Chapter 17: Gene Expression

Question 1

Template and coding strand

Answer 1

The template strand provides the pattern for the sequence of nucleotides transcribed by mRNA

The non-template strand or coding strand is the DNA strand that is complementary to the template strand

• Its condons are identical to the mRNA sequence with the substitution of thymine instead of uracil

Codons are read by the translation machinery in the 5’ → 3’ direction

Question 2

Stop and start codons

Answer 2

AUG is the sole start codon; also codes for methionine

UAA, UAG, and UGA are all stop codons

Question 3

Transcription components

Answer 3

RNA polymerase- enzyme that pries the two strands of DNA apart and joins complementary RNA nucleotides together

Promoter- sequence of a gene where RNA polymerase attaches to in order to initiate transcription

Transcription unit- the stretch of DNA downstream from the promoter that is transcribed

Terminator- sequence that signals the end of transcription; ONLY present in prokaryotes

Question 4

Transcription

In prokaryotes

Answer 4

Initiation

RNA polymerase binds itself directly to the promoter and begins transcription

• Untwists DNA and exposes 10−20 nucleotides at a time for pairing with RNA nucleotides

Elongation

Adds nucleotides to the 3’ end of the growing RNA molecule similar to DNA polymerase

Termination

Transcription proceeds through the terminator sequence in the DNA which causes the polymerase to detach and release the transcript which requires no further modification

Question 5

Transcription

In eukaryotes

Answer 5

Initiation

A collection of proteins called transcription factors help guide the binding of RNA polymerase II to the promoter

• Only after transcription factors are attached to the promoter does RNA polymerase II bind to it
• Entire complex of transcription factors and RNA polymerase II bound to the promoter is called a transcription initiation complex
• A crucial promoter DNA sequence called the TATA box helps form the initiation complex

Untwists DNA and exposes 10−20 nucleotides at a time for pairing with RNA nucleotides

Elongation

Adds nucleotides to the 3’ end of the growing RNA molecule similar to DNA polymerase at a rate of about 40 nucleotides per minute

Termination

RNA polymerase II transcribes the polyadenylation signal sequence; the RNA transcript is released 10−35 nucleotides past this polyadenylation sequence (AAUAAA)

Pre-mRNA then proceeds on for further processing

Question 6

RNA processing

In eukaryotes

Answer 6

Enzymes in the nucleus modify pre-mRNA before the genetic message is dispatched to the cytoplasm

Both ends of the primary transcript are usually altered

Usually certain interior sections of the molecule are also cut-out and the remaining parts spliced together

Question 7

Alteration of mRNA ends

In eukaryotes

Answer 7

The 5’ end which is synthesized first receives a 5’ cap of a modified form of guanine

At the 3’ end an enzyme adds 50−250 more adenines after the polyadenylation sequence AAUAAA forming a poly-A tail

5’ cap and poly-A tail have several function:

1. Facilitate the export of mature mRNA from the nucleus
2. Help protect the mRNA from degradation by hydrolytic enzymes
3. Help ribosomes attach to the 5’ end once it reaches the cytoplasm

Question 8

RNA splicing process

Answer 8

Large portions of the RNA primary transcript molecules are removed and the remaining portions reconnected

The removed segements are noncoding regions called intervening sequences or introns

The other regions called exons that remain are expressed and go to be translated into proteins

The terms introns and exons are use to describe RNA sequences and the DNA sequences that specify them

Question 9

RNA splicing enzyme

Answer 9

The removal of introns is accomplished by a large complex made up of proteins and small RNAs called spliceosomes

Spliceosomes consist of a variety of proteins and several small nuclear ribonucleoproteins (snRNPs) that recognize the splice sites

This complex binds to several short nucleotide sequences along and intron including key sequences at each end

The intron is then released and the spliceosoe joins together the two exons that flanked the intron

Question 10

Ribozymes

Answer 10

Ribozymes are catalytic RNA molecules that function as enzymes and can splice RNA

• Not all biological catalysts are proteins

Three properties of RNA enable it to function as an enzyme:

• It can form a three-dimensional structure because of its ability to base-pair with itself; a specific structure is essential to catalytic functioning
• Some bases in RNA contain functional groups that may participate in catalysis
• RNA can hydrogen-bond with other nucleic acid molecules which adds specificity to its catalytic activity

Question 11

Functional importance of introns

Answer 11

A single gene can encode more than one kind of polypeptide

Many genes are known to give rise to two or more dfferent polypeptides depending on which segements are treated as exons; a process known as alternative RNA splicing

Protein often have a modular architecture that consists of discrete functional and structural regions called domains that impart different properties; different exons code for different domains

Question 12

Molecular components of translation

Answer 12

A cell translates an mRNA message into protein with the help of transfer RNA or tRNA

Function is to transfer an amino acid from the cytoplasm to a growing polypeptide in a ribosome

Each tRNA molecule enables translation of a given mRNA codon into a specific amino acid

tRNA twists into a 3-D L-shapped structure

• Its 3’ end protrudes from one end and serves as an attachment site for a specific amino acid
• The loop extending from the other end of the L includes the anticodon which is a nucleotide triplet that base pairs with a specific mRNA codon

Question 13

tRNA-amino acid specificity

Answer 13

The correct matching of tRNA and amino acid is carried out by a family of enzymes called aminoacyl-tRNA synthetases

The active site of each type of aminoacyl-tRNA synthetase fits only a specific combination of amino acid and tRNA

There are 20 different synthetases, one for each amino acid

The synthetase catalyzes the covalent attachment of the amino acid to its tRNA in a process driven by the hydrolysis of ATP

Question 14

tRNA-mRNA specificity

Answer 14

Some tRNAs are able to bind to multiple codons coding for the same amino acid due to flexible base pairing between the third nucleotide base of a codon

45 tRNAs bind to more than one codon

This flexible base pairing is called wobble which is why synonymous codons for a given amino acid most often differ in their third nucleotide base

Question 15

Ribosomal structure

Answer 15

Consists of a large and a small subunit made up of ribosomal RNA or rRNA

Ribosome has one binding site for mRNA and three binding sites for tRNA:

• A site is where tRNA enters; holds the tRNA carrying the next amino acid to be added to the chain
• P site holds the tRNA carrying the growing polypeptide chain
• E site is where the empty tRNA exits from

Question 16

Stages of translation and total energy usage

Just the stages

Answer 16

Initiation

• Uses one molecule of GTP

Elongation

• Uses two molecules of GTP

Termination

• Uses two molecules of GTP

Total energy usage is five molecules of GTP

Question 17

Initiation stage of translaiton

Answer 17

Brings together an mRNA, a tRNA bearing the first amino acid, and the two subunits of a ribosome

AUG start signals the start of translation and establishes the reading frame

The union of mRNA, the initiator tRNA, and the small ribosomal subunit is followed by the attachment of a large ribosomal subunit completing the translation initiation complex

• Proteins called initiation factors are required to bring all these components together
• Cell also expends energy obtained by the hydrolysis of a GTP molecule to form the initiation complex

Question 18

Elongation stage of translation

Answer 18

A polypeptide is always synthesized in one direction from the initial methionine at the amino end, called the N-terminus, to the final amino acid at the carboxyl end, called the C-terminus

Amino acids are added one by one to the C-terminus of the growing chain

Each addition involves proteins called elongation factors and occurs in three steps:

1. Codon recognition; requires one molecule of GTP
2. Peptide bond formation
3. Translocation; requires one molecule of GTP

Energy expenditure occurs in the first and third steps

Translation proceeds along the mRNA in a 5′ → 3′ direction

Question 19

Termination of translation

Answer 19

Elongation occurs until a stop codon in the mRNA reaches the A site

Codons UAG, UAA, and UGA do not code for amino acids but instead act as stop signals

A release factor protein binds directly to the stop codon in the A site

The release factor causes the addition of a water molecule instead of an amino acid

This reaction releases the polypeptide and the translation assembly comes apart

• Breakdown of the translation assembly requires the hydrolysis of two more GTP molecules

Question 20

Post-translational modifications

Answer 20

During its synthesis a polypeptide chain begins to coil and fold spontaneously to form a protein with a specific shape

Post-translational modifications may be required before the protein can begin doing its particular job in the cell

Question 21

Targeting polypeptides to specific locations

Answer 21

There are two populations of ribosomes

1. Free ribosomes mostly synthesize proteins that function in the cytosol
2. Bound ribosomes make proteins of the endomembrane system and proteins that are secreted from the cell

Ribosomes are identical and can switch from free to bound

Polypeptide synthesis always begins and finishes in the cytosol unless the polypeptide signals the ribosome to attach to the ER

• Polypeptides destined for the ER or for secretion are marked by a signal peptide which targets the protein to the ER
• A signal-recognition particle (SRP) binds to the signal peptide and escorts it and its ribosome to a receptor protein translocation complex built into the ER membrane

Other kinds of signal peptides are used to target polypeptides to mitochondira, chloroplasts, or other organelles that are not part of the endomembrane system

• In these cases however translation is completed in the cytosol before the polypeptide is imported into the organelle

Question 22

Translation of multiple polypeptides

Answer 22

Multiple ribosomes can translate a single mRNA simultaneously forming a string of ribosomes called polyribosomes or polysomes

• Enable a cell to make many copies of a polypeptide very quickly

Cells can also increase the number of copies of a polypeptide by transcribing multiple mRNAs from the same gene

Question 23

Small scale genetic mutations

Answer 23

Point mutations are chemical changes in just one base pair of a gene and can lead to a range of effects

• Sickle-cell disease results from a point mutation which codes for a valine where a glutamic acid should be

Single nucleotide-pair substitutions

The replacement of one nucleotide and its complement with another pair of nucleotides

• Silent mutations- have no effect on the amino acid produced by a codon because of redundancy in the genetic code
• Missense mutations- still code for an amino acid but it is not the correct amino acid
• Nonsense mutations- change an amino acid codon into a stop codon nearly always leading to a nonfunctional protein

Nucleotide-pair insertions or deletions

Additions or losses of nucleotide pairs in a gene

• Frameshift mutations- occur whenever the number of nucleotides inserted or deleted is not a multiple of three; all nucleotides downstream will be improperly grouped into codons and will result in extensive missense mutations unless it occurs at or near the end of the gene

Question 24

New mutations

Answer 24

Spontaneous mutations can occur during DNA replication, recombination, or repair

Mutagens are physical or chemical agents that can cause mutations