chapter 9 part 1 Flashcards
how many different amino acids serve as building blocks for peptides
20
components of amino acids
- central carbon
- amino group
- carboxyl group
what does enzymes of ribosomes catalyze
peptide bond between amino acids
where are the peptide bonds formed between amino acids
between carboxyl group of one and amino group of next
R-group of amino acids
distinct parts - some charged, some polar
ribosome
machines that contain multiple rRNAs and proteins
which direction do ribosomes translate mRNA
5’ to 3’ direction
ribosome structure
- large ribosomal subunit
- small ribosomal subunit
how is ribosomal size measured
Svedberg units (S) based on size, shape, and hydration state
boundaries of translation
- start codon at N-terminus of protein
- stop codon at C-terminus
are the 5’ and 3’ UTRs inside or outside of the translated regions
outside
4 levels of peptide structure
- primary
- secondary
- tertiary
- quarternary
primary structure
peptide bonds
secondary structures
H-bonding between groups along peptide-bonded backbone
tertiary
bonds and other interactions between R-groups, or between R-group and peptide-bonded backbone
quaternary structure
bonds and other interactions between R-groups and between peptide backbones of dif polypeptdies
small subunit of E. coli ribosomes
- 30S
- 21 proteins
- one 16S rRNA molecule
large subunit of E. coli ribosomes
- 50S
- 31 proteins
- small 5S rRNA
- large 23S rRNA
how big is fully assembly ribosome of E. coli
70 S
3 important sites on ribosome
- A-site (aminoacyl)
- P-site (peptide)
- E-site (exit)
aminoacyl site
binds incoming tRNA molecule carrying next amino acid to be added to growing polypeptide chain
peptide site
holds tRNA to which the growing polypeptide chain is attached
exit site
provides pathway for exit of tRNA after its amino acid has been added to the growing chain
what are the most fully characterized of eukaryotic ribosomes
Mammalian ribosomes
small subunit of eukaryotic ribosome
- 40S
- 3 proteins
- one 18S rRNA
large subunit of eukaryotic ribosome
- 60S
- 45-50 proteins
- three rRNA molecules (5S, 5.8S, and 28S)
start codon
AUG
translation initiation overview
- small ribosomal subunit binds near 5’ end of mRNA and identifies start codon
- initiator tRNA binds to start codon
- large subunit joins small subunit to form intact ribosome, translation begins
initiator tRNA
carries first amino acid of polypeptide and binds to start codon
initiation factors
proteins that help direct ribosome assembly and binding of initiator tRNA
what provides energy for initiation
GTP
charged tRNAS
tRNAS carrying amino acids
uncharged tRNAs
tRNAs without amino acids
bacterial translation initiation
- small subunit-IF3 complex binds near the 5’ end of mRNA searching for start codon
- pre initiation complex
- initiator tRNA binds to start codon where P-site will be once the ribosome is fully assembled
- 30S initiation complex
- 50S subunit joins 30S subunit to form intact ribosome
- IF1,2,3 accompanies joining of subunits to create 70S initiation complex
what is the bacterial 30S subunit affiliated with
initiation factor (IF3), which prevents the 30S subunit from binding the 50S subunit
bacterial pre initiation complex
forms when 16S rRNA base pairs with Shine-Dalgarno sequence on mRNA
Shine-Dalgarno sequence
purine-rich (A/G) sequence of about 6 nucleotides 3-9 nucleotides upstream of start codon
where is a complementary pyrimidine-rich sequence in bacteria
near 3’ end of 16S rRNA (part of small subunit)
where does the initiator tRNA bind to in bacteria
start codon where P-site will be once the ribosome is assembled
amino acid on initiator tRNA
modified amino acid
- N-formylmethionine (fMet)
charger initiator tRNA name
tRNA(fmet)
30S initiation complex
initiation factor (IF-2) and GTP molecule bound to tRNA(fmet) and IF-1 joins the complex
what is the union of the 2 ribosomal subunits in bacterial translation initiation driven by
hydrolysis of GTP to GDP
70S initiation complex
dissociation of IF1, IF2, and IF3 accompanies the joining of subunits
eukaryotic translation initiation
- euk. 40S subunit complexes w/ euk. initiation factor
- pre initiation complex
- pre initiation complex joins initiation tRNA and eIF5
- joins group of at least 4 eIF4 proteins that assemble at 5’ cap of mRNA
- small subunit scans along 5’ UTR for start codon
- recruitment of 60S subunit to complex
preinitiaton complex of eukaryotes
eIF1, eIF1A, and eIF3 bind to small subunit
initiation complex of eukaryotes
pre initiation complex joins group of at least 4 eIF4 proteins that assemble at 5’ cap of mRNA
what is required for scanning for start codon in eukaryotes
ATP hydrolysis
approximately _______ of euk. mRNAs use AUG as start codon
90%
where is start codon located in eukaryotes
Kozak sequence (consensus)
what energy does location of start codon use in eukaryotes
GTP hydrolysis and dissociation of eIF proteins
what is archaeal translation initiation similar to?
eukaryotes
archaeal translaiton initaition
- met first aa
- some have Shine-Dalgarno sequences
- archaeal initiation factor proteins (aIFs) homologous in structure/function to eIFs
what carry out elongation in a series of steps?
several different elongation factors (EF) and ribosomal proteins
bacteria polypeptide elongation
- charged tRNAs affiliated with EF-Tu and GTP try to enter A site
- tRNA with correct anticodon sequence pairs with codon
- when tRNA pairs w/ mRNA codon, hydrolysis of GTP releases EF-Tu-GDP from tRNa
- peptidyl transferase catalyzes peptide bond
- elongated peptide transferred to the tRNA at the A-site while tRNA from the P-site exits through the E-site
- using GTP hydrolysis, EF-G translocates the ribosome, moving 3 nucleotides toward the 3’ end of the mRNA
- tRNa moved from A to P site, opens A site for next charged tRNA carrying anticodon
peptidyl transferase
catalyzes peptide bond formation between amino acids at the P and A sites
are archaeal/eukaryotic or archaeal/bacteria homologs more alike?
archaeal/eukaryotic
