Ch. 17 From Gene to Protein

Inherited traits are determined by

genes

the trait of albinism is caused by

a recessive allele of a pigmentation gene

The information content of genes is in the form of specific sequences of

nucleotides along strands of DNA, the genetic material

what is the genetic materia?

DNA

Albino deer has a _version of a key protein, an

faulty enzyme required for pigment synthesis

Why the protein is faulty?

the gene that codes for it contains incorrect information

The DNA inherted by an organism leads to

specific traits by dictating the synthesis of proteins and of RNA molecules involved in protein synthesis.

who are the link between genotype and phenotype?

proteins

Gene expression

the process by which the information encoded in DNA directs the synthesis of proteins or, in some cases, RNAs that are not translated into proteins and instead function as RNAs

the expresion of genes that code for proteins includes two stages:

-transcription -translation

Genes specify proteins via

transcription and translation

who provides the information to create specific proteins?

genes

Does genes build proteins directly?

NO they do not, they only provided the information

Who is the bridge between DNA and proteins synthesis?

nucleic acid RNA

Differences between DNA and RNA?

-RNA contains ribosa insteadof deoxyrobose sugar -RNA has the nitrogenous base uracil -DNA has the nitrogenous base thymine -DNA is a double helix strand -RNA is a single strand -nucleotides in DNA: A, G, C, or T -nucleotides in RNA: A, G, C, or U

what polymers have specific sequences of monomers that convey information?

nucleic acids and proteins

who are the monomers in DNA and RNA? what differ between each other?

the monomers are four types of nucleotides, which differ in nitrogenous bases

Each polypeptide of a protein also has monomers arranged in a particular linear order, but its monomers are_

amino acids

nucleic acids and proteins contain information written in two different_

chemical languages

Getting from DNA to protein requires two major stages:

-transcription -translation

Transcritption

Synthesis of RNA using information in the DNA. The two nucleic acids are written in different forms of the same language, and the information is simply transcribed, or "rewritten", from DNA to RNA.

Just as DNA strand provides the template for making a new complementary strand during DNA replication, it can also serve as

a template for assembling a complementary sequence of RNA nucleotides

messenger RNA (mRNA)

A type of RNA, synthesized using a DNA template, that attaches to ribosomes in the cytoplasm and specifies the primary structure of a protein. (In eukaryotes, the primary RNA transcript must undergo RNA processing to become mRNA.)

mRNA is a faithful

transcript of the gene’s protein-building instructions

The messenger RNA is called like this because,,,

Because it carries a genetic message from the DNA to the protein-synthesis machinery of the cell.

translation

The synthesis of polypeptide using the genetic information encoded in an in the mRNA molecule. There is a change of "language" form molecule nucleotides to amino acids.

The cell must translate the nucleotide sequence of an mRNA molecule into

the amino acid sequence of a polypeptide

The site of translation are_.

ribosomes

ribososmes

complex particles that facilitate the orderly linkage of amino acids into polypeptide chains

Transcriptions and translation occur in which organisms?

In all organisms. Eukayotes and prokaryotes

What is the difference between the mechanism of transcription and translation between bacteria and eukaryotes?

The flow of genetic information within the cells

Flow of genetic information in bacteria? (transcription and translation)

-Because bacteria does not have nuclei, its DNA is not separated by nucelar membranes from ribosomes and the other protein synthesizing equipment -This allows translation of an mRNA to begin while its transcription is still in progress.

Flow of genetic information in eukaryotes? (transcription and translation)

-nuclear envelope separates transcription from translation in space and time. -Transcription occurs in nucleus, and mRNA is then transported to the cytoplasm, where translation occurs.

what happens before mRNA leaves the nucleus?

They are modified in various ways to produce the final, functional mRNA

The transcription of a protein-coding eukaryotic gene results in_, and further processing yields the

pre-mRNA finished mRNA

Primary transcript

-An initial RNA transcript from any gene; also called pre-mRNA when transcribed from a protein-coding gene -Including those RNA that is not translated into protein

Summarize protein synthesis.

Genes program protein synthesis via genetic messages in the form of messenger RNA

Cells are governed by a molecular chain of command with a directional flow of genetic information, which is:

DNA –> RNA –> Protein

Central dogma

Concept that said that cells are governed by a molecular chain of command with a directional flow of genetic information, which is DNA-> RNA-> Protein

who created and in what year the central dogma?

Francis Crick 1956

RNA molecules can act as

templates for DNA synthesis

Where does the instructions for assembling amino acids into a specific order are encoded?

nucleic acids

How many nucleotides correspond to an amino acid?

3 (triplets of nucleotide bases)

what is the smallest unit of uniform length that can code for all the amino acids (20)?

Triplets of nucleotide bases (3)

If each arrangement of 3 consecutive nucleotide bases specifies an amino acid there can be_possible code words. what is the formula to determine this?

64 4^3

The flow of information from gene to protein is based on

a triplet code

triplet code

The genetic instructions for a polypeptide chain are written in the DNA as a series of nonoverlapping, three-nucleotide words.

the series of words in a gene is transcribed into a_, which is then translated into a _

complementary series of nonoverlaping, three-nucleotide words in mRNA chain of amino acids

During transcription what happens?

the gene determines the sequence of nucleotide bases along the length of the RNA molecule that is being synthesized

For each gene how many of the strands is or are transcribed?

only one of the two DNA strands is transcribed

Template strand

-The DNA strand that provides the pattern, or template, for ordering, by complementary base pairing, the sequence of nucleotides in an RNA transcript -For any given gene,the same strand is used as the template every time the gene is transcribed -However, for other genes on the DNA molecule, the opposite strand may be the one that always functions as the template.

what is the difference of the base-pairing rules between DNA synthesis and transcription? other difference between both?

-Uracil (U) takes the place of Thymine (T) in RNA (transcription) -mRNA nucleotides contain ribose instead of deoxyribose

during translation, the mRNA is read as a

sequence of nucleotide triplets, codons

Codon

a three-nucleotide sequence of DNA or mRNA that specifies a particular amino acid or termination signal; the basic unit of the genetic code.

a mRNA molecules is_to its DNA template, why?

complementary because RNA nucleotides are assembled on the template according to base-pairing rules

RNA molecules is synthesized in an_direction to the template strand of DNA

antiparallel

codons are customarily written in the_direction

5′->3′

The term codon is also used for the DNA nucleotide triplets along the _strand

nontemplate strand

The codons of the_are identical in sequence to mRNA, except that they have_instead of _

nontemplate strand T U

coding strand

nontemplate DNA strand

During translation what happens to the sequence of codons along an mRNA molecule?

it is decoded, or translated, into a sequence of amino acids making up a polypeptide chain

the codons are read by the translation machinery in what direction along the mRNA?

5′->3′

What does the codons specify?

each codon specifies which one of the 20 amino acids will be incorporated at the corresponding position along a polypeptide

Because codons are nucleotides triplets, the number of nucleotides making up a genetic message must be_times the number of amino acids in the protein product.

three times

How many nucleotides along the mRNA do we need to produce a protein with 100 amino acids long?

300 nucleotides

Molecular biologists cracked the genetic code of life in the early _ when a series of elegant experiments disclosed the _

-1960s -amino acid translations of each of the RNA codons

When and by who was the first codon deciphered? what was this codon?

1961 Marshall Nirenberg UUU (poly-U)

the UUU codon specifies what amino acid?

Phenylalanine

The _ codons of the 64 that do not designate amino acids are_, or_, marking the _. These codons are:

3 "stop" signals Termination codons the end of translation These codons are: UAA, UGA, UAG.

AUG codes for…

-the amino acid methionine (Met) -functions as "start" signals, or initiation codons, that signals the protein-synthesizing machinery to begin translating the mRNA at that location

genetic messages on mRNA usually begin with which codon?

AUG

Polypeptide chains usually begin with what amino acid? why? Does this amino acid stay or is removed after synthesis?

methionine because AUG codes for it usually removed

Codons show_because_;however they do not show _ because

redundancy because multiple codons code for the same amino acid. ambiguity because neither of the codons specify any other amino acid

Usually the codons that show redundancy (code for the same amino acid) differ only in the _

the third nucleotide base of the triplet

reading frame

-On an mRNA, the triplet grouping of ribonucleotides used by the translation machinery during polypeptide synthesis -the ability to extract the intended message from a written language depends on reading the symbols in the correct groupings

How reading frame applies to translating process?

The poypeptide will be made correctly only if the mRNA nucleotides are read in the direction of 5′->3′ and reading the message of mRNA as a series of nonoverlapping three-letter words. (EX. UGG UUU GGC UCA).

Evolution relationship between organisms?

-all the organism share the genetic code -CCG (RNA codon) is translated into the amino acid proline in all organisms whose genetic code has been examined

Using the genetic code in biotechnology

bacteria can be programmed by the insertion of human genes to synthesize certain human proteins for medical use (insulin)

Exeptions to the universality of the genetic code include

-translation systems in which a few codons differ from the standard ones (unicellular eukaryotes and organelle genes of some species )

A_is a reminder of the kinship that bonds all life on Earth

shared genetic vocabulary

Messenger RNA

the carrier of information from DNA to the cell’s protein-synthesizing machinery

Messenger RNA is transcribed from

the template strand of a gene

RNA polymerase

-an enzyme that links ribonucleotides into a growing RNA chain during transcription, based on complementary binding to nucleotides on a DNA template strand -it pries the 2 strands of DNA apart and joins togetherRNA nucleotides complementary to the DNA template strand, thus elongating the RNA polynucleotide

Stages of transcription

-initiation -elongation -termination

Which stage of transcription is different between bacteria and eukaryotes?

termination

In bacterium, the RNA transcript is _ usable as mRNA

immediately

In eukaryote, the RNA transcript must_

undergo processing

what direction does RNA polymerase can assemble a polynucleotide only?

5′->3′

What is the difference between DNA polymerase and RNA polymerase used in transcription?

RNA polymerase are able to start a chain from scratch; they do not need a primer

what marks where transcription of a gene begins and ends?

specific sequence of nucleotides (codons)

Promoter

-the DNA sequence,specific nucleotide sequence, where RNA polymerase attaches and initiates transcription -Positioning RNA polymerase to start transcribing RNA at the appropriate place

terminator

-in bacteria -the sequence of nucleotides in DNA that signals the end of transcription -signals RNA polymerase to release the newly made RNA molecule – RNA polymerase detach from DNA

molecular biologist refer to the direction of transcription as_and the other direction as_. This terms are also used to describe _. Ex?

downstream upstream the positions of nucleotides sequence withing DNA or RNA Ex: the promoter sequence in DNA is said to be upstream from the terminator

transcription unit

-stretch of DNA that is transcribed into an RNA molecule

Bacteria has a _type of RNA polymerase that synthesizes_

single synthesizes not only mRNA but also other tupes of RNA that function in protein synthesis (ribosomal RNA)

Eukaryotes have _types of RNA polymerase in their_

at least 3 types nuclei

in eukaryotes, the type of RNA polymerase used to mRNA synthesis is called…

RNA polymerase II

In eukaryotes, the other RNA polymerases, besides RNA polymerase II, what they do?

transcribe RNA molecules that are not translated into protein

describe the first step of transcription

1) Initiation: -After RNA polymerase binds to the promoter, the DNA strands unwind. -Polymerase initiates RNA synthesis at the start point on the template strand

describe the second step of transcription

2) elongation: -The polymerase moves downstream, unwinding the DNA and elongating the RNA transcripts 5′->3′. -In the wake of transcription, the DNA strands re-form a double helix

Describe the third step of transcription

3) termination: -eventually, the RNA transcript is released -the polymerase detaches from the DNA

The promoter of a gene includes within it the_and typically extends_

-transcription start point -several dozen or more nucleotide pairs upstream from the start point

start point

-nucleotide where RNA synthesis by RNA polymerase actually begins

RNA polymerase binds in a precise_and_on the promoter, therefore determining_

-location -orientation -determining: -where transcription stars -which of the two strands of the DNA helix is used as the template

In bacteria, the RNA polymerase recognizes and binds to…

to the promoter on its own

In eukaryotes, the RNA polymerase binding process and initiation of transcription are…

mediated by a collection of proteins called transcription factors

transcription factors

a regulatory protein that binds to DNA and affects transcription of specific genes

In eukaryotes, the RNA polymerase (specifically RNA polymerase II) recognizes and binds to…

to the promoter, after transcription factors are attached to it (promoter)

transcription initiation complex

The whole complex of transcription factors and RNA polymerase II bound to a promoter

TATA box

-A DNA sequence in promoters crucial in forming the transcription initiation complex (in eukaryotes) -about 25 nucleotides upstream from the transcriptional start point -compose of "T" and "A" nucleotides

The interactions between eukaryotic _and _is an example of the importance of protein-protein interaction in controlling eukaryotic transcription

RNA polymerase II Transcription factors

Eukaryotic chromosomes is complexed with histones and other proteins in the form of_. The roles of this proteins in making the DNA _

chromatin accessible for transcription factors

Once the appropriate transcription factors are firmly attached to the promoter DNA and the polymerase is bound in the correct orientation, the enzyme_

unwinds the two DNA strands and starts transcribing the template strand

A eukaryotic promoter is composed of

-TATA box -start point

Several transcription factors, one recognizing the_, must bind to the DNA_RNA polymerase II can bind in the correct_and_

-TATA box -before -position and orientation

Additional_bind to DNA along with_, forming the transcription initiation complex. _then unwinds the DNA double helix, and RNA synthesis begins at the _on the template strand

-transcription factors -RNA polymerase II -RNA polymerase II -start point

As RNA polymerase moves along DNA, it continues untwist the _, exposing about_DNA nucleotides at a time for pairing with_. This process is _

-double helix -10-20 DNA nucleotides -RNA nucleotides -elongation

The RNA polymerase II adds_ nucleotides to_end of the growing RNA molecules as it continues along the double helix during the process of

-complementary -3′ end -elongation

In the wake of this advancing wave of RNA synthesis, the the new RNA molecule_from its DNA template, and the DNA double helix_. This process is part of _

-peels away -reforms -elongation

What the progress rate of transcription?

40 nucleotides per second in eukaryotes

A single gene can be transcribed_by_

-simultaneously -several molecules of RNA polymerase following each other like trucks in a convoy

A growing strand of RNA trails off from each polymerase, with the length of each new strand reflecting how_

far along the template the enzyme has traveled from the start point

The congregation of many polymerase molecules simultaneously transcribing a single gene increases_, which helps the cell make_

-the amount of mRNA transcribed from it -the encoded protein in large amounts

The mechanism of termination differs between_ and _

-bacteria -eukaryotes

In bacteria how is the termination process?

transcription proceeds through a termination sequence in the DNA. the transcribed terminator (an RNA sequence) functions as the termination signal, causing the polymerase ti detach from the DNA and release the transcript, which requires no further modification before translation

In eukaryotes how is the termination process?

RNA polymerase II transcribes a sequence on the DNA called the polyadenylation signal sequence, which codes for a polydenylation signal (AAUAAA) in the pre-mRNA. Then, at the point about 10-35 nucleotides downstream from AAUAAA signal, proteins associated with the growing RNA transcript cut it free from the polymerase, releasing the pre-mRNA. The pre-mRNA then undergoes processing to be converted into the mRNA

Compare DNA polymerase and RNA polymerase in therms of how they function, the requirement for a template and primer, the direction of synthesis, and the type of nucleotides used.

-Both assemble nucleic acid chains from monomer nucleotides whose order is determined by complementary base pairing to a template strand -Both synthesize in the 5′->3′ direction, antiparallel to the template – DNA polymerase requires a primer, but RNA polymerase can start a nucleotide chain form scratch. -DNA polymerase uses nucleotides with the sugar deoxyribose and the base T, RNA polymerase uses nucleotides with the sugar ribose and the base U

What is the promoter, and is it located at the upstream or downstream end of a transcription unit?

-The promoter is the region of DNA to which RNA polymerase binds to begin transcription -It is located at the upstream end of the gene (transcription unit)

What enables RNA polymerase ti start transcribing a gene at the right place on the DNA in a bacterial cell? In a eukaryotic cell?

-In a bacterial cell,RNA polymerase recognizes the gene’s promoter and binds to it. -In an eukaryotic cell, transcription factors mediate the binding of RNA polymerase to the promoter. -In both cases, sequences in the promoter bind precisely to the RNA polymerase, so the enzyme is in the right location and orientation.

Enzymes in the eukaryotic nucleus_

modify pre-mRNA in specific ways before the genetic messages are dispatched to the cytoplasm

RNA processing

-modification of the RNA primary transcripts, including splicing out of introns, joining together of exons, and alteration of the 5′ and 3′ ends -these modifications produce an mRNA molecule ready for translation

how does the 5′ end of the pre-mRNA is modified?

The 5’end is sysnthezised first; it receives a 5′ cap, a modified form of a guanine (G) nucleotide added onto the 5′ end after transcription of the first 20-40 nucleotides

How does the 3′ end of the pre-mRNA is modified?

Recall that the pre-mRNA is released soon after the polyadenylation signal (AAUAAA), is transcribed. At the end 3′ end, an enzyme adds 50-250 more adenine (A) nucleotides, forming a poly-A tail.

5′ cap

-a modified form of guanine nucleotide added onto 5′ end of a pre-mRNA -After transcription, the messenger RNA strand is modified by covalently adding a modified GTP (with a methyl group) to the 5′-end of the mRNA. -It protects the RNA from degradation by enzymes -It also helps the ribosome recognize the attachment site

3′-Tail Modification

-Poly-A tail: a sequence of 50-250 adenine nucleotides added onto 3′ end of a pre-mRNA molecule

The 5′ cap and poly-A tail share several important functions. What are these?

1st. they seem to facilitate the export of the mature mRNA from nucleus 2nd. they help protect the mRNA from degradation by hydrolytic enzymes 3rd. they help ribosomes attach to the 5′ end of the mRNA once the mRNA reaches the cytoplasm

Does 5′ cap and poly-A tail translated into a protein? who else?

-No they are not translated into a protein -Nor are the regions called 5′ untranslated region (5′ UTR) and 3′ untranslated region (3′ UTR)

What is the one of the other functions that have the UTR?

ribosome binding

the 3′ UTR is conformed of…

the polyadenylation singal (AAUAAA)

RNA splicing

After synthesis of a eukaryotic primary RNA transcript, the removal of portions of the transcript (introns) that will not be included in the mRNA and the joining together of the remaining portions (exons)

Most eukaryotic genes and their RNA transcripts have _. Most of these noncoding sequences are_. Thus the sequence of DNA nucleotides that codes for a eukaryotic polypeptide is usually_; it is_

-long non coding stretches of nucleotides, regions that are not translated. -interspersed between coding segmeents of the gene and thus between coding segments of the pre-mRNA -not continuous -split into segments

Introns

-intervening sequences -A noncoding, intervening sequence within a primary transcript that is removed from the transcript during RNA processing; also refers to the region of DNA from which this sequence was transcribed

Exons

-a sequence within a primary transcript that remains in the RNA after RNA processing; also refers to the region of the DNA from which this sequence was transcribed -eventually they are expressed, usually by being translated into amino acid sequences -exceptions include UTRs of the exons at the ends of the RNA (make up mRNA but not translated into a protein).

in making a primary transcript frp, a gene, RNA polymerase II _, but the mRNA molecule that enters the cytoplasm is an_

-transcribes both introns and exons form the DNA -abridged version

How is pre-mRNA splicing carried out?

-the signal for the RNA splicing is a short nucleotide sequence at each end of an intron. -The splicesome interacts with the previous sites on the intron, releasing the intron, which is rapidly degraded, and joining together the two exons that flanked the intron -snRNA catalyze these processes, as well as participating in spliceosome assembly and splice site recognition

small nuclear ribonucleoproteins

-abbreviated snRNPs -recognize the signal for the RNA splicing, which is a short nucleotide sequence at the end of each intron. – located in the cell nucleus -composed of RNA and protein molecules -RNA in an snRNP particle is called small nuclear RNA (snRNA)

small nuclear RNA

-snRNA -RNA in an snRNP particle -about 150 nucleotides long -These join with additional proteins to form an even largely assembly called a splicesome

splicesome

a large complex made up of proteins and RNA molecules that splices RNA by interacting with the ends of an RNA intron, releasing the intron and joining the two adjacent exons

who within the splicesome base-pairs with nucleotides at specific sites along the intron?

snRNA

Ribozymes

-RNA molecules that function as enzymes -by their discover thecatalytic role of snRNA arose

In some organisms does not need_for splicing, the intron RNA functions as a_

-proteins or even additional RNA molecules -ribozyme and catalyzes its own excision

What are the 3 properties of RNA enable some RNA molecules to function as enzymes?

1st. because RNA is single stranded, a region of an RNA molecule may base-pair with a complementary region elsewhere in the same molecule, which gives the molecule a particular 3-dimensional structure. A specific structure is essential to the catalytic function of ribozymes, just as it is for enzymatic proteins. 2nd. like certain amino in an enzymatic protein, some of the bases in RNA contain functional groups that may participate in catalysis. 3rd. the ability of RNA to hydrogen-bond with other nucleic acid molecules (RNA or DNA) adds specificity to its catalytic activity.

Complementary base pairing between the RNA of_and the RNA of _ precisely locates the region where the _catalyzes the splicing.

-spliceosome -primary RNA transcript -rybozyme

some of the Introns’ functions

-contain sequences that regulate gene expression -affect gene product

Important consequence of the presence of introns

is that a single gene can encode more than one kind of polypeptide.

alternative RNA splicing

A type of eukaryotic gene regulation at the RNA-processing level in which different mRNA molecules are produced from the same primary transcript, depending on which RNA segment are treated as exons and which as introns

Because of alternative RNA splicing, the number of_

different products and organism produces can be much greater than its number of genes

domains

a discrete structural and functional region of a protein

different exons may code for different

domains of a protein

one domain of an enzyme might include the_, while other micght allow the enzyme to_

-active site -bind to a cellular membrane

The presence of intorns may facilitate the_

evolution of a new potentially beneficial proteins as a result of a process known as Exon shuffling

Exon shuffling

introns increase the probability of crossing over between the exons of alleles of a gene–simply by providing more terrain for crossovers without interrupting coding sequences.

what is the results of exon shuffling?

-new combinations of exons and proteins with altered structure and function. -usually results in non-beneficial changes, occasionally a beneficial variant might arise

How can human cells make 75,000-100,000 different proteins, given that these are about 20,000 human genes?

Due to alternative splicing of exons, each can gene can result in multiple different mRNAs and can this direct synthesis of multiple different proteins.

what would be the effect of treating cells with an agent that removed the cap from mRNAs?

Once an mRNA gas exited the nucleus, the cap prevents it from being degraded by hydolytic enzymes and facilitates its attachment to ribosomes. If the cap were removed from all mRNAs, the cell would no longer be able to synthesize any protein and would probably die

process of translation is the flow from_to_

mRNA to protein

In the process of translation, a cell "reads" _ and build a _

-a genetic message polypeptide accordingly.

The message in translation is_, and the translator is called_

-a series of codons along an mRNA molecule -transfer RNA (tRNA)

Transfer RNA (tRNA)

an RNA molecule that functions as a translator between nucleic acid and protein languages by carrying specific amino acids form a the cytoplasmic poolof amino acids to the growing polypeptide in a ribosomes, where they recognize the appropriate codons in the mRNA

A cell has always_in its cytoplasm. This is accomplished by

-the 20 amino acids -by synthesizing them from other compounds or by taking them up from the surrounding solution

the ribosome is made of

-proteins and RNAs (ribosomal RNA)

The ribosomes add each_brought to it by_to the growing end of a _chain

-amino acid -tRNA -polypeptide chain

The key of translating a genetic message into a specific amino acid sequence is the fact that

molecules of tRNA are not all identical, and each type of tRNA molecule translates a particular mRNA codon into a particular amino acid

A tRNA molecule arrives at a ribosomes having a_at one end

specific amino acid

At the other endof the tRNA is a nucleotide triplet called_, which_

-anitcodon -base-pairs with a complemetnarhy codon on mRNA

anticodon

a nucleotide triplet at one end of a tRNA molecule that base-pairs with a particular complementary codon on an mRNA molecule

When the tRNA base pairs with the codon on mRNA by_it carries the respective _to the other side. As an mRNA molecule is moved through a ribosome,_whenever the codon that match its anticodon is presented for translation. Codon by codon, the genetic message is translated as tRNAs deposit _ in the order prescribed, and the _joins the amino acids into a chain.

-hydrogen bonding -amino acid -the amino acid that this tRNA produces will be added to the polypeptide chain -amino acids -ribosome

The tRNA molecule is a _ int he sense that it can _

-translator -read a nucleic acid word (mRNA codon) and interpret it as a protein word (the amino acid)

The basic concept of translation: as a molecule of mRNA is moved through a ribosome, _are translated into_, one by one. The interpreters are_, each type with a specific _at one end and a _at the other end. A _adds its amino acid cargo to a growing_when the anitcodon _to a complementary_on the mRNA.

-codons -amino acids -tRNA molecules -anticodon -corresponding amino acid -tRNA -polypeptide chain -hydrogen-bonds -codon

How do we obtain transfer RNA molecules?

they are transcribed from DNA templates

In eukaryotic cells how do we obtain tRNAs?

-As mRNAs -They are made in the nucleus and then travels from the nucleus to the cytoplasm, where translation occurs

In both bacteria and eukaryotic cells, each tRNA molecule is used_

repeatedly, picking up its designated amino acid in the cytosol, depositing its cargo onto a polypeptide chain at the ribosome, and then leaving the ribosome, ready to pick up another amino acid.

tRNA molecule features

-consist of a single RNA strand that is only about 80 nucleotides long -because of the presence of complementary stretches of nucleotides bases that can hydrogen-bond to each other, this single strand can fold upon itself and form a molecule with a three-dimensional structure. -flattened into one plane to clarify its base pairing, a tRNA looks like a cloverleaf (2D) -it twists and folds into a compact 3D structure that is roughly L-shaped

describe the two-dimensional structure of tRNA

-4 base-paired tregions -3 loops -the base sequence of 3’end is the same for all tRNAs. (amino acid attachment site) -the anticodon triplet is unique to each tRNA type, as are some sequences in the other two loops. -The modified bases contribute to tRNA function in a way that is not yet understood.

Describe the different features of the L-shaped of tRNA

-The loop extending from one end of the L includes the anticodon (particular nucleotide triplet that base-pairs to a specific mRNA codon) -The other end of the L-shaped tRNA molecule protrudes its 3′ end (which is the attachment site for an amino acid)

the accurate translation of a genetic message requires two instances of molecular recognition, which are

1st. a tRNA that binds to an mRNA codon specifying a particular amino acid must carry that amino acid, and not other to the ribosome. 2nd. is the pairing of the tRNA acticodon wit the appropriate mRNA codon.

The correct matching up of tRNA and Amino acid (first instance for accurate translation) is carried out by a family of related enzymes called_

aminoacyl-tRNA synthetases

aminoacyl-tRNA synthetases

an enzyme that joins each amino acid to the appropoate tRNA

The acitve site of each type of aminoacyl-tRNA synthestase _

fits only a specific combination of amino acid and tRNA (both the amino acid attachment end and the enticodon end of tRNA are instrumental in ensuring the specific fit)

how many different aminoacyl-tRNA synthases are? what are capable each of the synthases?

-20, one for each amino acid -each synthase is able to bind all the different tRNAs that code for its particular amino acid

anticodons on tRNAs are written in what direction? why?

-3′->5′ to align properly with codons written 5′->3′

for base pairing RNA strand must be

antiparallel, like DNA.

steps for aminoacyl-tRNA synthetase joining a specific amino aicd to a tRNA

1. active site binds the amino acid and ATP 2. ATP loses two Phosphate groups and bonds to the amino acid as AMP (adenosine monophosphate) 3. Appropriate tRNA covalently bonds to amino acid, displacing AMP 4. The tRNA charged with amino acid is released by the enzyme

the process of linkage to tRNA and amino acid that aminoacyl-tRNA synthetase does is an_process

endergonic

The synthetase catalyzes the covalent attachment of the amino acid to its tRNA in a process driven by_. The resulting aminoacyl tRNA , or_, is released from the enzyme and is then available to_

-hydrolysis of ATP -charged tRNA -to deliver its amino acid to a growing polypeptide chain on a ribosome

If one tRNA variety existed for each mRNA codon specifying an amino acid, there would be _ tRNAs. In fact there are only about_, signifying that some tRNAs must _. Such versatility is possible because_.

-61 -45 -be able to bind to more than one codon. -the rules for base pairing between the 3rd nucleotide base of a codon and the corresponding base of a tRNA anticodon are relaxed compared to those at other codon positions.

wobble

flexibility in the base-pairing rules in which the nucleotide at the end 5′ end of a tRNA anticodon can form hydrogen bonds with more than one kind of base in the third position (3′ end) of a codon

the term wobble explains

why synonymous codons for a given amino acid most often differ in their third nucleotide base, but not in the other bases.

Ribosomes facilitate

the specific coupling of tRNA anticodons with mRNA codons during protein synthesis.

a ribosome consitst of

-a large subunit and a small subunit -each made up of proteins and one or more ribosomal RNAs (rRNAs)

ribosomal RNAs (rRNAs)

-RNA molecules that, together with proteins, make up ribosomes -the most abundant type of RNA

where are the subunits made to build ribosomal RNA in eukaritoic cells?

in the nucleus

describe the binding sites of the ribosome

A ribosome has an mRNA binding site and 3 tRNA binding sites, known as the A, P, and E sites.

when a tRNA fits into its binding site on the ribosome?

it fits into a binding site when its anticodon base-pairs with an mRNA codon.

which of the binding sites holds the tRNA attached to the growing polypeptide?

P site

Which of the binding sites hold the tRNA carrying the next amino acid to be added to the polypeptide chain?

site A

Which of the binding site is the place to discharge the tRNA that already has passed its amino acid to the growing polypeptide?

E site

after the ribosomal RNA is transcribed in the nueclues, what happens?

it is processed and assembled with proteins imported from the cytoplasm (in nucleus)

after the ribosome is made? what happens?

the resulting ribosomal subunits are then exported via nuclear pores to the cytoplasm

In both bacteria and eukaryotic cells, the the formation of ribosome condition is?

large and small subunits join to form a functional ribosome only when they are attach to mRNA molecule.

about_of the mass of one ribosome is made of proteins, the rest consist of_

-one third -rRNA

In eukaryotes how many subunits have the ribosomes?

4

In bacteria how many subunits have the ribosomes?

3

what are the differences between the ribosomes of eukaryotes and bacterias?

-differ in molecular composition -certain antibiotic drugs can inactivate bacterial ribosomes without inhibiting the ability of eukaryotic ribosomes to make proteins.

the structure of the ribosome reflects its function of…

bringing mRNA together with tRNAs carrying amino acids

P site

-one of a ribosome’s three binding sites for tRNA during translation. -The P site holds the tRNA carrying the growing polypeptide chain -stands for Peptidyl tRNA

A site

-one of a ribosome’s three binding sites for tRNA during translation. -The A site holds the tRNA carrying the next amino acid to be added to the polypeptide chain. -stand for aminoacyl tRNA

E site

-one of a ribosome’s three binding sites for tRNA during translation. -The E site is the place where discharged tRNAs leave the ribosome -E stands for Exit

Describe the process carry out insite the ribosome

-The ribosome holds the tRNA and mRNA in close proximity and position the new amino acid for addition to the carboxyl end of the growing polypeptide -It then catalyzes the formation of the peptide bond -As the polypeptide becomes longer, it passes through an exit tunnel in the ribosome’s large subunit. -When the polypeptide is complete, it is released through the exit tunnel

who, depending on the scientific evidene, is primarly responsible for both the strucutre and function of the ribosome? proteins or rRNA?

rRNA

what is the funciton of proteins in the ribosome?

-Proteins are largely on the exterior -support the shape changesof the rRNA molecules as they carry put catalysis during translation

Ribosomal RNA is the main constituent of_, and it is the catalyst of_

-interface between the two subunits and of the A and P sites -peptide bond formation

rRNA for its catalyst functions is considered to be

a ribozyme

3 stages of translation

-initiation -elongation -termination

what does all of the three stages of translation required?

protein "factors" that aid in the translation process

translation is the

synthesis of a polypeptide chain

In what stages does energy is required in translation?

initiation and elongation

how does the energy needed in certain aspects of initiation and elongation is provided?

by the hydrolysis of GTP (Guanosine triphosphate), molecule closely related to ATP

the initiation stage of translation brings together

-mRNA -tRNA containing the first amino acid of the polypeptide – two subunits of a ribosome

Describe the first step of initiation in translation

-a small ribosomal subunit binds to both a molecule of mRNA and a specific initiator tRNA, which carries the amino acid methionine and its anticodon is UAC

Describe the first step of initiation in translation inside bacteria

-the small subunit can bind the mRNA and the tRNA (containing methionine) in either order -the mRNA binding site on this subunit recognizes a specific nucleotide sequence on the mRNA just upstream of the start codon (AUG)

Describe the first step of intitiation in translation inside eukaryotes

-The small subunit, with the initiator tRNA already bound, binds to the 5′ cap of the mRNA and then move, or scans, downstream along the mRNA until it reaches the start codon -the initiator tRNA then hydrogen-bonds to the AUG start codon. -In either case, the start codon signals the start of translation; this is important because it establishes the codon reading frame for the mRNA

The union of what things completes the translation initiation complex?

union of mRNA, initiator tRNA, and a small ribosomal subunit is followed by the attachment of a large ribosomal subunit

what is required to bring all these components together? (mRNA, initiatior tRNA, ribosomal subunit, and large ribosomal subunit)

Proteins called initiation factors

the cell also spends energy obtained from_to form the_

-hydrolysis of GTP -initiation complex

At the completion of the initiation process…

the initiator tRNA sits in the P site of the ribosome, and the vacant A site is ready for the next aminoacyl tRNA.

A polypeptide is always synthesized in one direction, which is…

from the initial methionine at the amino end (N-terminus) toward the final amino acid at the carboxyl end (C-terminus)

Describe the second step in initiation in translation.

-arrival of a large ribosomal subunit completes the initiation complex -proteins called initiation factors are required to bring all the translation components together. -Hydrolysis of GTP provides the energy for the assembly -The initiator tRNA is in the P site -The A site is available to the tRNA containing the next amino acid

In the elongation stage of translation, amino acids are added

one by one to the previous amin acid at the C-terminus of the growing chain.

Each addition of amino acids requires the participation of_ and occurs in_

-several proteins called elongaiton factors -a three-step cycle

Energy expenditure occurs in which steps?

in the first and third step

for what processes in elongation does the hydrolysis of GTP is needed?

-codon recognition, which increases accuracy and efficiency of this step -translocation step

Describe the three-step cycle of elongation

1) codon recognition -The anticodon of an incoming amynoacyl tRNA base-pairs with the complementary RNA -Hydrolysis of GTP increases the accuracy and efficiency of this step -Many different aminoacyl tRNAs are present, but only one with the appropiate anticodon will bind and allow the cycle to progress 2) Peptide bond formation -An rRNA molecule of the large ribosomal subunit catalyzes the formation of a peptide bond between the amino a group of the new amino acid in the A site and the carboxyl end of the growing polypeptide in the P site. -This step removes the polypeptide from the tRNA in the p site and attaches it to the amino acid in the tRNA in the A site 3) translocation -The ribosome translocates the tRNA in the A site to the P site -At the same time, the empty tRNA in the P site is moved to the E site, where it is released. -The mRNA moves along with its bound tRNAs, bringing the next codon to be translated into the A site

The mRNA is moved through the ribosome in one direction only

5′ end first; this is equivalent to the ribosome moving from 5′ -> 3′ on the mRNA

the important point of the movement of mRNA and ribosome is

that the ribosome and the mRNA move relatively to each other, unidirectionally, codon by codon

The elongation cycle takes_in bacteria and is repeated as each_until the _is completed

-less than a tenth of a second -amino acid is added to the chain -polypeptide

Elongation continues until

a stop codon in the mRNA reaches the A site of the ribosome

what are the codons that are the stop signals and at the same time does not code for any amino acid?

UAG UAA UGA

A way to remember is "the gorilla wags to the baby"

-gorilla talks like: UGA -The baby cries: UAA -Wag would be with "U" UAG

release factor

-protein shaped like an aminoacyl tRNA -binds directly to the stop codon in the A site -causes the addition of a water molecule instead of an amino acid to the polypeptide chain

the addition of water to the polypeptide chain by the release factor what produces?

this reaction breaks (hydrolyses) the bond between the completed polypeptide and the tRNA in the P site, releasing the polypeptide through the exit tunnel of the ribosome’s large subunit

The remainder of the translation assembly (in termination step) then comes apart in a multistep process, aided by other_

protein factors

Breakdown of the translation assembly requires

hydrolysis of two more GTP molecules

termination of translation requires:

-GTP hydrolysis -Protein factors

Describe termination steps

1) when a ribosome reaches a stop codon on mRNA, the A site of the ribosome accepts a "release factor," a protein shaped like a tRNA, instead of an aminoacyl tRNA 2) The release factor promotes hydrolysis of the bond between the tRNA in the P site and the last amino acid of the polypeptide, thus freeing the polypeptide from the ribosome 3) the two ribosomal subunits and the other components of the assembly dissociate by the hydrolysis of 2 GTP

Polyribosomes

-also called polymes -A group of several ribosomes attached to, and translating, the same messenger RNA molecule -enable the cell to make many copies of a polypeptide very quickly -ribosomes trailing along the mRNA -found in both bacteria and eukaryotic cells

THE process of translation is often_to make a functional protein. Thus the polypeptide require further_

-not sufficient -modifications and mechanisms used to target completed proteins to specific sites in the cell

During synthesis, a polypeptide chain begins_, forming_

to coil and fold spontaneously as a consequence of its amino acid sequence (primary strucutre) -a protein of specific shape: 3D molecule with secondary and tertiary strucutre

Genes determine which level(s) of proteins?

primary structure

who determines the shape of the protein?

the primary structure

who helps the polypeptide to fold correctly?

the chaperone protein (chaperonin)

What is the name of the additional steps that may be required before a protein can begin doing its particular job in the cell?

post-transitional modifications

describe some of the modifications that are carried out by the post-transitional modifications

-amino acids may be chemically modififed by the attachment of sugars, lipids, phosphate groups,or other additions -Enzymes may remove one or more amino acids from the leading (amino) end of the polypeptide chain -Polypeptide chain may be enzymatically cleaved into two or more pieces (Ex. insulin) -Two or more polypeptides that are synthesized separately may come together, becoming the subunits of a protein that has quaternary structure. (Ex. hemoglobin)

two types of ribosomes:

-free ribosomes -bond ribosomes

free ribosomes

-are suspended in the cytosol -mostly synthesize proteins that stay in the cytosol and function there

Bond ribosomes

-attached to the cytosolic side of the endoplasmic reticulum (ER) or nuclear envelope. -Make proteins of the endomembrane system (the nuclear envelope, ER, Golgi apparatus, lysosomes, vacuoles, and plasma membrane) -make proteins that are secreted form the cell (ex. insulin)

bond and free ribosomes are_

-identical -can change status from free to bound

what determines wheter a ribosome is free in the cytosol or is bound to rough ER?

It is determined by the polypeptides of proteins that are marked by the presence of signal peptides

Polypeptide synthesis always begins where? and when?

in the cytosol as a free ribosome starts to translate an mRNA molecule

In the cytosol the polypeptide synthesis continues until completion unless…, which (polypeptide of proteins) are destined for_marked by_

the growing polypeptide itself cues the ribosome to attach to the ER -the endomembrane system or for secretion -signal peptide

signal peptide

-a sequence of about 20 amino acids -at or near the leading (amino or N-terminus) end of a polypeptide -targets the polypeptide to the endoplasmic reticulum or to other organelles in a eukaryotic cell

The polypeptide is recognized as_by_

-it emerges from the ribosome – a protein-RNA complex called signal-recognition particle (SRP)

signal-recognition particle (SRP)

-a protein-RNA complex -recognizes a signal peptide as it emerges from a ribosome -helps direct the ribosome to the ER by binding to a receptor protein on the ER -the receptor is part of a multiprotein translocation complex

When the ribosome is attached to the ER the process continues there, and the growing_via_

-polypeptide snakes across the membrane into the ER lumen -protein pore

what happens to the signal peptide when the polypeptide is completed? what happens to the rest of the completed polypeptide?

-it is removed by an enzyme, for example the signal-cleaving enzyme -If the completed polypeptide is for secretion, it will be released into the solution within the ER lumen. If the polypeptide is to be a membrane protein, it will remain partially embedded in the ER membrane

Other kinds of signal peptides are used to_.

target polypeptides to mitochondria, chloroplasts, the interior of the nucleus, and other organelles that are not part of the endomembrane system.

The critical difference in the cases that polypeptides are send to mitochondria, chloroplasts, the interior of the nucleus, and other organelles that are not part of the endomembrane system are:

-translation is completed in the cytosol before the polypeptide is imported into the organelles -The mechanism of translocation also vary, but in all the cases, the "postal zip codes" that address proteins for secretion or to cellular locations are signal peptides of some sort

How does Bacteria use signal peptides?

It employs signal peptides to target proteins to the plasma membrane for secretion

describe the steps for signal mechanism for targeting proteins to the ER

1) Polypeptide synthesis begins on a free ribosome in the cytosol 2) An SRP binds to the signal peptide, halting synthesis momentarily 3) The SRP binds to a receptor protein in the AR membrane, This receptor is part of a protein complex (a translocating complex) that has membrane pore and a signal-cleaving enzyme 4) The SRP leaves, and polypeptide synthesis resumes, with simultaneous translocation across the membrane. (The signal peptide stays attached to the translocation complex) 5) The signal-cleaving enzyme cuts off the signal peptide 6) The rest of the completed polypeptide leaves the ribosome and folds into its final conformation

What two processes ensure that the correct amino acid is added to a growing polypeptide chain?

-First, each aminoacyl-tRNA synthase specifically recognizes a single amino acid and attaches it only to an appropiate RNA -Second, a tRNA charged with its specific amino acid binds only to an mRNA codon for that amino acid

Discuss the ways in which rRNA structure likely contributes to ribosomal function

The specific structure and function of the ribosome seem to depend more on the rRNA than on ribosomal proteins. Because: -it is single-stranded -an RNA molecule can hydrogen-bond with itself and with other RNA molecules -RNA molecules make up the interface between the 2 ribosomal subunits, so presumably RNA-RNA binding helps hold the ribosome together. -the binding site for mRNA in the ribosome includes rRNA that can bind to mRNA. -complementary bonding within an RNA molecule allows it to assume a particular 3D shape, and along with the RNA’s functional groups, presumably enables rRNA to catalyze peptide bond formation during translation

Describe how a polypeptide to be secreted is transported to the endomembrane system

A signal peptide on the leading end of the polypeptide being synthesized is recognized by a signal-recognition particle that brings the ribosome to the ER membrane, There the ribosome attaches and continues to synthesize the polypeptide, depositing it in the ER lumen

If a tRNA has the anticodon 3′-CGU-5′, what two different codons could it bind to?

Because of wobble, the tRNA could bind to either 5′-GCA-3′ or 5′-GCG-3′, both of which code for the same amino acid that is alanine. So alanine will attach to the tRNA opposite to its anticodon

_ and _ RNA polymerase differ significantly from each other, while single archeal RNA polymerase resembles the _.

-bacterial -eukaryotic -three eukaryotic ones

Archea and eukaryotes use a _, unlike the _in bacteria

-complex set of transcription factors -smaller set of accessory proteins

_differently in bacteria and eukaryotes. The little known about archeal _suggests that it is similar to_process

-transcription is terminated -transcription terminaiton -eukaryotic

As far as translation is concerned, archeal ribosomes are the same size as_ribosomes, but their sensitivities to chemical inhibitors more closely match those of_ribosomes.

-bacterial -eukaryotic

The initiation of translation is slightly different in_and_. in this respect, the archeal process is more like that of_

-bacteria -eukaryotes -bacteria

The most important differences between bacteria and eukaryotes with regard to gene expression arise from the_. Thus the coupling of transcription and translation is similar in archeal cells is like_

-bacterial cell’s lack of compartmental organization -bacteria, because archea lacks nucleus

In bacteria the protein synthesis is_becuase of_. In eukaryotes the protein synthesis is_because of_. This processing stage (eukaryotes) includes_

-unregulated -lack of compartmental organization. Thus activities can happen simultaneously -regulated -presence of membranes which segregate transcription from translation and provides compartment for extensive RNA processing. -additional steps whose regulation can help coordinate the eukaryotic cell’s elaborate activities

In spite of the differences cataloged here between the three domains, however, the_

idea of the gene itself is a unifying concept among all forms of life.

Functional definition of a gene depending of all the previous information in this chapter:

DNA sequence that codes for a specific polypeptide chain

The definition of a gene by the Mendelian concept

discrete unit of inheritance that affects a phenotypic character

Morgan and his collagues assigned such genes to

specific loci on chromosomes

View gene as

region of specific nucleotide sequences along the length of the DNA molecule of a chromosome

What parts of the gene are not transcribed? why they can be part of the gene’s definition?

-introns and promoters and certain other regulatory regions of DNA. Also rRNA, tRNA, and other RNAs. -they can be considered part of the functional gene because they must be present for transcription to occur

defintion taking into account non transcribed parts of the gene

A gene is a region of DNA that can be expressed to produce a final functional product that is either a polypeptide or an RNA molecule

when considering phenotypes, Proteins bring about an _

organism’s observable phenotype

A given type of cell expresses only a_

subset of its genes (essential feature in multicellular organisms)

Gene expressions is regulated or nonregulated?

regulated

Does polyribosomes happen in eukaryotic cells?

no

In eukaryotic cells, mRNAs have been found to have a circular arrengement in which proteins hold teh poly-A tail near the 5′ cap. How might this increase translation efficiency?

when one ribosome terminates translation and dissociates, the two subunits would be very close to the cap. This would facilitate their rebinding and initiating synthesis of a new polypeptide, thus increasing the efficiency of translation

summary of transcription and translation in a eukaryotic cell

-Transcription= 1)RNA is transcribed from a DNA template -RNA processing= 2) In eukaryotes, the RNA transcript (pre-mRNA) is spliced and modified to produce mRNA, which moves from the nucleus to the cytoplasm. 3) The mRNA leaves the nucleus and attaches to a ribosome. -Amino Acid Activation= 4) Each amino acid attaches to its proper tRNA with the help of a specific enzyme and ATP -Translation= 5) a succession of tRNAs add their amino acids to the polypeptide chain as the mRNA is moved through the ribosome one codon at a time. When completed, the polypeptide is released from the ribosome.

The final products of some genes through transcription and translation are not polypeptides but_

RNA molecules,including tRNA and rRNA

All the polypeptides start with_provided by_. However it can be removed in later phases.

-Methionine (MET) -by the start codon AUG

Does prokaryotes have exons and introns? why?

no because their translation and transcription process are not separate by membrane (like in eukaryotes) Thus this processes can be simultaneous

Prokatyoes express_portion of the genes
Eukaryotes express_portion of the genes

-the whole thing -the exon

Genes code for_

-Proteins (majority) -RNA which is the final product that is not turned into protein (rRNA, tRNA, mRNA)

Inherited instructions in DNA direct the _. Thus, the DNA that forms alleles (genotype) codes for a _ that performs a specific function in the cell (enzyme, structural, etc.)… producing the _

-synthesis of proteins -protein -phenotype

How do we get from DNA sequence to protein?

DNA is transcribed into mRNA and mRNA is translated into polypeptide (central dogma of biology)

Why bother with RNA?
Why not just make proteins directly from DNA?

1) DNA can stay pristine and protected, away from the caustic chemistry of the cytoplasm. 2) Gene information can be amplified (make many copies of RNA made from one copy of DNA). 3) Regulation of gene expression is enhanced by having specific controls at each element of the pathway between DNA and proteins. The more elements in the pathway, the more opportunities there are to control protein production under different circumstances.

RNA vs. DNA

1)-OH group on 2′ carbon of the sugar (RNA) 2) Uracil (RNA) vs. thiamine (DNA) 3) -OH groups prevent stable double helixfrom forming – though hairpin loops can form (secondary structure) 4) No double helix Means RNA (depending On its bases) can form Unique 3-D structures (tertiary structure)

Transcription is performed by what enzyme?

RNA polymerase

Translation is done by?

Ribosomes

Transcription in matters of molecular language is _

the same language just transcribing (differences T and U)

Translation in matters of molecular language is_

from one molecular language (nucleotides) to other molecular language (amino acids)

RNA processing consist of

breaking and separating of exons and introns

Exons_
Introns_

-diffuse back together by splisosome add tails to the mRNA and is mature mRNA -> ready to leave the nucleus -stay in nucleus

Genes are composed of what three elements?

-promoter -coding region -terminator

promoter

-The region of a gene that is required for the initiation of transcription. Recognized by RNA polymerase (+ accessory proteins called transcription factors) -It is not translated into amino acids

coding region

The actual region of the gene that will be converted into a protein (lies between the promoter and the terminator)

Terminator

A sequence of DNA in the gene that causes the end of transcription.