Substituting purine for purine or pyrimidine for pyrimidine
Substituting purine forpyrimidine or vice versa.
Define tRNA wobble
Accurate base pairing isrequired only in the first 2nucleotide positions of anmRNA codon, so codonsdiffering in the 3rd 'wobble'position may code for thesame tRNA/amino acid.
Describe DNA replication.
Origin of replication: continuous DNAsynthesis on leading strand anddiscontinuous (Okazaki fragments) onlagging strand. Primase makes an RNAprimer on which DNA polymerase caninitiate replication. DNA polymerasereaches primer of preceding fragment;5'®3' exonuclease activity of DNApolymerase I degrades RNA primer;DNA ligase seals;
Describe DNA replication(continued answer)
3'->5' exonuclease activity ofDNA polymerase 'proofreads'each added nucleotide. DNAtopoisomerases create a nickin the helix to relievesupercoils
Less condensed (vs.Heterochromatin),transcriptionally active
1) Purines (A,G) have 2 rings.2) Pyrimidines (C,T,U) have 1ring 3) Guanine has a ketone.4) Thymine has a methyl
Describe single-strand,excision repair.
Excision repair-specificglycosylase recognizes andremoves damaged base.Endonuclease makes a breakseveral bases to the 5' side.Exonuclease removes shortstretch of nucleotides. DNApolymerase fills gap. DNA ligase seals
Describe the differencebetween Eukaryotic Vs.Bacterial, viral and plasmidorigin of replications
Eukaryotic genome hasmultiple origins ofreplication. Bacteria, virusesand plasmids have only oneorigin of replication.
Describe the main differencein eukaryotic and prokaryoticsynthesis of RNA.
Eukaryotes have 3 differentRNA polymerases ('I, II, IIIsynthesize RMT') andprokaryotes have 1 RNApolymerase (which makes all3 kinds of RNA).
Describe the method bywhich introns are removedfrom primary mRNAtranscript.
Introns are precisely spliced outof primary mRNA transcripts. Alariat-shaped intermediate isformed. Small nuclearribonucleoprotein particles(snRNP) facilitate splicing bybinding to primary mRNAtranscripts and formingspliceosomes.
Describe the number ofbonds per purine-pyrimidinepair. Which is stronger?
G-C bond (3 H-bonds) A-Tbond (2 H-bonds G-C bond isstrongerDescribe the structure ofChromatin.
Describe the structure ofChromatin.
Condensed by (-) chargedDNA looped around (+)charged histones(nucleosome bead). H1 tiesthe nucleosome together in astring (30 nm fiber)
Describe tRNA structure.
75-90 nucleotides, cloverleafform, anticodon end is opposite3' aminoacyl end. All tRNAs botheukaryotic and prokaryotic, haveCCA at 3' end along with a highpercentage of chemicallymodified bases. The amino acidis covalently bound to the 3' end of the tRNA
Does RNA polymerase have aproof reading function?
How do purines andpyrimidines interact,molecularly?
Purines and pyrimidines pair(A-T, G-C) via H-bonds
How does RNA polymerase II open DNA?
RNA polymerase II opens DNA at promoter site (A-T rich upstream sequence- TATA and CAAT)
How is the original RNAtranscript processed ineukaryotes? (3)
1) Capping on 5' end (7-methyl G) 2)Polyadenylationon 3' end ( =200 As) 3)Splicing out of introns
In eukaryotes, what mustoccur before an newlysynthesized RNA transcriptleaves the nucleus?
Only processed RNA istransported out the nucleusof eukaryotes.
Name 3 types of RNA
1) mRNA 2) rRNA 3) tRNA
Name the charged histonesaround which (-) chargedDNA loops (nucleosomecore).
H2A, H2B, H3, H4 histones
Name the enzyme responsiblefor the synthesis of RNA inprokaryotes.
Name the enzymes involvedin ss-DNA repair. (5)
1) specific glycosylase. 2)endonuclease. 3)exonuclease. 4) Danpolymerase. 5) DNA ligase.
Name the enzymesresponsible for the synthesisof eukaryotic RNA.
RNA polymerase I RNApolymerase II RNApolymerase III
What are exons?
Exons contain the actualgenetic information codingfor a protein
What are four types ofmutations that can occur inDNA?
What changes occur in DNAstructure during mitosis?
In mitosis, DNA condenses toform mitotic chromosomes
What codon sequence isfound at the 3' end of all tRNAs?
All tRNAs, both eukaryoticand prokaryotic, have CCA at 3' end.
What direction is DNA synthesized in?
5' > 3'. Remember that the5' of the incoming nucleotide bears the triphosphate (energy source for the bond).The 3' hydroxyl of the nascent chain is the target.
What direction is protein synthesized in?
Protein synthesis alsoproceed in the 5' to 3' (5' >3')
What direction is RNA synthesized in?
5' > 3'. Remember that the5' of the incoming nucleotide bears the triphosphate(energy source for the bond).The 3' hydroxyl of the nascent chain is the target.
What does the AUG mRNA sequence code for?
AUG codes for methionin,which may be removed before translation is completed. In prokaryotes the initial AUGcodes for a formyl-methionin(f-met).
What does the P in P-sitestand for? What does the A inA-site stand for?
P-site: peptidyl; A-site:aminoacyl;
What does the statement, 'the genetic code is commaless' mean? What is the exception to this rule?
The code is non-overlapping.The exception are some viruses
What does the statement, 'the genetic code is degenerate'mean?
More than one codon may code for the same amino acid
What does the statement, 'the genetic code is unambiguous' mean?
Each codon specifies only one amino acid
What does the statement, 'the genetic code is universal' mean? What are the exceptions (4)?
The same code is used in all life forms. The exceptions are 1. mitochondria, 2.archaeobacteria, 3.Mycoplasma, 4. some yeasts
What enzyme is responsible for 'charging' tRNA? How does it work?
Aminoacyl-tRNA synthetase.This enzyme (one per aa, uses ATP) scrutinizes aa before and after it binds to tRNA. If incorrect, bond is hydrolyzed by synthetase. The aa-tRNA bond has energy forformation of peptide bond.
What inhibits RNA polymerase II?
alpha-amanitin inhibits RNA polymerase II
What is a conservative missense mutation?
Mutation results in a different aa encoded, but that new aa is similar in chemical structure to the original code
What is a frame shift mutation? What is usually the effect on the encoded protein?
A change in DNA resulting in misreading of all nucleotides downstream. Usually results in a truncated protein.
What is a missense mutation?
Mutation results in a different aa encoded.
What is a nonsense mutation?
A change in DNA resulting in an early stop codon.
What is a promoter?
Site where RNA polymerase and multiple other transcription factors bind toDNA upstream from gene locus.
What is a silent mutation?What usually causes a silent mutation?
Mutation results in the same aa encoded. Often the base change is in the 3rd position of the codon
What is a snRNP? What is its function?
snRNP = small nuclear ribonucleoprotein. snRNPs facilitate splicing by binding to primary mRNA transcriptsand forming spliceosomes.
What is an enhancer?
Stretch of Dan that alters gene expression by binding transcription facts. May belocated close to, far from, or even within (an intron) the gene whose expression it regulates.
What is an Okazaki fragment?
The discontinuous DNA synthesized on the lagging strand during DNA replication
What is hnRNA?
hnRNA = heterogeneous nuclear RNA The initial RNA transcript is called hnRNA
What is responsible for the accuracy of amino acid selection during peptide synthesis?
Aminoacyl-tRNA synthetase and binding of charged tRNA to the codon are responsible for accuracy of amino acid selection.
What is the broad classification of nucleotides?
Purines (A, G) and Pyrimidines(C, T, U)
What is the difference between hnRNA and mRNA?
hnRNA = the initial RNA transcript mRNA = capped and tailed transcript
What is the differencebetween thymine and uracil?
Uracil found in RNA Thymine found in DNA
What is the function of DNA ligase during DNA Replication?
DNA ligase seals synthesized DNA into a continuous strand
What is the function of DNA polymerase during DNA Replication? (2)
5'®3' exonuclease activity of DNA polymerase I degrades RNA primer; 3'®5' exonuclease activity of DNA polymerase 'proofreads' each added nucleotide.
What is the function of DNA topoisomerase during DNA Replication?
DNA topoisomerases create a nick in the helix to relieve supercoils
What is the function of primase in DNA Replication?
Primase makes an RNA primer on which DNA polymerase can initiate replication.
What is the function of RNA polymerase I?
RNA polymerase I makes rRNA
What is the function of RNA polymerase II?
RNA polymerase II makes mRNA
What is the function of RNApolymerase III?
RNA polymerase III makes tRNA
What is the mRNA initiation codon?
AUG, or rarely GUG
What is the mRNA stop codons? (3)
UGA (U Go Away) UAA (U Are Away) UAG (U Are Gone)
What is the result of'mischarged' tRNA?
A mischarged tRNA (bound to wrong aa) reads usual codon but inserts wrong amino acid.
What is the role of endonuclease in ss-DNA repair?
Endonuclease makes a break several bases to the 5' side.
What is the role of excision repair-specific glycosylase in ss-DNA repair
Recognizes and removes damaged base.
What is the role of exonuclease in ss-DNA repair?
Exonuclease removes short stretch of nucleotides.
What prevents an incorrect aa-tRNA pairing?
If incorrect, the aa-tRNA bond is hydrolyzed by aminoacyl-tRNA synthetase.
What role does histone H1 play in chromatin structure?
H1 ties the nucleosome together in a string (30nmfiber)
What supplies the energy for formation of peptide bond?
The aa-tRNA bond has energy for formation of peptidebond.
What would most likely be the result of a mutation of the promoter sequence?
Promoter mutation commonly results in dramatic decrease in amount of gene transcribed.
When is ATP used in protein synthesis? When is GTP used in protein synthesis?
ATP is used in tRNA charging,whereas GTP is used in binding of tRNA ribosome and for translocations.
When is recombination involved in DNA repair?
If both strands are damaged,repair may proceed viarecombination withundamaged homologouschromosome.