Replication, Transcription, Translation Flashcards
What are the major differences between DNA and RNA?
DNA–deoxyribose sugar, thymine
RNA-ribose sugar, uracil
what does dNMPs stand for?
Deoxynucleoside monophosphates
What are they four different DNA bases?
dAMP-deoxyadenosine
dGMP-deoxyguanosine
dCMP-deoxycytidine
dTMP-deoxythymidine
How do nucleotides link together?
- Base attaches to 1’ C of sugar by a glycosidic bond
2. Adjacent nucleotides connect by phosphodiester linkages formed between3’ and 5’ hydroxyls of pentose sugar
How does hydrogen bonding occur within the DNA double helix?
Purines hydrogen bond with pyrimidines
A with T and C with G
What does it mean that the two strands of DNA are antiparallel?
5’ end of one strand bonds with 3’ end of its complement strand
Where do the nitrogenous bases point? Why?
Inside the helix because they are hydrophobic
Where do the sugar phosphate backbones point?
Outside because they are hydrophilic
Explain the differences between A, B, and Z DNA
B DNA–predominates–double helix
A DNA–right handed hell that is shorter and wider (RNA structure)
Z DNA–left handed helix that’s longer and narrower
What is the function of a histone?
To help package DNA
Describe the structure of a histone
made of basic (arg and lys) amino acids
What does semiconservative replication mean?
the old strand serves as a template for the new strand for every round of replication
Why is DNA not conservative?
two entirely new strands were not made in the same round of replication
Describe the role of DNA polymerase
Carries out DNA synthesis and proof reads
what is the function of a sliding clamp
prevents DNA polymerase from falling off the template so that synthesis can happen more quickly
What is the function of helicase
to separate the double stranded DNA
What is the function of single stranded binding protein (ssBP)
prevents the DNA from reannealing once helicase has separated it
Once separated, superhelical stress occurs. What helps relieve this stress?
topoisomerases relieve stress ahead of the replication fork by cutting a strand and allowing it to unwind a little and reseal
Which way does DNA polymerase synthesize DNA
5’ to 3’
what is a primer?
short sequence of RNA already complementary to strand that will serve as a template
How does DNA polymerase begin
Recognizes primer and attacks 3’ hydroxyl
How does the final strand remove the RNA primer?
it is removed by the 5’ to 3’ exonuclease activity of DNA polymerase I
What are the gaps called on the lagging strand of DNA?
Okazaki fragments
What fills in the okazaki fragment gaps and removes the RNA primer?
DNA polymerase I
What is the function of ligase?
It seals the nicks left after DNA polymerase fills in the gaps on the lagging strand
What is the end replication problem?
Gaps that cannot be filled in at the end
How is the end replication problem solved?
Telomerase fixes it by extending the 3’ end of telomeres
Describe what telomerase does
an RNA dependent DNA polymerase that adds DNA to 3’ ends of chromosomes to avoid loss of genetic material
How does smoking cause damage to DNA
oxidizes benzopyrene which then reacts with guanine residues forming bulky adducts
How does UV light cause damage to DNA?
causes formation of pyrimidine dimers which block replication and transcription
Nucleoside excision repair
acts on lesions causing large distortions like pyrimidine dimers
Base excision repair
acts on small lesions involving damage to one base
Mismatch repair pathway
fixes replication errors that escape proofreading
You always use undamaged strand as a template. This is the original strand. Once replicated, how can you tell which strand is the original?
Methylation of A bases (eventually new strand will have these too via addition by methylase)
Lynch Syndrome
impairs the mismatch repair pathway
Xerodermia pigmentosum
impairment of nucleotide excision repair
RNA polymerase
synthesizes mRNA 5’ to 3’
Promoter
RNA polymerase needs to recognize promoter to begin synthesis
Actions of RNA polymerase (4)
Search and bind promoters
Unwind DNA
Initiate polymerization
Detect termination signals
What is the sense strand?
the coding strand
What is the +1 base?
The first base of the official transcript of mRNA
What value are points to the left of +1 give?
negative values (they are not transcribed)
Cis acting elements of promoters
they are on the same molecule of DNA and near the gene they regulate
Trans-acting elements
any protein that binds to the DNA to facilitate or inhibit binding of RNA polymerase
operons in prokaryotes
several protein producing genes are linked together and are controlled by a single promoter
how does RNA polymerase II bind in eukaryotes
proteins bind to TATA box
- TATA binding protein (TBP) binds
- Cofactors bind
- TFIIA and TFIIB interact with TBP
- TFIIF recruits polymerase
- TFIIE and TFIIH bind, cleaving ATP and transcription is initiated
How does RNA polymerase nine in prokaryotes
sigma subunit recognizes promoter region–it will dissociate after initiation
How does termination of transcription occur?
RNA polymerase reaches terminal sequence with UUUU sequence following a hairpin
What is Rho proteins involvement in transcription?
It travels along mRNA, catches the polymerase and terminates transcription
Drug Rifampin
blocks initiation of transcription by blocking exit channel for RNA
What is the differences between cistronic and polycistronic DNA
Cistronic–only one gene from transcript
Poly–multiple genes from a transcript
Describe the functions of the three RNA polymerases in eukaryotes
I–makes rRNA
II–makes mRNA
III–makes tRNA
List some of the promoters in eukaryotes
TATA box
TFIIB recognition element
Downstream promoter (DPE)
Motif ten element (MTE)
What is the purpose of a guanine cap?
It seals the 5’ end of the primary transcript and decreases rate of degradation
Also serves as a site for ribosomal binding for translation
How it the 5’ cap made?
Terminal triphosphate loses phosphate–diphosphate
Diphosphate attacks alpha phosphate of dGMP
Methyl group transferred to guanine ring
What is the purpose of the poly A tail
added to the 3’ end and serves as a protein binding site that protects from degradation
How is the poly A tail made?
Polyadensylation signal after stop codon
Enzyme binds signal and cleaves transcript about 10 nucleotides downstream
PolyA polymerase adds nucleotides
Exons
Contain coding region of RNA
Introns
Contain regions that do not code for proteins and must be spliced out
Spliceosome
ensure that eons are spliced together with great accuracy
How is protein synthesized? (From what end to what end)
Amino terminus to carboxy terminus
Codons
3 base pairs read together–gives amino acid
Degenerative code
almost all amino acids have more than one codon
Unambiguous
each codon only specifies one amino acid
Wobble position
Accurate base pairing is required only in the first 2 positions of an mRNA codon. the third position can wobble–still code for same amino acid
Point mutation
single base pair change
silent mutation
change that specifies for the same amino acid
missense
change that specifies a different amino acid
nonsense
change that leads to a stop codon
Insertion/deletion
add or delete a base which causes an entire frameshift
Amino-acyl tRNA
binds to mRNA using anitcodon–corresponding amino acid is attached at the 3’ end
Aminoacyl-transferase
attaches the amino acid to the tRNA via an ester bond
Initiation of Translation
Initiated by GTP hydrolysis; initiation factors (eIFs) help assemble 40S with initiator tRNA and are released when the mRNA and 60S assemble with complex
Elongation
- Amino-acyl tRNA binds A site
- rRNA catalyzes peptide bond formation, transfers growing peptide to A site
- Ribosome advances 3 nucleotides towards 3’ end of mRNA, moving tRNA to P site
Termination
Stop codon is recognized by release factor and completed polypeptide is released from ribosome
What are some molecules that inhibit translation
Ricin–targets large subunit
Diptheria toxin–modifies His residue blocking translocation
Translation machinery is targeted by antibiotics
Types of post translational modifications
Trimming–removal of C terminus or N termini pro peptides from zygomens to make mature proteins
Phosphorylation, glycosylation, hydroxylation, methylation, acetylation, and ubiquitination
Spinal Muscular Atrophy (SMA)
Neuromuscular disease characterized by dysfunction and death of motor neurons
What causes SMA
Mutation in both SMN 1 genes
Mutation C to T in SMN 2 (occurs in exon and is then not spliced correctly)
What sequence is located at the 5’ splice site?
GU
What sequence is located at the 3’ splice site
AG
How does the spliceosome assemble
- U1 (5’ splice site) and U2 (branch site) bind
- U4-6 form complex
- U1 and U4 kicked out and left with catalytic complex
Exonic splicing enhancers and intronic splicing enhancers
Work by binding proteins that will recruit U1 and U2 and direct splicing
Exonic splicing silencers and intronic splicing silencers
bind proteins that interfere with identification of splice sites
Why can’t SMN2 substitute for SMN1?
C-T mutation causes incorrect splicing because exon 7 is skipped (mutation in enhancer)
What do insulator elements do?
Keep it so that one gene does not influence another
Structure of Histones
tetramer of two dimers with 146 bp of DNA wrapped around
Heterochromatic
proteins cannot access DNA and therefore the genes cannot be turned on
Euchromatic
proteins can access the DNA so these genes can be turned on
What charge do the amino terminal tails of histones have and why?
+ charge because of basic amino acids of lys and arg (interacts well with - charge DNA which causes compacting)
effects of acetylation of histones
once acetylated, there is no positive charge on histone tail–DNA therefore does not want to compact
How does acetylation of histones occur
Histone acetyl-transferase–transfers acetate from acetyl Co A to amino group on lysine
effects of methylation of histones
NONE! don’t affect the charge at all!
Bromo domain
recognized acetylated lysines
Chromo domain
recognizes methylated histones
What is the purpose of modifying chromatin?
To create a scaffold to attract different proteins to influence transcription
