Replication
Describe the model that DNA replication follows
Semiconservative model - each DNA strand contains one parental strand and one daughter strand (parental strand is used as a template)
List 3 differences between DNA & RNA
-DNA has deoxyribose sugar, RNA has oxyribose sugar (extra oxygen at 2' carbon)
-DNA has T, RNA has U (both pair with A)
-DNA usually double-stranded, RNA usually single-stranded (but there are exceptions, be careful!)
-RNA can form secondary structures which have important biological roles
Where does a peptide bond form and what type of reaction this is?
Between the carboxyl group of one amino acid and the amino group of the next amino acid?
Dehydration reaction (H2O released)
How is DNA packaged?
DNA wraps around histones, form nucleosomes (8 histones) which makes up chromatin
What is a synonymous vs a nonsynonymous mutation?
synonymous = different codon but same amino acid
nonsynonymous = different codon and different amino acid
What direction does DNA replication occur?
5' to 3'
What is transcription?
the process of transforming DNA to mRNA
What determines the specificity between tRNA and amino acid binding?
aminoacyl-tRNA synthetases (only 20!)
What are the main components that make up DNA?
Nucleotide bases (C/G, A/T), phosophate-sugar backbone (deoxyribose)
What allows for the greater diversity of proteins in eukaryotes compared to prokaryotes?
Different splicing of introns/exons so the same genes can code for multiple different proteins
What are Okazaki fragments and why do they form?
They are short strands that from on the lagging strand it is forming away from the helicase so it gets behind and has to start a new strand farther back, resulting in a bunch of fragments
Draw the mRNA strand that results from the following TEMPLATE DNA strand, include 5' and 3' labels
5' AGGCTAAGA 3'
3' UCCGAUUCU 5'
What are the sequences used for initiation called in prokaryotes and eukaryotes, what are the important bases in these sequences called, and what binds to these sequences?
Shrine-Dalgrano (prokaryotes), Kozak (eukaryotes), start codons, small ribosomal subunit (prokaryotes = 30S, eukaryotes = 40S)
Explain the difference between euchromatin and heterochromatin
Euchromatin - Loosely condensed, easily transcribed
Heterochromatin - Tightly condensed, not transcribed
Why can large ribosomal subunits not bind to mRNA right away, and what are they waiting for?
They can't bind because they are blocked by initiation factors, they wait for the first tRNA with Methionine to bind to the start codon.
Describe replication in prokaryotes
Theta: 9-mer and 13-mer A-T rich consensus sequences form OriC, bind DnaA, DnaB (helicase), DnaC, and SSB proteins, form open complex, replication occurs bidirectionally, single ori
rolling circle: no OriC, replication initiated by break in nucleotide strand, unidirectional, forms multiple circular DNA molecules
Explain transcription initiation in prokaryotes & eukaryotes
Prokaryotes: -35 and -10 consensus sequences in promoter, RNA pol holoenzyme and sigma subunit bind DNA unwinds at transcription start site, form open promoter complex, RNA pol begins transcription
Eukaryotes: -25 TATA box (other consensus sequences), enhancers/silencers bind activator/repressor transcription factors to promoter region, RNA pol binds and transcribes
What are the sites of the ribosome called and what happens in each?
E (exit site, empty tRNA leaves), A (aminoacyl site, tRNA carrying polypeptide chain passes it to the new tRNA in P site), P (peptidyl site, new tRNA with next amino acid enters)
What does Chargraff's rule state?
Purines pair with pyrimidines resulting in a 1:1 ratio, specifically, there will be equal amounts of cytosine and guanine and equal amounts of adenine and thymine nucleotide bases in DNA
Explain the third base wobble
The third base of anticodons is more relaxed and can pair with multiple different bases. Pyrimidines still usually pair with purines, and Inosine (I) can pair with A, C, and U
Name the main enzymes used for replication and describe their roles
Topoisomerase - relaxes super coiling
Helicase - unwinds/unzips strands
Primase - adds RNA primers
DNA Polymerase III - adds nucleotide bases
DNA Polymerase I - switches RNA bases to DNA
Ligase - joins strands together
Explain mRNA processing and why it is important
Addition of a 5' guanine cap, 3' poly-A tail (protect from degradation as it exits the nucleus), splicing of introns by the spliceosome (introns stay IN the nucleus)
Explain translation termination
Release factors bind to stop codon, RF-1 binds to A site, RF-3 forms complex with GTP, GTP hydrolysis to GDP provides energy to release polypeptide, everything else released from ribosome
Where does a phosphodiester bond form?
Between the 3' hydroxyl group and the 5' phosphate group
Explain the differences between the two types of prokaryotic termination and eukaryotic termination in transcription
Rho dependent - Rho protein (with helicase activity) binds to rho utilization site, moves toward 3' end, RNA pol stops when it reaches termination sequence, waits for Rho, Rho unwinds complex
Intrinsic/Rho-independent - Stem loop forms between a set of inverted sequences, causes RNA pol to pause, A=U bonds destabilize RNA pol & it loses contact
Eukaryotic - Poly-A signal sequence (downstream of stop codon) attracts enzyme to cleave @ cleavage site