Chapter 17: Gene Expression: From Gene to Protein

Question 1

Blank are the link between genotype and phenotype.

Answer 1

Proteins

Question 2

What is gene expression?

Answer 2

Gene expression is the process by which 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

Question 3

Three ways in which RNA differs from DNA.

Answer 3

1. RNA contains ribose instead of deoxyribose as its sugar.
2. RNA has the nitrogenous base uracil rather than thymine.
3. RNA molecule usually consists of a single strand rather than DNA’s double strand

Question 4

What are the monomers of DNA and RNA? Of proteins?

Answer 4

Monomers of DNA and RNA - The four types of nucleotides which differ in their nitrogenous bases (a pentose sugar, phospate group, and a nitrogonous base)
Monomers of proteins - amino acids

Question 5

Describe the two processes that are essential to the formation of a protein.

Answer 5

transcription: The synthesis of RNA using a DNA template

translation: The synthesis of a polypeptide using the genetic information encoded in an mRNA molecule. There is a change of “language” from nucleotides to amino acids.

Question 6

Where does transcription take place? What is used as the template and what is the product?

Answer 6

Nucleus
DNA
RNA (mRNA)

Question 7

Where does translation take place? What is used as the template and what is the product?

Answer 7

cyoplasm
mRNA
polypeptide

Question 8

In eukaryotes, what is the pre-mRNA called?

Answer 8

primary transcript

Question 9

What is the Central Dogma as proclaimed by Francis Crick?

Answer 9

The essential direction of flow of genetic information. It refers to the unidirectional flow of biochmical information from DNA to protein.

DNA is transcribed to RNA and RNA is translated to Protein.

Note: DNA can replicate and RNA can be reverse-transcribed into DNA

Question 10

How many nucleotide bases are there? How many amino acids?

Answer 10

4 nucleotide bases
20 amino acids

Question 11

How many nucleotides are required to have a unique code for each of these 20 amino acids?

Answer 11

3

Question 12

The language of DNA is a triplet code. How many unique triplets exist?

Answer 12

64

Question 13

DNA is double-stranded; however, for each protein, only one of these two strands is used to produce an mRNA transcript. What is the strand called?

Answer 13

The template strand

Question 14

Here is a short DNA template. Assemble the complementary mRNA strand.
Recall that DNA-to-DNA, DNA-to-RNA, and RNA-to-RNA strand interactions are antiparallel.

3ʹ A C G A C C A G T A A A 5ʹ

Answer 14

5’ UGCUGGUCAUUU 3’

Question 15

Name the start codon and the three stop codons.

Answer 15

AUG - Met (Methionine)
UAA, UAG, UGA

Question 16

Of the possible 64 codons, how many code for amino acids?

Answer 16

61 remember the three stop codons do not code for amino acids - UAA, UAG, UGA

Question 17

Label the template strand, coding strand, and codons in the image.

Answer 17

Template strand top strand of DNA, coding strand is the bottom strand that is most like the mRNA strand except for the Ts are replaced with Us.

Question 18

Why is the genetic code said to be redundant but not ambiguous?

Answer 18

Although more than one codon may specify a particular amino acid, neither codon specifies any other amino acid.

Question 19

The enzyme that uses the DNA template strand to transcribe a new mRNA strand.

Answer 19

RNA polymerase

Question 20

Recall from Chapter 16 that DNA polymerase III adds new nucleotides to the template DNA strand to assemble each new strand of DNA. Both enzymes can assemble a new polynucleotide only in the 5ʹ to 3ʹ direction. Which enzyme, DNA polymerase III or RNA polymerase, does not require a primer to begin synthesis?

Answer 20

RNA polymerase

Question 21

Why is the promoter area important in beginning transcription?

Answer 21

The promoter is a specific nucleotide sequence in the DNA of a gene that binds RNA polymerase, positioning it to start transcribing RNA at the appropriate place.

Question 22

How are DNA polymerase and RNA polymerase alike, and how do they differ?

Answer 22

Like the DNA polymerases that function in DNA replication, RNA polymerases can assemble a polynucleotide only in its 5’ to 3’ direction, adding onto its 3’ end.
Unlike DNA polymerases, RNA polymerases are able to start a chain from scratch; they don’t need to add the first nucleotide onto a pre-existing primer.

Question 23

What happens in the initiation stage of trascription?

Answer 23

RNA polymerase attaches to a promoter region in front (upstream) of the gene. The enzyme moves down stream in the 3’ to 5’ direction on the template strand as it prepares to produce a transcript in the 5’ to 3’ form.

Note: a eukaryotic promotor, commonly includes a TATA box and requires transcription factor proteins to bind to the promotor region before RNA polymerase can bind in the correction position. They bind with the RNA polymerase, forming a TRANSCRIPTION complex. RNA polymerase then unwinds the DNA and RNA synthesis begins at the start point for the template strand.

Eukaryotes

Question 24

Upstream
Downstream

Answer 24

The direction of transcription is called downstream. Upstream is the oposite direction.

Question 25

What is a TATA box?

Answer 25

The TATA box is a DNA sequence in eukaryotic promoters crucial in forming the transcription initiation complex.
The name TATA box is from the thymine (T) and adenine (A) that make it up. It is a nucleotide sequence that contains the sequence “TATA” about 25 nucleotides upstream of the
transcriptional start point.

Question 26

What happens in the elongation stage of transcription?

Answer 26

As RNA polymerase moves along the DNA, it untwists the double helix, exposing about
10-20 DNA nucleotides at a time for pairing with RNA nucleotides (adding them to the 3’ end, U in RNA pairs with A in DNA). As transcription proceeds forward, the newly synthesized RNA molecule behind the RNA polymerase peels away from its DNA template, and the DNA double helix re-forms.

Question 27

How does the termination of transcription occur in bacteria?

Answer 27

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

Question 28

How does termination of trascription occur in eukaryotes?

Answer 28

In eukaryotes, RNA polymerase II transcribes a sequence on the DNA called the polyadenylation signal sequence, which specifies a polyadenylation signal (AAUAAA) in the pre-mRNA. This is called a “signal” because once this stretch of six RNA nucleotides appears, it is immediately bound by certain proteins in the nucleus. Then, at a point about 10-35 nucleotides downstream from the AAUAAA, these proteins cut the RNA transcript free from the polymerase, releasing the pre-mRNA.

Question 29

RNA processing, sometimes also called mRNA editing, occurs only in eukaryotic cells.
Prokaryotic cells lack the enzymes to edit mRNA. The primary transcript is altered at both
ends, and sections in the middle are removed.

a. What happens at the 5ʹ end?
b. What happens at the 3ʹ end?

Answer 29

a. The 5’ end is synthesized 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.

b. The 3’ end of the pre-mRNA molecule is also modified before the mRNA exits the nucleus. An enzyme adds 50–250 more adenine (A) nucleotides, forming a poly-A tail.

Question 30

What are three important functions of the 5ʹ cap and poly-A tail?

Answer 30

1. They seem to facilitate the export of mature mRNA from the nucleus.
2. They help protect the mRNA from degradation by hydrolytic enzymes.
3. They help ribosomes attach to the 5’ end of the mRNA once the mRNA reaches the
   cytoplasm

Question 31

Use the following figure to label all the sections of the RNA molecule including the 5ʹ cap
and the poly-A tail. This RNA molecule is still in the nucleus but has not yet undergone
RNA splicing.

Answer 31

Question 32

The following figure is the next step in preparing the RNA transcript to leave the nucleus: RNA splicing. Completely label both the pre-mRNA and the mRNA strand.

Answer 32

Question 32

Distinguish between introns and exons.

Answer 32

Exons are expressed and exit the nucleus. Introns intervene and stay in the nucleus.
Introns are the noncoding segments of nucleic acid that lie between coding regions, also
called intervening sequences.
Exons are the segments of nucleic acid that are eventually expressed by being translated
into amino acid sequences.

Question 32

What are the two components of spliceosomes? How do spliceosomes work?

Answer 32

Spliceosomes are made of proteins and small RNAs. The small RNAs within the spliceosome recognize the intron–exon boundary, catalyze the excision of introns from the
pre-mRNA, and join together the exons that flank the intron.

Question 33

Label the following image.

Answer 33

Question 34

What is a ribozyme? And what commonly held idea was rendered obsolete by its discovery?

Answer 34

An RNA molecule that functions as an enzyme, such as an intron that catalyzes its own
removal during RNA splicing.
The idea that all biological catalysts are proteins was rendered obsolete by its discovery.

Question 35

What are three properties of RNA that allow it to function as an enzyme?

Answer 35

a. 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 three-dimensional structure. A specific structure is essential to the catalytic
function of ribozymes, just as it is for enzymatic proteins.

b. Like certain amino acids in an enzymatic protein, some of the bases in **RNA contain
functional groups **that may participate in catalysis.

c. This ability of RNA to hydrogen-bond with other nucleic acid molecules (either RNA or DNA) adds specificity to its catalytic activity.

Question 36

What is the consequence of alternative splicing of identical mRNA transcripts?

Answer 36

The number of different protein products an organism produces can be much greater than
its number of genes.

Question 37

Structure and function of mRNA

Answer 37

Messenger RNA

Single-stranded

Carries genetic material from the
DNA to the protein-synthesizing machinery of the cell

Question 38

Structure and function of tRNA

Answer 38

Transfer RNA

About 75 nucleotides long; folds
into a clover-leaf shape due to hydrogen bonds among its bases

Transfers amino acids from the cytoplasmic pool of amino acids to a growing polypeptide in a ribosome. Acts as the “translator”.

note: The tRNA actually twists and folds into a compact structure that is roughly L-shaped, with the 5’ and 3’ ends of the linear tRNA both located near one end of the structure. The protruding 3’ end acts as the attachment site for an amino acid. The loop extending from the other end of the L includes the anticodon, the particular nucleotide triplet that base-pairs to a specific mRNA codon.

Question 39

Function of rRNA

Answer 39

Ribosomal RNA
Together with proteins, makes up ribosomes; the most abundant type of RNA

Question 40

What is an anticodon?

Answer 40

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

Question 41

Transfer RNA has two attachment sites. What binds at each site?

Answer 41

A specific anticodon binds at one end of tRNA, and a corresponding amino acid at the other end (on the 3’ end).

Question 42

What is the function of aminoacyl-tRNA synthetases? How many different aminoacyl-tRNA synthetases are there?

Answer 42

The active site of each type of aminoacyl-tRNA synthetase fits only a specific combination
of amino acid and tRNA to combine them. There are 20 different types of aminoacyl-tRNA
synthestases.

Question 43

Scientists expected to find one aminoacyl-tRNA synthetase per codon, but far fewer have
been discovered. How does wobble explain this?

Answer 43

Wobble is flexibility in the base-pairing rules in which the nucleotide at the 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. This flexibility explains why there are only about 45 tRNAs.

Question 44

What are the three key points in matching the correct amino acid with the proper tRNA?

Answer 44

1. The amino acid and the appropriate tRNA enter the active site of the specific
   synthetase.
2. Using ATP, the synthetase catalyzes the covalent bonding of the amino acid to its specific tRNA.
3. The tRNA, charged with its amino acid, is released by the synthetase.

Question 45

Describe the structure of a eukaryotic ribosome.

Answer 45

A ribosome consists of a large subunit and a small subunit, each made up of proteins and
one or more rRNAs.

Question 46

How does a prokaryotic ribosome differ from a eukaryotic ribosome? What is the medical
significance of this difference?

Answer 46

Eukaryotic ribosomes are slightly larger in structure and differ somewhat from bacterial
ribosomes in their molecular composition.

Certain antibiotic drugs can inactivate bacterial
ribosomes without inhibiting the ability of eukaryotic ribosomes to make proteins. These
drugs, including tetracycline and streptomycin, are used to combat bacterial infections

Question 47

On the following figure, label the large subunit; small subunit; A, P, and E sites; and
mRNA binding site. To the right of the figure, explain the functions of the A, P, and E sites.

Answer 47

The P site holds the tRNA attached to the growing polypeptide. The A site holds the tRNA
carrying the next amino acid to be added to the polypeptide chain. Discharged tRNAs
leave from the E site.

Question 48

What happend during the initiation stage of translation?

Answer 48

A small ribosomal subunit binds to a molecule of mRNA. In a bacterial cell, the mRNA
binding site on this subunit recognizes a specific nucleotide sequence on the mRNA just
up stream of the start codon. An initiator tRNA, within the anticodon UAC, base-pairs with
the start codon, AUG. This tRNA carries the amino acid methionine (Met). The arrival of a
large ribosomal subunit completes the initiative complex.

Question 49

Summarize the two key events in forming the translation initiation complex.

Answer 49

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 bearing the next amino acid

Question 50

What is always the first amino acid in the new polypeptide?

Answer 50

methionine

Question 51

Three key events occur in elongation. Explain the important features of each event.

Answer 51

a. Codon recognition: The anticodon of an incoming aminoacyl tRNA base-pairs with the
complementary mRNA codon in the A site. Hydrolysis of GTP increases the accuracy
and efficiency of this step.

b. Peptide bond formation: An rRNA molecule of the large ribosomal subunit catalyzes
the formation of a peptide bond between the carboxyl end of the growing polypeptide
in the P site and the anmino grop of the new amino acid in the A site.

c. 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.

Question 52

What is a release factor? By what mechanism is termination accomplished?

Answer 52

A release factor is a protein shaped like an aminoacyl tRNA, which 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 to the polypeptide chain, thereby hydrolyzing and releasing the polypeptide through the exit tunnel of the ribosome’s large subunit.

Question 53

Which of the three events, codon recognition, peptide bond formation, and translocation, require energy.

Answer 53

Codon recognition and translocation both require energy from the hydroloysis of GTP.

Question 54

What happens during the termination stage of translation?

Answer 54

The final stage of translation is termination. Elongation continues until a stop codon in the mRNA reaches the A site. The nucleotide base triplets UAG, UAA, and UGA do not code for amino acids but instead act as signals to stop translation.