Lecture 9 Flashcards
what enzymes and proteins are essential to DNA synthesis?
DNA polymerase 3, SSBPs, DNA gyrase, DNA helicase, and RNA primers
DNA polymerase 3
elongates and edits
SSBPs
single stranded binding proteins; keeps ssDNA template ss
DNA gyrase
relieves the coiling tension created by unwinding
DNA helicase
pushes open the replication fork; unwinds to create single strands to be used as templates
RNA primers
polymerase needs a 3’ end to add onto
what features are similar in eukaryotic and bacterial DNA replication?
- dsDNA unwounded at ORI
- replication fork formed
- bidirectional synthesis creates leading and lagging strands
- eukaryotic polymerases also require 4 deozyribonucleoside triphosphates
how does eukaryotic DNA differ from bacterial DNA?
- more DNA
- DNA is complexed with nucleosomes
- linear chromosomes
- have multiple ORIs
bacterial and viral chromosomes
- single nucleic acid molecule
- largely devoid of associated proteins
- much smaller
- contain less genetic information
viral chromosomes
- DNA or RNA; ds or ss
- circular or linear
- genetic material is nactive until released into host
- packages long DNA into a small volume
bacterial chromosomes
- circular, ds DNA
- associated with histone proteins
- readily replicated and transcribed
supercoiled DNA
- closed-circular molecules
- more compact
topoisomerases
- enzymes that cut one or both DNA strands
- wind or unwind helix before releases strands
histones
-positively charged proteins associated with chromosomal DNA in eukaryotes
at what phase can DNA make RNA?
when the chromatin is a relaxed structure; when it is tightly wound no transcription can be occur
methylation
activates genes
can also repress genes
depends on what chemistry you are altering
phosphorylation
can promote demethylation
-can recruit proteins, those proteins can bind to this region and undo the work of the methyl group
acetylation
represses genes
euchromatin
-uncoiled and active
heterochromatin
condensed areas, mostly inactive
pseudogenes
single copy noncoding regions
codon
triplet code, every three ribonucleotides
what does unambiguous mean in the genetic code?
each triplet codon specifies for only one amino acid
what does degenerate mean in the genetic code?
a given amino acid can be specified by more than one triplet codon
what does commaless in genetic code mean?
once translation begins, there are no breaks in codons
mRNA
messenger RNA
serves as intermediate in transferring genetic information from DNA to proteins
how many codons are there? how many code for amino acids? what do the others do?
- 64 codons
- 61 coding
- the other 3 are termination signals
how many amino acids do the codons code for?
20
frameshift mutation
-insertions or deletions shift the reading frame and change the codons downstream
what are termination codons?
UAG, UAA, and UGA
reading frame
-contiguous sequence of nucleotides
nonoverlapping
- genetic code reads three nucleotides at a time in a continuous, linear manner
- during translation, genetic code is nonoverlapping
triple binding assay
- developed by Nitenberg and Leder
- ribosomes bind to a single codon of three nucleotides
- complementary amino acid charged tRNA can bind
how does the genetic code show order?
chemically similar amino acids share one or two middle bases in triplets encoding them
wobble hypothesis
- the initial two ribonucleotides of triplet codons are often more critical than the third
- the third position is less spatially constrained; need not adhere as strictly to established base-pairing rules
initiation codons
- methionine (AUG)
- initial amino acid incorporated into all proteins
- AUG is the only one to code for methionine
overlapping genes
- single mRNA has multiple initiation points
- creates different reading frames
- specifies more than one polypeptide
Open Reading Frame (ORF)
- overlapping genes
- DNA sequence produces RNA with start and stop
- series of triplet codons specify amino acids to make a polypeptide
transcription
- RNA synthesized on DNA template
- genetic info stored in DNA transferred to RNA
- serves as intermediate molecule between DNA and proteins
- each triplet codon is complementary to anticodon of tRNA
what does transcription result in?
- in ssRNA
- template is transcribed
- transcription begins with template binding by RNA polymerase at promoter
- alpha subunit is responsible for promoter recognition
promoter
specific DNA sequences in 5’ region upstream of initial transcription point
RNA polymerase
- enzyme directs synthesis of RNA using DNA template
- nucleotides contain ribose
- no primer needed for initiation
transcription start site
- DNA double helix is unwound to make template strand accessible for RNA pol
- interaction of promoter and RNA polymerase regulates efficiency of transcription
how does transcription differ in eukaryotes?
- occurs within a nucleus
- mRNA must leave nucleus for translation
- chromatin remodeling
- RNA polymerase rely on transcription factors to scan/bind to DNA
- enhancers and silencers control transcription regulation
chromatin remodeling
chromatin must uncoil to make DNA accessible to RNA pol
what are the three forms of RNA pol in eukaryotes?
RNA Polymerases 1,2,3
RNA Polymerase 2
-responsible for transcription of wide range of genes in euk
-activity of RNAP2 is dependent on cis-acting elements and trans-acting transcription factors
RNAP2 core-promoter determines where RNAP2 binds to DNA
what are the regulation sequences that influence the efficiency of transcription by RNAP2?
- proximal-promoter elements
- enhancers
- silencers
TATA box
- core promoter element
- determines start transcription site
enhancers
- binds activators
- increase transcription levels
silencers
- binds repressors
- decrease transcription factors
enhancers and silencers
- found unpstream, within, or downstream of a gene
- modulate transcription from a distance
posttranscriptional factors
- addition of 5’ cap (7-mG cap)
- addition of 3’ tail (poly-A tail)
- excision of introns
introns
- regions of initial RNA transcript not expressed in amino acid sequence of protein
- DNA sequence not represented in final mRNA product
- prokaryotes do not have them
heteroduplexes
introns present in DNA but not mRNA loop out
splicing
- introns are removed by splicing
- exons are joined together in mature mRNA
- mature mRNA is smaller than initial RNA
