Midterm Terms

law of inheritance

law of inheritance

each individual has 2 copies of each gene, one from each parent

law of segregation

maternal and paternal chromosomes segregate during meiosis

law of independent assortment

alleles do not influence each other when sorting into gametes

9:3:3:1

AaBb x AaBb ratio

bivalent

tetrad

pair of homologous chromosomes, one from each parent

same genes, different alleles

sister chromatids

found on X shaped chromosomes, will be seperated

identical genetic information

cohesion

protein complex that holds sister chromatids together before separation

kinetochore

connects centromeres of chromosome to microtubule of the mitotic spindle

3-5 phosphodiester linkage

joins nucleotides together

alternates between sugar and phosphate

5-3

directionality of DNA

right handed spiral

usual direction DNA coils

Chargaff’s rule

[A]=[T] & [G]=[C]

purines

two rings in nitrogenous base

A&G

pyrimidine

one ring on nitrogenous base

C&T&U

supercoiling

DNA twists on itself

chromatin

DNA with histones and associated proteins

histones

highly positive due to Lys & Arg

interacts with negative charge on DNA

nucleosomes

8 histone central core with DNA wrapped around it

uses H2A, H2B, H3 & H4 pairs

histone handshake

histone dimer interaction of H2A&H2B and H3&H4

H1

linker histone

regulates how tightly nucleosomes are backed together

binds to linker DNA

linker DNA

connections nucleosomes together

looped domains

30nm chromatin fibers gather and attach to protein scaffolds

30nm fibers

H1 histones + core nucleosome

increased DNA packing ratio 6-fold (total 40-fold)

euchromatin

functional DNA that is accessible for protein binding and transcription

heterochromatin

highly compact, non-functional DNA

at least 10% of genome

constitutive heterochromatin

permanently silenced DNA

found at telomeres and centromeres

contains repeats and few genes

facultative heterochromatin

inactivated DNA during an organism’s life

ex - X-inactivation

Barr body

inactivated X-chromosomes found in mammals

epigenetics

covalent modifications to DNA and histones

influence if section will be euchromatin or heterochromatin

acetylation

opens DNA structure and leads to more transcription

done on histone tails

methylation

closes DNA structure and leads to less transcription

done on histone tails

histone acetyltransferase

HAT

transfer acetyl group from acetyl-CoA to lysine on histone tail

histone deacetylase

HDAC

removes acetyl group from histone tail

histone methyltransferase

HMT

adds methyl groups (1-3) to lysine or arginine on histone tails

histone demethylase

removes methyl groups from histone tails

cytosine methylation

stabilizes nucleosome and prevents proteins from binding to DNA

often prevents initiation of transcription

DNA methyltransferase

adds methyl group to DNA where C is followed by G

read 5’-3’ CpG

symmetry of CpG

DNA methylation is replicated on both strands so it is passed on to daughter cells

genomic imprinting

methylation passed from parent to offspring

reader complex

“reads” histone code and position and activates enzymes (“writers”) that act on adjacent histones/DNA

chromatin remodeling enzymes

alter position of nucleosomes on DNA, removing histones and switching histone variants

work with histone readers/writers

barrier DNA sequences

recruit protein complexes that block the spread of reader-writer complexes and separate chromatin into domains

insulators

tandem repeat

repeats over and over without interruption

satellite DNA

5-500bp tandem repeats up to 100kbp

found in centromeres and telomeres

minisatellite DNA

10-100bp with up to 3000 repeats

highly variable/polymorphic, different between individuals and generations

basis for DNA fingerprinting

microsatellite DNA

1-5bp in clusters up to 10-40bp throughout genome

highly variable/many mutations

used to compared populations

SINE

short interspersed elements

short non-coding sequences scattered throughout the genome

retrotransposon

LINE

long interspersed elements

long non-coding sequences scattered throughout the genome

retrotransposon

non repetitive DNA

present as a single copy per haploid set

codes for almost all proteins

misalignment

error that expands or destroys repetitive sequences

microsatellite instability

misalignment related to progression of some diseases in humans

synteny

conserved blocks of genes in different species that are now in different positions

intrachromosomal rearrangement

synteny within the same chromosome

predisposed to deletions, inversions or duplications

usually in euchromatic regions

intrerchromosomal rearrangement

synteny in different chromosomes

common in pericentromeric and subtelomeric regions

transposition

movement of DNA/transposable elements around the genome

transposable element

mobile genetic section that moves in transposition

DNA transposons

move by cut & paste

catalyzed by transposase

inverted repeat at end are recognized by transposase

retrotransposon

copy & paste mechanism that involved an RNA intermediate catalyzed by reverse transcriptase to produce DNA from RNA

examples - LINEs & SINEs

ortholog

duplication that creates speciation

paralog

duplication and divergence

pseudogenes

paralog gene that has so many mutations it is non-functional

single nucleotide polymorphism

SNP

reason for alleles

caused by point mutation

copy number polymorphism

CNP

variation in amount of coding regions for a particular gene

structural variation

large segments of DNA changed by duplication, inversion, deletion, etc.

halotypes

combination of alleles on a chromosome that are typically inherited together

DNA polymerase

added nucleotides to DNA in 5’-3’ direction to 3’OH

has separate sites for adding and editing

distortions in the double helix

how mismatch base-pairing is recognized

2 UV light

single strand DNA (ssDNA) absorbs # as much _____ ______ as double stranded DNA (dsDNA)

G/C

base pair that denatures slowest?

c0t value

DNA concentration and incubation time of renaturation

A/T

origin of replication (ori) is rich with which base pair?

helicase

pulls apart double stranded DNA for replication

ahead of replication fork

single stranded binding protein

prevents single stranded DNA from folding in on itself during replication

DNA primase

Adds RNA chain so DNA polymerase can start replication

RNA polymerase

sliding clamp

keeps DNA polymerase on DNA template

3-5 exonuclease

proofreading mechanism after DNA polymerase

removes mismatch nucleotides

5-3 exonuclease

removes RNA primer from template strand

topoisomerase I

breaks the backbone of one DNA strand to relieve supercoiling

topoisomerase II

causes double stranded break to relieve supercoiling

detangles DNA

DNA ligase

covalently connects broken DNA backbone

usually to connect Okazaki fragments

trombone model

leading and lagging strand’s proteins touch and both strands are synthetized together due to loop of lagging strand

replicon

small unit of eukaryotic DNA being replicated

has its own origin of replication (ori)

origin of replication complex (ORC)

initiates replicon

telomers

tandem repeats at the end of chromosomes

GGGTTA x1000 in humans

telomerase

extends template strand with RNA so DNA polymerase can fill the end of lagging strand

prevents telomeres shrinking

reverse transcriptase

ionizing reaction

breaks DNA backbone

pyrimidine dimer

caused by UV radiation, damage DNA

depurination

removal of base from DNA due to thermal energy

deamination

removal of amino group on nitrogenous base, changing the base

usually conversion of cytosine to uracil in DNA

sometimes 5-methylcytosine to thymine

8 oxo guanine

most common DNA oxidation damage

excision nuclease

cut damaged strands on either side

nucleotide excision repair (NER)

damaged DNA is cut on either side using excision nucleases

DNA helicase separates the cut strand

DNA polymerase fills, DNA ligase seals

base excision repair (BER)

DNA glycosylase recognizes altered base and cleaves glycosidic bond

AP endonuclease nicks damaged strand

Phosphodiesterase removed deoxyribose phosphate that remains

DNA polymerase fills, DNA ligase seals

DNA glycosylase

cleaved glycosidic bond attaching base to sugar in base excision repair

non homologous end joining (NHEJ)

Ku detects double strand break (DSB) and binds to both ends

ends are processed and through together

DNA ligase seals

Ku

ring shaped heterodimer protein used in nonhomologous end joining to fix double strand breaks

loss of heterozygosity (LOH)

double strand repair gone wrong, homologous chromosome is used as a template for lost section

opposite strand

sense strand

coding strand

5’-3’ DNA strand that matches RNA sequence

template strand

antisense strand

noncoding strand

3’-5’ DNA strand that is used to synthetize RNA

RNA polymerase holoenzyme

5 RNA polymerases + sigma factor