Untitled Deck

Question 1

What is translation’s role in the central dogma?

Answer 1

Translation is the process by which the information encoded in mRNA is used to synthesize proteins.

Question 2

Draw the general structure of an amino acid zwitterion.

Answer 2

An amino acid zwitterion has both a positive and a negative charge, typically with an amino group (NH3+) and a carboxyl group (COO-).

Question 3

Define ‘proteinogenic amino acid’. Why are non-proteinogenic amino acids often toxic?

Answer 3

Proteinogenic amino acids are the 20 standard amino acids used to build proteins. Non-proteinogenic amino acids can disrupt normal protein function or interfere with metabolic processes, leading to toxicity.

Question 4

If a protein is a homodimer what does that mean? Heterotrimer?

Answer 4

A homodimer consists of two identical subunits, while a heterotrimer consists of three different subunits.

Question 5

Give the key features that define primary, secondary, tertiary, and quaternary structure of a protein.

Answer 5

Primary structure is the sequence of amino acids. Secondary structure includes alpha helices and beta sheets. Tertiary structure is the overall 3D shape, and quaternary structure involves multiple polypeptide chains.

Question 6

What stabilizes each level of protein organization?

Answer 6

Primary structure is stabilized by peptide bonds. Secondary structure is stabilized by hydrogen bonds. Tertiary structure is stabilized by various interactions including hydrogen bonds, ionic bonds, and hydrophobic interactions. Quaternary structure is stabilized by similar interactions between subunits.

Question 7

What are the 5’ and 3’ UTRs? What functions do they serve?

Answer 7

The 5’ and 3’ untranslated regions (UTRs) are segments of mRNA that are not translated into protein. They play roles in regulation of translation, stability of the mRNA, and localization.

Question 8

How many sequences are possible for a protein with a length of 100 amino acids?

Answer 8

There are 20^100 possible sequences for a protein with a length of 100 amino acids.

Question 9

What are three functions that are shared by both prokaryotic and eukaryotic ribosomes?

Answer 9

Both prokaryotic and eukaryotic ribosomes facilitate translation, decode mRNA, and catalyze peptide bond formation.

Question 10

What is the role of IF3 in translation initiation in bacteria?

Answer 10

IF3 prevents the premature association of the ribosomal subunits and helps the ribosome recognize the start codon.

Question 11

What is the role of IF2 and IF1 in translation initiation in bacteria?

Answer 11

IF2 facilitates the binding of the initiator tRNA to the ribosome, while IF1 helps to stabilize the initiation complex.

Question 12

How is the authentic start codon oriented to the P site in bacterial mRNA by the ribosomes?

Answer 12

The ribosome positions the start codon in the P site through the interaction of the initiator tRNA with the codon.

Question 13

Define consensus sequence.

Answer 13

A consensus sequence is a sequence of DNA or RNA that is derived from the alignment of similar sequences and represents the most common nucleotides at each position.

Question 14

Suppose a bacterial gene acquired a mutation in its Shine-Dalgarno sequence, what might be an expected consequence of this?

Answer 14

A mutation in the Shine-Dalgarno sequence could lead to decreased translation efficiency or failure to initiate translation.

Question 15

Explain the role of f-Met in translation. Is it present in eukaryotes?

Answer 15

f-Met is the first amino acid incorporated during protein synthesis in bacteria, serving as a marker for the start of translation. It is not present in eukaryotes.

Question 16

What are the roles of eIF1, eIF3, and eIF1A in eukaryotic translation initiation? eIF5? eIF4?

Answer 16

eIF1 and eIF1A help to ensure the correct start codon is recognized, eIF3 assists in the recruitment of the ribosome, eIF5 promotes the joining of the large ribosomal subunit, and eIF4 is involved in mRNA binding.

Question 17

Explain the process of ‘scanning’ for the authentic eukaryotic start codon.

Answer 17

Scanning involves the ribosome moving along the mRNA from the 5’ cap until it encounters the start codon.

Question 18

How does scanning differ from how bacteria identify start codons?

Answer 18

Bacteria use the Shine-Dalgarno sequence for ribosome binding, while eukaryotes scan from the 5’ end of the mRNA.

Question 19

What is the Kozak sequence?

Answer 19

The Kozak sequence is a specific sequence surrounding the start codon in eukaryotic mRNA that helps to identify the start site for translation.

Question 20

Suppose a mutation causes a Kozak-like sequence to appear upstream of an authentic start in the 5’ UTR of a eukaryotic gene. What is the expected consequence?

Answer 20

The mutation may lead to the ribosome initiating translation at the Kozak-like sequence instead of the authentic start codon, potentially resulting in a truncated protein.

Question 21

The Kozak sequence is generally not ‘free to vary’ from an evolutionary perspective. What does this mean?

Answer 21

This means that the sequence is conserved across species due to its importance in translation initiation.

Question 22

What is a leaderless mRNA? What types of organisms have them?

Answer 22

Leaderless mRNA lacks a 5’ untranslated region and is typically found in some bacteria and organelles.

Question 23

What is the role of EF-tu in translation elongation?

Answer 23

EF-tu is responsible for delivering the correct aminoacyl-tRNA to the ribosome during translation elongation.

Question 24

Immediately after peptide bond formation, in which site is the tRNA bound to the nascent polypeptide?

Answer 24

The tRNA bound to the nascent polypeptide is located in the P site.

Question 25

What is the role of EF-G in translation elongation? How would the function of this protein differ if the genetic code were a quadruplet code?

Answer 25

EF-G facilitates the translocation of the ribosome along the mRNA. If the genetic code were a quadruplet code, EF-G would need to accommodate the movement of four nucleotides at a time.

Question 26

Eukaryotes have fewer release factors than bacteria. Explain this based on the functional capabilities of the proteins.

Answer 26

Eukaryotic release factors can recognize multiple stop codons, allowing fewer factors to perform the same function as multiple factors in bacteria.

Question 27

Consider a misincorporation/mistranslation rate of 1/10,000. What percentage of copies of a protein of length 300 amino acids would NOT contain an error?

Answer 27

99.97% of copies of the protein would not contain an error.

Question 28

In eukaryotes transcription and translation cannot happen simultaneously. Why?

Answer 28

In eukaryotes, transcription occurs in the nucleus and translation occurs in the cytoplasm, preventing simultaneous processes.

Question 29

Define polycistronic mRNA. What organisms are they typically found in?

Answer 29

Polycistronic mRNA contains multiple coding sequences and is typically found in prokaryotes.

Question 30

How does the genetic code evidence a single origin of life on earth? Are there any exceptions? Do these exceptions cast meaningful doubt on the single origin idea? Why or why not?

Answer 30

The genetic code is nearly universal among all organisms, suggesting a single origin. Exceptions exist but do not cast meaningful doubt as they are rare and often involve minor variations.

Question 31

How is it possible for an organism with 50 tRNA genes to decode all 61 codons? Give two reasons.

Answer 31

An organism can use wobble base pairing and some tRNAs can recognize multiple codons.

Question 32

Mutations in tRNA synthetases are often lethal. Explain why this is.

Answer 32

Mutations in tRNA synthetases can lead to incorrect amino acid charging of tRNAs, resulting in faulty protein synthesis.

Question 33

What is post-translational modification?

Answer 33

Post-translational modification refers to the chemical modifications made to a protein after its synthesis, affecting its function and activity.

Question 34

Suppose the genetic code were overlapping. What two properties would this introduce in terms of (1) protein sequence and (2) point mutations?

Answer 34

(1) Overlapping would lead to multiple proteins being produced from a single mRNA. (2) Point mutations could affect multiple amino acids in a protein.

Question 35

In a gene there are three nearby mutations that each insert a single base pair. When this gene is transcribed and translated it is only marginally less biochemically active than the unmutated version. Explain this phenomenon and contrast it to the expectation given two single base pair insertions in close proximity in a gene.

Answer 35

The presence of three nearby mutations may lead to a compensatory effect, maintaining some function, unlike two single base pair insertions which could disrupt the reading frame more significantly.

Question 36

What pattern demonstrated that the genetic code lacks a delimiter?

Answer 36

The continuous nature of the genetic code, where codons are read in sequence without punctuation, demonstrates the lack of a delimiter.

Question 37

Explain in as much detail as possible how the genetic code was deciphered using radiolabeled tRNAs, synthetic mRNAs, ribosomes, and size selection. Use the codon 5’-AGA-3’ as an example and explain the expected result with this codon.

Answer 37

The genetic code was deciphered by synthesizing mRNAs with known sequences, using radiolabeled tRNAs to identify which amino acids were incorporated into proteins. For the codon 5’-AGA-3’, the expected result would be the incorporation of arginine into the growing polypeptide chain.