Ch16.1
Ch16.2
Ch17
Ch18
100
What are the two main characteristics of DNA structure? Is DNA charged?
Double helix and antiparallel.
Yes, Negative
100
Proteins used in the initiation of replications and their functions?
Topoisomerase: Relieves overwinding strain ahead of replication forks.
Helicase: Unwinds parental double helix at replication forks by breaking H bonds.
Single-Stranded Binding proteins: Binds to and stabilizes single-stranded DNA until it is used as a template
Primase: Synthesizes an RNA primer at 5′ ends of the leading strand and at 5′ ends of each Okazaki fragment of a lagging strand
100
What are the steps of gene expression for Eukaryotic cells? Where does each step take place?
NUCLEUS Transcription: DNA --> pre-mRNA
NUCLEUS RNA processing pre-mRNA: --> mRNA
CYTOPLASM Translation: mRNA --> Protein
100
What is an operon?
A unit of genetic function found in bacteria and phages. Consisting of a promoter, operator, and regulatory section of a gene.
200
What is a nucleotide made of? What is the backbone called?
Phosphate group, deoxyribose (sugar), nitrogenous base.
Sugar-phosphate backbone.
200
What is the leading strand template direction and lagging strand direction
Leading Template: 5' --> 3'
Leading strand: 3' --> 5'
Lagging Template: 3' --> 5'
Lagging strand: 5' --> 3'
200
Things needed for transcription? In what direction is the RNA strand created?
1. Promoter sequence (TATA Box) + Transcription factors + RNA Poly II = Transcription Initiation Complex
DNA 3' --> 5'
mRNA 5' --> 3'
200
What are the repressor and the corepressor?
repressor: inhibits gene transcription. Bind near the promoter.
Corepressor: binds to the repressor and changes its shape allowing it to bind to the operator.
300
What nitrogenous bases are purines? Which are pyrimidines? What types of bond binds them? Who pairs with who? How many bonds are in each?
Purines: G, A. Pyrimidines: T, C, U (RNA).
Hydrogen bonds.
A=T (2 H bonds), C=G (3 H bonds)
300
Remaining enzymes for actual replication and their functions?
DNA Polymerase III: synthesizes new DNA strands by adding nucleotides to the RNA primer.
DNA Polymerase I: Removes RNA nucleotides of primer from 5′ ends and replaces them with DNA nucleotides added to 3′ ends of the adjacent fragment
DNA Ligase: Joins Okazaki fragments of lagging strand; on the leading strand, joins 3′ end of DNA that replaces primer to rest of leading strand DNA
300
Is the termination for transcription the same for Eukaryotes and Prokaryotes?
NO
For prokaryotes: terminator sequence stops RNA poly II
Eukaryotes: Polyadenylation signal. Protein-bound to this poly-A-Tail cuts the mRNA from the polymerase.
300
What is Euchromatin and Heterochromatin?
Euchromatin: a less condensed form of chromatin; available to transcribe.
Heterochromatin: chromatin is very condensed; NOT available to transcribe.
Chromatin: complexes (nucleosomes) of DNA wrapped around histone proteins (positively charged proteins)
400
What are the three models of DNA replication? Which one do we think is correct nowadays?
Conservative, semiconservative, dispersive
400
You have a drug that blocks the activity of Primase. How will this drug affect DNA replication?
Synthesis of both complete lagging and leading strands will stop.
400
Three things to remember about RNA processing (What is added to both ends and what is actually changed)
Addition of a 5' cap (modified guanine)
Poly-A-tail: 50-250 A sequence to 3' end
RNA splicing: RNA cut and paste
400
How can chemical modifications regulate gene expression?
1. Histone acetylation: addition of acetyl group to histone tails (neutralize the positive charge of histones); promotes transcription by opening chromatin up.
2. DNA Methylation: addition of methyl group on DNA bases (mostly C); promote or inhibit translation
500
Difference between DNA and RNA
1. RNA has a ribose, while DNA has deoxyribose sugar
2. RNA single-stranded, DNA double-stranded
3. RNA has Uracil, rather than Thymine in DNA
500
Two types of mistakes repair of DNA replication
Mismatch repair: other enzymes remove and replace incorrectly paired nucleotides.
Nucleotide excision repair: a nuclease (DNA-cutting enzyme) removes and correctly replaces damaged segments of DNA.
500
What are the binding sites of the ribosomes in translation?
EPA sites
500
Inducible vs Repressivble
Inducible operons: off can be turned on. (i.e. lac operons (metabolism starts when allolactose is detected); catabolic (break down)
Repressive: on but can be turned off when the corepressor binds to the repressor; anabolic (building up)