KH2 Flashcards
describe central dogma of biology
theory that DNA (heredity) leads to RNA leads to protein
this gives rise to physiology and development biology = organism form/function
describe langue analogy (central dogma)
DNA synthesis replication = making perfect copy (thymine)
RNA synthesis transcription = resetting in a different nucleotide font (using uracil)
protein synthesis translation = rewriting in a different language (nucleotide vs aa)
describe replication (biopolymer, template and enzyme)
DNA
DNA
DNA polymerase
describe transcription (biopolymer, template and enzyme)
RNA
DNA
RNA polymerase
describe translation (biopolymer, template and enzyme)
protein
mRNA
ribosome
describe most enzymes
most enzymes are proteins (includes DNA and RNA polymerase)
describe ribosomes (composition)
ribosome includes protein and RNA components - both contribute to enzymatic function
RNA = critical catalytic component
what is template of transcription
exposed DNA strand
specifies RNA sequence by watson crick base pairing
describe the reaction of transcription
nascent RNA chain antiparallel
chain growth at 3’ end by RNA polymerase
joins last nulceotide to new selected one
catalyzes attack of 3’OH on alpha phosphate of incoming rNTP
beta diphosphate dropped and released
describe the direct interaction of template with incoming monomer (rNTP)
watson crick base pairs
rNTPs diffuse randomly
RNA polymerase will only link incoming rNTP to growing chain if it is the right base
must have the correct base and polymerase can sense when the right one comes in
what is the sequence of RNA transcribed correspond to
the non template strand which is not used to make RNA
both the non template and the new RNA strands are complementary and antiparallel to the template DNA strand
*RNA has U instead of T tho
describe the transcription bubble
local unwinding of 2 turns ~ 20 bases of double stranded DNA
what happens in transcription bubble
template DNA strand exposed by local unwinding of duplex DNA by helicase associated with RNA polymerase
one is used as template strand and other is non template (which is pushed away)
does transcription bubble stay in same spot the whole time
nOOO IT moves along the DNA with the RNA polymerase
what happens after DNA is unwound in transcription bublle
original duplex DNA reforms behind RNA polymerase as it moves unidirectionally along DNA
this reforming duplex kicks out newly synthesized RNA strand
RNA strand exits through a channel in polymerase 5’ end first
describe bacterial RNA polymerase transcribing DNA
growing RNA chain is extruded through exit channel of the RNA polymerase
transient transcription bubble moves with the RNA polymerase to the right
describe starting of RNA polymerase
promoters (certain DNA sequence) facilitate the initial binding (recruit RNA polymerase) of RNA polymerase to DNA
describe stopping of RNA polymerase
certain DNA sequences destabilize the attachment of RNA polymerase to the DNA as it moves
RNA polymerase falls off the DNA and releases the completed RNA chain and RNA will be exported
name and describe the things DNA replication and transcription have in common = 6 similarities
template is DNA
DNA duplex unwound by helicase at initiation sites and exposes template (replication origins)
new strand synthesized 5’-3’ antiparallel to template *chain growth at 3’ end
monomers = NTPs
direct interaction between template DNA and incoming monomer
attack of 3’OH on alpha phosphate of incoming dNTP and beta diphosphate dropped (same chemistry)
name and describe how transcription differs (from DNA replication) ~ 5 things
monomers = rNTPs
start and stop sites on template
newly synthesized strand separates from template
only one of original DNA strands is template
start with one molecule of duplex DNA and end with one molecule of duplex DNA + RNA molecule
name and describe how DNA replication differs (from transcription) ~ 5 things
monomer = dNTPs
start sites but no stop sites (never stops)
newly synthesized DNA never separates from template strand - is there until next replication and then they are separated
both of original DNA strands serve as templates
start with one molecule duplex DNA and end with 2 molecules duplex DNA
what is protein synthesis
translation
nucleotides into amino acids
words = codons (mRNA sequence)
dictionary = protein sequence
describe codons - and possible sequences (gen)
4 nucleotides
20 aas
3 nucleotides = codon
4x4x4x = 64 possible codons
describe the genetic code table
dictionary of codons (3 nts) and their corresponding amino acids
64 entries for 64 possible codons
what is genetic code (characteristic)
degenerate meaning that several different codons code for the same amino acid
explain punctuation codons
3 codons/64 do not code for any aas - they are stop codons = UAA UAG & UGA
one codon = start = AUG (met, all proteins start their synthesis with methionine, but is also found in protein chain)
describe monomer contacts for biopolymer synthesis
can be that there is direct contact where the energized monomer touches the template or could be indirect using an adaptor
name energized monomers
dNTP
rNTP
aminoacyl tRNA
describe monomer contacts for biopolymer synthesis - replication and transcription
direct interaction of template with next monomer molecule to be incorporated
describe monomer contacts for biopolymer synthesis - translation
indirect interaction between template and next monomer (aa) to be incorporated
tRNA acts as am adaptor between template and growing chain
describe adaptors (gen analogy)
transform signal from one system to another
2 ends - one to interact with each of the two systems being bridged
describe aminoacyl tRNAs
adaptors for transforming nucleotide signal into aa signal
amino acid monomers used in translation are in form of high energy amino acyl-tRNA esters
describe components of amino acyl tRNAs
amino acid signal end
nucleotide signal end - 3 nucleotide anticodon sequence that is complementary to a codon
describe how amino acyl tRNA does its job
peptidyl transferase reaction is catalyzed by the large subunit rRNA molecule
ribozyme at heart of protein synthesis
mRNA moves and tRNA comes along and attaches (anticodon with codon) keeps going following sequence
ribosome - a ribonucleo protein consisting of large and small subunits
describe translational reading frames
ribosome translocation is 3 bases at a time
count 3 - starts with AUG
what determines which reading frame is used
position of initiation codon
describe the 3 reading frames
natural mRNA sequence = starts and has correct sequence
displace by one base = start but now amino acids added are different
displace by 2 bases = same thing but now it creates a stop codon
*frameshift mutations
describe RNA world hypothesis
hypothesis that RNA evolved as an informational biopolymer before proteins and even before DNA (and before cells)
RNA world hypothesis of the evolution of life
