chapter 9

Question 1

proteins

Answer 1

polymers of amino acids attached end to end

Question 2

amino acids are determined by…

Answer 2

R group

Question 3

peptide bonds

Answer 3

connect amino acids between carboxyl end of one and amino group of the next, releasing H2O as byproduct

Question 4

amino acid directionality

Answer 4

first in chain has amino end sticking out and last one has carboxyl end

Question 5

primary

Answer 5

linear sequence of amino acids in polypeptide

Question 6

secondary

Answer 6

3D hydrogen bonds between polypeptide backbone’s amino and carboxyl groups

Question 7

tertiary

Answer 7

folding secondary into the final 3D polypeptide (beta polypeptide)

Question 8

quartenary

Answer 8

several tertiarys or subunits packed into a complex (hemoglobin is two alpha and two beta chains)

Question 9

two common types of secondary structure

Answer 9

alpha helix and beta pleated sheet

Question 10

amino acid side chains determine…

Answer 10

folding and provide functionality to interaction surfaces and active sites of enzymes

Question 11

codon

Answer 11

3 nucleotide sequence that encodes for amino acid

Question 12

nonoverlapping meaning

Answer 12

mutation of single base results in only one amino acid change

Question 13

main discovery by Crick and Brenner (1961) (hint: confirmed…)

Answer 13

confirm codons are by threes

Question 14

how did crick and brenner (1961) check how many codons there are

Answer 14

used rll locus of T4 Phage to induce insertions and deletions, they checked the phenotypes of the rll mutants to see affects

Question 15

Rll mutants can’t grow on…

Answer 15

e.coli strain K

Question 16

revertants

Answer 16

can be true revertant or suppressor (i.e it can grow on e.coli stain K when it shouldn’t)

Question 17

suppressor

Answer 17

second mutation that counteracts the effects of the first mutation

Question 18

true revertant

Answer 18

second mutation restores WT (insertion then deleted or vice versa)

Question 19

suppressor V.S true revertant

Answer 19

if 2nd mutation doesn’t restore wild type –> suppressor
if 2nd mutation restores wild type –> true revertant

Question 20

two mutants can be separated with…

Answer 20

recombination

Question 21

results of crick and brenner (1961) (there are 3)

Answer 21

1. deletion and insertion can repress eachother
2. same sign can’t repress each other but triple same side can allow WT
3. mRNA read continously and unidirectionally by three nucleotides at a time

Question 22

crick and brenner (1961) mRNA discovery

Answer 22

read CONTINUOUSLY and UNIDIRECTIONALLY by 3 nucleotides at a time

Question 23

streisinger experiment

Answer 23

used proflavine to encode lysozome (protein with known sequence) to confirm reading frame

Question 24

frameshift mutations

Answer 24

alter 3 nucleotide frame via insert or delete

Question 25

degeneracy

Answer 25

genetic code is redundant, some amino acids are specified by more than one codon

Question 26

degeneracy's affect on frameshift mutations (2)

Answer 26

1. frameshift doesn't cause immediate termination 2. frameshift suppressors arise frequently

Question 27

nirenberg and mithai

Answer 27

synthesized RNA from scratch without DNA using enzyme (polynucleotide phosphorylase) and random nucleotides (ribonucleotides: ATP, CTP, GTP, TTP)

Question 28

why couldn't nirenberg and mithai use RNA polymerase?

Answer 28

because it requires a template

Question 29

RNA stop codons

Answer 29

UAG, UAA, UGA

Question 30

brenner and stop codons

Answer 30

isolated 6 mutants in T4 phage and determined stop codons by comparing mutants with WT to see what's missing

Question 31

intragenetic vs extragenic suppressor

Answer 31

intra: same gene as original mutation extra: diff gene than original mutation

Question 32

mini RNAs

Answer 32

3 nucleotide strands, helps differentiate which codons code for which protein

Question 33

tRNA

Answer 33

adapter molecule that binds amino acid to codon and ribosome

Question 34

anticodon is __ and ___ to codon

Answer 34

antiparallel and complementary

Question 35

aminoacytl-tRNA

Answer 35

joins each amino acid with it's tRNAs

Question 36

aax + tRNAx + ATP -->

Answer 36

aax - tRNA + AMP + PPi

Question 37

translation reaction is catalyzed by

Answer 37

aminoacyt tRNA synthase, each recognizes a specific amino acid

Question 38

accuracy of protein synthesis depends on...

Answer 38

enzyme's ability to distinguish amino acid and set of corresponding tRNA

Question 39

evidence aminoacytl tRNA provides specificity

Answer 39

chemically change amino acid on rRNA

Question 40

result of aminoacytl experiment

Answer 40

protein with alanine where there should be cytosine

Question 41

sources of degeneracy (2)

Answer 41

1. tRNA molecules with different anticodons can carry same amino acid 2. tRNA can recognize more than one codon due to wobble

Question 42

wobble

Answer 42

sloppy pairing by tRNA

Question 43

polymer

Answer 43

large molecules composed of repeating units (ex: DNA, RNA, polypeptides, glycogen, fats)

Question 44

requirement for polymerization (3 parts)

Answer 44

1. Ribosome (links subunits 2. tRNA and anticodon (specificity) 3. ATP and GTP (energy to drive reaction and decrease specificity)

Question 45

charging tRNA

Answer 45

attatch aax

Question 46

where is ATP stored

Answer 46

in aax - tRNA bond

Question 47

peptide bond formation in translation

Answer 47

catalyzed at peptidyl transferase center of ribosome

Question 48

how can components of translation be identified

Answer 48

centrifugtion through sucrose density gradient (to separated shape and size)

Question 49

in centrifugation, largest mass reaches...

Answer 49

bottom of the tube first and have larger S value (sedimentation coefficient)

Question 50

ribosome

Answer 50

two subunits (large (60s) and small (40s)), both have RNA molecules and many protein molecules

Question 51

subunits of ribosome are apart until...

Answer 51

initiation of translation and they disassociate at termination

Question 52

all ribosomal RNAs are coded by

Answer 52

proteins

Question 53

ribosomal proteins are

Answer 53

structural

Question 54

ribosomal RNAs are

Answer 54

catalytic

Question 55

A site

Answer 55

entry of aminoacyl RNA

Question 56

P site

Answer 56

growing polypeptide chain

Question 57

E site

Answer 57

tRNA exit

Question 58

initiation key points

Answer 58

ribosome complex assembly and ribosome finds AUG

Question 59

3 steps of initiation

Answer 59

1. small subunit binds to mRNA (requires IF3) 2. in prokaryotes, N form tRNA binds to PSITE (requires IF1 and IF2) 3. large subunit binds to complex, completing assembly (energy derived from hydrolysis of GTP bound to IF2)

Question 60

IFs in prokaryotes

Answer 60

IF1- IF3 help initiator tRNA position and is then replaced by large subunit

Question 61

IFs in eukaryotes

Answer 61

IFs find 5' cap and recruit small subunit (0S) to scan mRNA for AUG, then replaced with large subunit

Question 62

differenced in pro and euk initiation, prokaryotes

Answer 62

- uses fMet for initiation and methionine after - mRNA translated as it's being transcribed - ribosome needs to find more than one initiation codon on each mRNA

Question 63

differenced in pro and euk intiation, eukaryotes

Answer 63

- only uses methionine - messages are monogenic and have cap and tail

Question 64

shine dalgarno sequence

Answer 64

prokaryote sequences before start are complementary to 3' end of 16S rRNA, helps position ribosome

Question 65

kozak sequence

Answer 65

AUG on eukaryotes

Question 66

elongation factors

Answer 66

EF-Tu and EF-Tsand EF-G

Question 67

elongation requires __ more GTPs for each amino acid

Answer 67

3

Question 68

tRNA path

Answer 68

A to P to E

Question 69

peptide path

Answer 69

P to A to P to A

Question 70

UAG, UGA, and UAA are recognized by

Answer 70

release factors

Question 71

release factors

Answer 71

binds to A site and causes ribosome to disassociate