Exam 4 Flashcards
FOXP2
that the speech problem was caused by a mutation in the FOXP2 gene located on chromosome 7 region 7q31
Transcription
Initiation with enzyme
RNA polymerase binds to a specific DNA sequence called the promoter, initiating the synthesis of an RNA transcript
Transcription Elongation
RNA polymerase slides along the DNA in an open complex to synthesize RNA
Transcription Termination in bacteria
a terminator is reached that causes RNA polymerase and the RNA transcript to dissociate from the DNA
Promoter region sequence
-35 to -10 nucleotides
Transcription Initiation in Prokaryotes
- RNA polymerase binds to DNA and the omega searches for the promotor region
- An open complex is formed of the DNA structure
- A short RNA is formed
- Omega factor is release and core enzyme chugs down the DNA
Transcription Elongation in Prokaryotes
- Rewinding of DNA
- Reads 3’ to 5’ and transcribes 5’ to 3’
- RNA-DNA hybrid region
Transcription Termination in Prokaryotes
Enzyme traverses entire gene until a termination nucleotide sequence is encountered
Intrinsic termination – hairpin structure followed by a string of repeated U residues
Rho-dependent termination depends on the rho (r) termination factor and hairpin
Eukaryotic transcriptional terminology
Two types:
cis-acting elements
trans-acting factors
cis-acting elements
DNA sequences that exert their effect only over a particular gene
Example: TATA box, enhancers and silencers
trans-acting factors
Regulatory proteins that bind to such DNA sequences
Example: transcription factors
Promoters (core and proximal)
Nucleotide sequences that serve as recognition sites for transcription machinery
Located immediately adjacent to regulatory genes
Critical for transcription initiation
Core promoter
Proximal-promoter elements:
Core promotor
6 parts
Illegally taking time to dance malicious
Made up of DNA sequence elements including:
Initiator (Inr)
TATA box - Binds TATA-binding protein (TBP) of transcription factor
TFIID: determines start transcription start site
TFIIB recognition element (BRE)
Downstream promoter element (DPE)
Motif ten element (MTE)
Proximal-promoter elements
Modulate efficiency of basal levels of transcription
Formation of RNA Pol Initiation Complex
6 parts
-drinking badly for everyone’s happy moments-
General transcription factors (GTF)
Proteins (TFIID, TFIIB, TFIIF, TFIIE, TFIIH, mediator)
Required at promoter to initiate basal or enhanced levels of transcription
Assembly of proteins in specific order forms pre-initiation complex (PIC) - provides a platform for RNAP II to recognize
Regulatory elements
short DNA sequences that affect the binding of RNA polymerase to the promoter
Found upstream, within, or downstream of gene
Modulate transcription from a distance
Transcription factors
2 types on genes
(proteins) bind to these elements and influence the rate of transcription
Enhancers
Stimulate transcription
Bound by activators (proteins)
Silencers
Inhibit transcription
Bound to repressors (proteins)
Coactivators
Interact with proteins and enable activators to make contact with promoter-bound factors
Coactivators form complex “enhanceosome”
Enhanceosome
Interacts with transcription complex
Repressor proteins at silencer elements decrease rate of PIC assembly and RNA Pol II release
Termination in Eukaryotes
No termination sequence
Once the polyadenylation signal sequence has been incorporated, the transcript is cleaved and the RNA pol II falls off/apart
Eukaryotic Posttranscriptional RNA Modifications
Addition of 5’ cap (7-mG cap)
Addition of 3’ tail (poly-A tail)
Intron removal
Capping
The 7-methylguanosine cap structure is recognized by cap-binding proteins
Cap-binding proteins play roles in the
–Movement of some RNAs into the cytoplasm
–Early stages of translation
Splicing of introns
Poly-A Tail
Endonuclease cleave occurs about 20 nucleotides downstream from the AAUAAA sequence
PolyA-polymerase adds adenine nucleotides to the 3’
Splicing Removes Introns
Introns (intervening sequences)
Regions of initial RNA transcript not expressed in amino acid sequence of protein
DNA sequences not represented in final mRNA product
Exons are sequence retained and expressed
Prokaryotes do not have introns
Heteroduplexes: Introns present in DNA but not mRNA loop out
Posttranscriptional modification: Splicing
Introns are removed by splicing
Exons are then joined together in mature mRNA
Mature mRNA is smaller than initial RNA
Spliceosome
Pre-mRNA introns spliced out by spliceosome
Reaction involves:
Formation of lariat structure
Splice donor and acceptor sites
Branch point sequence
Intron Advantage?
One benefit of genes with introns is a phenomenon called alternative splicing
A pre-mRNA with multiple introns can be spliced in different ways
This will generate mature mRNAs with different combinations of exons
This variation in splicing can occur in different cell types or during different stages of development
Alternative Splicing example
Baker’s yeast contains about 6,300 genes
~ 300 (i.e., 5%) encode mRNAs that are spliced
Only a few of these 300 have been shown to be alternatively spliced
Humans contain ~ 20,000 genes
Most of these encode mRNAs that are spliced
It is estimated that about 70% are alternatively spliced
Note: Certain mRNAs can be alternatively spliced to produce dozens of different mRNAs
The genetic code: General features
Written in linear form using RNA bases that compose m R N A
Each “word” consists of three ribonucleotide letters, or a triplet code
Codon: Every three ribonucleotides
Unambiguous—each triplet specifies only one amino acid
mutation
a heritable change in the genetic material
Mutations provide allelic variations
Since mutations can be quite harmful, organisms have developed ways to repair damaged DNA
Mutations can be divided into three main types where the mutation occurs
- Chromosome mutations
Changes in chromosome structure - Genome mutations
Changes in chromosome number - Gene mutations
Relatively small change in DNA structure that affects a single gene
point mutation – transition
a change of a pyrimidine (C, T) to another pyrimidine or a purine (A, G) to another purine
point mutation – transversion
a change of a pyrimidine to a purine or vice versa
Transitions are more common than transversions
Spontaneous mutation
Changes in nucleotide sequence that occur naturally
Arise from normal biological or chemical processes that alter nitrogenous bases
Spontaneous mutation rates vary, but are exceedingly low for all organisms
Spontaneous depurination
the natural, non-enzymatic removal of a purine base (adenine or guanine) from a DNA molecule, resulting in a site where there is no base (an abasic or apurinic site)
Spontaneous Deamination
a natural, random process where an amino group is removed from a nitrogenous base in DNA, leading to mutations, particularly when cytosine converts to uracil, or 5-methylcytosine to thymine.
Spontaneous Tautomeric Shifts
the spontaneous rearrangement of the positions of protons and electrons within a molecule, forming an isomer
Induced Mutations - Alkylating agents
Donate alkyl group to amino or keto groups
Alters base-pairing affinity
Intercalating Agents
Chemicals with dimensions and shapes that wedge between D N A base pairs
This causes base-pair distortions and D N A unwinding
Example: Ethidium bromide
Base analogs (mutagenic chemicals)
Can substitute for purines or pyrimidines during nucleic acid biosynthesis
Increase tautomeric shifts
Increase sensitivity to U V light—mutagenic
U V light
Electromagnetic spectrum
Purines and pyrimidines absorb U V at 260 n m
U V radiation creates pyrimidine dimers
Two identical pyrimidines that distort D N A conformation
Errors can be introduced during D N A replication
Nucleotide Excision Repair Removes Damaged DNA Segments
An important general process for DNA repair is nucleotide excision repair (NER)
This type of system can repair many types of DNA damage, including
–Thymine dimers and chemically modified bases
–missing bases, some types of crosslinks
Two types of excision repair
Base excision repair (BER)
Nucleotide excision repair (NER)
Base excision repair (BER)
Corrects DNA containing a damaged DNA base
DNA glycosylase recognizes altered base
Nucleotide excision repair (NER)
Repairs bulky lesions that alter/distort double helix
Base Excision Repair
Light-independent D N A repair mechanisms exist in all prokaryotes and eukaryotes and involve excision repair
Exonuclease recognizes and cuts distortion/error
D N A polymerase inserts complementary nucleotides in missing gap
D N A ligase seals final “nick”
Proofreading and mismatch repair
D N A polymerase “proofreads,” removes and replaces incorrectly inserted nucleotides
Mismatch repair (if proofreading fails) becomes activated
Mismatches are detected, cut, and removed (endonuclease and exonuclease). Correct nucleotide inserted by D N A polymerase
Strand Discrimination
Based on D N A methylation
Adenine methylase (enzyme in bacteria) recognizes D N A sequences and adds methyl group to adenine residues
Newly synthesized strand of replication remains unmethylated
Mismatch repair recognizes unmethylated strand and repairs
Postreplication Repair
Responds after damaged D N A has escaped repair and has failed complete replication
RecA protein directs recombination exchange with corresponding region on undamaged parental strand (donor DNA)
Gap can be filled in by repair synthesis
Double-Strand Break Repair
Double-strand breaks are extremely dangerous
Results in chromosomal rearrangements, cancer, cell death
D S B repair pathway reattaches strands
Two pathways involved in D S B repair
Homologous Recombination Repair
Recognizes break, digests 5’ end, and leaves 3’ overhang
3’ end aligns with sequence complementary on sister chromatid
Occurs during late S or early G2 phase of cell cycle
Nonhomologous End Joining Pathway
Activated in G1 prior to replication
Repairs double-strand breaks
Complex of proteins is involved in end joining
May include kinase and BRCA1
Proteins bind free ends and ligate ends back together
The genetic code specifics
Degenerate: A given amino acid can be specified by more than one triplet codon
Contains “start” and “stop” signals: triplets that initiate and terminate translation
Commaless
Once translation begins, codons are read with no break
Nonoverlapping
Any single ribonucleotide within m R N A is part of one triplet
Colinear
Sequence of codons in a gene is colinear
Nearly universal
A single coding dictionary is used by viruses, prokaryotes, archaea, and eukaryotes
wobble hypothesis
The initial two ribonucleotides of triplet codes are often more critical than the third
Third position - Less spatially constrained
Need not adhere as strictly to established base-pairing rules
Ribosome
Have an essential role in expression of genetic information
Consist of ribosomal proteins and ribosomal RNAs (rRNAs)
Consists of large and small subunits
Prokaryote ribosomes are 70S
Eukaryote ribosomes are 80S
t R N A s—transfer R N A s
Small in size and very stable
75–90 nucleotides
Transcribed from D N A
t R N A s have a cloverleaf structure
Contain anticodon
Amino acid covalently linked to the 3’ end
Charging tRNA
Aminoacylation: tRNA charging
Before translation can proceed, tRNA molecules must be chemically linked to respective amino acids
Aminoacyl tRNA synthetase
Enzyme that catalyzes aminoacylation
20 different synthetases, one for each amino acid
Highly specific; recognize only one amino acid
Initiation of Translation
Shine–Dalgarno sequence (AGGAGG)
Precedes AUG start codon in bacteria
Base-pairs with region on 16S r R N A of 30S small subunit, facilitating initiation
Initiation complex
Small ribosomal subunit + initiation factors + m R N A at codon A U G
Combines with large ribosomal subunit
Elongation
Both ribosomal subunits assembled with m R N A
Forms P site and A site
Catalyzes peptide bond formation between amino acid on t R N A at A site and growing peptide chain bound to t R N A in P site
Uncharged t R N A moves to E (exit) site
t R N A bound to peptide chain moves to P site
Sequence of elongation and translocation is repeated over and over
Termination
Signaled by stop codons (U A G, U A A, U G A) in A site
Codons do not specify any amino acid
G T P-dependent release factors
–Stimulates hydrolysis of polypeptide from peptidyl t R N A—released from translation complex
