Chapter 12 Flashcards
Transcription definition
The copying of DNA sequence into RNA sequence
Protein-encoding genes (structural genes)
encode aa sequence of polypeptide
messenger RNA (mRNA)
made by transcription of protein-coding gene, mRNA base sequence determines aa sequence of polypeptide during translation
Translation definition
produces polypeptide using info in mRNA
DNA replication
makes DNA copies that are transmitted from cell to cell and parent to offspring
Gene expression
overall process by which info within gene is used to produce functional product which can determine trait (with help of environment)
Regulatory sequences
site for binding of regulatory proteins, influences the rate of transcription (usually found upstream)
Promoter
site for RNA polymerase binding, signals beginning of transcription
Terminator
signals end of transcription
Ribosome-binding site
site for ribosome binding to mRNA in bacteria (translation begins near this site in mRNA
In eukaryotes, the ribosome binds to the _________ in the mRNA, and the ribosome scans the RNA for a ______ codon.
7-methylguanosine cap, start
What is the start codon in eukaryotes vs. bacteria?
Eukaryotes —> methionine
Bacteria —-> formylmethionine
Polycistronic
bacterial mRNA that encodes for two or more polypeptides
Template strand
DNA strand that’s actually used as a template/guide to be transcribed into mRNA
Coding strand/sense strand/nontemplate strand
Strand opposite to the coding strand (identical to base sequence in mRNA made from template strand)
Transcription factors
recognize promoter and regulatory sequences to control transcription
3 stages of transcription
initiation (start), elongation (grow), termination (stop)
Initiation
Promoter is recognition site for transcription factors, which enable RNA polymerase to bind to promoter. DNA is then denatured into bubble known as open complex.
Elongation/synthesis of RNA transcript
RNA polymerase slides along DNA in open complex to synthesize RNA
Where do promoters vary?
at -35 and -10 sequences
Most common sequence in promoter
consensus sequence - likely to result in high level of transcription, sequences that deviate from consensus sequence typically result in lower levels of transcription
What’s in the RNA polymerase holoenzyme? What’s it do?
Core enzyme (five subunits) and sigma factor (one subunit). Holoenzyme binds to DNA, scans along until it encounters promotor. When it does, sigma factor recognizes -35 and -10 sequences.
Helix-turn-helix structure in sigma factor
involved in tighter binding to DNA
Closed complex
binding of RNA polymerase to promoter
Open complex
formed when TATAAT box in the -10 sequence is unwound, a short RNA strand is made within open complex (sigma factor released at this point, marking end of initiation)
RNA polymerase directionality
RNA polymerase slides along template strand in 3’ to 5’ direction, RNA synthesized in 5’ to 3’ direction using nucleoside triphosphates (NTPs) as precursors
Location of _____ determines template strand and therefore direction of transcription.
promoter
2 different mechanisms of termination in E. coli
rho-dependent and rho-independent (facilitated by uracil-rich sequence at 3’ of RNA and stem-loop upstream) (both mechanisms have hairpin structure)
3 different RNA polymerases that transcribe Nuclear DNA
RNA pol I - transcribes all rRNA genes (except 5S rRNA)
RNA pol II - transcribes all protein-encoding genes (synthesizes mRNAs) and some snRNA genes for splicing
RNA pol III - transcribes all tRNA genes, 5S rRNA gene, microRNA genes
Conserved sequences
usually upregulated, an example is the TATA box
Basal transcription
basal=general, baseline amount of transcription factors needed for RNA pol to function
Regulatory elements (name 2 types)
short DNA sequences that affect binding of RNA pol to core promoter
1. Enhancers - stimulate transcription
2. Silencers - inhibit transcription
cis-acting elements that regulate gene transcription
DNA sequences that exert their effect only over particular gene (ex: TATA box, enhancers, silencers)
trans-acting factors that regulate gene transcription
regulatory proteins that bind to such DNA sequences
3 categories of proteins required for basal transcription to occur at promoter
RNA pol II, 5 different proteins called general transcription factors (GTFs), protein complex called mediator
2 models of termination
Allosteric model - “do nothing” model, RNA pol II destabilized & dissociates from DNA
Torpedo model - exonuclease binds to 5’ end of RNA and degrades it in 5’ to 3’ direction, catches up to pol and causes termination
Colinearity of gene expression
sequence of DNA in the coding strand corresponds to the sequence of nucleotides in the mRNA
Does RNA modification occur in eukaryotes or prokaryotes?
eukaryotes
Exons vs. introns
exons = coding sequences, introns don’t code for anything and are spliced out
4 ways to modify RNA
- Splicing
- Processing of rRNA and tRNA transcripts to smaller functional pieces
- 5’ Capping
- 3’ polyA tailing of mRNA transcripts
RNA processing
larger RNA transcripts cleaved into smaller functional pieces (ex: rRNAs and tRNAs)
RNA processing - transfer RNAs
also made as large precursors, cleaved at both 5’ and 3’ ends to produce mature, functional tRNAs
RNaseP
an endonuclease, also a ribozyme (catalyst composed of RNA)
3 splicing mechanisms (all 3 involve removal of intron RNA and covalent linkage of exon RNA fragments)
Group I intron splicing (self-splicing)
Group II intron splicing (self-splicing)
Spliceosome (pre-mRNA)
(slide 52 chart)
Self-splicing
can occur in vitro w/out proteins, not aided with additional enzyme, instead the RNA itself functions as its own ribozyme
Maturases
protein that enhances rate of splicing
What is the spliceosome made of?
several subunits called snRNPs (small nuclear RNA and a set of proteins = combo of active RNA and proteins, displays active RNA), pulls back pieces we don’t need & they dip somehow
Functions of spliceosome subunits
bind to intron sequence and recognize intron-exon boundaries, hold pre-mRNA in correct configuration, catalyze rxns that remove introns and covalently link exons (occurs via metalloribozyme)
Alternative splicing
pre-mRNA with multiple introns can be spliced in different ways, two or more polypeptides can be derived from a single gene
Constitutive vs. alternative exons
constitutive - always exons
alternative - sometimes bits of info (sometimes cut out like introns if not used)
Uses of 5’ cap (7-methyl-guanosine)
protect poly-A tail from degradation, protects from breakage while free floating, protect against enzymes,
important for exiting nucleus
RNA editing
can occur by changing one type of base to another, modifying (not pulling old out and putting new in)
Important table on slides ____
77 & 78
FuG
gUh
