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chapter 9 Flashcards

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Biology 101 flashcards
1
Q

proteins

A

polymers of amino acids attached end to end

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2
Q

amino acids are determined by…

A

R group

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3
Q

peptide bonds

A

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

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4
Q

amino acid directionality

A

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

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5
Q

primary

A

linear sequence of amino acids in polypeptide

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6
Q

secondary

A

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

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7
Q

tertiary

A

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

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8
Q

quartenary

A

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

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9
Q

two common types of secondary structure

A

alpha helix and beta pleated sheet

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10
Q

amino acid side chains determine…

A

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

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11
Q

codon

A

3 nucleotide sequence that encodes for amino acid

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12
Q

nonoverlapping meaning

A

mutation of single base results in only one amino acid change

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13
Q

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

A

confirm codons are by threes

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14
Q

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

A

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

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15
Q

Rll mutants can’t grow on…

A

e.coli strain K

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16
Q

revertants

A

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

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17
Q

suppressor

A

second mutation that counteracts the effects of the first mutation

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18
Q

true revertant

A

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

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19
Q

suppressor V.S true revertant

A

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

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20
Q

two mutants can be separated with…

A

recombination

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21
Q

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

A
  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
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22
Q

crick and brenner (1961) mRNA discovery

A

read CONTINUOUSLY and UNIDIRECTIONALLY by 3 nucleotides at a time

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23
Q

streisinger experiment

A

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

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24
Q

frameshift mutations

A

alter 3 nucleotide frame via insert or delete

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25
Q

degeneracy

A

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

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26
Q

degeneracy’s affect on frameshift mutations (2)

A
  1. frameshift doesn’t cause immediate termination
  2. frameshift suppressors arise frequently
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27
Q

nirenberg and mithai

A

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

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28
Q

why couldn’t nirenberg and mithai use RNA polymerase?

A

because it requires a template

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29
Q

RNA stop codons

A

UAG, UAA, UGA

30
Q

brenner and stop codons

A

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

31
Q

intragenetic vs extragenic suppressor

A

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

32
Q

mini RNAs

A

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

33
Q

tRNA

A

adapter molecule that binds amino acid to codon and ribosome

34
Q

anticodon is __ and ___ to codon

A

antiparallel and complementary

35
Q

aminoacytl-tRNA

A

joins each amino acid with it’s tRNAs

36
Q

aax + tRNAx + ATP –>

A

aax - tRNA + AMP + PPi

37
Q

translation reaction is catalyzed by

A

aminoacyt tRNA synthase, each recognizes a specific amino acid

38
Q

accuracy of protein synthesis depends on…

A

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

39
Q

evidence aminoacytl tRNA provides specificity

A

chemically change amino acid on rRNA

40
Q

result of aminoacytl experiment

A

protein with alanine where there should be cytosine

41
Q

sources of degeneracy (2)

A
  1. tRNA molecules with different anticodons can carry same amino acid
  2. tRNA can recognize more than one codon due to wobble
42
Q

wobble

A

sloppy pairing by tRNA

43
Q

polymer

A

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

44
Q

requirement for polymerization (3 parts)

A
  1. Ribosome (links subunits
  2. tRNA and anticodon (specificity)
  3. ATP and GTP (energy to drive reaction and decrease specificity)
45
Q

charging tRNA

A

attatch aax

46
Q

where is ATP stored

A

in aax - tRNA bond

47
Q

peptide bond formation in translation

A

catalyzed at peptidyl transferase center of ribosome

48
Q

how can components of translation be identified

A

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

49
Q

in centrifugation, largest mass reaches…

A

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

50
Q

ribosome

A

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

51
Q

subunits of ribosome are apart until…

A

initiation of translation and they disassociate at termination

52
Q

all ribosomal RNAs are coded by

A

proteins

53
Q

ribosomal proteins are

A

structural

54
Q

ribosomal RNAs are

A

catalytic

55
Q

A site

A

entry of aminoacyl RNA

56
Q

P site

A

growing polypeptide chain

57
Q

E site

A

tRNA exit

58
Q

initiation key points

A

ribosome complex assembly and ribosome finds AUG

59
Q

3 steps of initiation

A
  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)
60
Q

IFs in prokaryotes

A

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

61
Q

IFs in eukaryotes

A

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

62
Q

differenced in pro and euk initiation, prokaryotes

A
  • 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
63
Q

differenced in pro and euk intiation, eukaryotes

A
  • only uses methionine
  • messages are monogenic and have cap and tail
64
Q

shine dalgarno sequence

A

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

65
Q

kozak sequence

A

AUG on eukaryotes

66
Q

elongation factors

A

EF-Tu and EF-Tsand EF-G

67
Q

elongation requires __ more GTPs for each amino acid

A

3

68
Q

tRNA path

A

A to P to E

69
Q

peptide path

A

P to A to P to A

70
Q

UAG, UGA, and UAA are recognized by

A

release factors

71
Q

release factors

A

binds to A site and causes ribosome to disassociate

genetics (13 decks)

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