week 5 (unit 2) Flashcards
RNA
- single-stranded (most)
- bases: UTCG and ribose sugar
DNA
- double-stranded, genetic material
- bases: ATCG and deoxyribose sugar
- semiconservative
eukaryotic DNA characteristics
(fungi and protists)
- linear, in nucleus, telomeres, introns, multiple chromosomes, and strands twist
prokaryotic DNA characteristics
(bacteria and archaea)
- circular, in cytoplasm, one chromosome, one origin of replication -> bidirectional replication
levels of protein structure
- primary: amino acid sequence
- secondary: alpha helix or beta sheets
- tertiary: 3D structure (polypeptide structure)
- quaternary: 2 or more polypeptide structures
—– hemoglobin
7 enzymes involved in DNA synthesis
- helicase: breaks the H bonds
- ssDNA binding proteins: protects the DNA and keeps the strands apart
- topoisomerases: relieves twisting and keeps it loose
- primase: synthesizes the short RNA primers on the lagging strand for the DNA polymerase
- clamp loader complex: holds teh DNAP at the DNA strand
- Tau: binds E. Coli replication proteins
- DNA ligase: joins the Okazaki fragments
leading strand
- primase and DNAP replicate easily in the 5’ to 3’ direction (MEANING THE DNA STRAND THAT IS 3’ FROM THE LEFT SIDE)
lagging strand
- primase and DNAP replicate in many fragments and DNA ligase joins them when done
what enzyme has exonuclease activity (proofreading) , remove wrong nucleotide and out the correct one in
DNAP
what does central dogma refer to?
DNA-> RNA -> protein
is it in prok. or euk. that transcription and translation occur at the same time (coupled)?
prokaryotes
difference between DNAP 1 and DNAP 3?
- DNAP 1 is used to synthesize the DNA from the RNA primers
- DNAP 3 does the proofreading
bacterial RNAP
pic
for transcriptional initiation, whats the composition of the promoter fro both prok and euk?
- euk: TATA box
- prok: pribnow box
—- both are heavy TATA heavy regions
promoter region
- -35 bps upstream: sigma factor recognizes and binds
- -10: Pribnow box: strands start to separate
- +1: transcription starts
what proteins block the RNAP from binding?
repressor proteins on the operator region
what proteins help the binding of RNAP?
activator proteins on the enhancer region
bacterial transcriptional elongation
the mRNA strand continues to grow
bacterial transcriptional termination: 2 ways
- intrinsic (stem loop): RNA sequence makes a hairpin which is weak bc of AU base pairs and then strand is released
—— 1. hairpin structure: pause
2. poly U sequence: ends - factor dependent Rho protein (helicase): Rho binds to the rut site and moves along the strand and until it catches up to the termination site and then teh strand is released
bacterial translational initiation
- rRNA is w/ mRNA and tRNA binds to the Shine Dalgarno sequence (start codon) on the mRNA
—–initiator tRNA = N-formylmethionine
—–archaea and euk: initiator tRNA= methionine
euk translational initiation
the tRNA binds to the 5’ cap and 3’ polyadenine tail instead of the shine dalgarno sequence (euk doesn’t have this)
bacterial translational elongation
-mRNA strand is moving along teh ribsome and the tRNA is providing teh amino acid
- tRNA is moving form A-> P -> E sites
- 2 rare stop codon: selenocysteine and pyrrolysine
bacterial translational termination
when the stop codon is reached the ribosome disassembles and the polypeptide chain is released
where do the proteins go when they are synthesized?
from cytoplasm to across the plasma membrane
2 protein movement systems
sec: general secretion pathway
tat: specialized for folded proteins
protein secretion in gram (-) bacteria
