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Myogenic Mechanism

How arteries and arterioles react to an increase or decrease of blood pressure to keep the blood flow within the blood vessel constant.

Vascular Smooth Muscle

VSM

Calponin

Calcium binding protein. Tonically inhibits the ATPase activity of myosin in smooth muscle. Phosphorylation of this protein by a protein kinase, which is dependent upon calcium binding to calmodulin, releases the this protein’s inhibition of the smooth muscle ATPase. Thin filament regulatory protein.

1

The influx of calcium, triggering the exposure of binding steps on actin. Which CBC step? Number (X/6).

2

Cross bridge formation: phosphorylated myosin head attaches/binds to an actin myofilament. Which CBC step? Number. (X/6).

3

The power stroke: 1) ADP and Pi are released from the myosin head 2) Myosin head changes to bend, low-energy state 3) Shape change pulls the actin towards the M line Which CBC step? Number. (X/6).

4

Cross bridge detachment: ATP attaches to myosin, breaking the cross bridge. Which CBC step? Number. (X/6).

5

Cocking of the myosin head: attached ADP is hydrolyzed by myosin ATPase into ADP + Pi, bringing it back to a high-energy state. Which CBC step? Number. (X/6).

6

The transport of calcium ions back into the sarcoplasmic reticulum (SR). Which CBC step? Number. (X/6).

Phosphorylase

An enzyme that introduces a phosphate group into an organic molecule, notably glucose. A type of phosphotransferase.

Kinase

An enzyme that catalyzes the transfer of phosphate groups from high-energy, phosphate-donating molecules to specific substrates.

Phosphatase

A type of hydrolase that removes a phosphate group.

Synthase

An enzyme that catalyzes the linking together of two molecules, especially without the direct involvement of ATP.

Phosphotransferase

Any of a class of enzymes, including the kinases, that catalyze the transfer of phosphorus-containing groups from one compound to another. Also called transphosphatase.

Cross Bridge Cycle

Microtubule

A microscopic tubular structure present in numbers in the cytoplasm of cells, sometimes aggregating to form more complex structures.

Microfilament

A small rodlike structure, about 4-7 nanometers in diameter, present in numbers in the cytoplasm of many eukaryotic cells.

Intermediate Filament

Cytoskeletal component found in the cells of many animal species. They are composed of a family of related proteins sharing common structural and sequence features.

Thick Filament

One of the two types of protein filaments that, together form cylindrical structures call myofibrils which extend along the length of muscle fibres.

Myofibril

Any of the elongated contractile threads found in striated muscle cells. Contain thick filaments and thin filaments.

Actin

Main component of thin filament.

Troponin and Tropomyosin

The other two protein molecules that form the thin filaments are called _____ and ___________.

Sarcomere

Thick filaments plus thin filaments =

H

Single letter. This is the band in the sarcomere which there are only thick filaments, and no thin filaments.

I

Single letter. This band is the region between adjacent A bands, in which there are only thin filaments, and no thick filaments. Each of these bands extends across two adjacent sarcomeres.

A

Single letter. This band is a relatively darker area within the sarcomere that extends along the total length of the thick filaments.

Z

Single letter. This band is a thick squiggly line cutting down the center of the I band. Separates one sarcomere from the next.

M

Single letter. This band is supporting proteins that hold the thick filaments together in the H zone

Neuromuscular Junction

The connection between the motor neuron and muscle fiber.

Transverse Tubules

Invaginations, or deep indentations, of the sarcolemma into the sarcoplasm of the skeletal muscle cell

Sarcoplasmic Reticulum

Stores and releases calcium into sarcoplasm after nervous stimulation

Sarcolemma

The plasma membrane of a muscle cell.

Sarcoplasm

The cytoplasm of a muscle fiber.

Phosphoesters

When serine, threonine and tyrosine are phosphorylated (most common, since they have -OH) the products are…

Western Blot

Lab technique used to identify specific amino-acid sequences in proteins.

Anomeric Carbon

In a cyclic carbohydrate, the carbon that was the carbonyl carbon in acyclic form.

Right

In a glycosidic bond, which oxygen gets eliminated at water? Left or right?

Epimer

Each of two isomers with different configurations of atoms around one of several asymmetric carbon atoms present.

Diastereomer

Occurs when two or more stereoisomers of a compound have different configurations at one or more (but not all) of the equivalent (related) stereocenters and are not mirror images of each other.

Geometric Isomer

Each of two or more compounds that differ from each other in the arrangement of groups with respect to a double bond, ring, or other rigid structure.

Tropomyosin

In a relaxed muscle it covers the binding sites of actin for cross-bridges of myosin.

Troponin

Has a binding site for Ca2+. When Ca2+ joins troponin undergoes conformational change and pulls the tropomyosin away and exposes the binding sites.

Neuromuscular Junction

A motor neuron has many terminal branches ending in knobs. A terminal knob neuron and motor end plate of sarcolemma lie very close across synaptic cleft and form a neuromuscular junction. Motor end plate has receptors for acetylcholine secreted by terminal knob.

Nervous stimulus pass through synaptic cleft

a. Depolarization of presynaptic membrane opens Ca2+ channels. b. Influx of Ca2+ causes exocytosis of vesicles releasing Acetylcholine in synapse. c. Acetylcholine binds to receptors in postsynaptic membrane = motor end plate and opens Na+ channels. d. Influx of Na+ depolarizes the motor end plate.

Cholinesterase

Acetylcholine detaches from receptors when the motor end plate gets depolarized. What is the enzyme present in the synapse that breaks acetylcholine into acetate + choline? Terminal knob reabsorbs the choline.

Ca2+

Depolarization of t-tubules causes depolarization of terminal cisternae that lie on each side of t-tubule. The fall in voltage activates Dihydropyridine receptors; that open Ryanodine receptors. This is how which compound gets released into the cytosol of muscle fiber?

Summation

When a 2nd stimulus is applied before the completion of 1st twitch, it results in a greater contraction called summation because it sums the 2 contraction.

Tetanus

Continued contraction at maximum level due to fast series of stimulations. It can be incomplete if you can see individual contractions. A very fast series of stimulations causes it to be complete when we cannot see individual contractions.

Southern Blot

A method used in molecular biology for detection of a specific DNA sequence in DNA samples. It combines transfer of electrophoresis-separated DNA fragments to a filter membrane and subsequent fragment detection by probe hybridization.

Hybridization Probe

A fragment of DNA or RNA of variable length (usually 100-1000 bases long) which can be radioactively labeled. It can then be used in DNA or RNA samples to detect the presence of nucleotide sequences (the DNA target) that are complementary to its sequence.

Restriction Site

Generally palindromic. Location on a DNA molecule containing specific (4-8 base pairs in length) sequences of nucleotides, which are recognized by restriction enzymes.

Restriction Digest

The process of cutting DNA molecules into smaller pieces with special enzymes called Restriction Endonucleases (sometimes just called Restriction Enzymes or RE’s).

Retroviral Integrase (IN)

An enzyme produced by a retrovirus (such as HIV) that enables its genetic material to be integrated into the DNA of the infected cell.

Phosphodiester Bond

The linkage between the 3′ carbon atom of one sugar molecule and the 5′ carbon atom of another.

Phosphodiester Bond

Retrovirus

Type of virus that replicates in a host cell through the process of reverse transcription.

Retrovirus

A single-stranded positive-sense RNA virus with a DNA intermediate and, as an obligate parasite, targets a host cell.

Retrovirus

The virus uses its own reverse transcriptase enzyme to produce DNA from its RNA genome — the reverse of the usual pattern, thus retro (backwards).

Provirus

This new DNA is then incorporated into the host cell genome by an integrase enzyme, at which point the retroviral DNA is referred to as a…?

Retrovirus

Viral DNA integrated into a host cell genome by integrase originates from a…? mRNA transcribed from retroviral DNA is either used to synthesize viral proteins, or used as the RNA genome for progeny viruses. The sequence of the nucleotide in the original viral genome will be the same as that of the transcribed mRNA.

Retrovirus

A vDNA sequence encoding a protein is inserted into a host genome by IN. The protein is translated from the hypothetical mRNA sequence shown. 5-GGCAACUGACUA-3 Therefore, the segment of the original viral genome that encoded this protein had what nucleotide sequence?

Inhibition

Can be determined by through rate experiments. Keep [E] constant. Vary [S]. Either include or exclude the inhibitor. One word.

110 Da

Average molecular weight of an amino acid.

siRNA

Interferes with the expression of specific genes with complementary nucleotide sequences by degrading mRNA after transcription, resulting in no translation.

Hill Coefficient

It describes the fraction of the macromolecule saturated by ligand as a function of the ligand concentration; it is used in determining the degree of cooperativeness of the ligand binding to the enzyme or receptor. n>1 positive cooperative binding n<1 negative cooperative binding n=1 noncooperative binding

Gallbladder

Stores bile.

Pancreas

Secretes glucagon.

Parietal Cell

Secretes HCl

Liver

Detoxifies drugs.

Noncompetitive

One word. Inhibitor that binds to the E and the ES Complex with same affinity.

Effector

One word. A small molecule that selectively binds to a protein and regulates its biological activity. In this manner, these molecules act as ligands that can increase or decrease enzyme activity, gene expression, or cell signalling.

True

True or False? Bacteria can lyse cells.

Asparagine and Glutamine

Only amino acid with amide group. ___and____ (alphabetical).

Isoelectric Focusing

A technique of electrophoresis in which the resolution is improved by maintaining a pH gradient between the electrodes.

Autoradiograph

An image on an x-ray film or nuclear emulsion produced by the pattern of decay emissions (e.g., beta particles or gamma rays) from a distribution of a radioactive substance.

Acetyl

A functional group, the acyl with chemical formula CH3CO. It is sometimes represented by the symbol Ac (not to be confused with the element actinium). This group contains a methyl group single-bonded to a carbonyl.

Allele

Different protein isoforms are synthesized through the same gene via alternative splicing, NOT from a different _____ on another chromosome?

Post-Translational Modification

Refers to the covalent and generally enzymatic modification of proteins during or after protein biosynthesis. Proteins are synthesized by ribosomes translating mRNA into polypeptide chains, which may then undergo PTM to form the mature protein product.

Peptide

FSH what kind of hormone?

Connective

One word. Type of tissue that connects, supports, binds, or separates other tissues or organs, typically having relatively few cells embedded in an amorphous matrix, often with collagen or other fibers, and including cartilaginous, fatty, and elastic tissues.

Epithelial

One word. Type of tissue found to line the cavities and surfaces of blood vessels and organs throughout the body.

Nervous

One word. Type of tissue. Component of the two parts of the nervous system; the brain and spinal cord of the central nervous system (CNS), and the branching peripheral nerves of the peripheral nervous system (PNS), which regulates and controls bodily functions and activity.

Kd

Higher affinity corresponds to lower…? (Which constant?)

In Vitro

Conclusions on therapeutic treatments should not be draw from experiments done…?

Glycosylation

Post-translational _________ can promote protein folding and improve stability as well as serving regulatory functions?

Lipidation

Post-translational ___________often targets a protein or part of a protein to the cell membrane.

Phosphorylation

Most common post-translational modification. Helps regulate activity of enzymes.

Noncompetitive

Which type of inhibitor does NOT alter the KM/Vmax ratio of an enzyme?

Mixed

One word. Type of enzyme inhibition in which the inhibitor may bind to the enzyme whether or not the enzyme has already bound the substrate but has a greater affinity for one state or the other. Conceptual mixture of both competitive inhibition, in which the substrate is not bound, and uncompetitive inhibition, in which the inhibitor can only bind the enzyme if the substrate has already bound.

Uncompetitive

One word. Type of inhibitor that binds the enzyme once the substrate has already bound. Works better in higher substrate concentrations in which ES Complexes are more abundant.

Immunoprecipitation

AKA – "Pulldown." Precipitating a protein antigen out of solution using an antibody that specifically binds to that particular protein. This process can be used to isolate and concentrate a particular protein from a sample containing many thousands of different proteins.

Capase

Family of protease enzymes playing essential roles in programmed cell death (including apoptosis, pyroptosis and necroptosis) and inflammation.

Consensus Sequence

Sequence alignments in which related sequences are compared to each other and similar sequence motifs are calculated. Calls RNA Polymerase or nuclear factors to the scene.

Nuclear Localization Domain

Amino acid sequence that ‘tags’ a protein for import into the cell nucleus by nuclear transport.

Signal Peptide

(Sometimes referred to as signal sequence, targeting signal, localization signal, localization sequence, transit peptide, leader sequence or leader peptide) is a short (5-30 amino acids long) peptide present at the N-terminus of the majority of newly synthesized proteins that are destined towards the secretory pathway.

Nuclear Localization Domain

Amino acid sequence that ‘tags’ a protein for import into the cell nucleus by nuclear transport.

Signal Peptide

(Sometimes referred to as signal sequence, targeting signal, localization signal, localization sequence, transit peptide, leader sequence or leader peptide) is a short (5-30 amino acids long) peptide present at the N-terminus of the majority of newly synthesized proteins that are destined towards the secretory pathway.

Nuclear Localization Domain

Amino acid sequence that ‘tags’ a protein for import into the cell nucleus by nuclear transport.

Signal Peptide

(Sometimes referred to as signal sequence, targeting signal, localization signal, localization sequence, transit peptide, leader sequence or leader peptide) is a short (5-30 amino acids long) peptide present at the N-terminus of the majority of newly synthesized proteins that are destined towards the secretory pathway.

Nuclear Localization Domain

Amino acid sequence that ‘tags’ a protein for import into the cell nucleus by nuclear transport.

Signal Peptide

(Sometimes referred to as signal sequence, targeting signal, localization signal, localization sequence, transit peptide, leader sequence or leader peptide) is a short (5-30 amino acids long) peptide present at the N-terminus of the majority of newly synthesized proteins that are destined towards the secretory pathway.

Nuclear Localization Domain

Amino acid sequence that ‘tags’ a protein for import into the cell nucleus by nuclear transport.

Signal Peptide

(Sometimes referred to as signal sequence, targeting signal, localization signal, localization sequence, transit peptide, leader sequence or leader peptide) is a short (5-30 amino acids long) peptide present at the N-terminus of the majority of newly synthesized proteins that are destined towards the secretory pathway.

Nuclear Localization Domain

Amino acid sequence that ‘tags’ a protein for import into the cell nucleus by nuclear transport.

Signal Peptide

(signal sequence, targeting signal, localization signal, localization sequence, transit peptide, leader sequence or leader peptide) is a short (5-30 amino acids long) peptide present at the N-terminus of the majority of newly synthesized proteins that are destined towards the secretory pathway.

Nuclear Localization Domain

Amino acid sequence that ‘tags’ a protein for import into the cell nucleus by nuclear transport.

Transcription Factor

(Sometimes called a sequence-specific DNA-binding factor) is a protein that binds to specific DNA sequences, thereby controlling the rate of transcription of genetic information from DNA to messenger RNA.

Capase

Family of protease enzymes playing essential roles in programmed cell death (including apoptosis, pyroptosis and necroptosis) and inflammation.

Transcription Factor

Nuclear factor is a…?

Enhancer

A short (50-1500 bp) region of DNA that can be bound by proteins (activators) to increase the likelihood transcription that will occur at a gene. These proteins are usually referred to as transcription factors.

Promoter

A region of DNA that initiates transcription of a particular gene. Usually located near the transcription start sites of genes, on the same strand and upstream on the DNA (towards the 5′ region of the antisense strand).

Hydrophobic

Side chains of what kind of amino acids (one word) are most likely to be at dimer interface if protein is present in cytosol?

Affinity Mass

SDS-PAGE separates molecules based on ____ and ____? (alphabetical)

Isoelectric Point

Isoelectric focusing separates molecules based on…?

Charge

Ion-Exchange Chromatography separates molecules based on net…?

Glucokinase

Enzyme that facilitates phosphorylation of glucose to glucose-6-phosphate.

Hexokinase

An enzyme that phosphorylates hexoses (six-carbon sugars), forming hexose phosphate.

Glucose-6-Phosphatase

An enzyme that hydrolyzes glucose-6-phosphate, resulting in the creation of a phosphate group and free glucose.

Phosphoglucomutase

An enzyme that transfers a phosphate group on an α-D-glucose monomer from the 1′ to the 6′ position in the forward direction or the 6′ to the 1′ position in the reverse direction.

Binding

After an amino acid substitution in an enzyme, if the Kd didn’t change, then that residue was not involved in the ____ site?

DNA Amplification

In cloning cDNA, DNA Polymerase does what?

Ligates cDNA to DNA vector

In cloning cDNA, Ligase does what?

Inverse transcription of RNA to cDNA

In cloning cDNA, Reverse Transcriptase does what?

Nothing

In cloning cDNA, RNA Polymerase does what?

dNTPs

The building blocks for DNA (they lose two of the phosphate groups in the process of incorporation).

Stability

π-stacking increases what?

Glucagon

Mobilizes hepatic glycogen so we can burn it.

Gluconeogenesis

A metabolic pathway that results in the generation of glucose from certain non-carbohydrate carbon substrates.

Glycogenolysis

The biochemical breakdown of glycogen to glucose whereas.

Glycogenesis

The formation of glycogen from sugar.

Acetyl-CoA

Its main function is to convey the carbon atoms within the acetyl group to the citric acid cycle (Krebs cycle) to be oxidized for energy production.

Oxaloacetate

A metabolic intermediate in many processes. It takes part in the: gluconeogenesis, urea cycle, glyoxylate cycle, amino acid synthesis, fatty acid synthesis and citric acid cycle.

Key intermediate in the Krebs cycle, coming after isocitrate and before succinyl CoA.

Alpha-Ketoglutarate

Glutamine is synthesized from glutamate by glutamine synthetase, which utilizes an ATP to form glutamyl phosphate; this intermediate is attacked by ammonia as a nucleophile giving glutamine and inorganic phosphate.

Alpha-Ketoglutarate

One of the most important nitrogen transporters in metabolic pathways. The amino groups of amino acids are attached to it (by transamination) and carried to the liver where the urea cycle takes place.

Alpha-Ketoglutarate

Is transaminated, along with glutamine, to form the excitatory neurotransmitter glutamate. Glutamate can then be decarboxylated (requiring vitamin B6) into the inhibitory neurotransmitter GABA.

Gluconeogenesis

Lactate, glycerol, and glucogenic amino acids are all possible substrates for…?

G-Protein

Activation of ______promotes dissociation of bound GDP and its exchange for GTP on the alpha subunit.

G-Protein

Activation of coupled ________ leads to activity of adenylate cyclase and protein kinase.

Adenylate Cyclase

Catalyzes the conversion of adenosine triphosphate (ATP) to 3′,5′-cyclic AMP (cAMP) and pyrophosphate.

cAMP

A second messenger important in many biological processes. cAMP is a derivative of adenosine triphosphate (ATP) and used for intracellular signal transduction in many different organisms, conveying the _____-dependent pathway.

Glycogen Phosphorylase

Catalyzes the rate-limiting step in glycogenolysis in animals by releasing glucose-1-phosphate from the terminal alpha-1,4-glycosidic bond.

Phosphogluconate

Which of the following compounds is NOT a gluconeogenic precursor or substrate? Glycerol, Lactate, Phosphogluconate, Oxaloacetate

Cyclase

An enzyme, almost always a lyase, that catalyzes a chemical reaction to form a cyclic compound

Lyase

An enzyme that catalyzes the joining of specified molecules or groups by a double bond.

Acetylase

Any enzyme catalyzing acetylation or deacetylation, as in the formation of N-acetylglutamate from glutamate plus acetyl-CoA, or the reverse; acetylases are usually called acetyltransferases.

GTP and Succinate

Under physiological conditions, increased activity of succinyl-CoA synthetase will most likely result in greater levels of the reaction products, "__XXX___ and _____".

NADPH

The pentose phosphate pathway results in the generation of…?

NADPH

A reductive agent in cellular respiratory processes resulting from the PPP pathway.

Competitive

The Vmax of an enzymatic reaction is altered by all but which? Competitive Noncompetitive Uncompetitive Mixed

Substrate Analog

Two words. Are chemical compounds with a chemical structure that resemble the substrate molecule in an enzyme-catalyzed chemical reaction.

Cofactor

A substance (other than the substrate) whose presence is essential for the activity of an enzyme

Prosthetic Group

Two words. A nonprotein group forming part of or combined with a protein.

Coenzyme

A nonprotein organic compound that is necessary for the functioning of an enzyme.

Scavenger

One word. A chemical substance added to a mixture in order to remove or de-activate impurities and unwanted reaction products.

Lipoic Acid

An organosulfur compound derived from octanoic acid. Is essential for aerobic metabolism.

Glucose-6-Phosphate Dehydrogenase

In the pentose phosphate pathway, which enzyme catalyzes the production of 6-phosphogluconolactone?

Coding Strand

Two words. The DNA strand which has the same base sequence as the RNA transcript produced. "Sense"

Template Strand

Two words. The DNA strand from which RNA Polymerase reads to produce mRNA.

Myogenic activity

Myogenic activity refers to the ability of a muscle to contract without nervous stimulation in response to other stimuli like stretching. Smooth and cardiac muscle both possess myogenic activity.

Blood pressure in the aorta compared to the rest of the body

Blood pressure is higher in the aorta of an interest of the body

What are micro filaments composed of?

Actin

Amino acids that can be phosphorylated

Have a hydroxyl group that allow an esterification type reaction to occur ie: serine, threonine, tyrosine, histidine (rare) In prokaryotes: serine, threonine, tyrosine, very rarely: histidine arginine and lysine residues

What is the difference between alpha and beta designators

They distinguish epimers at anomeric carbon atoms

What is a signal sequence?

Protein domains required for proteins that are directed toward secretory pathways.

What is a palindromic sequence

A sequence is a palindrome if it is the same as its reverse complement. Most often serves as a restriction site Ex: 5′ AAGCTT 3′ 3′ TTCGAA 5′

Compare the viral DNA sequence that encodes a protein to the hypothetical mRNA sequence

Viral DNA integrated into a host cell genome by integrates would originate from a retrovirus. mRNA transcribed from retroviral DNA is either used to synthesize viral proteins or is used as the RNA genome for progeny viruses. The original viral DNA sequence will be the same as that of the transcribed mRNA

How would you determine the mechanism of inhibition for reaction

Competitive inhibition can be determined through rate experiments by applying the principles of the Michaelis Menton equation. By keeping enzyme concentration constant, varying substrate concentration and either including or excluding the inhibitor the effect of the inhibitor on the vmax and apparent KM of the reaction can be determined

What are the only elements that vary in different cells and therefore can confer both temporal and spatial regulation on their target genes?

Nuclear Factors

What is a gene promoter?

Promoter sequences are DNA sequences that define where transcription of a gene by RNA polymerase begins. Promoter sequences are typically located directly upstream or at the 5′ end of the transcription initiation site.

What is a gene enhancer?

In genetics, an enhancer is a short (50-1500 bp) region of DNA that can be bound by proteins (activators) to activate transcription of a gene. These proteins are usually referred to as transcription factors.

Which type of interactions are common to dimerizations of proteins?

Hydrophobic Protein-Protein Interactions

Auto phosphorylation

Type of post-translational modification of proteins. It is generally defined as the phosphorylation of the kinase by itself. requires ATP

What are protein isoforms?

Different isoforms of a protein that are expressed from the same gene; alternative splicing.

What is the average molecular weight of an amino acid?

110Da

What is "native" gel electrophoresis?

"Native" or "non-denaturing" gel electrophoresis is run in the absence of SDS. While in SDS-PAGE the electrophoretic mobility of proteins depends primarily on their molecular mass, in native PAGE the mobility depends on both the protein’s charge and its hydrodynamic size.

What is the effect of SDS-Page?

A detergent that denatures proteins and surrounds them with negative charge.

How does isoelectric focusing separate proteins?

Based on their isoelectric point. must establish a pH gradient gel

How does ion exchange chromatography separate proteins?

Based on their net charge.

How does SDS-Page separate proteins?

Based on their mass.

How does affinity chromatography separate charge?

Based on their interactions with specific ligands.

How many molecules of reduced electron carrier are generated during conversion of α-ketoglutarate to oxaloacetate in the citric acid cycle?

3 → 1 FADH₂ & 2 NADH

What enzyme catalyzes the final step of both gluconeogenesis and glycogenolysis?

Glucose-6-Phosphatase

How is the efficiency of an enzyme measured?

kcat/Km Remember, at constant concentration, Vmax = kcat[E]

Hill coefficient

Hill coefficient greater than one indicates positive cooperativity

Nitrogenous bases

Lineweaver-Burk Plot

What does an increase in Kd suggest concerning protein stability?

A decrease in stability. Kd is representative of a propensity to dissociate

What TCA intermediates can be used for gluconeogenesis?

Oxaloacetate and α-ketoglutatrate

To which type of receptor does glucagon bind?

GPCR

peptide versus steroid hormones

Peptide hormones are hydrophilic and soluble in blood, they do not require transport proteins to remain soluble in the bloodstream. Steroid hormones must bind transport proteins which are lipophilic

What enzyme catalyzes the rate-limiting step in glycogen breakdown?

Glycogen Phosphorylase

Uncompetitive inhibition effect on Km, vmax. what makes uncompetitive inhibition more effective

Decreases both, ratio stays the same. uncompetitive inhibitors bind to their target enzymes only one substrate is first bound to the enzyme, at a higher substrate concentration the substrate enzyme complex are more abundant and to be on competitive inhibitor will work more effectively when the substrate concentration is highest.

What types of peptide sequences are likely to be found in the transmembrane helix of the protein

transmembrane helices are made of mostly unbroken stretches of hydrophobic amino acids

What are the bond types of glycogen?

Linear: α(1→4) Branch Points: α(1→6)

What is the difference between lactase (lactic acid) and lactose?

What does the PPP produce?

NADPH

Which type of inhibitors affect Vmax?

Noncompetitive, Uncompetitive, Mixed

What is the effect of free radical scavengers?

To mitigate the effects of reactive oxygen species (ROS).

What is the cofactor of pyruvate dehydrogenase and what is the function of this enzyme?

Lipoic Acid, Catalyzes the conversion of pyruvate to acetyl-CoA.

What is the structure of succinate?

What is the structure of fumarate?

What is the structure of malate?

What is the structure of oxaloacetate?

In the PPP, which enzyme catalyzes the production of 6-phosphogluconolactone?

Glucose-6-phosphate dehydrogenase

What is catalytic efficiency

kcat/Km

Whenever you see enzyme modifications that affect Tm and Kcat think that the enzyme’s conformational stability has been affected.

What is a glycoside bond?

In chemistry, a glycoside is a molecule in which a sugar is bound to another functional group via a glycosidic bond.

Definition of kcat?

Described the rate-limiting step of catalysis under saturating conditions of substrate.

cDNA cloning steps

Prior to cloning: take given mRNA sequence + reverse transcriptase gives us complimentary (single) DNA strand. Addition of DNA polymerase generates double stranded DNA which is starting point for cDNA. 1) isolate DNA from organism 2) cut DNA with restriction enzyme 3) cut cloning vector with same restriction enzymes 4) ligate sequence into cloning vector to make recombinant DNA molecule (DNA ligase) 5) insert recombinant DNA into host 6) host replicates, so that we get large collection of recombinant DNA

Steps of G-coupled protein receptor

When a ligand binds to the G receptor, GTP (active) replaces inactive GDP which binds to the alpha subunit. The alpha GTP complex dissociates leaving the Gamma Beta dimer behind. The GTP alpha subunit can activate the enzyme adenylyl cyclase which catalyze the formation of cAMP, amplifying the signal. CAMP goes on to bind and activate protein kinase a which phosphorylates genes on target proteins

the pentose phosphate pathway results in the generation of

NADPH which is used as a reductive agent and cellular respiratory processes

What is a signal sequence?

Protein domains required for proteins that are directed toward secretory pathways.

What are the only elements that vary in different cells and therefore can confer both temporal and spatial regulation on their target genes?

Nuclear Factors

What is a gene promoter?

Promoter sequences are DNA sequences that define where transcription of a gene by RNA polymerase begins. Promoter sequences are typically located directly upstream or at the 5′ end of the transcription initiation site.

What is a gene enhancer?

In genetics, an enhancer is a short (50-1500 bp) region of DNA that can be bound by proteins (activators) to activate transcription of a gene. These proteins are usually referred to as transcription factors.

Which amino acid is indicated by "Gln"?

Glutamine

Which amino acid is indicated by "Asn"?

Asparagine

Which type of interactions are common to dimerizations of proteins?

Hydrophobic Protein-Protein Interactions

What are protein isoforms?

Different isoforms of a protein that are expressed from the same gene; alternative splicing.

What is the average molecular weight of an amino acid?

110Da

What is "native" gel electrophoresis?

"Native" or "non-denaturing" gel electrophoresis is run in the absence of SDS. While in SDS-PAGE the electrophoretic mobility of proteins depends primarily on their molecular mass, in native PAGE the mobility depends on both the protein’s charge and its hydrodynamic size.

What is the effect of SDS-Page?

A detergent that denatures proteins and surrounds them with negative charge.

How does isoelectric focusing separate proteins?

Based on their isoelectric point.

How does ion exchange chromatography separate proteins?

Based on their net charge.

How does SDS-Page separate proteins?

Based on their mass.

How does affinity chromatography separate charge?

Based on their interactions with specific ligands.

How many molecules of reduced electron carrier are generated during conversion of α-ketoglutarate to oxaloacetate in the citric acid cycle?

3 → 1 FADH₂ & 2 NADH

What enzyme catalyzes the final step of both gluconeogenesis and glycogenolysis?

Glucose-6-Phosphatase

How is the efficiency of an enzyme measured?

kcat/Km Remember, at constant concentration, Vmax = kcat[E]

Lineweaver-Burk Plot

What does an increase in Kd suggest concerning protein stability?

A decrease in stability.

What TCA intermediates can be used for gluconeogenesis?

Oxaloacetate and α-ketoglutatrate

To which type of receptor does glucagon bind?

GPCR

What enzyme catalyzes the rate-limiting step in glycogen breakdown?

Glycogen Phosphorylase

What are the bond types of glycogen?

Linear: α(1→4) Branch Points: α(1→6)

What is the difference between lactase (lactic acid) and lactose?

What does the PPP produce?

NADPH

Which type of inhibitors affect Vmax?

Noncompetitive, Uncompetitive, Mixed

What is the effect of free radical scavengers?

To mitigate the effects of reactive oxygen species (ROS).

What is the cofactor of pyruvate dehydrogenase and what is the function of this enzyme?

Lipoic Acid, Catalyzes the conversion of pyruvate to acetyl-CoA.

What is the structure of succinate?

What is the structure of fumarate?

What is the structure of malate?

What is the structure of oxaloacetate?

In the PPP, which enzyme catalyzes the production of 6-phosphogluconolactone?

Glucose-6-phosphate dehydrogenase

What is catalytic efficiency

kcat/Km

Whenever you see enzyme modifications that affect Tm and Kcat think that the enzyme’s conformational stability has been affected.

What is a glycoside bond?

In chemistry, a glycoside is a molecule in which a sugar is bound to another functional group via a glycosidic bond.

What is competition isothermal titration calorimetry?

Definition of kcat?

Described the rate-limiting step of catalysis under saturating conditions of substrate.

What is the difference between hyperbolic and parabolic?

move through both structures

the appendix, being located next to the colon, allows bacteria to do what?

the mesoderm

what germ layer gives rise to the heart and blood vessels?

subdomains in the membrane that contain high concentrations of cholesterol and glycosphingolipids

what is a lipid raft?

microtubules

what type of filament (microtubule, microfilament, intermediate) are responsible for chromosome movement in cell division?

no, they are enucleated and thus have no DNA

do erythrocytes have DNA?

obligate parasite

a parasitic organism that cannot complete its life-cycle without exploiting a suitable host

negative symptoms

thoughts, feelings, or behaviors normally present that are absent or diminished in a person with a mental disorder

implicit memory refers to memory used unconsciously (like procedural memory), whereas explicit is conscious, intentional recollection of factual information, previous experiences and concepts (e.g. semantic and episodic)

what’s the difference between implicit and explicit (declarative) memory?

new, unusual information retrieved by senses; requires conscious processing

what is novel information, and does it require conscious or unconscious processing?

signal detection theory

proposes that detection of stimulus is dependent on its strength and the individual’s alert status

cross-sectional

a type of data collected by observing many subjects (such as individuals, firms, countries, or regions) at the same point of time or without regard to differences in time

sanctions

mechanisms for social control; can either be punishments or rewards

the "Me" represents the socialized and conforming part of self, whereas the "I" represents the spontaneous, less socialized part of self

what is the difference between the "Me" and "I" parts of Mead’s theory of identity?

E=hf=h(c/λ)

what is the formula for energy of photon?

using its steric number (# of atoms bonded + # of lone pairs)

how do you determine an atom’s hybridization?

kcat = Vmax/[E]

what does kcat equal formula wise?

daughter nuclei (may or may not be radioactive after the decay)

radioactive decay produces daugher or radioactive nuclei?

removing the amino acid residue (knockout mice)

are variants made by removing the titular amino acid (e.g. Y229) or adding?

reduction (electrons being donated = reduced)

donation of hydride = reduction or oxidation?

venturi effect

characteristic of Bernoulli’s equation; basically fluid pressure decrease while velocity increases at a constricted area of the pipe

triacylglycerols (three fatty acid chains ester-linked to a single glycerol)

storage lipids are also known as what common name? what is their structure?

Lewis acids accept electrons, whereas Lewis bases donate electrons

what’s the difference between Lewis acid and base?

Eq constant larger than one with equal a negative ∆G° value, thus will be spontaneous [according to ∆G° = -RTln(Eq)]

what equilibrium constant values are associated with a negative ∆G°?

a covalent bond (a shared pair of electrons) in which both electrons come from the same atom (e.g.

what is a coordinate covalent bond?

the number of atoms or ions immediately surrounding a central atom in a complex

what is the coordination number?

atomic radius of atoms involved (e.g C-H is very short bond because H has a very small atomic radius)

bond length is determined primarily by what?

under standard conditions, each mole occupies 22.4 L of space

how much space does each mole occupy at STP?

W = .5kx^2

what is the equation for the work done by a spring?

series are added, parallel are added and inverted (reverse for capacitor)

what are the equations used for resistors in series and parallel? capacitors?

positively charged at physiological pH

what’s the charge of a protein that has an isoelectric point around 9?

a nuclear localization sequence

proteins that are translocated into the nucleus usually contain what kind of sequence?

prion

an abnormally folded protein that encourages other proteins to adopt an abnormal structure, which is often damaging

centrosome

where do microtubules originate from?

ratio refers to number, whereas interval refers to time

what is the difference between fixed interval and ratio schedules?

dependency ratio

the ratio of the number of economically dependent members of the population to the number of economically productive members

affective (how one emotional reacts), behavioral (how one behaviorally reacts), and cognitive (thoughts and beliefs one has about an object)

what are the three components of attitude?

social desirability

bias that refers to the fact that in self-reports, people will often report inaccurately on sensitive topics in order to present themselves in the best possible light

social stratification

society’s categorization of people into socioeconomic strata, based upon their occupation and income, wealth and social status, or derived power (social and political)

usually individuals in groups are less creative, rather than when they are alone

groups have more/less creativity?

vocabulary – left
visuospatial, music perception, and emotion processing – right

where are the following cognitive functions lateralized in the brain? (visuospatial skills, music perception, vocabulary, and emotional processing)

formation of plaques around brain cells cause them to die, accompanied by formation of tangles that prevent brain cells from receiving proper nutrients [AB (B-amyloid) and NFT (neurofibrillary tangle proteins)]

what is the biological bases for Alzheimer’s disease?

hyperactive dopaminergic signal transduction, overactivation of brain’s D2 receptors

what is the biological bases for Schizophrenia disease?

abnormal levels of dopamine, norepinephrine, and serotonin; high levels of cortisol

what is the biological bases for depression disease?

degeneration of substantia nigra cells leads to low dopamine levels

what is the biological bases for Parkinson’s disease?

neural stem cells can regenerate brain cells (neurons, astrocytes, oligodendrocytes), repairing damage from degenerative diseases

how can stem cell-based therapy be used to regenerate neuronal cells?

Hawthorne effect

describes changes in research participants as a result of their awareness that they are being observed

Thomas theorem

states that if an individual believes something to be real, then it is real in its consequences

E=V/d

Electric field intensity equation in regards to voltage

P = IV = V^2/R = I^2R

power equals what in terms of voltage, current, and resistance?

anodes are positively charged, whereas cathodes are negatively charged (anions flow toward the anode and vice versa)

what are the charges of anodes and cathodes respectively?

DNA

DNA is connected by phosphodiester bond.

Retroviruses

are viruses that are RNA viruses ( they are able to convert their genome into DNA inside their host cell)

Tetramer

4 of this molecule

Western Blot

we want to confirm if a small molecule induces formation of integrates tetramers by binding the protein ( the protein has to be in native state). – use of denaturing agent will disrupt the interaction between monomers – reducing agent with disrupt disulfide bonds.

Hill Coefficient

A hemoglobin saturation curve under various oxygen levels show that the saturation of oxygen is not linearly dependant on oxygen levels. As more oxygen binds –positive cooperativity. The hill coefficient is a measure of tendency of cooperative binding. – greater than 1- means positive cooperativity – less than 1- means negative cooperativity =1 – it neither increase nor decrease

Kd

dissociation constant of a particular set of substrate interaction. In case of substrate- protein interaction, it indicates the propensity to dissociate ( break of substrate from protein).

K cat

is the turnover number- it s calculate by Vmax/ [E]. It is the units: 1/ seconds. The higher the Kcat means more substrate are turned over per one second.

Kcat/ Km

specificity constant ( it tells you the catalytic coefficient ) – which means how fast in M/sec the enzyme reacts with the substrate once it encounters the substrate.

Competitive inhibitors

bind to enzyme

Non competitive inhibitor

can bind to the enzyme and enzyme substrate couple with the SAME affinity

Uncompetive inhibitor

only bind to the ES complex.

Indépendant variable

variable in experiment that is varied by researcher to determine the effect.

deamidation

involves the release of NH3

Isoelectric focusing

is a method of separating molecules which differ in their charge characteristics. In isoelectric focusing- the protein mixture is subjected to an electric field iin a stable pH gradient. The anode region is

Kcat is the

turnover number. it is calculated by Vmax/E. it is unit are 1/seconds.

Kcat/ Km

is the speificifity constant. ( it tells you catalytic effcicenty which measure how fast the enzyme reacts with substrate

Tertiary structure of protein

stabilized by- disulphide bonds- Hydrogen bonds – Salt bridge

Uncompetitive Inhibitors does not alter

the slope of line weaver blood . this result in equal Km max, bind to the es complex only

Uncompetitivie inhibitor

binds to the ES complex only. Uncompetitive inhibitors binds to the target enzyme only when the substrate is 1st bound to enzymes at complex is more abundant, more inhibitors can bind.

Nuclear Factors

are the only elements that vary in cells + confer temporal and spatial regulation of target genes.

1 aa=

110 Datons

Native gel

it is not denatured into its subunits. Heterodimers- subunits are joint covalently.

Ion Exchange Chromatography

separate proteins based on net charge

affinity chromatography

bind to proteins based on interaction with ligand.

Catalytic efficiency

is pretty much how good is the enzyme at measuring catalytic efficency

Guconogenic precursors

lactate, oxalocate, glycerol, and others glucongoenic precurso

pentose phosphate pathway

Guclose 6 phosphate—- 6-phosphogluconate ( via Glucose 6 phosphate dehyrodgenase_

Coding strand is identical

to mRNA

Transcription

occrus at the noncoding template strand. The coding strand is identical to the mRNA`

Catalytic efficiency

is the measure of how well a cell is able to grab an enzyme and turn it into product.

q5- Function of filaments

Thick filament- made out of myosin microfilament- actin Intermediate filaments- provide structural support Microtubules– make up spindle apparatus, cilia, and flagella. http://www.ivyroses.com/HumanBody/Muscles/Muscle_Filaments.php https://courses.washington.edu/conj/motor/musclereview.htm

Amino acid questions

q6, q8 ( asked for hydrophilic amino acids) q13- branched and unbranched side chains … question 21 (?) 42, 56, 66– which amino acid is most similar to Gln (glutamine)– options: Glu, Gly, Asn, Ala), Answer: Asn – because both glutamine and asparagine are polar amino acids

q17-Enantiomers

each of a pair of molecules that are mirror images of each other.

Epimers

each of two isomers with different configurations of atoms around one of several asymmetric carbon atoms present. – the stereochemical designators a & B distinguish between epimers at an anomeric carbon ( The anomeric carbon is a stereocenter. An important feature is the direction of the OH group attached to the anomeric carbon. Depending on the direction of the OH group, the anomeric carbon is either α or β. α: equatorial DOWN or axial DOWN. β)

Isomers

each of two or more compounds with the same formula but a different arrangement of atoms in the molecule and different properties.

Epimeric carbon

Epimeres, differ at only one chiral center, not the anomeric carbon. See difference between epimers and anomers. https://biochemanics.wordpress.com/2013/03/31/anomers-vs-epimers/ http://www.ochempal.org/index.php/alphabetical/e-f/epimers/

Figure out question 15.

a hint is found here: http://forums.studentdoctor.net/threads/help-gen-chem-question-osmotic-pressure.1192752/ https://answers.yahoo.com/question/index?qid=20080916112855AA4xM1U

q- 16- Which event is directly mediated by a ligand-gated ion channel?

The influx of Na+ across a motor end-plate occurs when NA+ ion channels bind the ligand acetylcholine Influx of NA+ across the motor end plate result in the depolarization of the muscle fiber membrane.

q16- Calcium Pump

Calcium pumps are a family of ion transporters found in the cell membrane of all animal cells. They are responsible for the active transport of calcium out of the cell for the maintenance of the steep Ca2+ electrochemical gradient across the cell membrane. The plasma membrane Ca2+ ATPase and the sodium-calcium exchanger are together the main regulators of intracellular Ca2+ concentration

What removes calcium back to the sarcoplasmic reticulum?

The plasma membrane Ca2+ ATPase (PMCA) is a transport protein in the plasma membrane of cells and functions to remove calcium (Ca2+) from the cell. There is a very large transmembrane electrochemical gradient of Ca2+ driving the entry of the ion into cells, yet it is very important that they maintain low concentrations of Ca2+ for proper cell signalling. Thus, it is necessary for cells to employ ion pumps to remove the Ca2+.

Role of Actylcholine

Acetylcholine is the neurotransmitter used at the neuromuscular junction—in other words, it is the chemical that motor neurons of the nervous system release in order to activate muscles. This property means that drugs that affect cholinergic systems can have very dangerous effects ranging from paralysis to convulsions. Acetylcholine is also used as a neurotransmitter in the autonomic nervous system, both as an internal transmitter for the sympathetic nervous system and as the final product released by the parasympathetic nervous system. It is the ligand that mediates the ligand-gated ion channel that allows the influx of Na+ at the motor end plate allowing for the depolarization of the muscle fiber membrane

Action Potential Information

•Action potential is a brief reversal of membrane potential where the membrane potential changes from -70mV to +30mV •The action potential has three main stages: depolarization, repolarizaton, and hyperpolarization. •Depolarization is caused when positively charged sodium ions rush into a neuron with the opening of voltage gated sodium channels. •Repolarization is caused by the closing of sodium ion channels and the opening of potassium ion channels. •Hyperpolarization occurs due to an excess of open potassium channels and potassium efflux from the cell Source: Boundless. "The Action Potential and Propagation." Boundless Anatomy and Physiology. Boundless, 08 Aug. 2016. Retrieved 19 Aug. 2016 from https://www.boundless.com/physiology/textbooks/boundless-anatomy-and-physiology-textbook/overview-of-the-nervous-system-11/neurophysiology-113/the-action-potential-and-propagation-615-8485/

Hyperpolarization

Hyperpolarization is a change in a cell’s membrane potential that makes it more negative. It is the opposite of a depolarization. It inhibits action potentials by increasing the stimulus required to move the membrane potential to the action potential threshold.

Types of Mutations

https://ghr.nlm.nih.gov/primer/mutationsanddisorders/possiblemutations

q-18 What bond is cleaved by IN during the first reaction of integration?

In the first reaction of integration, integrase cleaves a dinucleotide from the 3’end of a strand of viral DNA. This involves the cleavage of a P-O bond. The question falls under the category of "transmission of genetic information from the gene to the protein"

Amino Acid Flash Cards

https://quizlet.com/80449523/aamc-structure-and-function-of-proteins-and-their-constituent-amino-acids-1a-55-flash-cards/

q22- Weight of an amino acid

110 Da- if an integrase monomer is composed of 288 amino acids ( also called 288 residue protein) – It will have an approximate weight of 32kDa. Thus the tetrameter will have an approximate molecular weight of 128KDa.

q23- What are denaturing gells used for?

use denaturing gels for: •Estimating/confirming the molecular weight of a protein •Isolation of proteins based on size •Separation of protein complexes into individual components •Estimating purity level of a sample •Western blotting •Preparation for protein sequencing

What are native gells used for?

Determining the aggregation state of a protein •Isolation of enzymes •Studying protein complexes

what are reducing gells used for?

Used if there is a desire to confirm if a molecule induces the formation of another. See question 23

q32- What is KCAT

Kcat is the turnover number — the number of substrate molecule each enzyme site converts to product per unit time

q32- What is KM

Km is the concentration of substrate which permits the enzyme to achieve half Vmax. An enzyme with a high Km has a low affinity for its substrate, and requires a greater concentration of substrate to achieve Vmax

q32- Definition of Hill coefficient

a measure of coperativity. When the hill coefficient is greater than one it means that the enzyme exhibits coperativity. If it’s essentially one ( such as 1.1, or 1.2) it does not.

q 35- Deamidation
— Amino acid question.
Which amino acids undergo deamidation

Deamidation is a chemical reaction in which an amide functional group is removed from an organic compound. Which amino acids contiain an amide group. (NH3). A deamidation reaction releases NH3 – question 37.

q40- Isoelectric focusing ( or electrofocusing)

a technique of electrophoresis in which the resolution is improved by maintaining a pH gradient between the electrodes.

q42- Which residue can act as a substitute for serine?

Alanine is similar to serine, cannot be phosphorylated, and will not add a positive or negative charge to the protein.

q47- relationship between affinity and Kd

KD, is the equilibrium disassociation constant between an antibody and its antigen. The higher the affinity, the lower the Kd

q52- What hold protein structures together

https://www.premedhq.com/protein-structures https://www.khanacademy.org/test-prep/mcat/biomolecules/amino-acids-and-proteins1/v/four-levels-of-protein-structure

Competitive inhibition

Competitive inhibition is a form of enzyme inhibition where binding of the inhibitor to the active site on the enzyme prevents binding of the substrate and vice versa. –Same Vmax, Different Km Uncompetitive inhibition: Same Km/Vmax ratio

noncompetitive inhibitor

A noncompetitive inhibitor binds to the enzyme away from the active site, altering the shape of the enzyme so that even if the substrate can bind, the active site functions less effectively. – Same Km, different Vmax

mixed inhibition

It is called "mixed" because it can be seen as a conceptual "mixture" of competitive inhibition, in which the inhibitor can only bind the enzyme if the substrate has not already bound, and uncompetitive inhibition, in which the inhibitor can only bind the enzyme if the substrate has already bound either causes an increase in KM and decrease in Vmax or the opposite. When Km goes up, Vmax goes down

q56- Which peptide sequence is most likely found in a transmembrane helix of a protein?

Transmembrane helixes are mostly made out of unbroken pieces of hydrophobic amino acids Ala-Ile-Phe-Val-Leu

q66- which amino acid is most similar to Gln (glutamine)–
options: Glu, Gly, Asn, Ala

Answer: Asn – because both glutamine and asparagine are polar amino acids

q6- Which amino acid is LEAST likely found in one of the transmembrane domains of GPCR43?

Options: Gly, Trp, Phe, Asp

Answer: Asp, because it has a negatively charged R group, and is very hydrophilic.

Which amino acid contains an unbranched alkyl side chain?
Ala, Ile, Leu, Val

The answer is alanine, since it contains a methyl side chain which is not considered an branched alkane.

Which ideal solution exhibits the greatest osmotic pressure?

https://www.reddit.com/r/Mcat/comments/4z766f/aamc_scored_cp_15_simple_stoichiometry_question/

Myogenic Mechanism

How arteries and arterioles react to an increase or decrease of blood pressure to keep the blood flow within the blood vessel constant.

Vascular Smooth Muscle

VSM

Calponin

Calcium binding protein. Tonically inhibits the ATPase activity of myosin in smooth muscle. Phosphorylation of this protein by a protein kinase, which is dependent upon calcium binding to calmodulin, releases the this protein’s inhibition of the smooth muscle ATPase. Thin filament regulatory protein.

1

The influx of calcium, triggering the exposure of binding steps on actin. Which CBC step? Number (X/6).

2

Cross bridge formation: phosphorylated myosin head attaches/binds to an actin myofilament. Which CBC step? Number. (X/6).

3

The power stroke: 1) ADP and Pi are released from the myosin head 2) Myosin head changes to bend, low-energy state 3) Shape change pulls the actin towards the M line Which CBC step? Number. (X/6).

4

Cross bridge detachment: ATP attaches to myosin, breaking the cross bridge. Which CBC step? Number. (X/6).

5

Cocking of the myosin head: attached ADP is hydrolyzed by myosin ATPase into ADP + Pi, bringing it back to a high-energy state. Which CBC step? Number. (X/6).

6

The transport of calcium ions back into the sarcoplasmic reticulum (SR). Which CBC step? Number. (X/6).

Phosphorylase

An enzyme that introduces a phosphate group into an organic molecule, notably glucose. A type of phosphotransferase.

Kinase

An enzyme that catalyzes the transfer of phosphate groups from high-energy, phosphate-donating molecules to specific substrates.

Phosphatase

A type of hydrolase that removes a phosphate group.

Synthase

An enzyme that catalyzes the linking together of two molecules, especially without the direct involvement of ATP.

Phosphotransferase

Any of a class of enzymes, including the kinases, that catalyze the transfer of phosphorus-containing groups from one compound to another. Also called transphosphatase.

Cross Bridge Cycle

Microtubule

A microscopic tubular structure present in numbers in the cytoplasm of cells, sometimes aggregating to form more complex structures.

Microfilament

A small rodlike structure, about 4-7 nanometers in diameter, present in numbers in the cytoplasm of many eukaryotic cells.

Intermediate Filament

Cytoskeletal component found in the cells of many animal species. They are composed of a family of related proteins sharing common structural and sequence features.

Thick Filament

One of the two types of protein filaments that, together form cylindrical structures call myofibrils which extend along the length of muscle fibres.

Myofibril

Any of the elongated contractile threads found in striated muscle cells. Contain thick filaments and thin filaments.

Actin

Main component of thin filament.

Troponin and Tropomyosin

The other two protein molecules that form the thin filaments are called _____ and ___________.

Sarcomere

Thick filaments plus thin filaments =

H

Single letter. This is the band in the sarcomere which there are only thick filaments, and no thin filaments.

I

Single letter. This band is the region between adjacent A bands, in which there are only thin filaments, and no thick filaments. Each of these bands extends across two adjacent sarcomeres.

A

Single letter. This band is a relatively darker area within the sarcomere that extends along the total length of the thick filaments.

Z

Single letter. This band is a thick squiggly line cutting down the center of the I band. Separates one sarcomere from the next.

M

Single letter. This band is supporting proteins that hold the thick filaments together in the H zone

Neuromuscular Junction

The connection between the motor neuron and muscle fiber.

Transverse Tubules

Invaginations, or deep indentations, of the sarcolemma into the sarcoplasm of the skeletal muscle cell

Sarcoplasmic Reticulum

Stores and releases calcium into sarcoplasm after nervous stimulation

Sarcolemma

The plasma membrane of a muscle cell.

Sarcoplasm

The cytoplasm of a muscle fiber.

Phosphoesters

When serine, threonine and tyrosine are phosphorylated (most common, since they have -OH) the products are…

Western Blot

Lab technique used to identify specific amino-acid sequences in proteins.

Anomeric Carbon

In a cyclic carbohydrate, the carbon that was the carbonyl carbon in acyclic form.

Right

In a glycosidic bond, which oxygen gets eliminated at water? Left or right?

Epimer

Each of two isomers with different configurations of atoms around one of several asymmetric carbon atoms present.

Diastereomer

Occurs when two or more stereoisomers of a compound have different configurations at one or more (but not all) of the equivalent (related) stereocenters and are not mirror images of each other.

Geometric Isomer

Each of two or more compounds that differ from each other in the arrangement of groups with respect to a double bond, ring, or other rigid structure.

Tropomyosin

In a relaxed muscle it covers the binding sites of actin for cross-bridges of myosin.

Troponin

Has a binding site for Ca2+. When Ca2+ joins troponin undergoes conformational change and pulls the tropomyosin away and exposes the binding sites.

Neuromuscular Junction

A motor neuron has many terminal branches ending in knobs. A terminal knob neuron and motor end plate of sarcolemma lie very close across synaptic cleft and form a neuromuscular junction. Motor end plate has receptors for acetylcholine secreted by terminal knob.

Nervous stimulus pass through synaptic cleft

a. Depolarization of presynaptic membrane opens Ca2+ channels. b. Influx of Ca2+ causes exocytosis of vesicles releasing Acetylcholine in synapse. c. Acetylcholine binds to receptors in postsynaptic membrane = motor end plate and opens Na+ channels. d. Influx of Na+ depolarizes the motor end plate.

Cholinesterase

Acetylcholine detaches from receptors when the motor end plate gets depolarized. What is the enzyme present in the synapse that breaks acetylcholine into acetate + choline? Terminal knob reabsorbs the choline.

Ca2+

Depolarization of t-tubules causes depolarization of terminal cisternae that lie on each side of t-tubule. The fall in voltage activates Dihydropyridine receptors; that open Ryanodine receptors. This is how which compound gets released into the cytosol of muscle fiber?

Summation

When a 2nd stimulus is applied before the completion of 1st twitch, it results in a greater contraction called summation because it sums the 2 contraction.

Tetanus

Continued contraction at maximum level due to fast series of stimulations. It can be incomplete if you can see individual contractions. A very fast series of stimulations causes it to be complete when we cannot see individual contractions.

Southern Blot

A method used in molecular biology for detection of a specific DNA sequence in DNA samples. It combines transfer of electrophoresis-separated DNA fragments to a filter membrane and subsequent fragment detection by probe hybridization.

Hybridization Probe

A fragment of DNA or RNA of variable length (usually 100-1000 bases long) which can be radioactively labeled. It can then be used in DNA or RNA samples to detect the presence of nucleotide sequences (the DNA target) that are complementary to its sequence.

Restriction Site

Generally palindromic. Location on a DNA molecule containing specific (4-8 base pairs in length) sequences of nucleotides, which are recognized by restriction enzymes.

Restriction Digest

The process of cutting DNA molecules into smaller pieces with special enzymes called Restriction Endonucleases (sometimes just called Restriction Enzymes or RE’s).

Retroviral Integrase (IN)

An enzyme produced by a retrovirus (such as HIV) that enables its genetic material to be integrated into the DNA of the infected cell.

Phosphodiester Bond

The linkage between the 3′ carbon atom of one sugar molecule and the 5′ carbon atom of another.

Phosphodiester Bond

Retrovirus

Type of virus that replicates in a host cell through the process of reverse transcription.

Retrovirus

A single-stranded positive-sense RNA virus with a DNA intermediate and, as an obligate parasite, targets a host cell.

Retrovirus

The virus uses its own reverse transcriptase enzyme to produce DNA from its RNA genome — the reverse of the usual pattern, thus retro (backwards).

Provirus

This new DNA is then incorporated into the host cell genome by an integrase enzyme, at which point the retroviral DNA is referred to as a…?

Retrovirus

Viral DNA integrated into a host cell genome by integrase originates from a…? mRNA transcribed from retroviral DNA is either used to synthesize viral proteins, or used as the RNA genome for progeny viruses. The sequence of the nucleotide in the original viral genome will be the same as that of the transcribed mRNA.

Retrovirus

A vDNA sequence encoding a protein is inserted into a host genome by IN. The protein is translated from the hypothetical mRNA sequence shown. 5-GGCAACUGACUA-3 Therefore, the segment of the original viral genome that encoded this protein had what nucleotide sequence?

Inhibition

Can be determined by through rate experiments. Keep [E] constant. Vary [S]. Either include or exclude the inhibitor. One word.

110 Da

Average molecular weight of an amino acid.

siRNA

Interferes with the expression of specific genes with complementary nucleotide sequences by degrading mRNA after transcription, resulting in no translation.

Hill Coefficient

It describes the fraction of the macromolecule saturated by ligand as a function of the ligand concentration; it is used in determining the degree of cooperativeness of the ligand binding to the enzyme or receptor. n>1 positive cooperative binding n<1 negative cooperative binding n=1 noncooperative binding

Gallbladder

Stores bile.

Pancreas

Secretes glucagon.

Parietal Cell

Secretes HCl

Liver

Detoxifies drugs.

Noncompetitive

One word. Inhibitor that binds to the E and the ES Complex with same affinity.

Effector

One word. A small molecule that selectively binds to a protein and regulates its biological activity. In this manner, these molecules act as ligands that can increase or decrease enzyme activity, gene expression, or cell signalling.

True

True or False? Bacteria can lyse cells.

Asparagine and Glutamine

Only amino acid with amide group. ___and____ (alphabetical).

Isoelectric Focusing

A technique of electrophoresis in which the resolution is improved by maintaining a pH gradient between the electrodes.

Autoradiograph

An image on an x-ray film or nuclear emulsion produced by the pattern of decay emissions (e.g., beta particles or gamma rays) from a distribution of a radioactive substance.

Acetyl

A functional group, the acyl with chemical formula CH3CO. It is sometimes represented by the symbol Ac (not to be confused with the element actinium). This group contains a methyl group single-bonded to a carbonyl.

Allele

Different protein isoforms are synthesized through the same gene via alternative splicing, NOT from a different _____ on another chromosome?

Post-Translational Modification

Refers to the covalent and generally enzymatic modification of proteins during or after protein biosynthesis. Proteins are synthesized by ribosomes translating mRNA into polypeptide chains, which may then undergo PTM to form the mature protein product.

Peptide

FSH what kind of hormone?

Connective

One word. Type of tissue that connects, supports, binds, or separates other tissues or organs, typically having relatively few cells embedded in an amorphous matrix, often with collagen or other fibers, and including cartilaginous, fatty, and elastic tissues.

Epithelial

One word. Type of tissue found to line the cavities and surfaces of blood vessels and organs throughout the body.

Nervous

One word. Type of tissue. Component of the two parts of the nervous system; the brain and spinal cord of the central nervous system (CNS), and the branching peripheral nerves of the peripheral nervous system (PNS), which regulates and controls bodily functions and activity.

Kd

Higher affinity corresponds to lower…? (Which constant?)

In Vitro

Conclusions on therapeutic treatments should not be draw from experiments done…?

Glycosylation

Post-translational _________ can promote protein folding and improve stability as well as serving regulatory functions?

Lipidation

Post-translational ___________often targets a protein or part of a protein to the cell membrane.

Phosphorylation

Most common post-translational modification. Helps regulate activity of enzymes.

Noncompetitive

Which type of inhibitor does NOT alter the KM/Vmax ratio of an enzyme?

Mixed

One word. Type of enzyme inhibition in which the inhibitor may bind to the enzyme whether or not the enzyme has already bound the substrate but has a greater affinity for one state or the other. Conceptual mixture of both competitive inhibition, in which the substrate is not bound, and uncompetitive inhibition, in which the inhibitor can only bind the enzyme if the substrate has already bound.

Uncompetitive

One word. Type of inhibitor that binds the enzyme once the substrate has already bound. Works better in higher substrate concentrations in which ES Complexes are more abundant.

Immunoprecipitation

AKA – "Pulldown." Precipitating a protein antigen out of solution using an antibody that specifically binds to that particular protein. This process can be used to isolate and concentrate a particular protein from a sample containing many thousands of different proteins.

Capase

Family of protease enzymes playing essential roles in programmed cell death (including apoptosis, pyroptosis and necroptosis) and inflammation.

Consensus Sequence

Sequence alignments in which related sequences are compared to each other and similar sequence motifs are calculated. Calls RNA Polymerase or nuclear factors to the scene.

Nuclear Localization Domain

Amino acid sequence that ‘tags’ a protein for import into the cell nucleus by nuclear transport.

Signal Peptide

(Sometimes referred to as signal sequence, targeting signal, localization signal, localization sequence, transit peptide, leader sequence or leader peptide) is a short (5-30 amino acids long) peptide present at the N-terminus of the majority of newly synthesized proteins that are destined towards the secretory pathway.

Nuclear Localization Domain

Amino acid sequence that ‘tags’ a protein for import into the cell nucleus by nuclear transport.

Signal Peptide

(Sometimes referred to as signal sequence, targeting signal, localization signal, localization sequence, transit peptide, leader sequence or leader peptide) is a short (5-30 amino acids long) peptide present at the N-terminus of the majority of newly synthesized proteins that are destined towards the secretory pathway.

Nuclear Localization Domain

Amino acid sequence that ‘tags’ a protein for import into the cell nucleus by nuclear transport.

Signal Peptide

(Sometimes referred to as signal sequence, targeting signal, localization signal, localization sequence, transit peptide, leader sequence or leader peptide) is a short (5-30 amino acids long) peptide present at the N-terminus of the majority of newly synthesized proteins that are destined towards the secretory pathway.

Nuclear Localization Domain

Amino acid sequence that ‘tags’ a protein for import into the cell nucleus by nuclear transport.

Signal Peptide

(Sometimes referred to as signal sequence, targeting signal, localization signal, localization sequence, transit peptide, leader sequence or leader peptide) is a short (5-30 amino acids long) peptide present at the N-terminus of the majority of newly synthesized proteins that are destined towards the secretory pathway.

Nuclear Localization Domain

Amino acid sequence that ‘tags’ a protein for import into the cell nucleus by nuclear transport.

Signal Peptide

(Sometimes referred to as signal sequence, targeting signal, localization signal, localization sequence, transit peptide, leader sequence or leader peptide) is a short (5-30 amino acids long) peptide present at the N-terminus of the majority of newly synthesized proteins that are destined towards the secretory pathway.

Nuclear Localization Domain

Amino acid sequence that ‘tags’ a protein for import into the cell nucleus by nuclear transport.

Signal Peptide

(signal sequence, targeting signal, localization signal, localization sequence, transit peptide, leader sequence or leader peptide) is a short (5-30 amino acids long) peptide present at the N-terminus of the majority of newly synthesized proteins that are destined towards the secretory pathway.

Nuclear Localization Domain

Amino acid sequence that ‘tags’ a protein for import into the cell nucleus by nuclear transport.

Transcription Factor

(Sometimes called a sequence-specific DNA-binding factor) is a protein that binds to specific DNA sequences, thereby controlling the rate of transcription of genetic information from DNA to messenger RNA.

Capase

Family of protease enzymes playing essential roles in programmed cell death (including apoptosis, pyroptosis and necroptosis) and inflammation.

Transcription Factor

Nuclear factor is a…?

Enhancer

A short (50-1500 bp) region of DNA that can be bound by proteins (activators) to increase the likelihood transcription that will occur at a gene. These proteins are usually referred to as transcription factors.

Promoter

A region of DNA that initiates transcription of a particular gene. Usually located near the transcription start sites of genes, on the same strand and upstream on the DNA (towards the 5′ region of the antisense strand).

Hydrophobic

Side chains of what kind of amino acids (one word) are most likely to be at dimer interface if protein is present in cytosol?

Affinity Mass

SDS-PAGE separates molecules based on ____ and ____? (alphabetical)

Isoelectric Point

Isoelectric focusing separates molecules based on…?

Charge

Ion-Exchange Chromatography separates molecules based on net…?

Glucokinase

Enzyme that facilitates phosphorylation of glucose to glucose-6-phosphate.

Hexokinase

An enzyme that phosphorylates hexoses (six-carbon sugars), forming hexose phosphate.

Glucose-6-Phosphatase

An enzyme that hydrolyzes glucose-6-phosphate, resulting in the creation of a phosphate group and free glucose.

Phosphoglucomutase

An enzyme that transfers a phosphate group on an α-D-glucose monomer from the 1′ to the 6′ position in the forward direction or the 6′ to the 1′ position in the reverse direction.

Binding

After an amino acid substitution in an enzyme, if the Kd didn’t change, then that residue was not involved in the ____ site?

DNA Amplification

In cloning cDNA, DNA Polymerase does what?

Ligates cDNA to DNA vector

In cloning cDNA, Ligase does what?

Inverse transcription of RNA to cDNA

In cloning cDNA, Reverse Transcriptase does what?

Nothing

In cloning cDNA, RNA Polymerase does what?

dNTPs

The building blocks for DNA (they lose two of the phosphate groups in the process of incorporation).

Stability

π-stacking increases what?

Glucagon

Mobilizes hepatic glycogen so we can burn it.

Gluconeogenesis

A metabolic pathway that results in the generation of glucose from certain non-carbohydrate carbon substrates.

Glycogenolysis

The biochemical breakdown of glycogen to glucose whereas.

Glycogenesis

The formation of glycogen from sugar.

Acetyl-CoA

Its main function is to convey the carbon atoms within the acetyl group to the citric acid cycle (Krebs cycle) to be oxidized for energy production.

Oxaloacetate

A metabolic intermediate in many processes. It takes part in the: gluconeogenesis, urea cycle, glyoxylate cycle, amino acid synthesis, fatty acid synthesis and citric acid cycle.

Key intermediate in the Krebs cycle, coming after isocitrate and before succinyl CoA.

Alpha-Ketoglutarate

Glutamine is synthesized from glutamate by glutamine synthetase, which utilizes an ATP to form glutamyl phosphate; this intermediate is attacked by ammonia as a nucleophile giving glutamine and inorganic phosphate.

Alpha-Ketoglutarate

One of the most important nitrogen transporters in metabolic pathways. The amino groups of amino acids are attached to it (by transamination) and carried to the liver where the urea cycle takes place.

Alpha-Ketoglutarate

Is transaminated, along with glutamine, to form the excitatory neurotransmitter glutamate. Glutamate can then be decarboxylated (requiring vitamin B6) into the inhibitory neurotransmitter GABA.

Gluconeogenesis

Lactate, glycerol, and glucogenic amino acids are all possible substrates for…?

G-Protein

Activation of ______promotes dissociation of bound GDP and its exchange for GTP on the alpha subunit.

G-Protein

Activation of coupled ________ leads to activity of adenylate cyclase and protein kinase.

Adenylate Cyclase

Catalyzes the conversion of adenosine triphosphate (ATP) to 3′,5′-cyclic AMP (cAMP) and pyrophosphate.

cAMP

A second messenger important in many biological processes. cAMP is a derivative of adenosine triphosphate (ATP) and used for intracellular signal transduction in many different organisms, conveying the _____-dependent pathway.

Glycogen Phosphorylase

Catalyzes the rate-limiting step in glycogenolysis in animals by releasing glucose-1-phosphate from the terminal alpha-1,4-glycosidic bond.

Phosphogluconate

Which of the following compounds is NOT a gluconeogenic precursor or substrate? Glycerol, Lactate, Phosphogluconate, Oxaloacetate

Cyclase

An enzyme, almost always a lyase, that catalyzes a chemical reaction to form a cyclic compound

Lyase

An enzyme that catalyzes the joining of specified molecules or groups by a double bond.

Acetylase

Any enzyme catalyzing acetylation or deacetylation, as in the formation of N-acetylglutamate from glutamate plus acetyl-CoA, or the reverse; acetylases are usually called acetyltransferases.

GTP and Succinate

Under physiological conditions, increased activity of succinyl-CoA synthetase will most likely result in greater levels of the reaction products, "__XXX___ and _____".

NADPH

The pentose phosphate pathway results in the generation of…?

NADPH

A reductive agent in cellular respiratory processes resulting from the PPP pathway.

Competitive

The Vmax of an enzymatic reaction is altered by all but which? Competitive Noncompetitive Uncompetitive Mixed

Substrate Analog

Two words. Are chemical compounds with a chemical structure that resemble the substrate molecule in an enzyme-catalyzed chemical reaction.

Cofactor

A substance (other than the substrate) whose presence is essential for the activity of an enzyme

Prosthetic Group

Two words. A nonprotein group forming part of or combined with a protein.

Coenzyme

A nonprotein organic compound that is necessary for the functioning of an enzyme.

Scavenger

One word. A chemical substance added to a mixture in order to remove or de-activate impurities and unwanted reaction products.

Lipoic Acid

An organosulfur compound derived from octanoic acid. Is essential for aerobic metabolism.

Glucose-6-Phosphate Dehydrogenase

In the pentose phosphate pathway, which enzyme catalyzes the production of 6-phosphogluconolactone?

Coding Strand

Two words. The DNA strand which has the same base sequence as the RNA transcript produced. "Sense"

Template Strand

Two words. The DNA strand from which RNA Polymerase reads to produce mRNA.

Which recombinant processes depends on the F factor plasmid?

Conjugation

Inflation of the lungs occurs by __.

Negative pressure pumping

Which of the following occurs during mitosis but NOT during meiosis I?
-Synapsis
-Splitting of centromeres
-Pairing of homologous chromosomes
-Breakdown of nuclear membrane

Splitting of centromeres

T/F: During oocyte meiosis/division, the polar bodies have an equal amt of nuclear mat’l.

F-they have an unequal amt of cytoplasmic mat’l

A higher rate of reabsorption of a sustance in the kidney =&gt; __ rate of clearance.

Lower

INC’d vasocronstriction has an important role in which of the following situations?
A) Causing DEC’dBP assoc’d w/ fainting
B) INC’ing blood flow to skin during exercise
C) INC’ing bloodflow to skin during blushing
D) Maintaining BP during hemorrhage

D) Maintaining BP during hemorrhage

Low Ca in blood will trigger INC in:
I. PTH
II. Osteoclast activity
III. Vitamin C (needed for bone formation)

I & II only

What would trigger release of calcitonin?

When blood Ca2+ too high

The chemical valinomycin inserts into membranes &amp; causes movement of K+ into the mito. If mitochondria are treated w/ it what will happen to the rate of ATP synthesis &amp; why?

Would DEC b/c would disrupt the movement of H+ into the intermembrane space

Sliding filament model = ?

Delayed ovulation would be assoc’d w/ delayed secretion of which hormone?

Luteinizing hormone

Hill coeff &gt; 1 means __.

Enz exhibits cooperativity

Noncompetitive inhibitors bind the enzyme &amp; ES complex w/ same/different affinity?

Same

Reducing cond’ns in SDS PAGE serve what purpose?

Cleave diS bonds

Which does NOT contribute to stabilization of 4º structure of protein?
-diS
-Phosphodiester bond
-H bond
-Salt bridge

-Phosphodiester bond

Which type of inhibition does NOT alter the Km/Vmax ratio?

Uncompetitive

Uncompetitive inhibition = ?

Inhibition in which I can only bind the ES complex

An enz is more effectively inhibited by uncompetitive inhibitors when:
I. [S] DEC’s
II. [S] INC’s
III. [I] INC’s

II & III

What is the avg MW of an AA?

110 Da

Which methods separate proteins based on charge?
I. SDS-PAGE
II. Ion Exchange Chromatography
III. Isoelectric focusing
IV. Affinity chromatography

II & III

How many molecules of reduced e- carrier are generated during conversion of a-KG to OAA during the TCA cycle?

3: 2 NADH & 1 FADH2

Which enz is used in both gluconeogenesis &amp; glycogenolysis?
A) Phosphoglucomutase
B) G-6-Phosphatase
C) Hexokinase
D) Glucokinase

B) G-6-Phosphatase

Which is NOT a gluconeogenic pre-cursor/substrate?
A) Lactate
B) Glycerol
C) OAA
D) Phosphogluconate

D) Phosphogluconate

Under physiological cond’ns, INC’d activity of Succinyl-CoA Synthetase would most likely result in:
I. INC’d levels of Succinyl-CoA
II. INC’d levels of Succinate
III. INC’d levels of GTP

II & III

___ inhibitors are the only ones that don’t alter the Vmax of an enz.

Competitive

In the PPP which enz catalyzes the production of 6-phosphogluconolactone?

G-6-P DH

What is the seq of the corresponding mRNA for the DNA coding strand below?
5′-GACATGGACTCGCTA-3′

5′-GACAUCGACUCGCUA-3′

Which CANNOT be used to analyze gene exp’n?
A) W blot
B) S blot
C) N blot
D) RT PCR

B) S blot

Microfilaments are composed of __.

Actin

What is best control for autophosphorylation of an enz? Why?

-Enz alone + ATP w/o substrate -To make sure that detected phosphorylation is due to autophisphorylation & not the substrate being phosphorylated

What is the best way to test for competitive inhibition?

-Keep [E] constant -Vary [S] w/ & w/o inhibitor present

The tissues of the heart &amp; blood vessels are derived from which germ layer?

Mesoderm

For different cells w/in the same organism containing the same DNA,

Trans-acting element = ?

Regulatory gene sequences that will be used in the regulation of another target gene

__ AA’s are most likely to be involved in dimerization b/c __.

Hydrophobic Free & not interacting w/ H2O

According to the sliding filament model of muscle contraction, which event most directly causes muscle relaxation?

ATP binds myosin head

When glycogen stores are depleted, which of the following can be used as precursors to maintain blood glucose levels?
I. Acetyl-CoA
II. Lactate
III. OAA
IV. alpha-KG

II, III & IV

What is the cofactor for PDC?

Lipoic acid

The heart, kidneys, and skeletal muscle are derived from which germ layer?

Mesoderm

In the sliding filament model for muscle contraction, what is the role of ATP?

-Binds the myosin head & causes it to be released from binding sites on actin filament -> leads to relaxation -Then is hydrolyzed & re-positions myosin head for another contraction

Proteins that are translocated to the nucleus must contain __.

Nuclear localization sequence

Histone acetylation would be best analyzed by __.

W blot

Post-translational modifications are best analyzed by __.

W blot

Blood from the small intestine is first transported to __.

Liver

Microtubules originate from __.

Centrosome

SDS-PAGE separates proteins based on __ &amp; grants a uniform __ charge to all of them.

-Size only -Negative

How does the anti-sense RNA seq compare to the original DNA seq?

Same, but w/ sub T -> U

Stereochemical designators a &amp; ß distinguish b/w ?

Epimers @ anomeric C atom

Depolarization of the muscle fiber membrane is mediated by what kind of channel &amp; ion?

-Influx of Na+ across motor end plate thru ligand-gated ion channel

How does S blot differentiate b/w mutant &amp; WT alleles?

Restriction digest- elimination/creation of restriction site (4-6 bp palindrome)

cDNA contains what parts of mRNA?

Exons only

A Hill coeff = 1 means __.

Enx doesn’t exhibit cooperativity

Phosphorylation of which AA residues is most likely?

-Ser, Thr (& His)

FSH is a __ hormone.

Peptide

Mixed vs uncompetitive inhibition?

-Uncomp: only binds ES complex -Mixed: can bind ES or E alone but has greater affinity for 1

Signal sequence domains are required for __.

Proteins directed toward secretory pathways

Temporal &amp; spatial gene regulation = ?

-Temporal = when genes are exp’d only @ specific times -Spatial = when genes are exp’d only @ specific location in organism

Nuclear factors are __-acting elements

Trans

What types of proteins are involved in dimerization &amp; protein-protein interactions?

Hydrophobic

SDS PAGE non-reducing vs reducing = ?

-Non-red: only breaks 4º structure -Red: breaks 4º structure & reduces diS bridges

In cation exhcange chromatography, the stationary phase binds __ &amp; __ elute first.

-Binds cations (+), anions elute (-)

Glucose-6-Phosphatase catalyzes the final step in which processes?

Gluconeogenesis & glycogenolysis

Anything that can __ can serve as gluconeogenic pre-cursors.

Generate pyruvate/OAA & be fed into the TCA cycle

What happens to the C atoms from acetyl-coA when it enters the TCA cycle?

Form CO2

PDC catalyzes conversion of ___.

Pyruvate to Acetyl-CoA

Phosphatase

Removes a phosphate group

Phosphorylase

Adds a phosphate group

Kinase

Transfers a phosphate group from ATP to an organic molecule

Microfilaments are made of…

Composed of actin (movement!!!!!)

Osmotic pressure

Directly related to osmolarity. Greater osmolarity = greater osmotic pressure

Average molecular weight of an amino acid

110 Da

Hill coefficient

Describes cooperativity of ligand binding. n>1 –> Positively cooperative (e.g. hemoglobin). n<1 –> Negatively cooperative n=1 –> Noncooperative

Vmax and kcat relationship

Direct. Vmax = kcat[E]

Signal sequence domains

Protein domains required for proteins that are directed toward secretory pathways

Enhancers

DNA sequences that activators (proteins) bind to to promote/enhance transcription

Nuclear factors

A type of transcription factor

Protein-protein interactions (such as dimerization) typically involve what kind of amino acid residues?

Hydrophobic

Possible starting materials for gluconeogenesis

Lactate, oxaloacetate, a-ketoglutarate, glycerol, …

Glucagon

Promotes mobilization of endogenous glucose storage

Rate-limiting enzyme of glycogenolysis

Glycogen phosphorylase

Linear linkages in glycogen

alpha (1–>4)

Branch point linkages in glycogen

alpha (1–>6)

Proton gradient

More protons in the IMS Proton pumping in the ETC pumps protons into the IMS

Coding strand

Complementary to the template strand. Has the same sequence as the mRNA strand except with T’s instead of U’s (also introns)

ATP per glucose: Glycolysis

2

ATP per glucose: Cellular respiration overall

30-32

Myoglobin

Holds oxygen in muscles & organs

Two primary factors that determine the level of blood pressure

1. Cardiac output 2. Resistance to blood flow

Relationship between blood pressure and amount of substance in the urine

Low b.p. decreases the glomerular filtration rate, allowing more time for reabsorption & decreasing the amount of the substance in the urine.

Oxidoreductase

catalyze oxidation-reducation reactions Examples: Dehydrogenase Reductase

Transferase

Catalyze the movement of a functional group from on molecule to another Examples: Kinase: Catalyze the transfer of phosphate group, generally from ATP, to another molecule Phosphorylase: Catalyzes the transfer of a phosphate group from an inorganic group to an acceptor

Kinase

Catalyze the transfer of phosphate group, generally from ATP, to another molecule

Hydrolase

Catalyze the BREAKING of a compound into two molecules using the addition of water. Creates two products Example: Phosphatase: cleaves phosphate Peptidases: Cleave peptides Nucleases: Cleave nucleic acids Lipase: cleaves lipids

Lyases

Catalyze the cleavage of a single molecule into two produces without the addition of water WHEN WATER IS PRESENT: the addition of water breaks a double bond or triple bond so that other bonds can form (hydratase) the REVERSE is the removal of water to form a double or triple bond, HOWEVER, there is only ONE substrate and ONE product + water (dehydratase) Examples: Aldolase Enolase citrate synthase

Isomerases

Catalyze the rearrangement of bonds within a molecule within stereoisomers as well as constitutional isomers

Ligases

Catalyze addition or synthesis reactions, generally between large similar molecules and often require ATP nucleic acid synthesis and repair

Synthase

Can be a ligase or lyase create a bond between two molecules without ATP

Synthetase

Creates a bond between two molecules with the addition of ATP Only a ligase

Sympathetic nervous system does what to the blood vessels?

Constricts

Sarcomere

Process of action potential in muscles

1. ACh binds and causes the Na+ ligand-gated channels at the motor end plates to open (-70mv) 2. Influx of Na+ depolarizes inside the cell causing voltage gated Na+ channels to open (-55mV) 3. Cell depolarizes which initiates action potential and the sodium gated voltage-gated channels close (35mv) 4. Action potential propagates along entire sarcolemma down each T-tubule causing VGC Ca2+ channels to open

Van’t Hoff factor for non ionic bonds

1

Van’t Hoff factor for MgCL2

3

Van’t Hoff factor for NaCl

2

Kd

dissociation constant and measures the dissociation of SUBSTRATE from the ES complex The higher the Kd, the lower the substrate-enzyme affinity

Kcat

Kcat is a measure of the catalytic production of product per second Measured as Kcat/s Therefore, the reciprical of Kcat can be thought of as the time it takes for a certain amount of product to be produced the higher the Kcat, the higher Vmax

Vmax

maximum initial velocity of the enzyme catalyzed by a reaction under certain conditions Kcat * [Enzyme]

Ki

Measures affinity of an inhibitor Higher Ki, the lower the enzyme affinity is to the substrate

Km

concentration of a substrate in which the system would be working at HALF of Vmax

Ka

Is the association constant, which measures the ratio of enzyme-ligand to free enzymes. This measures only binding affinity Ka = 1/Kd

Competitive inhibition

Occupies only the active site INCREASES Km Vmax stays the same can be overcome by adding more substrate

Noncompetitive inhibition

Binds at an allosteric site Cannot be overcome by adding more substrate Binds equally well to the enzyme and the substrate-enzyme complex Decreases Vmax, but Km statys the same

Southern Blot

Detects specific DNA sequences using restriction endonucleases and gel electrophoresis

Restriction endonucleases

An enzymes that recognizes specific double stranded sequences. The sequence must be palindromic ->GAATTC <-CTTAAG Mutations must cause or delete a palindromic sequence to be useful in southern blot testing

Polymerase Chain Reaction (PCR)

automated process that can produce millions of copies of DNA sequences without amplifying the DNA bacteria Requires primers that are complementary to the DNA that flanks the region of interest Requires high amounts of G-C in the primers, because G-C have 3 H-bonds, while A-T only have 2 H-bonds. PCR requires heating to unneal the DNA strand

Western Blot

detects specific proteins in a sample of tissue using gel electrophoresis to separate native proteins by structure or length best for measuring gene expression

Northern blot

adaptation of the southern blot procedure used to detect specific RNA sequences by hybridization with complementary DNA

Bond type between nucleic acids

Phosphodiester bonds

Bond type between amino acids

Retrovirus

Carries reverse transcriptase which synthesizes DNA from an RNA strand DNA is then implemented into it’s DNA strand where it will produce that DNA the RNA strand that is transcribed to a protein is the same as the reverse transcriptase

Weight of an amino acid

110 Da 0.110 kDA

PAGE electrophoresis

analyzes proteins in their native state Limited by varying mass-to-charge and mass-to-size ratios of cellular protein because multiple different proteins may experience the same level of migration Proteins can be recovered in this method if they are not stained (because stains denature protein) Most useful in comparing molecular size or charge of proteins known to be in similar size from other analytic methods like SDS-PAGE or size-exclusion chromatography

SDS-PAGE electrophoresis

Sodium dodecyl sulfide separates based on mass SDS binds to proteins and creates large chains with net negative charges, thereby neutralizing the protein’s original charge and denaturing the protein The only variable affecting their velocity is f, the frictional coefficient, which depends on mass SDS page can not reduce disulfide bonds (covalent bonds) requires a stronger reducing agent

Isoelectric focusing

must establish a stable pH gradient on the gel pI = pH the protein or amino acid is neutral positive anode, negative cathode protein stops moving at the pH the atom is negative, because the anode or cathode won’t be drawing it towards it any longer

Column Chromatography

Column with silica or alumina beads as adsorbent Size and polarity are the limiting factors More polar, less speed

Ion-Exchange chromatography

Beads in column are coated with charged substances to attract compounds salt is used to elute charged molecules

Size-exclusion chromatography

Beads in the column contain pores

Affinity chromtography

Coat beads with receptors that binds the protein

What happens when you use a reducing agent in gel electrophoresis?

It disrupts the disulfide bonds

Gallbladder

stores bile

Liver

creates bile receives all blood from abdomen from the hepatic portal vein crates glycogen and stores fats into triacyglycerol detoxifies compounds

Pancreas

Secretes insulin, glucagon and somatostatin

Isoform

Two similar proteins that are almost identical in amino acid sequence Resulted from alternative splicing in post transcriptional modification

3 Bp =

1 residue

Deamidation

results in the formation of NH3

cDNA

complentary DNA DNA that is made from reverse transcribing RNA does not require RNA polymerase, because it starts as an mRNA

Transcription

1. Helicase and topoisomerase prevent supercoiling as well as uncoil the strand 2. RNA polymerase II transcribes mRNA. It binds at the TATA box. Transcription factors help RNA polyermase locate and bind 3. RNA polymerase travels along the 3′ to 5′ strand so it can synthesize in the 5′ to 3′ direction

Bacteria promotor for DNA

-10 and -35

Epithelial tissue

forms outer layer of the skin, lines cavities of the digestive and respiratory system; covers the walls of organs of the closed ventral body cavity. Also lines some parts of the FEMALE reproductive tract

Connective tissue

adipose tissue, cartilage, bone and blood

Peptide Hormone

Made of amino acids Derived from larger polypeptides that are cleaved during posttranslational modification released via exocytosis Charged and cannot pass through plasma membrane First messenger Soluble in blood

Steroid Hormone

Derived from cholesterol and produced by the gonads and adrenal cortex Nonpolar Receptors usually intracellular or intranuclear Receptors can bind directly to DNA, altering transcription rate slower, but longer lived

GLUT-2

Low affinity transporter in hepatocytes and pancreatic cells Captures excess glucose for storage Does not respond to insulin Km is high (low affinity). High Km allows for glucose sensing

GLUT-4

In adipose tissue and muscles and responds to glucose concentration Rate is increased by insulin Low Km to maintain a constant rate of glucose influx

Michaelis-Menten Equation

measures velocity of the enzyme-substrate reaction

PCR Steps

1. Heat up the DNA and the strands will separate 2. Add a shit ton of primer and Taq polymerase w/ nucleotides 3. Taq polymerase will attach the nucleotides for gene amplification

Souther blot steps

1. Cleave DNA to create smaller pieces (with an enzyme) 2. Gel electrophoresis to separate strands 3. Transfer Gel onto filter and the fragments will transfer onto the filter 4. Expose to radiolabeled complementary DNA 5. Expose filter to x-ray film to visualize

cDNA steps

1. Take mRNA and add reverse transcriptase 2. cDNA will form, but it is only single stranded, so we add DNA polymerase 3. DNA is now double stranded 4. Inject DNA into cloning vector (plasmid or virus) and infect a bacteria

How many phosphate groups do nucleotides have?

3 phosphate groups before being bound to a chain of nucleic acids, where then it will have only 1

5′ to 3′ of nucleic acid

5′ is phosphate group 3′ is hydroxyl group

rRNA

helps mRNA bind to the right spot can act as enzymes to catalyze reactions known as rybozymes

tRNA

bring amino acids to ribosomes

miRNA and si RNA

about 22 nucleotides long bind to specific mRNA molecules to increase stability or interfere with translation

Which is stronger T-A or G-C?

G-C because 3 hydrogen bonds

Purines

Purines always glow Adenine, Guanine

A-T

G-C

Where does Beta-Oxidation occur?

In the mitochondria

What is the rate limiting step in Glycolysis?

Conversion of Fructose-6-phosphate to fructose-1,6-bisphosphate by PFK-1

What is the rate limiting step of Gluconeogenesis?

Conversion of Fructose-1,6-bisphosphate to fructose-6-phosphate by fructose-1,6-bisphosphatase

What is the rate limiting step of Glycogenesis

Glycogen synthase which forms the alpha (1,4) linear linkages in glycogen

What is the rate limiting step of Glycogenolysis?

Glycogen phosphorylase breaks the alpha 1,4 linkages of glycogen and releases glucose-1-phosphate

What is the rate limiting step of the pentose phosphate pathway?

Glucose-6-phosphate is converted into 6-phosphogluconate (or 6-phosphoglucanolactone) by glucose-6-phosphate dehydrogenase (G6PD)

What is the rate limiting step of fermentation?

Lactate dehydrogenase reduces pyruvate to lactate, which in return oxidizes NADH to NAD+

Steps of PDH

1. Pyruvate is oxidized to yield CO2 and is bonded to TPP to form Acyl-TPP 2. Acyl-TPP is oxidized by lipoic acid to become Acyl-lipoate and frees the TPP. 3. Lipoic acid acts as an oxidizing agent to oxidize Acyl to become an acetyl group. Lipoic acid is now reduced 4. Dihydrolipoyl transacetylase catalyzes the interaction of CoA-SH to the acetyl group to form Acetyl-CoA. Lipoc acid is still reduced 5. Reduced Lipoic acid reacts with FAD. FAD becomes FADH2 and lipoic acid is now oxidized 6. FADH2 reacts with NAD+ to produced FAD and NADH to replenish the FAD

microfilaments

made of the protein actin and help support the shape of the cell

microtubules

hollow rod composed of tubulin proteins that makes up part of the cytoskeleton in all eukaryotic cells and is found in cilia and flagella

intermediate filaments

cytoskeletal components that are composed of various proteins

thick filaments

relatively massive bundles of subunits made of myosin

thin filaments

composed of actin, troponin, tropomyosin

antagonist

a type of receptor ligand or drug that blocks or dampens a biological response by binding to a receptor rather than provoking the response

agonist

a chemical that binds to a receptor and activates the receptor to produce a biological response

anomeric carbon

the new chiral center formed in ring closure; it was the carbon containing the carbonyl in the straight-chain form

epimer

diastereomers that differ in configuration at only one chiral carbon

enantiomers

molecules that are mirror images of each other

Southern Blot

uses restriction enzymes to ID mutations (fragments made are shown during electrophoresis)

110 Da

average molecular weight of an amino acid

positive cooperativity

Hill coefficient > 1

no cooperativity (enzyme follows normal M-M kinetics)

Hill coefficient = 1

negative cooperativity

Hill coefficient < 1

adenine

guanine

cytosine

thymine

nuclear factors

elements affecting DNA transcription that vary between cells

2 NADH 1 FADH2

alpha ketoglutarate to oxceloacetate makes

glycogen phosphorylase

enzyme that catalyzes the rate limiting step in glycogen breakdown

pentose phosphate pathway

NADPH created to make 5 carbon sugars

hf

E =

wavelength * frequency

c =

Vmax/[Etotal]

Kcat =

gamma

kinases use which ATP phosphate

Venturi effect

eduction in pressure of a fluid resulting from the speed increase as fluids are forced to flow faster through narrow spaces

Doppler effect

an observed change in the frequency of a wave when the source or observer is moving

coordinate covalent bond

bond in which the shared electron pair comes from the lone pair of one of the atoms in a molecule

coordination number

the number of ions of opposite charge that surround the ion in a crystal

pH = pKa + log([A-]/[HA])

Henderson Hasselbach equation

[A]^b[C]^d

Ksp of [AbCd] =

ubiquitination

proteins are targeted for degradation by a proteasome

proteasome

recognize ubiquitin-tagged proteins and degrade them.

GADPH

G3P to 1,3-bisphosphoglycerate

Schwann Cells

supporting cells of the PNS responsible for the formation of myelin

microglia

small, wandering cells that engulf cell debris and pathogens in the CNS are called

astrocytes

nourish neurons and form the blood-brain barrier, which controls the transmission of solutes from the bloodstream into nervous tissue

oligodendrites

nervous system cell that myelinates multiple CNS axons

conflict theory

views society in terms of competing groups that act according to their own self-interests, rather than according to the need for societal equilibrium

functionalism

factions of society work together to maintain stability; claims that society, like an organism, is a system that consists of different components working together

life course perspective

an approach to human behavior that recognizes the influence of age but also acknowledges the influences of historical time and culture

source monitoring error

a specific type of error of recollection where a memory is incorrectly attributed to the wrong source

right

hemisphere for visuospatial skills, music perception, and emotion

interference

any new material introduced between initial learning (encoding) and retrieval

emotional intelligene

ability to perceive, express, understand and manage one’s emotions; can delay gratification in pursuit of long term rewards

cognitive behavioral therapy

first systematically modify maladaptive behavior then foster cognitive change through self assessments

symbolic interactionism

approach that focuses on the interactions among people based on mutually understood symbols

hydroquinone

hyperbolic

traditional Mechalis Menten curve

competitive

up Km, no change Vmax

noncompetitive

no change Km, down Vmax

uncompetitive

down Km, down Vmax

kcat/Km

catalytic efficiency

C

1 H bond donor, 2 H bond acceptors

G

2 H bond donor, 1 H bond acceptor

Why can’t you inject mouse antigen to humans?

Because they will recognize it but it will produce anti-mouse antibodies, which is not useful to fight human ones.

Cytochrome c carries how many electrons?

1e-

suffix for further oxidizable

-ic (ferric 3+)

suffix for further reduceable

-ous (ferrous2+)

Effects of ↑insulin

↑glucose uptake ↓[blood glucose]

effects of ↑glucagon

↓glucose uptake ↑[blood glucose]

When ↓E, what is more important? Transport capacity or affinity?

Km because it doesn’t require energy

antigenicity

capacity of a chemical structure (either an antigen or Hapten) to bind specifically with a group of certain products that have adaptive immunity: T cell receptors or antibodies. -used by parasites to "hide" from human immune system

pineal gland

How does bacteria replicate?

Not by mitosis! binary fission, they can also extend independent life.

What is the advantage of RBC passing in lung capillaries in single file?

more SA is exposed therefore, ↑efficiency for gas exchange

Operon

embryogenesis

endoderm

gut tube and its derived organs: cecum, intestine, stomach, thymus, liver, pancreas, lungs, thyroid and prostate.

mesoderm

cardio, skeletal, bone, report, RBC, gut (smooth cells).

ectoderm

skin, neuron, mouth, pigment

describe actin

has polarity, microfilament, can bind ATP

cytoskeleton, what kind of filament?

Intermediate, no polarity, doesn’t bind ATP

Northern Blot

detect RNA sequence by cDNA

Southern Blot

detect DNA sequence by probes, uses rest. sites to digest

Restriction sites

palindromes 4-6bp,

+RNA virus

must encode RNA-dep RNA polymerase

-RNA viruse

must encode and carry own RNA-dep RNA polymerase

Retrovirus

must encode reverse transcriptase

weight of 1 amino acid

110Da

SDS-PAGE using reducing agents disrupts what bonds?

disulfide aka 3°

advice

if the data doesn’t support it don’t choose it analyze what the y and x axis means

probability

event/all

isoforms

any of two or more functionally similar proteins that have a similar but not identical amino acid sequence and are either encoded by different genes or by RNA transcripts from the same gene which have had different exons removed.

cDNA

ds DNA from ssRNA via reverse transcriptase

Hill coefficient

cooperativity H > 1 cooperative H < 1 NOT

cooperativity

binding one ↑affinity for more binding

What can’t you phosphorylate?

non polar AA

(-) control

(-) results expected

(+) control

(+) results expected

are peptide hormones soluble?

yes, they are hydrophilic, can’t just diffuse, needs receptor

what stabilized 3° structures?

S-S H-bond Salt bridge

What are signal sequence domains?

protein domains required for proteins that are directed toward secretory pathways.

Tru or false: All cells of one indiv. has the same genes, promoters and enhancers.

True

In an individual, do all of his/her cells have the same nuclear factors?

NO. they vary in different cells and can confer both temporal and spatial regulation of their target genes.

Which types of A.A. are involved in dimerization interface?

Hydrophobic A.A. because polar and charged will face the water in the cytosol instead.

How are isoforms formed?

alternative splicing of eons of the primary transcript

If proteins don’t split up at a non-reducing SDS page, they are ______________ linked.

covalently linked.

What defines covalently linked?

S-S

What methods separate proteins based on their charge?

Isoelectric focusing (based on pI, pH where net charge is 0) Ion-exchange chromatography

Catalytic efficiency, which has more leverage?

Km (more important for this to be small than kcat to be big.

If Ka or Kd doesn’t change after you substitute A.A. for another, what does that suggest?

That residue is not involved in binding to the substrate.

What is a good indicator of blood pressure?

Reactive oxygen species

Can you use Acetyl-CoA as a source for gluconeogenesis?

No. Acetyl-CoA goes to TCA and gets decarboxylated.

GPCR

What happens after ligand (ex. glucagon) binds to G-protein receptor?

↑adenylate cyclase activity ↑cAMP ↑ protein kinase A

G-protein coupled receptors

What is the rate limiting step in glycogenolysis?

Glycogen phosphorylase

Rate limiting step of glycolysis

PFK (F6P →F1,6BP)

Rate limiting step of Krebs

isocitrate dehydrogenase (iso→a-ketoglutarate +CO2+NADH)

Rate limiting step of PPP

G6P dehydrogenase (G6p→6Phosphygluconate + NADPH + H+)

Rate limiting step of FA synthesis

Acetyl-CoA carboxylase (Acetyl-CoA →Malonyl CoA

Rate limiting step of FA oxidation

none. entry way is carnitine acyltransferase 1 (palmitoylcarnitine–>palmitoyl CoA)

Rate limiting step of urea cycle

carbamoyl phosphate synthase 1 (ATP+HCO3+ammonia–>carbamoyl phosphate), mito only

Rate limiting step of glycogenesis

Glycogen synthase

Rate limiting step of gluconeogenesis

F1,6,Phosphatase (F1,6BP →F6P)

glycogen

alpha glycosidic linkage

Beta glycosidic linkage

Can phosphogluconate (from PPP) go through gluconeogenic pathway?

No.

Free radical scavengers mitigate the effects of ROS

What causes the electrochemical gradient in ETC?

H gradient (not e- gradient)

know the structures of citric acid cycle

coding DNA strand is the same as _______

mRNA strand

phosphorylase
phosphatase
kinase

adds P onto acceptor removes P from substrate (using H2O/hydrolysis) transfers P from ATP onto acceptor

Glycogen phosphorylase

adds P onto glycogen to make glucose-1-P, together with de-branching enzyme

Glycogen de-branching enzymes
-mechanism
-product
-how many?

Transfers a1–>4 from branch onto a1–>4 main chain, then cleaves off single a1–>6 branched glucose off. Results in glucose-1-P 2

What is the rate limiting step in glycogenolysis

glycogen phosphorylase step. glycogen –> glucose 1 P

how is glycogenolysis/glycogenesis connected to glycolysis?

glucose 1 P converts to glucose 6 P that feeds into gluconeogenesis or glycolysis

Glycogenesis

glucose 1 P (from converting glucose 6 P from glycolysis) is converted to UDP-glucose using UTP and glycogen synthase + 1 branching enzyme.

what does branching enzyme do?

transfers a1–>4 of main chain to a1–>6 of branch. Hydrolyze and attach.

nicotinic receptor
muscarinic receptor
cholinergic receptor
adrenergic receptor

Ach –> Ach Ach –> muscle receives Ach and secretes Ach (2 types: nicotinic, muscarinic) receives Ach and secretes norepinephrine

How do you use Southern Blot to differentiate between wildtype or mutant strands?

Use of the same restriction enzymes will tell you if mutant strand has a point mutation that makes the sequence no longer palindromic, thus not able to be cleaved by enzyme

Retroviruses have what in genome?

ssRNA

Steps of retroviral replication

vRNA (original HIV genome) –> vDNA –> mRNA vDNA via reverse transcriptase mRNA to start synthesizing proteins (viral proteins, though)

If effect is specific to Protein A, adding a different protein in experiment shows same results as…

control

Both parents are red (either heterozygous or homozygous dominant). What is the probability that both parents are heterozygotes?

2/3 x 2/3 = 4/9 because passage said parents are red

Cooperativity has Hill coefficient

greater than 1 Hill = Higher than 1; Hill < 1 means negative cooperativity (ligand binds, that decreases affinity for other ligands); Hill = 1 means NO cooperativity

GTPase is activated by….

GTP

Isoelectric focusing requires:

a stable pH gradient in gel

Osteoclasts are what kind of cells?
ovarian cells are what kind?

connective tissue epithelial tissue

nuclear factors

all cells within an organism have the same DNA. Nuclear factors vary in different cells, depending on cell type

2 domains of nuclear proteins

nuclear localization domain DNA binding domain

Krebs cycle, where is NADH produced? FADH2? GTP? CO2?

NADH: using and producing a-ketoglutarate, producing OAA FADH2: using succinate GTP: producing succinate CO2: along with NADH

glucose 6 phosphatase

catalyzes the final step of both gluconeogenesis and glycogenolysis.

– – – – –

Ligand gated ion channels

something binds to the receptor and then ions can flow through. examples: acetylcholine receptors (neuromuscular junction), serotonin receptor, GABA, and Glutamate receptor

Muscarinic receptors

parasympathetic

Nicotinic receptors

neuromuscular junction

Carbohydrate digestion where

Mouth and small intestine

Protein digestion where

Stomach and small intestine

Restriction site

usually palindromes of 4-6 base pairs

Southern blot uses

restriction sites

Restriction enzymes

attack the DNA that viruses inject into a bacteria but won’t attack bacteria’s DNA because it’s methylated (by methylase) Cut at a palindromic sequence. In a southern blot, given two alleles with a palindromic sequence, if you cut with the enzyme and run it in the blot, the allele that does not have the disruption in the palindromic sequence will be cut into two pieces while the other allele won’t be cut because it doesn’t have the restriction enzyme necessary

Structure of DNA

Average molecular weight of an amino acid

110 Da

Noncompetitive inhibitor

Bind to [E] and [ES] with same affinity, so K_m remains constant V_m decreases

Uncompetitive inhibitor

Bind to [ES] only K_m decreases ("lock" it in the conformation) V_m decreases

Mixed inhibitor

Binds to [E] and [ES] with different affinity V_m decreases K_m may increase or decrease

Competitive inhibitor

Binds only to [E] at active site V_m doesn’t change K_m increases

Isoforms

functionally similar proteins that have a similar but not identical amino acid sequence and are either encoded by different genes or by RNA transcripts from the same gene which have had different exons removed alternative splicing can form them take home point: same function

Isoelectric focusing

separation of proteins based on their isoelectric point (pI)

High affinity corresponds to

low k_d

Ovarian cells are

epithelial cells

SDS page

coats it in (-) charge breaks tertiary structure, not disulfide bonds

reducing agent like DTT

breaks disulfide bonds

Pull down assay

confirming the existence of a protein-protein interaction

Promoters and enhancers

both DNA, not proteins Promoter is initiation site of transcription Enhancers are before promoter and transcription factors (proteins) can bind at enhancers to increase the rate of transcription

Nuclear factors

type of transcription factor

nuclear localization signal

‘tags’ a protein for import into the cell nucleus by nuclear transport

signal sequence

tacked on to proteins that are destined towards the secretory pathway. These proteins include those that reside either inside certain organelles (the endoplasmic reticulum, golgi or endosomes), secreted from the cell, or inserted into most cellular membranes

Are covalent bonds destroyed with SDS page?

No

Affinity chromatography

Separates things based on their interactions and affinity with a specific ligand, not based on charge

glucose 6 phosphatase

Enzyme used in last step of glycogenlysis and gluconeogenesis in liver, because only liver can go from G6P -> glucose

Reverse transcription polymerase reaction

take mRNA, reverse transcription to get cDNA, then PCR the cDNA

alpha keto glutarate (can/cannot) be converted into glucose

can

All epithelial cells are

Avascular They separate and organize your body’s organs

All glandular cells (both endocrine and exocrine) are

epithelial cells

Malonyl coA is an inhibitor of

Carnitine Acyl transferase (the enzyme that attaches carnitine to a fatty acid)

What can make glucose?

Not fatty acids Amino acids can contribute

Can acetyl coA make glucose?

no

Actin myosin model

Bacterial membrane contains

phospholipids and proteins, not glycolypids or steroids

Blood clotting factors synthesized in the

liver

Platelets

cell fragments without nuclei

Epitope

part on the antigen that binds to antibody

After calcium released from sarcoplasmic reticulum, it’s taken up by

active transport using ATP energy

dehydrogenase

catalyzes oxidation reactions

Loading control

Used in western blot to make sure same amount of protein is loaded for each run usually an ubiquitous protein is used

Phosphorylase vs Kinase

Phosphorylase adds on an inorganic phosphate Kinase adds on a phosphate group from a donor like ATP

Retrograde transport

transporting things in opposite direction

How many electrons does cytochrome c accept?

1

Best PCR primer has

more GC content. More h bonds, more stable.

Nondisjunction occurs in which phases of meiosis?

anaphase 1 (homologous chromosomes) or anaphase 2 (sister chromatids)

High affinity transport

Means a LOW k_t value because you only need a little bit of substrate to make reaction go, so it’s very high affinity

Does k_t change when you add more proteins?

No, k_t is inherent to the enzyme itself and will not change if you add more proteins

An animal with (low/high) metabolic rate will be better suited against low nutrient conditions

low

Cellular respiration produces total of _____ ATP under aerobic conditions

38

Bacteria can regulate their gene expression based on their environmental conditions by

upregulating gene expression in presence of certain molecules in environment. for example in presence of lactose, you get transcription of lactose digesting enzyme.

Zwitterion

has both a positive and a negative charge, doesn’t necessarily cancel each other out

episome

genetic element inside some bacterial cells, especially the DNA of some bacteriophages, that can replicate independently of the host and also in association with a chromosome with which it becomes integrated

photoreceptors

visual receptor cells in retina rods and cones

Lining of mouth is derived from

invagination of ectoderm

vitamin D

increases gut absorption of calcium

CCK

When chyme in small intestine, duodenum secretes CCK to tell pancreas to secrete enzymes/bicarbonate and gallbladder to secrete bile

Chondroblasts

secrete stuff for cartilage

Fibroblasts

secrete collagen

chemiosmosis

movement of ions down gradient, like when H+ moves into mitochondrial matrix to form ATP

How many rings in steroid?

4. 3 6 membered, 1 5 membered

lipid raft

cholesterol, protein, receptor rich area of the plasma membrane

Enzymes

1. can NOT change the primary structure of a substrate (meaning the amino acid sequence) 2. co-localize substrates (bring them close together) 3. change the local pH by donating protons/accepting 4. altering substrate shape

Phosphate

it’s the GROUP, not just the phosphorous in the middle

aldosterone causes

absorption of Na+ and secretion of K+

endomembrane system

the nuclear membrane, the endoplasmic reticulum, the Golgi apparatus, lysosomes, vesicles, endosomes and the cell membrane

Diastole vs Systole

Systole = contraction Diastole = relaxation

Heart develops from which germ layer?

Mesoderm

Lungs develops from which germ layer?

Endoderm

Kidney develops from which germ layer?

Mesoderm

Reproductive system develops from which germ layer?

Mesoderm

Pancreas develops from which germ layer?

Endoderm

Liver develops from which germ layer?

Endoderm

cofactor

usually a metal ion

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