Quiz 2 Molecular Genetics

genome

complete haploid genetic complement of a cell

contig

a series of overlapping DNA segments that form a continuous sequence together

Sequence tagged sites (STS)

regions on the contigs that had been previously characterized

Expressed sequence tags (EST)

regions present on a contig whose expression can be measured

Shot gun sequencing

randomly sequence pieces from throughout the genome and then computers order the fragments

Genome annotation

identifies and locates genes

phenotypic function

effects of a gene product on the whole organism

cellular function

metabolic process the gene product is engaged in

molecular function

how a gene product works in the cell

homologs

two genes with sequence similarity even if functions are unreleated

Orthologs

two genes in different species have a clear functional and sequence relationship

Paralogs

genes that are in the same species and related to each other

Synteny

conserved gene order

Introns

interruptions in genes

Simple sequence repeats

less than ten bases long but repeated many times (often have functional importance)

Single nucleotide polymorphisms (SNPs)

single base variation between individuals

Haplotypes

features close together that will be inherited as a group

Systems biology

study of complex interconnected processes

transcriptome

genes expressed in a cell under given conditions (aka all of the RNA in the cell)

Proteome

all of the proteins in a cell under given conditions

2D gel electrophoresis

separates proteins based on their isoelectric point and then molecular weight

Mass spectrometry

used to partially sequence proteins of interest from 2D gel electrophoresis

Chromatin

DNA and its associated proteins

Centromeres

points of attachment for proteins that link to the mitotic spindle

Telomeres

small sequences repeated over and over at the end of chromosomes

DNA supercoiling

further coiling of the DNA double helix on itself

Plasmid

covalently closed circular DNA

DNA underwinding

DNA has fewer turns than the typical beta helix

Negative supercoiling

supercoiling induced by underwinding DNA

Positive supercoiling

supercoiling induced by overwinding DNA

Plectonemic supercoiling

right handed branches and makes a >-< shape

Solenoidal supercoiling

tight left-handed turns that produce a grater degree of compaction

Topoisomerases

enzymes that regulate the amount of over/underwinding of DNA

Structural Maintenance of chromosomes (SMC) proteins

create physical contact between parts of chromosomes that aren’t close to each other

Cohesion

two SMC proteins link sister chromatids together after replication

Condesin

two SMC proteins help chromosomes condense in phrophase

Histones

highly conserved basic proteins

Nucleosomes

basic unit of chromosome structure that controls access to DNA

Core histones

H2A, H2B, H3, and H4

N-terminal tails

forms intermolecular contacts and help with regulation of chromatin structure

Chromatosome

amount of DNA required to bind H1 along with the other histones (168bp)

Epigenetic inheritance

genetic properties not encoded for by DNA sequences

Activator chromatin remodeling complex

move nucleosome away from the promoter sequence

Repressor chromatin remodeling complex

position nucleosome over the promoter sequence

ChIP-Seq and ChIP-Chip

allow for the mapping of positions of nucleosomes throughout the genome

Histone chaperones

assist in the assembly of histone octamers on DNA by binding H3-H4 tetramer or a H2A-H2B dimer

Histone acetyltransferases (HATs)

make regions more accessible and promote transcription

Histone deacetylases

remove acetyl groups and depress transcription by reducing access to DNA

Bromodomains

recognize acetylated histones

Chromodomains

bind methylated lysines (maybe associated with repression)

Histone Code

events directed by histone modification to cause transcriptional activation and successfully transcribe a protein

DNA replication

duplication of the cellular genome

Daughter strand

newly made strand in DNA replication

Template strand

the original strand (aka parental strand)

Replication fork

the site where replication is taking place

Semi-discontinuous replication

how DNA is synthesized with a leading and lagging strand

Leading strand

continuously made and chases the replication fork

Lagging strand

discontinuously made and synthesizes away from the fork

Primer terminus

end of the primer

primed template

primer and the template strand

Proofreading

3’ to 5’ endonuclease activity that will test the new DNA to make sure the correct base was added

Proofreading exonucleasr

remove bases from the 3’ end of DNA

Nick translation

degrades DNA or RNA as a new strand is made

Core enzyme

number of subunits capable of the base function of the enzyme

Holo enzyme

when a core enzyme associates with additional components to enhance function

DNA helicase

opens up double stranded DNA using energy from ATP

Topoisomerases

relaxes positive supercoiling from helicase

Single stranded binding protein

binds cooperatively to single stranded DNA and keeps it single stranded

Primers

RNA that provides the first 3’Oh group for DNA polymerase

Primases

specialized enzymes that make primers

RNase H

recognizes and removes most of the primer (all but the last base)

ChIP-Seq and ChIP-Chip

cells treated with formaldehyde (covalently cross link nucleosome and DNA), cells disrupted and linker DNA digested with micrococccal nucelase, nucleosomes immunoprecipitated, protein crosslinks broken, and released DNA sequences or labeled and used to probe microarray

How does human IFN-B globin work

GCN5 activator binds specific DNA sequence upstream of gene, contains HAT that acetylated H4 and protein kinase that phosphorylates H3, attracts chromatin remodeler using bromodomain, moves nucleosomes and exposes TATA box, attracts transctiption factors, gene transcribed

Meselson and Stahl’s experiment

Grew E coli on N15, then switched to N14, collected samples after each generation, first gen = mixed, sexond gen = light and mixed DNA, proved semiconservative replication

Okazaki’s experiment

E. coli infected with phage, cells repeatedly exposed to radioactively labeled nucleotides, analyzed on alkaline CsCl gradient, isolated short intermediate fragments, disappeared as time went on

Process to remove a primer

RNase H removes all but last base of primer, DNA poly I fills gap by nick translation, DNA ligase seals the nick