Week 9

Question 1

Gene (3 definitions)

Answer 1

• the basic unit of genetic information
• also defined as the nucleic acid sequence that codes for a polypeptide, tRNA or rRNA
• linear sequence of nucleotides with a fixed start point and end point

Question 2

DNA gene structure

Answer 2

promoter = has RNA pol binding site
transcription starts -> leader —> trailer —> terminator

Question 3

mRNA gene structure

Answer 3

-leader (has shine-dalgarno sequence where ribosome binds)
-translation starts (start codon) –> stop codon –> trailer

Question 4

coding strand

Answer 4

5’ to 3’

Question 5

template strand

Answer 5

3’ to 5’

Question 6

Bacteria frequently cluster all of the genes required for ______

Answer 6

-formation of a particular structure

Question 7

Locus (def.)

Answer 7

position on a genome (this far from oriC)

Question 8

Gene cluster (def.)

Answer 8

cluster of gene encoding proteins involved in the biosynthesis of one structure

Question 9

Operon (def.)

Answer 9

series of genes contranscribed –> one mRNA for all the genes, same promoter + terminator (can determine by experimentation)

Question 10

operon produces ____ mRNA (has _____)

Answer 10

-polycistronic
-open reading frame for each gene

Question 11

mRNA matches which strand of DNA expect T/U

Answer 11

coding strand (5’ -> 3’)

Question 12

start codon ? codes for?

Answer 12

-AUG
-N-formylmethionine, a modified amino acid used to initiate protein synthesis in bacteria

Question 13

stop codon ?

Answer 13

-UAA, UAG, UGA

Question 14

stop codon is immediately followed by ______

Answer 14

trailer sequence which contains a terminator sequence used to stop transcription

Question 15

codon (def.) + ______ is complementary

Answer 15

-genetic code word, 3 base pairs long, that specifies an amino acid
-anticodon on tRNA

Question 16

start codon (def.) sense codon? stop (nonsense) codon?

Answer 16

-start site for translation
-the 61 codons that specify amino acids
-the three codons used as translation termination signals (do not encode amino acids)

Question 17

Code degeneracy (def.)

Answer 17

• up to six different codons can code for a single amino acid (61 codons for 20 a.a)

Question 18

Codon usage bias (def.)

Answer 18

some of a.a are used more often; fewer tRNA in TRNA pool for some codons; this slows down translation at these sites

Question 19

3rd base pair wobble

Answer 19

-3rd base pair of codon is more likely to be unique (loose base pairing)
-eliminate need for unique tRNA for each codon

Question 20

Reading frames

Answer 20

-reading frame specifies where the codons are
-ribosome binding site (shine sequence) is always 6-7 bp upstream of the start codon

Question 21

Polymers of amino acids linked by _____

Answer 21

-peptide bonds

Question 22

amino acids have _____ (4). a.a can be _____ depending on side chain

Answer 22

-central carbon, carboxy group (C-terminal), amino group (N-terminal), side chain
-polar, non-polar, or charged

Question 23

peptides have directionality

Answer 23

N -> C

Question 24

Translation initiation

Answer 24

1 – binding of mRNA to 30S subunit (mediated by Shine Dalgarno sequence)
2 – binding of initiator tRNA to complex
3 – Hydrolysis of GTP by initiation factors to bring 50S subunit

Question 25

Intact ribosome contains 3 sites:

Answer 25

* A site (amino acid) -> new tRNA * P site (peptide) -> peptide is extended (initial tRNA binds here) * E site (exit) -> empty tRNA leaves

Question 26

Translation elongation consists of three phases

Answer 26

* aminoacyl-tRNA binding * transpeptidation reaction * translocation -> whole ribosome moves over one codon

Question 27

Translation elongation involves several ______

Answer 27

elongation factors (EFs)

Question 28

Elongation: aminoacyltRNA binding

Answer 28

-aminoacyl-tRNA enters ribosome based on codon -requires EF-Tu and GTP hydrolysis

Question 29

Elongation: transpeptidation

Answer 29

-formation of peptide bond -catalyzed by peptidyl transferase activity of 23S rRNA (ribozyme) -amino group on the A site amino acid performs nucleophilic attack on the carboxyl group of the Cterminal amino acid on the P site tRNA (peptide bond formation) -peptide chain transferred from the P site to A site

Question 30

Elongation : translocation (three simultaneous events)

Answer 30

* peptidyl-tRNA moves from A site to P site * ribosome moves down one codon * empty tRNA moves to E site and dissociates * requires EF-G (translocase) and GTP hydrolysis

Question 31

Translation termination

Answer 31

-Takes place at any one of three codons (nonsense (stop) codons – UAA, UAG, and UGA) * Release factors (RFs) -> aid in recognition of stop codons, 3 RFs function in prokaryotes, only 1 RF active in eukaryotes) * GTP hydrolysis required * Ribosome dissociates into 30S and 50S components

Question 32

Protein maturation involves 4 things

Answer 32

* Folding * Posttranslational modifications * Complex formation * Localization

Question 33

Chaperone proteins do what? + examples + work by ____

Answer 33

* Help proteins fold properly -DnaKJ complex or GroEL-GroES complex -excluding water to allow hydrophobic regions to form properly

Question 34

Molecular chaperones

Answer 34

* proteins that aid the folding of nascent polypeptides * protect cells from thermal damage * e.g., heat-shock proteins * aid in transport of proteins across membranes

Question 35

posttranslational modifications descr. + function

Answer 35

-some go on for the life of the protein and some are dynamic - change the activity, localization, stability, binding partners of a protein

Question 36

posttranslational modifications examples

Answer 36

* acetylation * methylation * phosphorylation * glycosylation * uridylylation * proteolysis * prosthetic group

Question 37

Localization: Sec system

Answer 37

* transports unfolded proteins through membrane and helps integral membrane proteins fold * requires an N-terminal signal sequence * requires ATP hydrolysis

Question 38

Localization: Tat system

Answer 38

* transports folded proteins through membrane * requires an N-terminal signal sequence (twin arginine) * requires proton motive force

Question 39

protein with signal sequence + SecA =

Answer 39

protein secrted into periplasm

Question 40

protein with signal sequence + signal recognition particle =

Answer 40

protein inserted into membrane

Question 41

Secretion systems

Answer 41

Type I (ABC transporter) = cytoplasm to outside Type II (found in most bacteria) =require Sec/TAT; periplasm to outside but extends into cytoplasm; folded proteins Type V (found in most bacteria) =require Sec/TAT; periplasm to outside; unfolded Type III: injectisome (proteins), requires ATP, used by pathogenic bacteria (salmonella), injects toxins directly into host cells Type IV: injectisome (DNA), requires ATP, some secrete proteins, most are type IV pili & transfer DNA Type VI: retracted sheath -> contracted (needle); secretes proteins directly into other cells as part of bacterial warfare, requires ATP