Chapter 17 - From Gene to Protein

Question 1

What is gene expression, and what two stages does it include?

Answer 1

The process by which DNA directs protein synthesis.

The two stages are

1. Transcription
2. Translation

Question 2

Briefly describe the differences in the transcription/translation process for the synthesis of DNA for Prokaryotes and Eukaryotes

Answer 2

Prokaryotes

mRNA produced by transcription is immediately translated without processing.

Eukaryotes

Nuclear envelope separates transcription from translation

Eukaryotic RNA transcripts are modified through RNA processing to yield finished mRNA

Question 3

What is a codon?

Answer 3

• The flow of information from gene to protein is based on a triplet code:
• A series of non-overlapping, 3-nucleotide “words” called codons.
• These triplets are the smallest units of uniform length that can code for all amino acids
• Each codon specifies the amino acid to be placed at the corresponding position along a polypeptide (protein).

Question 4

Why do we use triplets for codons (or 3 nucleotides per codon in otherwords) ?

Answer 4

There are 4 nucleotides (A,G,T,C)

There are 20 amino acids

It must be a combination of more than one nucleotide that specifies one amino acid

Could a codon be 2 nucleotides long? if grouped in pairs there are 42 = 16 combinations… not enough combinations

With triplets there are 43 = 64 combinations More than enough combinations for all 20 amino acids.

Experimentation confirmed that codons are triplets of nucleotides

Question 5

During transcription, one of the two DNA strands, called the ____________ ________ provides a template for odering the sequence of nuecleotides in an RNA transcript

Answer 5

Template strand

Question 6

During translation (protein building) the mRNA base triplets (codons) are read in what direction on the carbon?

Answer 6

During translation, codons are read in the 5’ to 3’ direction

*Extra: The 5’ and 3’ mean “five prime” and “three prime”, which indicate the carbon numbers in the DNA’s sugar backbone. The 5’ carbon has a phosphate group attached to it and the 3’ carbon a hydroxyl group. This asymmetry gives a DNA strand a “direction”.

Question 7

How do we read DNA ?

Answer 7

During translation, codons along an mRNA molecule are read by translation machinery in the 5’ to 3’ direction.

Each codon specifies the addition of one of the 20 amino acids

For example, UGG particular position on the DNA strands results in the placement of the amino acid Tryptophan (Trp) at the corresponding position of the polypeptide to be produced.

Question 8

Why is genetic code redundant but not ambiguous?

Answer 8

Redundant……

because an amino acid can be specified by more than 1 codon.

Not Ambiguous…..

because no codon specifies more than one amino acid.

Question 9

In order for a specified polypeptide to be produced, codons must….

*Also review cracking the code Image*

Answer 9

….be read in the correct reading frame (correct groupings)

Question 10

Transcription is the first stage of gene expression, briefly describe how it begins.

Answer 10

RNA synthesis is catalyzed by RNA polymerase, which pries the DNA strands apart and hooks together the RNA nucleotides

RNA synthesis follows the same base-pairing rules as DNA, except uracil substitutes for thymine

• The DNA sequence where RNA polymerase attaches is called the promoter; in bacteria, the sequence signaling the end of transcription is called the terminator*
• The stretch of DNA that is transcribed is called a transcription unit*

Question 11

What is the DNA sequence where RNA polymerase attached to called? and what is the sequence signalling end of transcription?

Answer 11

Promoter

The DNA sequence where RNA polymerase attaches is called the promoter

Terminator

in bacteria, the sequence signaling the end of transcription is called the terminator

Question 12

What is the stretch of DNA that is transcribed called?

Answer 12

Transcription Unit

Question 13

What are the three (3) stages of transcription? (brief description)

Answer 13

1. Initation & RNA Polymerase Binding

• Promoters signal the initiation of RNA synthesis
• Transcription factors mediate the binding of RNA polymerase and the initiation of transcription
• Completed assembly of transcription factors and RNA polymerase II bound to a promoter is called a transcription initiation complex
• A promoter called a TATA box is crucial in forming the initiation complex in eukaryotes

2. Elongation of RNA strand

As RNA polymerase moves along the DNA, it untwists the double helix, 10 to 20 bases at a time.

Transcription progresses at a rate of 40 nucleotides per second in eukaryotes.

A gene can be transcribed simultaneously by several RNA polymerases.

3. Termination of Transcription

The mechanisms of termination are different in bacteria and eukaryotes

In bacteria, the polymerase stops transcription at the end of the terminator

In eukaryotes, the polymerase continues transcription after the pre-mRNA is cleaved from the growing RNA chain; the polymerase eventually falls off the DNA

Question 14

What is the first stage of transcription? Be descriptive

Answer 14

1. Initation & RNA Polymerase Binding

• Promoters signal the initiation of RNA synthesis
• Transcription factors mediate the binding of RNA polymerase and the initiation of transcription
• Completed assembly of transcription factors and RNA polymerase II bound to a promoter is called a transcription initiation complex
• A promoter called a TATA box is crucial in forming the initiation complex in eukaryotes

Question 15

What is the second stage of transcription? Be descriptive

Answer 15

2. Elongation of the RNA Strand

• As RNA polymerase moves along the DNA, it untwists the double helix, 10 to 20 bases at a time.
• Transcription progresses at a rate of 40 nucleotides per second in eukaryotes.
• A gene can be transcribed simultaneously by several RNA polymerases.

Question 16

What is the third stage of transcription? be descriptive..

Answer 16

3. Termination of Transcription

• The mechanisms of termination are different in bacteria and eukaryotes
• In bacteria, the polymerase stops transcription at the end of the terminator
• In eukaryotes, the polymerase continues transcription after the pre-mRNA is cleaved from the growing RNA chain; the polymerase eventually falls off the DNA

Question 17

What is RNA processing?

Answer 17

Each end of a pre-mRNA molecule is modified in a particular way:

The 5′ end receives a modified nucleotide 5′ cap and the 3′ end gets a poly-A tail.

These modifications share several functions:

• They seem to facilitate the export of mRNA
• They protect mRNA from hydrolytic enzymes
• They help ribosomes attach to the 5′ end

Question 18

Most eukaryotic genes and their RNA transcripts have long noncoding stretches of nucleotides that lie between coding regions, what is this called? and what is the counterpart to this?

Answer 18

Introns

Non-coding regions

Exons

Regions that are expressed

Question 19

What is RNA Splicing?

Answer 19

RNA Splicing

removes introns and joins exons, creating an mRNA molecule with a continuous coding sequence.

*exons exit the nucleus

Question 20

What the hell is a spliceosome?

Answer 20

Spliceosomes

in some cases, RNA splicing is carried out by spliceosomes. Spliceosomes consist of a variety of proteins and several small nuclear ribonucleoproteins (snRNPs) that recognize the splice sites.

Question 21

Some genes can encode more than one kind of polypeptide (depending on which segments are treated as exons during RNA splicing) what are these variations called?

Answer 21

Alternative RNA splicing

Because of alternative splicing, the number of different proteins an organism can produce is much greater than its number of genes.

Question 22

Proteins often have a modular architecture consisting of discrete regions called _________.

In many cases, different exons code for different domains in a protein

_________ __________ may result in the evolution of new proteins.

Answer 22

Proteins often have a modular architecture consisting of discrete regions called Domains.

In many cases, different exons code for different domains in a protein

Electron shuffling may result in the evolution of new proteins.

Question 23

After mRNA has been transcribed, spliced and modified, it is ready to produce protein. What happens to the mRNA to begin translation?

Answer 23

mRNA is shuttled out of the nucleus into the cytoplasm where it will bind to a ribosome and start Translation…

Question 24

Translation is RNA-directed synthesis of a polypeptide. A cell translates an mRNA message into protein with help of _ _ _ _ _ _ _ _ _ _ _ (_ _ _ _) ?

Answer 24

Translation is RNA-directed synthesis of a polypeptide. A cell translates an mRNA message into protein with help of Transfer RNA (tRNA)

Question 25

Describe tRNA

Answer 25

Molecules of tRNA are not identical:

• Each carries a specific amino acid on one end
• Each has an anticodon on the opposite end from the amino acid
• the anticodon on the tRNA base-pairs with a complementary codon on mRNA

Question 26

For translation of the RNA to be accurate, what two steps are required?

Answer 26

1. A correct match between tRNA and an amino acid, done by the enzyme aminoacyl-tRNA synthetase

2. A Correct match between the tRNA anticodon and an mRNA codon.

Question 27

In terms of codons, what is a wobble?

Answer 27

Wobble

Flexibile pairing at the third base of a condon. Allows some tRNA’s to bind to more than one codon.

Question 28

What is the relationship of Ribosomes to the process of translation?

Answer 28

Ribosomes facilitate specific coupling of tRNA anticodons with mRNA codons in protein synthesis

The two ribosomal subunits (large and small) are made of:

• Proteins and
• Ribosomal RNA (rRNA)

Question 29

A ribosome has three binding sites for tRNA, what are they?

Answer 29

A Site

holds the tRNA that carries the next amino acid to be added to the chain.

P Site

holds the tRNA that carries the growing polypeptide chain.

E Site

is the exit site, where the discharged tRNA’s leave the ribosome.

Question 30

What are the three stages of translation? (with a brief description of each)

Answer 30

1. Initiation of Translation

• Initiation stage of translation brings together mRNA, tRNA with the first amino acid, and the two ribosomal subunits

2. Elongation of polypeptide chain

• During the elongation stage, amino acids are added one by one to the preceding amino acid.

3. Termination

• Termination occurs when a stop codon in the mRNA reaches the A site of the ribosome.
• The A site accepts a protein called a release factor
• The release factor causes the addition of a water molecule instead of an amino acid.
• This reaction releases the polypeptide, and the translation assembly then comes apart.

Question 31

What is the first stage of translation? How does this proceed….

Answer 31

1. Ribosome Association and Initiation of Translation

• Initiation stage of translation brings together mRNA, a tRNA with the first amino acid, and the two ribosomal subunits
  1) First, a small ribosomal subunit binds with mRNA and a special initiator tRNA
  2) Then, the small subunit moves along the mRNA until it reaches the start codon (AUG)
  3) Proteins called initiation factors bring in the large subunit that completes the translation initiation complex

Question 32

Go through the process of the second stage of translation

Answer 32

2. Elongation of polypeptide chain

During the elongation stage, amino acids are added one by one to the preceding amino acid.

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

1. Codon recognition,
2. Peptide bond formation and
3. Translocation

Question 33

What is the third stage of translation? go through the process

Answer 33

3. Termination

Termination occurs when a stop codon in the mRNA reaches the A site of the ribosome.

The A site accepts a protein called a release factor

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

This reaction releases the polypeptide, and the translation assembly then comes apart.

Question 34

What two populations of ribosomes are evident in the cells?

Answer 34

Free Ribosomes

(in the cytosol)

Free ribosomes mostly synthesize proteins that function in the cytosol.

Bound ribosomes

(attached to the ER)

Make proteins of the endomembrane system and proteins that are secreted from the cell.

*Both types are identical and can interchange

Question 35

How do proteins enter the endoplasmic reticulum?

Answer 35

A signal-recognition particle (SRP) binds to the signal peptide

The SRP brings the signal peptide and its ribosome to the ER

Question 36

What are mutations and point mutations?

Answer 36

Mutations

changes in the genetic material

Point mutations

are chemical changes in just one base pair of a gene

Question 37

Point mutations (chemical changes in just one base pair of a gene) can be divided into what two general categories?

Answer 37

1. Base-pair substitutions

• A base-pair substitution replaces one nucleotide and its partner with another pair of nucleotides.
• Can result in 3 different outcomes:

1. Silent mutations have no effect on the amino acid produced by a codon because of redundancy in the genetic code
2. Missense mutations still code for an amino acid but not necessarily the right amino acid.
3. Nonsense mutations change an amino acid codon into a stop codon, nearly always leading to a non-functional protein

2. Base-pair insertions or deletions

• Insertions and deletions are additions or losses of nucleotides pairs in a gene.
• These mutations have a disastrous effect on the resulting protein more often than substitutions do.
• Insertion or deletion of nucleotides may alter the reading frame, producing a frameshift mutation.

Question 38

Within point mutations, the primer category it is divided into is called “base-pair substituions”. A base-pair substitution replaces one nucleotide and its partner with another pair of nucleotides, there is three outcomes.

What is the first outcome?

Answer 38

Silent mutations

have no effect on the amino acid produced by a codon because of redundancy in the genetic code

Question 39

Within point mutations, the primer category it is divided into is called “base-pair substituions”. A base-pair substitution replaces one nucleotide and its partner with another pair of nucleotides, there is three outcomes.

What is the second outcome?

Answer 39

Missense mutations

still code for an amino acid but not necessarily the right amino acid.

Question 40

Within point mutations, the primer category it is divided into is called “base-pair substituions”. A base-pair substitution replaces one nucleotide and its partner with another pair of nucleotides, there is three outcomes.

What is the third outcome?

Answer 40

3. Nonsense mutations

change an amino acid codon into a stop codon, nearly always leading to a non-functional protein

Question 41

Base-pair insertions or deletions are additions or losses of nucleotides pairs in a gene. Insertion or deletion of nucleotides may alter the reading frame, producing a frameshift mutation.

What are the three possibilities?

Answer 41

1. Frameshift causing immediate nonsense (1 base-pair insertion)
2. Frameshift causing extensive missense (1 base-pair deletion)
3. No frameshift, but one amino acid missing (3 base-pair deletion)

Question 42

What happens if a single nucleotide in a DNA template strand changed?

Answer 42

The change of a single nucleotide in a DNA template strand can lead to the production of an abnormal protein.

Question 43

What is a Gene? (be specific)

Answer 43

Gene

In summary, a gene can be defined as a region of DNA that can be expressed to produce a final functional product, either a polypeptide or an RNA molecule