geneticcccc Flashcards
What are the differences btw DNA and RNA?
DNA: Deoxyribose sugar, double helix structure, stable, no OH groups present
RNA: Ribose sugar, usually single strand, easily degraded, OH group present
What are the different types of RNA and their functions?
Ribosomal RNA = rRNA: carries out RNA interference part of the ribsome
Transfer RNA = tRNA: attaches to an amino acid
Messanger RNA = mRNA: carries coding info from DNA to ribosome
Small nuclear RNAs = snRNAs: processes pre-mRNA, maintain telomere, aid in regulation of TFs
Small nucleolar RNAs = snoRNAs: Processes rRNA, RNA modifications
MicroRNAs = miRNAs: bind to mRNA to mark destruction, gene expression regulation
Small interfering RNAs = siRNAs: helps process rRNA and making ribosome, inhibits gene expression
Which RNA polymerase synthesizes each type of RNA?
Polymerase 1: Syntheizes large rRNA
Polymerase 2: Syntheisizes Pre-mRNA, snoRNA, miRNA, and snRNA
Polymerase 3L Synthesizes tRNA, miRNA, snRNA, and small rRNA
What basic components are needed for transcription?
- A DNA Strand
- The raw materials (ribonucleotide triphosphates) to build the new RNA Strand
- The transcription apparatus
What are the steps of transcription? *Bacterial
- Initiation: assembly of the transcription apparatus and start of transcription
- Elongation: Polymerase unwinds DNA and adds nucleotides to RNA strand
- termination: recognition of end of transcription and RNA separates from DNA
INSIDE CYTOPLASM
What proteins and DNA elements are required for each step of transcription? *Bacterial
Initiation: RNA Polymerase, sigma factor
Elongation: RNA Polymerase
Termination: sequence rho independent/ dependent
What is meant by the template and non-template strands of DNA?
Template strand: The strand that is being used for synthesis
Non-Template Strand: The strand that is NOT being used for synthesis
What is the direction of RNA synthesis?
5’ to 3’
What is a consensus sequence?
the most common sequence of nucleotides found at a specific location of DNA or RNA
What consensus sequences are found in the promoter in bacteria and eukaryotes
In bacterial: it is at -35 and -10
In eukaryotic: Each RNA Polymerase has their own promoter type
- RNA Poly 2: TATA box btw -25 and -30
What are the differences of prokaryotic and eukaryotic transcription
Pro: Occurs in cytoplasm, one type of RNA Pol, uses sigma factor
Eu: Occurs in nucleus, 3 types of RNA Pol, uses general transcription factors
What are the similarities of prokaryotic and eukaryotic transcription
both processes use RNA polymerase to synthesize RNA from a DNA template, occur in three stages (initiation, elongation, and termination), and utilize a single strand of DNA as the template for RNA synthesis
How can auxotrophic mutants be used to identify the genes involved in a biochemical pathway?
EXAMPLE AND BIG PICTURE:
protein A turns substrate 1 into substrate 2, and then protein B turns it into substrate 3
If protein A is mutated and nonfunctional, the cell cannot make substrate 2. So substrate 2 will need to be supplied in the media for it to survive.
If protein B is mutated, the cell can make substrate 2 but not substrate 3. So substrate 3 will need to be added to the media.
What is the general structure of an amino acid?
R-CH(NH2)-COOH
Primary, secondary, tertiary, and quarterly
R = Specific to each amino acid
What is a transposable element?
Sequence that is cut and pasted and inserted into the DNA sequence in a different location, not from replication, kind of like duplication,
How many amino acids are there?
20: alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, proline, serine, threonine, tryptophan, tyrosine, and valine.
What kind of chemical bond joins two amino acids in a protein?
Peptide Bond
What are the roles of mRNA, tRNA, and rRNA in translation?
mRNA: codons and template strand
tRNA: anticodon and associated amino acid
rRNA: Part of the ribosome, catalyzes process and structure
What are the characteristics of the genetic code?
64 codons, lots of RNA nucleotide sequences that all code for a type of amino acid. 3 of them are stop codons: UAA, UGA, and UAG. AUG is the initiation codon. code is universal. 3 possible reading frames that are determined by the location of the start codon. degenerate: many different codon sequences can make the same amino acid.
What is a codon and how many nucleotides are in a codon?
3 nucleotides that code for one amino acid
How many codons can code for one amino acid?
1
How many amino acids can be encoded by one codon?
One!
What is a reading frame?
A way to divide a nucleic acid sequence into codons
What is the wobble hypothesis?
Only the 1st and 2nd have precise base pairing, the 3rd nucleotide of the codon and anticodon can wobble. The 3rd can pair with bases it usually doesn’t. This allows a single tRNA molecule to recognize and bind to more than one codon.
What are the start and stop codons?
Start: AUG
Stop: UAA, UGA, UAG
What are the steps of translation?
Initiation: tRNA attaches to AUG, small and large subunit binds to mRNA
Elongation: the creation of peptide bonds between amino acids is catalyzed by the large subunit.
Termination: stop codon enters A site
Where does translation take place?
Ribosome
What components are required for each step of translation?
Initiation: Start codon AUG is matched with its anticodon carrying Met.
Elongation: tRNA w/ amino acid enters P site, the tRNA with the next amino acid enters A site, amino acid from P site goes to A site, the empty tRNA goes to E site and leaves, the tRNA with the chain goes to P site, and repeat
Termination: Stop codon and release factor binding
What are the three sites a tRNA can occupy in the ribosome?
E: Exit site
A: Aminoacyl site
P: Peptide site
Where does the tRNA enter into the ribosome?
Aminoacyl site (A)
What causes tRNA to move to the next site?
Translocation: ribosome shifts along the mRNA, all tRNA shift to the next site
What causes tRNA to exit the ribosome?
Translocation: ribosome shifts along the mRNA, tRNA shifts to Exit site and get kicked out
How is Chromatin remodeling used to regulate gene expression at the chromatin level?
Chromatin remodeling complexes reposition the nucleosomes, allowing transcription factors and RNA polymerase to bind to promoters and initiate transcription.
How is Histone modifications used to regulate gene expression at the chromatin level?
Histone Methylation: DNA becomes more tightly wrapped around histone, methyl group added to histone protein tail, prevents DNA from being transcribed
Histone Acetylation: DNA becomes less tightly wrapped around histone, acetyl group added to histone protein, allows transcription to happen
How is DNA methylation used to regulate gene expression at the chromatin level?
methyl groups added to cytosine bases adjacent to guanine nucleotides, bases cannot be expressed because they are compressed, gene is silenced
How is gene expression regulated at the transcription level?
Transcription factors: Activator or repressor
Most transcriptional activator proteins affect transcription by interacting with the basal transcription apparatus.
General TFs bind to the core promoter as part of the basal transcription apparatus
What proteins and DNA elements are involved w/ gene expression?
Enhancer: DNA sequence stimulating transcription a distance away from promoter
Silencer: DNA sequence with an inhibitory effect on the transcription of distant genes
Insulators: DNA sequence that blocks or insulates the effect of enhancers when it lies between the enhancer and the promoter
RNA polymerase may pause or stall downstream of the promoter
General Transcription factors:
Give an example of gene regulation by alternative splicing.
With alternative splicing, there is the potential for multiple mRNAs to be produced from a single pre-mRNA by cutting out certain exons, this acts as a form of gene regulation
What is a mutation?
inherited change in the DNA sequence of genetic information
What are the possible causes of mutations?
errors in DNA replication during cell division, exposure to mutagens or a viral infection.
How do mutations arise spontaneously?
Tautomeric shifts: structural isomers of chemical compounds that readily interconvert each other by relocating a proton
Depurination: loss of purine
Deamination: loss of an amino group
Deletions and Insertions
Stand slipage or unequal crossover etc
What mutagens can lead to chemically induced mutations?
Oxidative reaction: like Hydrogen peroxide
Intercalating agents: proflavin, acridine orange, and ethidium bromide
Alkylating agents: donate alkyl group
- Example: Ethylmethylsulfonate (EMS) and Mustard gas
Deamination: nitrous acid
Hydroxylamine: add hydroxyl group
What kind of mutations are caused by ionizing radiation and UV light?
Ionizing radiation causes double-strand breaks
UV light causes pyrimidine dimers
What type of damage does each DNA Repair pathway generally repair?
Mismatch: Fixes Replication errors, including mispaired bases and strand slippage
Direct: Fixes Pyrimidine dimers; other specific types of alterations
Base excision: Fixes: Abnormal bases, modified bases, and pyrimidine dimers
Nucleotide excision: Fixes DNA damage that distorts the double helix, including abnormal bases, modified bases, and pyrimidine dimers
Homologous recombination: Fixes Double-strand breaks
Nonhomologous end joining: Fixes Double-strand breaks
What pathways can be used to repair DNA damage?
Mismatch: Enzymes cut out a section of the newly synthesized strand of DNA and replace it with new nucleotides. The old nucleotides are degraded.
Direct: Restores the correct structures of altered nucleotides
Base excision: excises modified bases and then replaces one or more nucleotides. 1 nick.
Nucleotide excision: removes bulky DNA lesions that distort the double helix. 2 nicks
Homologous recombination: uses a similar DNA sequence as a template to accurately repair broken DNA strands
Nonhomologous end joining: directly joins broken DNA ends without requiring a homologous template
How do transposable elements cause mutations?
when anything is added to the DNA sequence, that can give rise to DNA mutations since the sequence has been altered
What are the steps of silencing a gene by RNA interference?
The miRNA (people) or siRNA (plants) are cut up by a dcer, then bind to 3’ UTR and either destroy or prevent mRNA from binding to ribosome.
What types of RNA molecules can be used for silencing a gene by RNA interference?
miRNA and siRNA
What part of the mRNA is targeted for silencing a gene by RNA interference?
3’ UTR
What is a somatic mutation and what are the results from it?
Mutation that occurs in non reproductive cells, not hereditary and cannot be passed to offspring. Only passed to other cells via mitosis
What is a germline mutation and what are the results from it?
Mutations that are in sex cells. Able to be passed on to half of the next offspring.
What is a transversion and what are the effects from it?
type of base substitution. Purine to pyridine and vice versa. Alters a single codon
What is a transition and what are the effects from it?
type of base substitution purine to another purine or pyrimidine to another pyridine. Alters a single codon
What is a frameshift mutation and what are the effects from it?
the insertion or deletion of nucleotide bases in numbers that are not multiples of three, changes the reading frame and change many codons
What is a Nucleotide repeat expansion and what are the effects from it?
Increase in the number of copies of a set of nucleotides
Alters number of nucleotides in the gene, can cause diseases like huntingtons
What is a forward mutation and what are the effects from it?
Wild type to Mutant type
What is a reverse mutation and what are the effects from it?
Mutant type to wild type
What is a neutral mutation and what are the effects from it?
No change in function but there is still a change to the code
What is a silent mutation and what are the effects from it?
type of neutral mutation, changes the codon sequence, but it ends up making the same amino acid, no phenotypic change.
What is a missense mutation and what are the effects from it?
Amino acid to a different amino acid
What is a nonsense mutation and what are the effects from it?
Sense codon (makes amino acid) to nonsense codon (makes stop codon)
What is a intragenic suppressor mutation and what are the effects from it?
occurs when an original mutation is either fully or partially compensated for by a second mutation at a different location in the same gene
What is a intergenic suppressor mutation and what are the effects from it?
occurs when the original mutation and the suppressor mutation are located in different genes.
What is a Loss-of-function mutation and what are the effects from it?
a genetic alteration that significantly reduces or completely abolishes the normal function of a gene, resulting in a protein product with diminished or no activity
What is a gain-of-function mutation and what are the effects from it?
a genetic change that alters a gene in a way that causes the resulting protein to have a new or enhanced function, often leading to abnormal activity or an increased level of normal activity
What is the transcription apparatus made of? bacteria
2 alpha, one beta, one beta prime, and one omega. The sigma factor comes in and controls the binding of the promoter.
What proteins and DNA elements are required for each step of transcription? *Eukaryotic
initiation: general transcription factors, core promoter, enhancers, regulatory promoter
elongation: RNA Pol
termination: Sequence
What are the steps of transcription? *Eukaryotic
- Initiation: Binding of the TFIID transcription factor to the TATA box
- Elongation: Polymerase unwinds DNA and adds nucleotides to RNA strand
- termination: RNA polymerase II is terminated when an exonuclease enzyme
INSIDE NUCLEUS
