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What are the four most abundant elements found in living organisms?

C, O, H, N.

What are the seven moderately abundant elements found in living organisms?

Mg, Na, Cl, Ca, P, S, K.

An Acyl functional group


An Amido functional group


An Amino functional group


A Carbonyl functional group


A Carboxyl functional group


A Phosphoanhydride functional group


An Ester functional group


An Ether functional group


A Hydroxyl functional group


An Imino functional group


A Phosphate ester (Phosphoester) functional group


A Sulfhydryl functional group


A Phosphate diester (Phosphodiester) functional group


Cells contain what four major types of biological molecules?

– Amino acids – Carbohydrates (also called monosaccharides or sugars) – Nucleotides – Lipids

What macromolecules do Amino acids get assembled into?

Proteins and polypeptides

What macromolecules do Nucleotides get assembled into?

Nucleic acids

What do amino acids contain?

– An amino group (-NH) – A Carboxylic acid group (COO^-) – A side chain

What is the general chemical formula for carbohydrates?

(CH2O) n where n>or equal to 3

What are the polymers of sugars (carbohydrates, monosaccharides)?


Amino acids are linked by _____ bonds. Nucleotides are linked by _____ bonds. Polysaccharides are linked by _____ bonds.

Peptide bonds; Phosphodiester bonds; Glycosidic bonds.

Which statement below is false?
A.) Amino acids get assembled into proteins.
B.) Carbohydrate has an empirical formula of (CH20)n.
C.) Of the four major types of biomolecule lipid is the only one that cannot polymerize.
D.) Nucleic acids are made up of nucleotides.
E.) None of the above

E.) None of the above

What are the three major kinds of biological polymers?

– Polypeptides and proteins – Nucleic acid – Polysaccharides

Which of the major types of biomolecules is never found in a polymeric form?
A.) amino acids
B.) carbohydrates
C.) nucleotides
D.) lipids
E.) none of the above

D.) Lipids

Which of the following biopolymers is correctly paired with the bond that forms between the monomers?
A.) protein: ester bond
B.) polysaccharide: glycosidic bond
C.) DNA: phosphate bond
D.) RNA: phosphate bond
E.) all of the above

B.) Polysaccharide: glycosidic bond

What are the main functions proteins serve?

Carry out metabolic reactions and support cellular structures.

What is the main function nucleic acids serve?

Encode information

What are the main functions polysaccharides serve?

Store energy and support cellular structures.

Which of the biopolymers is correctly paired with its major function?
A.) polysaccharide: energy storage
B.) none of the above
C.) protein: information encoding
D.) nucleic acids: energy storage
E.) lipids: information encoding

A.) Polysaccharide: Energy storage

How is enthalpy (H) defined?

The heat content of a system.

How is entropy (S) defined?

A measure of the system’s disorder or randomness.

How is Gibbs free energy (G) defined?

A measure of the free energy of a system based on H and S.

What is the change in enthalpy of coffee that starts at 100kJ/mol and ends up at 50kJ/mol?

50kJ/mol -100kJ/mol = -50kJ/mol * It’s negative because energy is coming out into the surroundings.

Entropy is used to measure _____.
A.) free energy
B.) heat content
C.) temperature
D.) randomness
E.) all of the above

D.) Randomness

Referring to when water freezes, which of the statements is correct?
A.) The entropy is decreasing and the enthalpy is decreasing.
B.) The entropy is increasing and the enthalpy is decreasing.
C.) The entropy is increasing and the enthalpy is increasing.
D.) The entropy is decreasing and the enthalpy is increasing.
E.) The entropy is increasing and the enthalpy is the same.

A.) The entropy is decreasing and the enthalpy is decreasing.

What formula is used to calculate free energy from enthalpy and entropy?

ΔG = ΔH-TΔS – ΔG is Gibbs free energy change – ΔH is enthalpy change – ΔS is entropy change – Temp in Kelvin

When ΔG<0, the reaction is _____ or _____. When ΔG>0, the reaction is _____ or _____.

Spontaneous; Exergonic; Nonspontaneous; Endergonic.

If coffee gets colder, what is the sign of the enthalpy?

Negative, because energy is coming out into the surroundings.

If you spilled the coffee, what is the sign of entropy?


Thermodynamic law dictates enthalpy goes from_____ to______ and entropy goes from _______to_______.

Low to high; high to low

A reaction is spontaneous when it occurs with any size _____ in enthalpy and any size _____ in entropy.

Decrease; increase

For a reaction where A is converted to reactant B, tell whether this process is favorable at 4 degrees C.
A= H (54kJ) S (22J)
B= H (60kJ) S (43J)

– subtract 60-54 to get 6kJ (H) – convert 6kJ -> 6,000J – subtract 43-22 to get 21J (S) – convert 4C -> 277K ΔG = ΔH-TΔS ΔG = 6000J-277K(21J) ΔG = 183J/mol the reaction is not favorable (because it is positive).

An exergonic process _____.
A.) occurs without the addition of free energy
B.) has a ΔG< 0
C.) is spontaneous
D.) will have more products than reactants at equilibrium
E.) all of the above

E.) All of the above

Which oxidation state of carbon is the most oxidized (least reduced)? And what three come after that?

– Carbon dioxide – Followed by acetic acid, carbon monoxide, and formic acid.

Which oxidation state of carbon is the least oxidized (most reduced)? And what three come after that?

– Methane – Followed by ethane, ethene, and ethanol.

Which of the following molecules contains the most oxidized form of carbon?
A.) acetaldehyde
B.) ethylene
C.) carbon dioxide
D.) ethanol
E.) acetic acid

C.) Carbon dioxide

Photosynthetic organisms use energy from the sun to reduce _____ to _____.
A.) formaldehyde; ethanol
B.) CO2; ethanol
C.) CO2; carbohydrates
D.) CO2; oxygen
E.) none of the above

C.) CO2; carbohydrates

How to calculate oxidation state of carbon in a molecule?

– Overall oxidation # is 0 unless it has a charge on it, then it is just the charge. – O is usually 2- – H is usually 1+ – Add up all of oxidation number of H and O and the oxidation of C is the charge differences divided by the number of carbons.

What is the oxidation state of the carbons in this molecule?

O= 2(Oxygen) x -2 = -4 H= 4(Hydrogen) x 1 = 4 carbon = 0/2 = 0

What are the physical differences between prokaryotes vs. eukaryotes?

– Eukaryotes contain a nucleus and prokaryotes do not. – Eukaryotes have organelles and prokaryotes do not. – Eukaryotes are generally bigger than prokaryotes. – Eukaryotes can form multicellular organisms, prokaryotes can not.

One of the things that make eukaryotes different from prokaryotes is that?
A.) Prokaryotes can form multicellular organisms but prokaryotes can not.
B.) Eukaryotes can form multicellular organisms but prokaryotes can not.
C.) Eukaryotes have ribosomes but prokaryotes do not.
D.) In general prokaryotes are a lot bigger than eukaryotes.
E.) None of the above

B.) Eukaryotes can form multicellular organisms but prokaryotes can not.

Which of the following is a major difference between eukaryotic and prokaryotic cells?
A.) eukaryotic cells contain a nucleus, prokaryotic cells do not
B.) eukaryotic cells contain organelles, prokaryotic cells do not
C.) eukaryotic cells are much larger than prokaryotic cells
D.) eukaryotic cells often form multicellular organisms, prokaryotic cells do not
E.) all of the above

E.) All of the above

Eukaryotes are multicellular organisms.

False; some eukaryotes are unicellular.

What are the properties of water?

– Water is polar – Has tetrahedral geometry

Which side of water is partially positive and which side is negative?

– Oxygen has a partial negative charge. – Hydrogen has a partial positive charge.

The ____% of human body weight is made up of water. Within that, ____% of it resides inside the cell, ____% resides in the interstitial space, and ____% resides in the circulatory system.

60%, 40%, 15%, 5%.

What gives water molecules its polarity?


The lifespan of H-bonds is incredibly short, what does that say about the property of water?

It is dynamic, always changing.

If hydrogen bonds are always breaking, how come surface tension can still exist?

They are always reform the bonds.

Why did the frozen beer break the bottle?

Ice crystal latice is more spacious. It expands when frozen and ice is more spacious.

What makes water expand when frozen?
A.) Breaking of hydrogen bonds
B.) Forming of hydrogen bonds
C.) Breaking of van der waals bonds.
D.) Formation of the crystal lattice by the water molecules.


What is electronegativity and how is it related to hydrogen bonds?

Electronegativity is a measure of an atom’s affinity for electrons. Water can form hydrogen bonds not just with other water molecules but with a wide variety of other compounds that bear N-, O, or S-containing functional groups.

Which of the following statements is not accurate when considering water and biological molecules?
A.) Water can act as a hydrogen bond donor.
B.) Water can act as a hydrogen bond acceptor.
C.) Polar substances are soluble because of their interaction with water.
D.) Non-polar substances associate with water to maximize their exposed surface area.

D.) This statement is not accurate. Non-polar substances cannot interact or associate with polar water molecules.

What is the dielectric constant?

A measure of a solvent’s ability to diminish the electrostatic attractions between dissolved ions. The higher the dielectric constant of the solvent, the less able the ions are to associate with each other.

Which of the following statements is not accurate when considering water and biological molecules?
A.) Polar substances are soluble because of their interaction with water.
B.) Water is more likely to act as a hydrogen bond donor than a hydrogen bond acceptor.
C.) The hydrogen bonding pattern of water is disrupted by the presence of hydrophobic molecules.

B.) Because Water molecules are equally likely to act as either a hydrogen bond donor or a hydrogen bond acceptor.

What is a hydrogen bond donor and a hydrogen bond acceptor?

– Hydrogen donors give H+, all Hydrogens bonded to F, O, or N. – Hydrogen bond acceptors are the N or O’s bonded to the Hydrogen.

The following molecule has ____ hydrogen bond acceptors and _____ hydrogen bond donors.

3; 4; All hydrogens become hydrogen donors. The N, N, and O bonded to the hydrogen are hydrogen acceptors.

What causes a hydrogen bond?

Partial stripping of hydrogen.

How does the hydrogen bonding property of water help it dissolve biomolecules?

Oxygen makes it more bond friendly.

What does the dielectric constant value of a solvent say about its property?

It’s ability to shield the charges.

What are some of the dielectric constants for solvents at room temperature?

– Formamide: 109 – Water: 80 – Methanol: 33 – Ethanol: 25 – 1-Propanol: 20 – 1-Butanol: 18 – Benzene: 2

Which solvent do you expect to be better at dissolving MgCl, methanol or ethanol?

Methanol, because you want the highest dielectric constant. Methanol is 33 and ethanol is 25.

Which of the molecules below would be very soluble in water due to the formation of H-bonds?
A.) O2
B.) Benzene
C.) NaCl
D.) Ethanol
E.) Sodium palmitate

D.) Because it has a hydroxy group and it needs an O or N. – A is wrong because it isn’t polar. – B is wrong because it doesn’t have N or O.

Which of the following would be the best solvent for ammonium ions?
A.) 1-butanol
B.) 1-propanol
C.) Methanol
D.) Formamide

D.) because formamide has the highest dielectric constant.

Water is not able to hydrogen bond with which of the following?
A.) Ethanol (CH3CH2OH)
B.) Ammonia (NH3)
C.) Methane (CH4)
D.) Acetic acid (CH3CO2H)
E.) Diethyl ether (CH3CH2OCH2CH3)

C.) Methane, because it doesn’t have an O or N to hydrogen bond with.

What is the hydrophobic effect?

The exclusion of non polar substances from an aqueous solution. Nonpolar molecules aggregate to avoid contact with hydrophilic molecules, particularly water.

What is the leading force that drives the hydrophobic effect?

The entropy of water molecules

Which of the following statements about water is FALSE?
A.) Water carries a dipole because of the geometry of the two oxygen-hydrogen bonds.
B.) Water will act as a hydrogen bond acceptor with hydroxyl groups.
C.) Substances with polar functional groups are generally soluble in water.
D.) A network of electrostatic interactions exists between the molecules in water.
E.) The hydrophobic effect is driven largely by the entropy of the non-polar substance.

E.) This statement is false. The hydrophobic effect is driven largely by changes in the entropy of water.

Which of the following functional groups could NOT act as a hydrogen bond donor?
A.) A hydroxyl group.
B.) An amino group.
C.) An aldehyde.
D.) Both aldehyde and ester.
E.) An ester.

D.) because neither an ester nor an aldehyde contains a hydrogen bond donor atom.

How do you identify if a molecule is hydrophobic or not?

The way to tell if a molecule is hydrophobic or not is to put it in water to see if the shape of the molecule changes, or to see if it will dissolve or not (like oil and water). This constraint on the structure of water represents a LOSS of entropy.

What does amphiphilic mean?

It likes both. Molecules that have both hydrophobic and hydrophilic portions.

An amphiphilic molecule:
A.) Has both polar and non-polar groups.
B.) Has non-polar groups.
C.) Has neither polar nor non-polar groups.
D.) Has polar groups.


Hydrophobic or nonpolar substances are insoluble in water.


Consider the transfer of benzene from water to pure benzene. Which statement is false?
A.) The ∆H of transfer is about zero.
B.)The ∆G of transfer is negative.
C.) T∆S is positive.
D.) The process is less favorable at higher temperature.

D.) Because Assuming that ∆S and ∆H do not change with temperature, higher temperatures will enhance the positive ∆S, making ∆G=∆H-T∆S even more negative and the process even more favorable at higher temperatures.

What is a micelle?

A particle with a solvated surface and a hydrophobic core that is formed by amphiphilic molecules. (hydrophobic tails go on the inside and hydrophilic heads go on the inside.)

What is a lipid bilayer?

A lipid bilayer is formed when the amphiphilic lipid molecules form two layers so that their polar head groups are exposed to the solvent while their hydrophobic tails are in the interior, away from the water. To eliminate solvent exposed edges, a lipid bilayer tends to close up to form a VESICLE.

What type of molecule do you want to look for that would form a micelle head?

Chain of hydrocarbons followed by COO-Na or a COO-

What is one of the main functions lipid bilayer does for the cell?

It is a barrier against diffusion.

What is able to cross a lipid bilayer?

A hydrophobic molecule

How is acidic defined?

Low; pH<7 -7 is neutral

How is basic defined?

High; pH>7

What is the concentration of H+ and OH- in pure water?

H+ and OH are represented as Kw which is the ionization constant. Kw=10^-14 at 25C so in a sample of pure water H+=10^-7 and OH-=10^-7.

How does the concentration of H+ and OH- affect each other?

They are inversely related. Since the product of H+ and OH- in ANY solution must be equal to 10^-14, a hydrogen ion concentration greater than 10^-7 is balanced by a hydroxide ion concentration less than 10^-7.

Solutions in which [H+] &gt; 10-7 are said to be acidic.


Solutions in which [H+] = [OH-] are said to be neutral.


What is the formula to find pH?

pH = -log[H+]

Calculate the pH of a solution that is 10 mM of NaOH in water.

– First need to find H+ [OH-] [H+] =10^-14 ALWAYS – convert 10mM to 0.01M which is 10^-2 [H+] = 10^-14/10^-2 = 10^-12 pH = -log[10^-12] pH = 12

What is the pH of 1 liter of water with an initial pH of 7.0 after 100 mL of 0.02M HCl has been added to it?

pH = (how much is added) x (concentration of what’s added)/TOTAL volume. – First convert 100 mL -> 0.1L 0.1 x .02M/1.1L(inital 1 liter+liter after) = 0.001818 pH = -log[0.001818] pH = 2.74

What is the difference between a weak acid vs a strong acid?

A strong acid dissociates completely in a solution while a weak acid partially dissociates in a solution.

Which statement about weak acids is false?
A.) A weak acid partially dissociates into its ionic form in water.
B.) A weak acid becomes a base once its deprotonated.
C.) The pK value of a weak acid decreases in an acidic environment.
D.) The pH of a solution decreases when a weak acid is added to it.

C.) is false because pK NEVER changes.

Which condition holds more H3O+ ions, acid or base?


The higher the pK value the _____ attraction and the _____ the acid.

Less; weaker

The lower the pK value the _____ attraction and the _____ the acid.

More; stronger

What is a conjugate base?

The molecule that is ready to accept a proton.

How to find the conjugate base

You take away one hydrogen and include a – at the end.

What is the conjugate base of H3BO3?


What is the conjugate base of H2BO3^-?


What is the conjugate base of HBO3^2-?


The pK of boric acid (H3BO3) is 9.24. What is the prodominant form of this molecule you are likely to find at pH 10.14?

– Depronated means take a proton off. H2BO^3-

What is the formula for pK?

pK = -log[pH]

Which of the following would be the strongest acid?
A.) Citrate, pK 4.76
B.) Citric acid, pK 3.75
C.) Formic acid, pK 3.13

C.) because the strongest acid has the smallest pK.

What is the buffering range of a weak acid?

The effective buffering capacity of an acid is generally taken to be within one pH unit of its pK. The range is pK-1 to pK+1.

Boric acid is suited to bugger _____ at pH 10.25 and _____ at pH 8.25.
A.) Acid, Base
B.) Base, Acid
C.) Strong acid, weak acid
D.) Strong base, weak base
E.) Neither because it is outside +1 and -1 of pK.


What is the formula for calculating the pH as it relates to the pK of an acid and the concentration of the acid(HA) and its conjugate base(A-).

pH = pK + log [A-]/[HA] A- is acetate HA is acetic acid

Calculate the pH of a 1L solution to which has been added 25mL of 30mM of acetic acid and 30 mL of 30mM of sodium acetate.

– First convert 25mL ->.025L 30mL -> .03L – Add up all Liters (.025+.03+1=1.055) – A- = 0.03L x 0.03M/1.055 = .00085M – HA = 0.025L x .02M/1.055= .000473 pH = 4.76 + log [.00085]/[.000473] pH = 5.014

What is the difference between purine and pyrimidine?

Purines have 2 rings and pyrimidines have 1.

_____ and _____ are purines in both DNA and RNA.

Adenine and Guanine

_____ and _____ are pyrimidines found in DNA.

Cytosine and thymine

_____ and _____ are pyrimidines found in RNA.

Cytosine and uracil

Adenine (A) is paired with _____ in DNA.

Thymine (T)

Adenine (A) is paired with _____ in RNA.

Uracil (U)

Guanine (G) is paired with _____.

Cytosine (C)

Which answer best fits the molecule Cytosine?
A.) This is a pyrimidine base and base pairs with adenine.
B.) This is a pyrimidine base and base pairs with guanine.
C.) This is a purine base and base pairs with thymine.
D.) This is a purine base and base pairs with cytosine.

B.) because Cytosine is a pyrimidine that pairs with guanine.

How is DNA different from RNA?

– DNA contains A,C,G,T and RNA contains A,C,G,U. – DNA is double stranded, and it’s the original. RNA is single stranded and it’s a copy of DNA. – RNA can form three dimensional shape and can fold back on itself. – RNA has a hydroxyl group on its 2′ position of ribose, DNA does not. #22 on test one

What is the structure of a DNA double helix?

– The TWISTING of the DNA double helix is caused by the hydrophobic effect. The two strands are antiparallel – The STABILITY is caused by not only the hydrogen bonding between pairs, but also the adjacent stacking interactions consisting of Van der waals interaction. – G&C have a tighter bond than A&T. – G&C has 3 hydrogen bonds and A&T has 2 hydrogen bonds.

Which statement correctly explains the reason for the twisting of the DNA helix?
A.) Twisting relaxes the ribose phosphodiester backbone.
B.) It is caused by the G:C and A.) T base pairings.
C.) It is caused by the antiparallel matching of the coding strand with the noncoding strand.
D.) It is caused by the hydrophobic effect of the base stacking.


What does denaturing of a DNA molecule mean?

Dentature means to break the hydrogen bonds between the base pairs by raising the temperature to be able to determine the melting point of DNA. Denaturation of DNA can be recorded as a melting curve by monitoring an increase in the absorbance of ultraviolet light.

Identify the DNA strand that this mRNA strand was made from.

– First write base pairings AGCTCATGC – Then read it backwards CGTACTCGA

What is the function of replication?

To make an exact copy of original DNA.

When does replication occur?

Prior to cell division.

What is the enzyme that carries out replication?

DNA polymerase

What are the building blocks of replication?


What is the direction of the elongation process of replication?

From 5′ to 3′

What is the function of transcription?

To make RNA copy of the gene encoded in the DNA.

When does transcription occur?

Prior to translation

What is the enzyme that carries out transcription?

RNA polymerase

What are the building blocks of transcription?


What is the direction of transcription?

From 5′ to 3′

What is the function of translation?

To assemble polypeptide based on the codon sequence encoded in the mRNA.

When does translation occur?

During protein expression

What is the enzyme that carries out translation?


What are the building blocks of translation?

tRNA and amino acids

What is the direction of the elongation process of translation?

From amine terminal to the carboxyl terminal.

Which statement about replication is FALSE?
A.) It is carried out by ribosomes.
B.) It happens prior to cell division.
C.) the growing strand grows from 5′ to 3′.
D.) The building blocks of the newly synthesized DNA are deoxyribonucleotides.


Which statement about transcription is FALSE?
A.) Transcription is carried out by RNA polymerase.
B.) The end product of transcription is mRNA.
C.) mRNA is made from the coding strand of the DNA.
D.) mRNA is made from ribonucleotides.


What is a codon?

A sequence of three nucleotides in DNA or RNA that specifies a single amino acid. – Codon -> nontemplate strand – Noncodon -> template strand

How is the DNA sequencing with the Sanger method used in genetic studies?

Uses ddNTP to synthesize the DNA. It adds ddNTP instead of dNTP, and halts further extension of the DNA chain. After primer is bound to the DNA, DNA polymerase extends the primer by sequentially adding nucleotides that complement the template strand.

How is the Polymerase Chain Reaction (PCR) used in genetic studies?

– Used to produce large amounts of particular DNA sequences. uses primers. Initiates DNA polymerase process / it is fast and does not require a pure sample of DNA. – PCR repeats 3 chemical reactions: 1. Denaturation: DNA is denatured by heat. dsDNA separates at a high temp to form ssDNA. 2. Annealing: Primers can base pair to ssDNA. 3. Extension: New strand is synthesized.

What is required to make PCR work?

1. DNA template 2. Two primers 3. Thermostable DNA polymerase 4. Four types of dNTPs 5. Buffer containing Mg2+

How is the restriction digest method used in genetic studies?

– Cutting DNA specifically – Enzyme: endonuclease – Annealing is done with ligating – Breaks into smaller fragments to work with in the laboratory.

How is the cloning with expression plasmid used in genetic studies?

– Mimicking the natural process of evolution. – Annealing is done naturally

The _____ method is used to sequence a gene. One crucial component you need for this method is _____. This is because they _____ the DNA polymerase process.

Sanger, ddNTPs, terminate.

The _____ method is used to amplify a gene. One crucial component you need for this method is _____. This is because they _____ the DNA polymerase process.

PCR, Primers, initiate.

Which one of these sequences is palindromic?

AAGCTT because it becomes TTCGAA which can be read backwards.

How to distinguish L from D.

– Wedge means it is coming towards you. – Dashes mean it is going into screen. – First you want H wedged, going towards you, then if it spells CORN going clockwise it is L.

What are the three categories of amino acids?

– Hydrophobic (have no Os besides the amine group) – Polar (has Os) – Charged (have large chains coming off of the Amine group) * Memorize paper!

Why is Proline a special amino acid?

It is the only amino acid where its side chain wraps back onto itself. This causes rigidity within the molecule which cause kink in the peptide where ever there is proline.

What makes Tryptophan (W) special?

What makes it the most unique is that its absorbance of light is so high that detection with light to find tryptophan is the most useful way to detect protein in a solution because ALL proteins have at least one tryptophan.

What makes methionine special?

Methionine is ALWAYS the "start" codon for the amino acids, and therefore initiates reading in the correct direction.

What makes Cysteine special?

Cysteine is known for its ability to form disulfide bonds to create linkages between molecules. This drastically changes the shape of a protein.

Which of the following amino acids contains a sulfur atom?
A.) Lys
B.) Pro
C.) Cys
D.) Trp

C.) Cys

Which of the following amino acids contains a charged side chain at pH 7.0?
A.) Asp
B.) Gly
C.) Tyr
D.) Trp
E.) none

A.) Asp

Which amino acid would disrupt the structure of an a-helix?
A.) Ala
B.) Gly
C.) Cys
D.) Pro

D.) Pro, because it is the only amino acid where the side chain wraps back onto itself.

How do amino acids come together?

They are linked via condensation reactions to form peptide bonds between each other. Byproduct: H2O

What is the secondary structure of amino acids? What are the secondary structures?

– The localized conformation of the peptide backbone. – Alpha helix, Beta sheets, and Irregular secondary structures.

How is Alpha helix stabilized?

It is stabilized by the H-bonds formed between the carbonyl oxygen and the amino hydrogen.

What is the direction of the turn in an Alpha helix?

Right handed helix, a complete turn is made of 3.6 amino acids.

How are Beta sheets stabilized?

By the H- bonds formed between the carbonyl oxygen and the amino hydrogen.

Beta sheets: Parallel vs antiparallel

– Parallel aligns in the same direction and creates an irregular secondary structure. – Antiparallel aligns in opposite directions.

Which statement below is FALSE?
A.) a-helix is held together by hydrogen bonds.
B.) B-sheet is stabilized by hydrogen bonds.
C.) The right handed coil in a a-helix is caused by hydrophobic resides.
D.) Irregular secondary structures do not have a general structural definition.


How to identify irregular secondary structures

Usually found in the linker region connecting the alpha helices and beta strands.

How is the tertiary structure defined?

The overall three-dimensional shape of the protein made up of the secondary structures.

What are the leading factors that hold tertiary structure together?

Hydrophobic forces and cross-linkers.

How does hydrophobicity play a role in tertiary structures?

Related to the location of a particular side chain in protein’s tertiary structure. The greater the hydrophobicity is, the more likely that side chain will be located in the interior of the protein. Causes protein folding.

How do Disulfide bonds (cross linkers) play a role in tertiary structures?

Can form within polypeptide chains. Plentiful in proteins that are secreted in an extracellular environment.

Which statement describes the tertiary structure of myoglobin?
A.) Its amino acids sequence began with Met-Ser-Ala-Ile-…
B.) It is a globular protein that contains a hydrophobic pocket with a heme group in the middle.
C.) The protein functions as a single subunit.
D.) It is made up of a-helices and irregular secondary structures.


Which of these factors does not play a role in protein folding?
A.) Primary structure
B.) Hydrophobic effect
C.) Steric hindrance of the peptide bond.
D.) Steric hindrance of the side chains.
E.) They all play a role


How to determine the quaternary structure.

Count the number of polypeptides present (Ex: Dimer [2things], homo trimer [3 things].

How does size exclusion/Gel filtration Chromatography work?

Shape is NOT destroyed, separated based on HYDRODYNAMIC volume, large proteins take the direct route (Comes out quicker) while small proteins take the indirect route (takes longer to come out). Limitation is that it can’t break up protein quaternary structure.

How does Ion exchange chromatography work?

Separates protein based on their change. Slightly bound proteins are caught first, where as tightly bound proteins come later.

How does SDS page work?

Separates protein based on ABSOLUTE SIZE. Detergent destroys natural shape (all proteins become linear). Large come out last, small proteins come out first (Opposite of size exclusion). Limitation: cannot purify proteins, only analyzes.

How does NMR (Nucleomagnetic resonance) work?

– Pros: Can study with movements (doesn’t need to be static), study protein within a solution. – Cons: Low resolution, can’t study large protein structures, can only see H & N isotope atoms.

How does X-ray crystallography work?

– Pros: High resolution, can study large protein structures. – Cons: Can only study in static condition (no movement), difficult.

Which of the following separates proteins based on net charge?
A.) Size-exclusion
B.) Ion-exchange chromatography


Size exclusion separates protein based on their hydrodynamic volume, which refers to?
A.) Absolute size of the protein
B.) The size of the protein in solution as it flows through the column.
C.) The volume of the protein in neutral pH.
D.) The volume and size ratio of the protein.


A student in the lab is told to purify a protein that contains a large number of Lys and Arg residues. Which purification technique should he/she use?
A.) Cation exchange column
B.) SDS Page
C.) X-ray crystallography
D.) Size exclusion

A.) Cation exchange column

One of the benefits NMR has over X-ray crystallography is?
A.) It can be used to study protein dynamics.
B.) It has higher resolution
C.) Magnetism doesn’t destroy protein
D.) It can see resonance structures.


How to determine the PI of a peptide.

1. Write all the pKs given in order from highest to lowest. 2. Depronate so that if it is + it becomes 0 and if it is neutral it becomes -1 and if it is -1 it becomes -2. 3. Add all the depronated numbers to get the number you start the graph at. 4. Fill the rest of the charges in the spaces between the pK values. 5. Take the two pK values that are surrounding the 0 and add them and divide by 2.

What is the function of myoglobin?

Cellular storage and transport of oxygen throughout muscles.

Where is myoglobin most commonly found?

In muscle cells

What is the tertiary structure of myoglobin?

Globular shaped protein with a hydrophobic pocket where a heme prosthetic group lies.

What is the binding mechanism of myoglobin?

Oxygen is sandwiched between the 6th coordination position of Fe(2) and His above it. It has no cooperative binding and graphs in a hyperbolic trend.

What is the function of hemoglobin?

Transport of oxygen from the lungs to the body tissues.

Where is hemoglobin most commonly found?

In red blood cells

What is the tertiary structure of hemoglobin?

Nearly identical to myoglobin

What is the quaternary structure of hemoglobin?


What is the binding mechanism of hemoglobin?

Oxygen binds to the heme group just as in myoglobin but its subject to steric regulation. It has cooperative binding with sigmoidal curve.

What is the physiological significance of cooperative of hemoglobin?

Tensed- deoxygenated Relaxed- Oxygenated

What role does BPG play for hemoglobin?

Decreases Hb’s affinity for oxygen, only binds to the tense (deoxy) conformation of Hb, stabilizes the T conformation of Hb.

Which one of these statements about myoglobin is false?
A.) It is found inside of the cell, specifically muscle cells.
B.) It contains one heme group and can bind to one oxygen molecule.
C.) In its tense state it is deoxygenated.
D.) Myoglobin does not have cooperative bonding property.

C.) is false because its hemoglobin that has a tense state.

Hemoglobin exhibits cooperative binding. What would happen to us if HB loses that?
A.) Our lungs would be filled with CO2.
B.) Our muscles would get too much O2
C.) The hemoglobin would never let go of the oxygen.
D.) The hemoglobin would never bind to the oxygen


What happens to the affinity of hemoglobin for oxygen as the pH is increased from 6 to 7?

It increases

Fetal hemoglobin is slightly different than adults because?

It binds to biphosphoglycerate with a lower affinity.

What are the intracellular and extracellular structural proteins?

– Intracellular: Microfilament, intermediate filament, Keratin, and microtubules. – Extracellular: Collagen

What is the function of microfilaments?

Skeletal support in eukaryotes and cellular migration.

What is the diameter of microfilaments?


What are the building blocks of microfilaments?

Actin monomers made up of 375 aa.

What is the overall structure of microfilaments?

Double strand coiled filament with each actin monomer contacts four of its neighbors.

What is the special property of microfilaments?

The filament is constantly assembling and disassembling from each end. The filament is said to be treadmilling when the rate of growing of one end match the rate disassembling of the other end.

What is the function of an intermediate filament?

Exclusively skeletal support.

What is the diameter of an intermediate filament?


What are the building blocks of an intermediate filament?

A dimer of a-helices in a left handed coiled coil conformation.

What are intermediate filaments assembled by?

Hydrophobic interactions

What is the overall structure of an intermediate filament?

Cable like structure with 16 to 32 polypeptides at the cross section.

What is the special property of intermediate filaments?

Each a-helix has a repeating pattern of seven amino acids where 1st and 4th positions are always hydrophobic residue. Crosslinking by disulfide bonds further stabilizes the intermediate filaments.

_____ is an intermediate filament.


What is a protein found in hair, horn, nails, and feathers?


What is the function of microtubules?

Skeletal support and cell mobility.

What is the diameter of microtubules?


What are the building blocks of microtubules?

Heterodimer made up of alpha and Beta tubulins.

What are microtubules assembled by?

Hydrophobic interactions and GTP and GDP interactions.

What is the regulatory mechanism in microtubules?

GTB bound tubulins assemble and GDP bound tubulins disassemble.

What is the overall structure of microtubules?

Rigid tube like structure made up of 13 protofilaments.

What is a special property of microtubules?

The + end of the microtubule grows and disassembles twice as fast as the – end.

How many protofilaments make up the wall of the microtubule?


What is the function of collagen?

Support of extracellular matrix.

What is the diameter of collagen?


What are the building blocks of collagen?

Triple helix made up of three polypeptide with a common repeating pattern of Gly-Pro-Hyp.

What is collagen assembled by?

Hydrogen bond interactions and covalent linkers.

Where is collagen typically found?

In tendons, connective tissues, and bones.

What is a special property of collagen?

Pound for pound, stronger than steel. The protein contains large amounts of proline and hydroxyproline. Hydroxyproline is converted from regular proline by a mechanism which involves vitamin C.

Which of these pairings is wrong?
A.) Microfilaments: actin
B.) Microtubule: Tubulin
C.) Extracellular support fibers: Collagen
D.) Intermediate filaments: Keratin
E.) They are all correct


Which of these statements is false?
A.) Microfilaments are associated with cell mobility.
B.) Collagen is made up of triple helices; each has a repeating pattern of Gly-Pro-Hyp.
C.) Microtubules have a larger diameter than microfilaments and intermediate filaments.
D.) Keratin always has hydrophilic residues on the 1st and 4th positions of their alpha helices.
E.) They are all correct


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