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42 Cards in this Set

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Difference btw uracil & thymine
5-position:
Thymine-CH3
Uracil-H
What conveys the information on RNA?

What remains consistant?
the sequence of bases

ribose-phosephate backbone
What is the polarity of the RNA chain?
top- 5'

bottom - 3'
_________ catalyzes the ____________ of DNA to RNA
-RNA polymerase

-translation?
RNA:
DNA strand template is read in what direction?

The RNA is synthed in what direction?
- 3'-5'

- 5'-3'
Procaryote RNA polymerase subunits (5)
2 alpha, 1 beta, 1 beta prime, 1 (gamma?)^70
Procaryote RNA:

gamma^70
recognizes and binds to promoter site on DNA template
What signals the termination of transcription (procaryotes only?)
-hairpin structure in RNA sequence, or

-rho protein
how does the rho protein stop transcription?
-pulls RNA away from DNA through ATP hydrolysis
rRNA:

amount
bases
role
-80%
-3700-120
-catalytic (part of ribosome)
tRNA:
aka
amount
bases
role
structure
-"transfer RNA"
-15%
-75
-amino acid "adaptors"
-has anticodon triplet, complementary to codon
mRNA:
aka
amount
bases
role
how
lifespan
-"messenger" RNA
-5%
-variable
-directs protein synth
-mRNA sequence of codons
-short
snRNA:
amount
bases
role
-v. low
-variable
-part of nucleoprotein catalysts
how does human rna synth differ from procaryotic?
more subunits and are specialized
Human rna polymerase 1 makes?
-rRNA
How many subunits are in human RNA polymerase 2?
What it it's product?
What is the end product, and how is it made?
-12
-primary transcript, with exons and introns
-mRNA and snRNA, by splicing out the introns
What does human RNA polymerase 3 produce?
-tRNA's
What enzyme catalyzes the removal of introns?

What are these enzymes made of?
-splyceosomes

-roboprotein complexes: snRNA and protein
Process of initiation (translation)
-30S ribosome binds IF1 & IF3
-IF2-GTP & mRNA bind
-fMet-tRNA binds in P-site
-IF3 leaves
-50S binds, IF1 leaves
-if codon/anticodon match, GTP hydrolyzed into GDP, IF2 leaves
Translation elongation:
aa-tRNA binding
-EF-Tu(GTP) binds and aa-tRNA binds at A
-If match, GTP->GDP and EFtu dissociates
-peptide bond forms (catalyzed in tunnel, no energy needed)
What is the "small motor" unit involved in the elongation cycle?
-EF-G(GTP): uses GTP hydrolysis to bump A-site one codon up the mRNA
Translation Termination
-Releasing factors (RF1 or 2) bind ribosome when "stop" codon in A
-released by hydrolysis
Initiation of protein synthesis uses ____ ATP to AMP.

Each elongation uses ___.
-1

-2
Acinomycin D
-binds to dsDNA
-inhibits exposure of ssDNA :. stops replication
-planer hydrophobic ring w/ 2 cyclic peptides
-antibacterium?
Rifampicin
("R" for RNA)
-binds to RNA polymerase (on beta unit)
-DNA binds, but synth stops after just a few bases
-(antibiotic)
Puromycin
-antibiotic
-binds A-site, blocking binding of aa-tRNA.
-reacts covalently w/ peptide in P-site, aborting growing protein
cycloheximide
-binds 60S
-inhibits peptide bond formation
tetracycline
-binds 30S
-inhibits aa-tRNA binding
Ricin
-binds ribosome
-removes specific ADENINE, inactivating cell ribosomes
What activates or represses transcription?
DNA-protein interactions
What modifies protein-DNA interactions
DNA-ligand interaction
What modifies protein-ligand and/or protein-DNA interactions?
Protein-protein interactions
CAP
-cAMP binding protein
-activates the expression of genes used when no glucose around
-cAMP/CAP dimer binds DNA and enhances RNA polymerase binding
oncogenes
-mutations of normal proteins involved in cell growth or differentiation
-result in cancer
-some retroviruses use reverse transcriptase and integrase to splice oncogene into host DNA
Tobacco Mosaic Virus
-ssRNA
-codes for RNA-directed RNA polymerase, coat protein, and other proteins
-coat is aggregate of only 1 protein
Influenza A Virus
-ssRNA
-8 segments
-lipid bilayer
-surface proteins help it bind to host
HIV
-ssRNA (retrovirus)
-lipid bilayer
-surface proteins help it bind
-RNA-directed DNA polymerase
-integrates with host DNA
Herpes Simplex (HSV-1)
-dsDNA
-nucleocapsid
-DNA copied in nucleus, capsid built in cytoplasm
prion
PrP^sc binds PrP and accelerates it's conversion into PrP^sc (bad stuff)
-caused by ingestion of PrP^sc
Types of enzymes (6)
-oxidoreductase (e- transfer)
-transferase (group transfer)
-hydrolases (hydrolysis)
-lyase (addn or removal of group across dbl bond
-isomerase (rearrangement w/in molec)
-ligase (condensation rxn with ATP cleavage)
4 classes of proteases
-serine
-zinc
-thiol (cysteine)
-aspartate
serine proteases
-specificity pocket favors nonpolar/cationic/small substrates
-eg. chymotrypsin/tripsin/elastase