Transcription
What are the four steps of transcription, and what is the goal of transcription?
1. Initiation - Transcription factors bind and recruit RNA polymerase
2. Elongation - reads 3'-5' and builds 5'-3'
3. Termination - RNA polymerase hits the termination sequence and falls off
4. Processing - splicing and adding poly a tails and 5' g caps
- to make an mRNA transcript to be translated later
What is the start codon? What are the stop codons?
Start: AUG - Methionine
Stop: UGA, UAG, UAA
What is the differnce between an intron and an exon?
What process do we see these terms in?
introns - stay in the nucleus
exons - exit the nucleus to be translated
This is alternative splicing
What is an operon and are they found in eukaryotes, prokaryotes or both?
Operons are a group of genes that are transcribed together and regulated by a shared promoter and operator
- found only in prokaryotes
What is a gene knockout? What does it accomplish?
making a gene nonfunctional and seeing what happens - this helps us understand the function of the gene
True or false: transcription occurs in the S phase
false - DNA replication occurs in the S phase. Try to differentiate these processes --> The purpose of transcription is NOT to replicate DNA. Remember, the end goal is to make a protein.
What are the three tRNA binding sites in the large ribosomal subunit?
A - site where anitcodon binds to complementary codon in mRNA
P - site where tRNA adds its amino acid to polypeptide chain (peptide bond formed)
E - exit site of tRNA
Describe CRISPR-Cas and why it is used.
CRISPR-Cas9 uses Cas9 (protein that makes the cut) guided by an sgRNA (derived from crRNA and tracrRNA) to cut DNA. The cell then repairs the cut using NHEJ (error-prone) or HDR (precise), allowing for gene editing.
- it is a way to alter a DNA sequence
Compare and contrast the lac operon and the trp operon.
Lac operon - has an inducible repressor; lactose bind to the repressor and repressor inactivates - proteins can be produced - lactose is an inducer
Trp operon - has repressible repressor; tryptophan binds to repressor and activates it - proteins not being produced
What are the steps in polymerase chain reaction (PCR)? What is the purpose?
1. Denaturing - separate strands of DNA
2. Annealing - attach primers to DNA
3. Extension - synthesize complementary DNA strands from dNTPs, starting at primer
Purpose: making many copies of DNA
Does transcription require an RNA primer to begin synthesis? Why or why not?
What are the different forms of RNA involved in translation?
mRNA - messenger RNA: what the ribosome reads or translates into a protein
rRNA - ribosomal RNA: ribosome made of two subunits that reads mRNA
tRNA - transfer RNA: carries an amino acid to A site of rRNA to add to growing peptide chain
Name the 6 different types of mutation. (there are some subcategories)
silent
missense conservative
missense non-conservative
nonsense
insertion (frameshift)
deletion (frameshift)
What is the term for passing on expression patterns (not necessarily the genes but specifically how they are expressed)
epigenetics
What is gene therapy, and how does it work?
Introducing a therapeutic allele into a person - can do so with vectors (genetically engineered viruses)
What is a nucleosome? What is a histone? What is chromatin
A nucleosome is 8 histones + DNA - a form of DNA organization
A histone is a protein that DNA wraps around for organization
Chromatin - DNA + proteins (histones)
non-overlapping - read three, the read three new ones
redundant - multiple codons code for one amino acid
unambiguous - a specific codon codes for only one amino acid
punctuated - start and stop codons
universal - found across many species
What is DNA fingerprinting, and what element did we discuss that helps with DNA fingerprinting?
It is a way to identify individuals based on their unique genomes
We talked about short tandem repeats (STRs) - vary in repeat numbers among individuals.
Which of the following are DNA sequences and which are proteins?
enhancer, insulator, activator, promoter-proximal, repressor, transcription factors, silencer, promoter
DNA: enhancer, insulator, promoter-proximal, silencer, promoter
Proteins: activator, repressor, transcription factors
What is the difference between a ddNTP and a dNTP? What process are these used in? Can you briefly describe the process and its purpose?
When ddNTPs attach to the sequence, the sequence ends because there is no free hydroxyl group to continue building off of. dNTPs are basically normal bases (A, G, C, T)
Used in Sanger Sequencing - making lots of fragments of DNA and using gel electrophoresis to sort the lengths of the fragments and using a laser to read the bases the sequencing stopped on.
this is done to learn the sequence of DNA
What is the difference between euchromatin and heterochromatin? What are the processes that promote each chromatin? Is this occurring in eukaryotes or prokaryotes?
Euchromatin: open form, ready for transcription, promoted by acetylation of histone tails
Heterochromatin: closed, harder for transcription factors to bind, methylation promoted
- This is regulation in eukaryotes
In what direction does the ribosome read mRNA?
5' to 3' ---> in most other cases, things are read 3' to 5' and built 5' to 3', but this is a special circumstance.
- Anticodons are still antiparallel to codons
DNA is replicated, but the copy is mutated. What is it called if that gene product is non-functional?
Pseudogene
Compare and contrast distal regulatory region and the promoter region. (What elements are in each?)
Distal regulatory region - region far away from (usually upstream) the protein coding DNA - silencer, enhancer, insulator
Promoter - close to protein-coding DNA - core promoter (where GTFs bind), promoter proximal elements (binding site for activator and repressor)
What are the different fates of gene duplication?
- both copies share original function
- one copy decays through mutations
- copies differentiate in expression
- one copy acquires new function