chapter 9 Flashcards
proteins
polymers of amino acids attached end to end
amino acids are determined by…
R group
peptide bonds
connect amino acids between carboxyl end of one and amino group of the next, releasing H2O as byproduct
amino acid directionality
first in chain has amino end sticking out and last one has carboxyl end
primary
linear sequence of amino acids in polypeptide
secondary
3D hydrogen bonds between polypeptide backbone’s amino and carboxyl groups
tertiary
folding secondary into the final 3D polypeptide (beta polypeptide)
quartenary
several tertiarys or subunits packed into a complex (hemoglobin is two alpha and two beta chains)
two common types of secondary structure
alpha helix and beta pleated sheet
amino acid side chains determine…
folding and provide functionality to interaction surfaces and active sites of enzymes
codon
3 nucleotide sequence that encodes for amino acid
nonoverlapping meaning
mutation of single base results in only one amino acid change
main discovery by Crick and Brenner (1961) (hint: confirmed…)
confirm codons are by threes
how did crick and brenner (1961) check how many codons there are
used rll locus of T4 Phage to induce insertions and deletions, they checked the phenotypes of the rll mutants to see affects
Rll mutants can’t grow on…
e.coli strain K
revertants
can be true revertant or suppressor (i.e it can grow on e.coli stain K when it shouldn’t)
suppressor
second mutation that counteracts the effects of the first mutation
true revertant
second mutation restores WT (insertion then deleted or vice versa)
suppressor V.S true revertant
if 2nd mutation doesn’t restore wild type –> suppressor
if 2nd mutation restores wild type –> true revertant
two mutants can be separated with…
recombination
results of crick and brenner (1961) (there are 3)
- deletion and insertion can repress eachother
- same sign can’t repress each other but triple same side can allow WT
- mRNA read continously and unidirectionally by three nucleotides at a time
crick and brenner (1961) mRNA discovery
read CONTINUOUSLY and UNIDIRECTIONALLY by 3 nucleotides at a time
streisinger experiment
used proflavine to encode lysozome (protein with known sequence) to confirm reading frame
frameshift mutations
alter 3 nucleotide frame via insert or delete
degeneracy
genetic code is redundant, some amino acids are specified by more than one codon
degeneracy’s affect on frameshift mutations (2)
- frameshift doesn’t cause immediate termination
- frameshift suppressors arise frequently
nirenberg and mithai
synthesized RNA from scratch without DNA using enzyme (polynucleotide phosphorylase) and random nucleotides (ribonucleotides: ATP, CTP, GTP, TTP)
why couldn’t nirenberg and mithai use RNA polymerase?
because it requires a template
RNA stop codons
UAG, UAA, UGA
brenner and stop codons
isolated 6 mutants in T4 phage and determined stop codons by comparing mutants with WT to see what’s missing
intragenetic vs extragenic suppressor
intra: same gene as original mutation
extra: diff gene than original mutation
mini RNAs
3 nucleotide strands, helps differentiate which codons code for which protein
tRNA
adapter molecule that binds amino acid to codon and ribosome
anticodon is __ and ___ to codon
antiparallel and complementary
aminoacytl-tRNA
joins each amino acid with it’s tRNAs
aax + tRNAx + ATP –>
aax - tRNA + AMP + PPi
translation reaction is catalyzed by
aminoacyt tRNA synthase, each recognizes a specific amino acid
accuracy of protein synthesis depends on…
enzyme’s ability to distinguish amino acid and set of corresponding tRNA
evidence aminoacytl tRNA provides specificity
chemically change amino acid on rRNA
result of aminoacytl experiment
protein with alanine where there should be cytosine
sources of degeneracy (2)
- tRNA molecules with different anticodons can carry same amino acid
- tRNA can recognize more than one codon due to wobble
wobble
sloppy pairing by tRNA
polymer
large molecules composed of repeating units (ex: DNA, RNA, polypeptides, glycogen, fats)
requirement for polymerization (3 parts)
- Ribosome (links subunits
- tRNA and anticodon (specificity)
- ATP and GTP (energy to drive reaction and decrease specificity)
charging tRNA
attatch aax
where is ATP stored
in aax - tRNA bond
peptide bond formation in translation
catalyzed at peptidyl transferase center of ribosome
how can components of translation be identified
centrifugtion through sucrose density gradient (to separated shape and size)
in centrifugation, largest mass reaches…
bottom of the tube first and have larger S value (sedimentation coefficient)
ribosome
two subunits (large (60s) and small (40s)), both have RNA molecules and many protein molecules
subunits of ribosome are apart until…
initiation of translation and they disassociate at termination
all ribosomal RNAs are coded by
proteins
ribosomal proteins are
structural
ribosomal RNAs are
catalytic
A site
entry of aminoacyl RNA
P site
growing polypeptide chain
E site
tRNA exit
initiation key points
ribosome complex assembly and ribosome finds AUG
3 steps of initiation
- small subunit binds to mRNA (requires IF3)
- in prokaryotes, N form tRNA binds to PSITE (requires IF1 and IF2)
- large subunit binds to complex, completing assembly (energy derived from hydrolysis of GTP bound to IF2)
IFs in prokaryotes
IF1- IF3 help initiator tRNA position and is then replaced by large subunit
IFs in eukaryotes
IFs find 5’ cap and recruit small subunit (0S) to scan mRNA for AUG, then replaced with large subunit
differenced in pro and euk initiation, prokaryotes
- 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
differenced in pro and euk intiation, eukaryotes
- only uses methionine
- messages are monogenic and have cap and tail
shine dalgarno sequence
prokaryote sequences before start are complementary to 3’ end of 16S rRNA, helps position ribosome
kozak sequence
AUG on eukaryotes
elongation factors
EF-Tu and EF-Tsand EF-G
elongation requires __ more GTPs for each amino acid
3
tRNA path
A to P to E
peptide path
P to A to P to A
UAG, UGA, and UAA are recognized by
release factors
release factors
binds to A site and causes ribosome to disassociate
