Biochem - Molecular (Transcription & Translation Part 2)

Question 1

Define exons versus introns.

Answer 1

Exons contain the acutal genetic information coding for protein; Introns are intervening noncoding segments of DNA; Think: “INtrons are INtervening sequences and stay IN the nucleus, whereas EXons EXit and are EXpressed.”

Question 2

What is alternative splicing?

Answer 2

Different exons are frequently combined by alternative splicing to produce a larger number of unique proteins.

Question 3

What are 2 types of conditions in which abnormal splicing variants are implicated?

Answer 3

Abnormal splicing variants are implicated in oncogenesis and many genetic disorders (e.g., Beta-thalassemia).

Question 4

Describe the structure of tRNA, mentioning number of nucleotides, structural level/order, form/shape, and its ends.

Answer 4

75-90 nucleotides, secondary structure, cloverleaf form, anticodon end is opposite 3’ aminoacyl end.

Question 5

What sequence do all tRNAs (eukaryotic and prokaryotic) have at their 3’ end? What function does this serve?

Answer 5

All tRNAs, both eukaryotic and prokaryotic, have CCA at 3’ along with a high percentage of chemically modified bases. The amino acid is covalently bound to the 3’ end of the tRNA. “Think: CCA Can Carry Amino acids.”

Question 6

What does the T-arm of tRNA contain, and for what is this necessary?

Answer 6

T-arm: contains the TPsiC (thymine, pseudouridine, cytosine) sequence necessary for tRNA-ribosome binding

Question 7

What does the d-arm of tRNA contain, and for what is this necessary?

Answer 7

D-arm: contains dihydrouracil residues necessary for tRNA recognition by the correct aminoacyl-tRNA synthetase

Question 8

What is its sequence and function of the acceptor stem of tRNA?

Answer 8

Acceptor stem: the 3’ CCA is the amino acid acceptor site.

Question 9

What is the aminoacyl-tRNA synthetase and its purpose? How does it accomplish this? What happens if there’s an error after aminoacyl-tRNA synthetase does its job?

Answer 9

Aminoacyl-tRNA synthetase (1 per amino acid; “matchmaker”; uses ATP) scrutinizes amino acid before and after it binds to tRNA. If incorrect, bond is hydrolyzed. The amino acid-tRNA bond has energy for formation of peptide bond. A mischarged tRNA reads usual codon but inserts wrong amino acid.

Question 10

What is responsible for the accuracy of amino acid selection?

Answer 10

Aminoacyl-tRNA synthetase and binding of charged tRNA to the codon are responsible for accuracy of amino acid selection

Question 11

Draw the reactions of Aminoacyl-tRNA synthetase and Initiation factor (IF2), showing the changes they create in tRNA.

Answer 11

See p. 74 in First Aid 2014 for visual at bottom of page

Question 12

Explain tRNA wobble. What property of the genetic code does it exemplify?

Answer 12

Accurate base pairing is required only in the first 2 nucleotide positions of an mRNA codon, so codons differing in the 3rd “wobble” position may code for the same tRNA/amino acid (as a result of degeneracy of genetic code).

Question 13

What are the 3 major steps in protein synthesis?

Answer 13

(1) Initiation (2) Elongation (3) Termination

Question 14

What process initiates initiation of protein synthesis? What factors are likewise involved in initiation?

Answer 14

Initiated by GTP hydrolysis; Initiation factors (eukaryotic IFs) help assemble the 40S ribosomal subunit with the initiator tRNA and are released when the mRNA and the ribosomal 60S subunit assemble with the complex.

Question 15

What are the ribosomal subunits in eukaryotes versus prokaryotes?

Answer 15

Eukaryotes: 40S + 60S => 80S (Think: “Even”); PrOkaryotes: 30S + 50S => 70S (Think: “Odd”)

Question 16

How is ATP versus GTP used in protein synthesis?

Answer 16

ATP - tRNA Activation (charging); GTP - tRNA Gripping and Going places (translocation)

Question 17

What are the 3 steps of elongation during protein synthesis?

Answer 17

(1) Aminoacyl-tRNA binds to A site (except for initiator methionine) (2) rRNA (“ribozyme”) catalyzes peptide bond formation, transfers growing polypeptide to amino acid in A site (3) Ribosome advances 3 nucleotides toward 3’ end of mRNA, moving peptidyl tRNA to P site (translocation); Think: “going APE: A site = incoming Aminoacyl-tRNA, P site = accommodates growing Peptide, E site = holds Empty tRNA as it Exits.”

Question 18

What occurs during the termination step of protein synthesis?

Answer 18

Stop codon is recognized by release factor, and completed polypeptide is released from ribosome

Question 19

What are 2 major types of posttranslational modifications?

Answer 19

(1) Trimming (2) Covalent alterations

Question 20

What defines the trimming posttranslational modification? Give an example.

Answer 20

Removal of N- or C-terminal propeptides from zymogen to generate mature protein (e.g., trypsinogen to trypsin)

Question 21

What are 6 examples of covalent alteration posttranslational modification?

Answer 21

(1) Phosphorylation (2) Glycosylation (3) Hydroxylation (4) Methylation (5) Acetylation (6) Ubiquination

Question 22

What is a Chaperone protein, and what function does it serve?

Answer 22

Intracellular protein involved in facilitating and/or maintaining protein folding

Question 23

What are a type of chaperone proteins found in yeast, and what function do they have? Give a specific example of such chaperone proteins.

Answer 23

In yeast, some are heat shock proteins (e.g., Hsp 60) that are expressed at high temperatures to prevent protein denaturing/misfolding