Chapter 4.2

Question 1

What governs how molecule folds into a stable 3D configuration?

Answer 1

sequence of amino acids along a polypeptide chain - primary structure

Question 2

What determines what a protein can do and how it works?

Answer 2

3D structure

- immense diversity in tertiary and quaternary structures among proteins explains wide range of functions

Question 3

What is the sequence of bases along DNA strand for in transcription?

Answer 3

used as a template in synthesis of complementary sequence of bases in a molecule of RNA

Question 4

What is the sequence of bases in mRNA for in translation?

Answer 4

used to specify the order in which successive amino acids are added to a newly synthesized polypeptide chain

Question 5

What are ribosomes?

Answer 5

complex structures of RNA and protein that bind with mRNA and are the site of translation
- has small subunit and large subunit composed of ribosomal protein and rRNA

Question 6

What are the binding sites of large subunit of ribosome?

Answer 6

• A (aminoacyl) site
• P (peptidyl) site
• E (exit) site

Question 7

What is a major role of ribosome?

Answer 7

ensure that when mRNA is in place on ribosome, sequence in mRNA coding for amino acids is read in successive, non-overlapping groups of three nucleotides called codons

Question 8

What happens while ribosome establishes correct reading frame for codons?

Answer 8

actual translation of each codon in mRNA into one amino acid in polypeptide is carried out by tRNA

Question 9

What are tRNAs?

Answer 9

small RNA molecules

• self-pairing structure that can be drawn as a cloverleaf
• in actual structure, three bases in anticodon loop make up anticodon (three nucleotides that undergo base pairing with corresponding codon
• CCA at 3’ end
• 3’ hydroxyl of ^A nucleotide is attachment site for amino acid corresponding to anticodon

Question 10

What do aminoacyl tRNA synthetases enzymes do?

Answer 10

connect specific amino acids to specific tRNA molecules

• directly responsible for translating codon sequence in nucleic acid to a specific amino acid in polypeptide chain
• most organisms have one aminoacyl tRNA for each amino acid
• binds to multiple sites on any tRNA that has an anticodon corresponding to the amino acid
• catalyzes formation of covalent bond between amino acid and tRNA

Question 11

What is a charged tRNA?

Answer 11

tRNA with its amino acid attached

Question 12

What is the genetic code?

Answer 12

correspondence between codons and amino acids, in which 20 amino acids are specified by 64 codons

Question 13

Describe amino acid methionine.

Answer 13

• always first amino acid coded by AUG
• polypeptide is synthesized from amino end to carboxyl end therefore methionine forms the amino end
• in many cases, methionine is cleaved off by enzyme after synthesis is complete

Question 14

What happens once initial methionine creates amino end of new polypeptide chain

Answer 14

• downstream codons are read one by one
• at each step, ribosome binds to tRNA with complementary anticodon, and amino acid on tRNA is attached to growing chain to become new carboxyl end of polypeptide chain
• process continues until STOP codon is reached

Question 15

Many amino acids are specified by more than one codon, and the genetic code is redundant, or degenerate. Redundancy has strong patterns however:

Answer 15

1. redundancy results almost exclusively from third codon position
2. when amino acid is specified by two codons, they differ either in whether third position is a U or a C (both pyrimidines) or an A or G (both purines)
3. when an amino acid is specified by four codons, identity of third codon position does not matter (could be U, C, A, or G)

Question 16

What two features of translation causes the chemical basis of these patterns?

Answer 16

1. in many tRNA anticodons, 5’ base that pairs with 3’ base in the codon is chemically modified into a form that can pair with two or more bases at the third position in the codon
2. in ribosome, there’s less than perfect alignment between third position of codon and base that pairs with it in anticodon, so the requirements for base pairing are somewhat relaxed: this is called wobble

Question 17

What are the 3 steps of translation?

Answer 17

1. initiation: AUG codon is recognized and Met is established as first amino acid in new polypeptide chain
2. elongation: successive amino acids are added to growing chain one by one
3. termination: addition of amino acids stop and completed polypeptide chain is released from ribosome

Question 18

What does initiation require?

Answer 18

proteins called initiation factors that bind to mRNA

Question 19

What do initiation factors do in eukaryotes?

Answer 19

binds to 5’ cap that is added to mRNA during processing

• recruit small subunit of ribosome
• other initiation factors bring up a tRNA charged with Met

Question 20

Describe initiation.

Answer 20

• initiation factors bind to 5’ cap that is added to mRNA during processing
• initiation complex then moves along mRNA until it encounters first AUG triplet (position establishes translational reading frame)
• AUG codon is recognized and Met is established as first amino acid in new polypeptide chain in P site

Question 21

Describe elongation.

Answer 21

• large ribosomal subunit joins complex, initiation factors are released, next tRNA is ready to join ribosome at A site
• once new tRNA is in place, reaction takes place in which bond connecting Met to its tRNA is transferred to amino group of next amino acid in line, forming a peptide bond (RNA in large subunit is catalyst)
• new polypeptide becomes attached to tRNA in A site
• ribosome shifts one codon to the right
• uncharged tRNA(met) shifts to E site and released into cytoplasm
• peptide-bearing tRNA shifts to P site
• movement of ribosomes empties A site, ready for next charged tRNA
• REPEATED
• continues until ribosome encounters stop codons

Question 22

What are elongation factors?

Answer 22

bound to GTP molecules and break their high-energy bonds to provide energy for elongation of polypeptide
- ribosome movement along mRNA and formation of peptide bonds require energy obtained by these proteins

Question 23

Describe termination.

Answer 23

• ribosome encounters stop codon
• release factor protein binds to A site and causes bond connecting polypeptide to tRNA to break, creating carboxyl terminus of polypeptide and completing chain
• polypeptide is released, small and large ribosomal subunits dissociate both from mRNA and from each other

Question 24

Describe the different of translation initiation between prokaryotes and eukaryotes.

Answer 24

prokaryotes: mRNA molecules have no 5’ cap, instead the initiation complex is formed at one or more internal sequences present in mRNA known as Shine-Dalgarno sequence with AUG codon downstream that serves as an initiation codon

Question 25

What does the ability of prokaryotes to initiate translation internally allow?

Answer 25

prokaryotic mRNAs to code for more than one protein

• mRNA known as polycistronic mRNA which results from transcription of a group of functionally related genes located in tandem along DNA and transcribed as a single unit from one promoter
• this type of gene organization is called an operon

Question 26

Why do prokaryotes have many of their genes organized into operons?

Answer 26

because the production of a polycistronic mRNA allows all protein products to be expressed together whenever needed

Question 27

What genes are typically organized into operons?

Answer 27

those whose products are needed for either successive steps in synthesis of essential small molecules (ie. amino acid) or for successive steps in breakdown of a source of energy (ie. complex carbohydrate)