BIOL 3010 Exam 2

Mismatch Repair

DNA repair mechanism that corrects mistakes in replication, discriminating between newly synthesized and parental DNA by the methyl groups on the parental strand

Correct polymerase errors

De Novo Mutation

any mutation or alteration in the genome of an individual organism that was not inherited from its parents

Point Mutation

Only effect one gene; small insertions and deletions

Interstrand Crosslink

the link between strands of DNAs with the covalent bond and prevent separation of DNA strands

Huntington’s Disease

Late on-set neurodegenerative disease

From trinucleotide repeats

Lariat

lasso‐shaped structure formed from the fragment of RNA to be excised during the process of splicing out the introns in the primary transcript of eukaryotic genes

Degeneracy

Several different codons can specify the same amino acid

Nonsense mutation

Cause premature termination of translation

Frameshift Mutation

insertions or deletions of base pairs that alter the grouping of nucleotides into codons

Co-linearity

Amino Acids correspond to proteins (e.g. if there in a mutation in the amino acid, there will be a mutation in the protein)

miRNA

RNA molecule 23 bases long that targets specific mRNAs for destruction or blocks their translation

Fanconi Anemia

From defective inter strand crosslink repair

Complementation

the process in which heterozygosity for loss-of-function mutant recessive alleles for two different genes produces a normal phenotype

Complementation Test

Method of discovering whether two mutations are in the same or separate genes.

Complementation Groups

a collection of mutations that do not complement each other. Often used synonymously with gene

Gene Body

entire gene from the transcription start site to the end of the transcript

includes introns and exons

Cis-regulatory Element (Enhancers)

DNA sequence that regulates transcription

Ribosomopathies

Phenotypes for ribosomal mutations

ex: Treacle Collins Syndrome, Diamond-Blackfan Anemia

Screen Saturation

when new alleles are at loci for which mutants have already found

Marker Loci

DNA sequence-based landmarks for identifying chromosome segments and constructing linkage maps

Missense Mutation

genetic alteration that causes the substitutions of one amino acid for another

Basal Factors

Protein (a transcription factor) that can bind directly to the DNA of all promoters in a genome

Required for the initiation of transcription by RNA polymerase

Beadle and Tatum

“one gene, one enzyme”

Genetic Mapping

use recombination, that occurs during meiosis, to narrow down where the affected gene must be

Forward Genetic Strategy

identify mutant phenotypes
of interest
↓
determine which gene has
been mutated
↓
infer something about how
that gene functions

Reverse Genetic Strategy

decide on gene of interest
↓
inactivate that specific gene
(homologous recombination,
knockdown, or CRISPR)
↓
infer something about how that
gene functions

Most common cause for DNA damage in human cells?

Replication Errors

Exonuclease

Recognizes and excises mismatches to proofread newly synthesized DNA strands

Why is it important to quickly fix errors in DNA?

Because there isn’t very much time until the DNA strand will be replicated

What does DNA damage trigger?

DDR (DNA Damage Respones)

ATM Kinase to trigger p53 phosphorylation

Deamination

Removal of amine group changes C to U

Depurination

Hydrolysis of purine base

Why are double stranded breaks harder to fix than single stranded?

There is no template strand

What causes double stranded breaks?

X-rays

What causes thymine dimers?

UV rays

DNA Glycosylases

recognize a specific type of altered base in DNA and catalyze its hydrolytic removal in base excision repair

AP Endonuclease

cuts the phosphodiester backbone in base excision repair

Nucleotide Excision Repair

repair the damage caused by almost any large change in the structure of the DNA double helix

Double Strand Break Repair

done by non homologous end joining which seals the ends together causing mutations OR homologous recombination using sister chromatids

Protein Coding Genes

Genes that code for mRNA

Non-protein Coding Genes

Any genes that make RNAs other than mRNA (ex: tRNA, rRNA, miRNA)

Open Chromatin (Euchromatin, light stain)

more accessible to RNA polymerase and transcription factors; more likely to be transcriptionally active

Closed Chromatin (Heterochromatin, dark stain)

tightly packed with nucleosomes, less accessible, less likely to be transcriptionally active

Trans-regulatory Factors (Transcription Factors)

Determine whether a gene is turned on or off

Can be repressors or activators

Nucleosome

DNA wrapped in histones

Post-translational modifications of histone tails

acetylation, methylation, phosphorylation, ubiquination

Acetylation

On Lysine to unwrap DNA

Histone Acetyl Transferase (HAT)

Changes affinity of nucleosomes

Methylation

Provides a binding site for the recruitment of additional proteins

CHD1 (Chromatin Remodeling Protein)

Binds after methylation

reposition or kick out nucleosomes to give access to proteins

exchange and eject histone dimers

Pioneer Transcription Factors

Bind target DNA sequence

Permit binding of other DNA transcription factors

Pleurypotency

the capacity of individual cells to initiate all lineages of the mature organism in a flexible manner directed by signals in the embryo or cell culture environment

What is needed for a gene to be transcribed into DNA?

Accessibility to TFs

Interactions of TFs with cis-regulatory elements

initiation, elongation, termination of RNA transcript

processing of newly transcribed RNA

transport of processes RNA to cytoplasm

RNA Polymerase I

rRNA

RNA Polymerase II

mRNA

RNA Polymerase III

tRNA

Splice Donor

GU

Splice Acceptor

AG

Alternative Splicing

Choosing to include or exclude certain introns to code for different proteins

What influences alternative splicing?

Splice site strength

Cis-regulatory sequences that favor or impair exon recognition

Expression of levels of trans-acting factors

Yanofsky Experiment

each nucleotide was associated with the identity of only one amino acid (co-linearity)

Crick and Brenner

Frameshift mutations indicate a triplet code

Wobble Position

5’ nucleotide in anticodon of tRNA

Ex: UCU to UCC is still serinine

Charged tRNA

tRNA with attached amino acid

Kozak Sequence

Directs PIC and ribosome to start codon and mediates ribosome assembly

Peptidyl Transferase

Adds new amino acids to growing polypeptide chain

How can upstream open reading frames work to regulate transcription?

By slowing it down

The ribosome has to stop at each start codon and figure out if it is the true start or not

Leads to reduction of proteins

Ethyl Methane Sulfonate (EMS)

Used to increase mutation rate per locus

Mechanistic consequences of mutation

Coding: deletions, insertions, frameshift, missense

Mis-splicing of RNA

Altered transcriptional efficiency

Temperature Sensitive Mutation

marked drop in the level or activity of the gene product when the gene is expressed above a certain temperature

Branch Site