genetics test 2

extranuclear inheritance / cytoplasmic inheritance

inheritance patterns involving genetic material outside the nucleus

nucleoid

where genetic material of mitochondria and chloroplasts are located, can contain several copies of the chromosome

oxidative phosphorylation

main function of the mitochondria, a process used to generate ATP

genome

all the genetic material an organism possesses

euploidy

variation in the number of complete sets of chromosomes

aneuploidy

variation in the number of particular chromosomes, occurs through nondisjunction

trisomy

textra copy of all the genes, can express too much of the genes on this chromosome

monosomy

one less copy of all genes, can express too little of the genes on this choromosome

nondisjunction

occurs when homologs are pulled to the same pole or the centromere does not split

familial down syndrome

trisomy 21, chromosome 21 and 14 are fused together

deletion / chromosomal deficiency

occurs when a chromosome breaks and a fragment is lost

cri-du-chat

results from a deletion of a small terminal portion of the short arm of chromosome 5

gene family

consists of two or more genes that are derived from the same ancestral gene

homology

descent from a common ancestor

orthology

decent from a common ancestor by genome division

paralogy

descent from a common acestor by duplication within a genome

globin gene

encode subunits of proteins that bind oxygen, 14 paralogs on three different chromosomes

inversion

total amount of genetic information stays the same, linear sequence is rearranged

balanced translocation

formed by breakage and reunion of chromosomes, recombination between repeate sequences

reciprocal translocations

DNA gets swapped between non-homologous chromosomes or broken DNA's reactive ends created by breaks are recognized by repair enzymes and joined together

nonreciprocal translations / unbalaned translocations

the transfer of genetic material occurs in only one directio

robertsoninan translocation

fusion of two telocentric chromosomes in the centromere region

PAR

psuedoautosomal regions, critical to segregation of x and y chromosomes during male gametogenesis

MSY

male-specific region Y

SRY

sex-determining region y

TDF

testis-determining factor, triggers testes formation, binds DNA and regulates gene expression

psuedoautosomal inheritance

the very few genes found on both X and Y chromosomes, has gotten shorter in evolutionary time

polypoid

have multiple complete sets of chromosomes

monoploid set

basic chromosome set, from which all the other genomes are formed

autopolyploids

have all chromosomes in the polyploid sepcies derive from a single diploid ancestral

allypolyploids

comeplete sets of chromosomes from two or more different ancestral species, much more common

anitbiotics

chemicals that kill or inhibit the growth of bacteria, used to treat bacterial infections. will target different cellular processes to restrict bacterial growth

carbon-source mutatns

cannot utilize a particular carbon source (sugar) for energy

lac-

a mutant that lost the ability to break down and use the sugar lactose as its only carbon source

auxotrophic

unable to synthesize an essential nutrient

leu-

a bacterium that has lost the ability to synthesize the amino acid leucine

prototroph

synthesizes all essential compounds

antibiotic resistance

bacterium can grow in the presence of antibiotic that it was formerly sensitive to

rich / complete media

all nutrients are supplied

minimal media

has very few nutrients

selection

only the organism with the phenotype of interest grows -- live or die only

screening

all phenotypes will grow, but they will be different (ie. colony shape, color, growth rate, enzyme production)

conjugation

direct DNA transfer between a donor and recipient bacterium, requires interaction between bacterial cells

transduction

transfer of DNA from one bacterium to another via a bacteriophage

transformation

uptake of extracellular DNA released from dead bacterium, requires a receptor and competence factors

lederberg and tatum experiment

demonstrated genetic transfer by bacterial conjugation, bacteria were able to transfer DNA so all necessary nutrients are produced

pilus

how bacteria physically interact during conjugation

fertility factor / f factor

confers the ability to donate DNA (fertility) during conjugation

episome / plasmid

small, extrachromosomal circular piece of DNA that determines f factor, also contains genes for tranferring itself to cells that lack f factor

f+ cells

have the f factor, serve as donors (recipients become f+)

f- cells

lack f factor, act as recipients, can act as donors once converted to f+

plasmid

small circular pieces of DNA, contain one or more genes, replicate independently of the bacterial chromosomr plasmidse

r plasmids

confer antibiotic resistance

col plasmids

encode colicins that can kill neighboring bacteria

virulence plasmids

carry genes that turn bacterium into pathogenic strains

conjugative plasmids

plasmids which are transmitted via conjugation, also carry the genes requires for conjugation

tra & trb

play a role in a the transfer of DNA

hfr cells

high frequency of recombination, derived from f+ strains. act as donor strains, created when an f factor integrates into the chromosome. recipients of hfr strains do not become f+ or hfr (stay f-)

interrupted mating experiments

demonstrated that specific genes in an hfr strain are transferred and recombined sooner than others, used a map gene order on the chromosome based on their time-of-entry from a donor hfr strain into a f- recipient strain

f' plasmids

f plasmids excised along with some chromosomal DNA, recipient cells become f'

merozygote / merodiploid

partially diploid, seen in f' plasmids

bacteriophage

a virus that specifically attacks bacterial cells, composed of genetic material surrounded by a protein coat, can follow the lytic cycle, the lysogenic cycle, or both

virulent phages

only undergo a lytic cycle

temperate phages

can follow both lytic and lysogenic cycles

generalized transduction

any piece of bacterial DNA can be incorporated into the phage

transduction step 1

infection of the donor cell, gene can be inseted in phage particle (rare)

transduction step 2

infection of the recipient cell, gene combined with recipient genome

natural transformation

DNA uptake occurs without help

artificial transformation

DNA uptake occurs with the help of special techniques

competence factors

proteins that facilitate the binding, uptake, and incorporation of DNA into the bacterial chromosome

competent

cells that can take up DNA

helicase (DnaB)

unwinds the DNA helix as replication proceeds, travels 5' to 3'

ssDNA binding protein (SSB)

binds and protects ssDNA

primase

RNA polymerase which can synthesize a RNA primer for initiation, requires DNA template and ribonucleotide triphosphates

DNA polymerase 1,3

synthesize DNA, prooofread, involved in replication

gyrase

reduce increased coiling generated during unwinding

DNA polymerase 1

remove RNA primers, active on the lagging end, proofreads, synthesizes DNA to fill in gaps from primer removal

ligase

join the gap-filling DNA to the adjacent strand, joins 3'-OH with 5'-phosphate

temperature sensitive mutants

can survive at a low/permissive temperature, and will fail to grow at the nonpermissive temperature (which is higher)

oriC

origin of replication, where replication starts

DnaA box

a DNA sequence that is bound by the protein DnaA

DnaA protein

binds DnaA boxes and to each other, causes DNA bending --> separation of strands in the AT-rich region

DNA adenine methyltransferase (Dam)

methylates the A on both strands of GATC immediately after replication -- the parental strands are methylated but it takes several minutes for the daughter strands

exonucleases

cut DNA from an end

endonucleases

cut DNA internally

DNA polymerase 2,4,5

involved in the repair of damaged DNA

DNA polymerase 3 holoenzyme

has all of it's protein subunits, processive (stays on the DNA template for a long time)

core enzyme

has just the bare essentals to do the job

processitivity

the measure of the number of nucleotides added by a DNA polymerase enzyme before it falls off/disassociates from the template

B-subunit clamp

prevents the core enzyme from falling off the template during DNA synthesis

leading strand

3' end points into the replication fork

lagging strand

5' end points into the replication fork

replication bubble

bidirectional synthesis of leading and lagging strands from one origin of replication

ter

termination sequence, on opposite side to oriC

protein tus

termination utilization substance, binds to the ter sequences, stops the movement of replication forks

catenanes

intertwined circular molecules as a result of DNA replication

ORC

origin recognition complex, multi-subunit protein binds to origins

MCM

mini-chromosome maintenance, includes helicase and ATPase

CDC6, CDT1

load MCM tonto DNA, considered RLF

RLF

replication licensing factors, their removal allows replication to proceed, which limits replication to once per cell cycle

geminin

inhibits CDT1

pol a

associates with the primase, adds DNA to RNA primers

PCNA

proliferating cell nuclear antigen, eukaryotic counterpart of the B sliding clamp in bacteria

telomeres

ends of linear chromosomes, long stretches of short repeating sequences, preseve the integrity and stability of chromosomes

telomerase

ribonucleoprotein (RNA and protein), inclides a reverse transcriptase domain

transcription

RNA mulecules are synthesized by an enzyme, RNA polymerase from DNA

processing

in the nucleus of eukaryotic cells, the RNA usually undergoes chemical modification-- adds 5' cap, introns are removed by splicing, adds poly-a tail. the cleavage of a large RNA transcript into smaller pieces, 1+ becomes a functional RNA molecule

translation

the processed RNA molecules is used to specify the order which amino acids are joined together to form a polypeptide chain

gene product

end protein made

RNA polymerase

a multi subunit enzyme that synthesizes RNA from a DNA template, consists of a RNA synthesizing core plus specifity factors, uses a DNA template to direct synthesis

specificity factors

needed to recognize and bind promoter DNA

promoters

DNA sequences that promote gene expression, direct the exact location where RNA polymerase binds to DNA to initiate transcription

coding strand

has the same sequence as the RNA

template strand

has the complement sequence as the RNA

consensus sequence

most commonly occuring bases for transcription initiation

LOGO alignment

graphical comparison of nucleotide or amino acid sequences

closed complex

promote DNA base-paired, DNA is not unwound

open complex

promoter DNA is unwound, hydrogen bonds are broken between the template and coding DNA strands, incoming NTPs can pair with the template strand

termination

end of RNA syntesis, occurs when the short RNA-DNA hybrid f the open complex is forced to separate

rho-dependent termination

requires a protein known as rho

stop signal

transcription terminantion sites are inverted repeat sequences which can form loops in RNA

TATA box

core promoter element in eukaryottes

introns

intervening sequences, regions of the initial RNA transcript that are not expressed in the amino acid dequence of the protein

RNA splicing

introns are removed and the exons are joined or spliced together in the mature mRNA

exons

regions that are retained in the mRNA

ribozyme

RNA enzyme / catalytic RNA

snRNPs

small nuclear ribonucleo-protein particles, composed of RNA and protein

alternative splicing

refers to the phenomenon that pre-mRNA can be spliced in more than one way, produced two or more polypeptides

proteome

the number of proteins that a cell can make

exosome

multiprotein RNase, main activity is 3'--5' exonuclease, degrades mRNA without a polyA tail

splicing repressor

repressor prevents recognition of a splice site, spliceosome cannot use that splice site, and skips it

complementarity

allows each strand to serve as a template for synthesis of the other

meselson and stahl

determined the mechanism of DNA replication using heavy 14-N

chromosomes

structures that contain the genetic material, complexes of DNA and proteins

genome

comprises all genetic material that an organism possesses

bacterial chromosomes

single circular chromosomes, looped with DNA-binding proteins and then supercoiled

centromere

requires for proper segregation during mitosis and meiosis

kinetochore protein

link the centromere to the spindle apparatus

telomere

prevent chromosome shortening

nucleosome

repeating structural unit within eukaryotic chromatin, composed of a double stranded segment of DNA wrapped around an octamer of histone proteins

histone octamer

composed of two copies each of four different histone proteins

histone h1

attaches to the DNA at its juncture with the nucleosome

solenoid model

regular, spiral configuration containing six nucleosomes per turn

zig-zag model

less regular nucleosomes do not contact each other

nuclear matrix

composed of two parts, nuclear lamina and internal matrix proteins

nuclear lamina

fibers that line the inner nuclear membrane

internal matrix proteins

connected to the nuclear lamina and fills interior of nucleus, structural and functional role remains controversial

matrix-attachment regions (MARs)

anchored to teh nuclear matrix, creating radial loops

radial loops

play a role in compaction, organizes chromosomes within the nucleus

chromosome territory

where each chromosome in the nucleus is located, discrete and nonoverlapping

nucleus

chromosome territories, where chromosomes occupy specific regions

heterochromatin

tightly compacted regions of chromosomes, transcriptionally inactive

euchromatin

less condensed regions of chromosomes, transcriptionally active

constitutive heterochromatin

regions that are always heterochromatic, permanently inactive with regard to transcription, usually contain highly repetitive sequences

facultative heterochromatin

regions that can interconvert between euchromatin and heterochromain, ie. barr body formation during development in females

prokaryotic alpha subunit

5'-3' polymerization, core enzyme: elongates

prokaryotic e subunit

3'-5' exonuclease, polynucleotide chain

repetitive sequences

can cause misalignment between homologous chromosomes

deletions and duplications

can be caused by abnormal crossing over/recombination between homologous chromosomes

break point effect

inversion break point occurs in a vital gene

position effect

a gene is repositioned in a way that alters its gene expression

pericentric inversion

centromere lies within inverted region

paracentric inversion

centromere lies outside inverted region

inversion loop

must form in order for the normal and inversion chromosome to synapse properly

inviable

occurs when there is no centrosome, if centrosomes move to opposite poles, and sometimes caused by deletion and duplication

y-linked genes

non-essential or male-specific functions

causes of antibiotic resistance

prescribed when not relevant, treatment not followed to completion, overuse (especially in agriculture)

p1 phage

infects E. coli

p22 phage

infects salmonella typhimurium

conditional mutant

can survive at a permissive condition, but will fail to grow at a nonpermissive condition

ts mutants

less stable at higher temperatures and therefore lose their function

rapid stop

subset of ts mutants, encoded enzymes needed for replication of DNA after it already started

slow stop

subset of ts mutants, completed their current round of replication but could not start another, encoded genes needed for initiation of replication

rapid stop mutants

dnaE, dnaX, dnaN, dnaZ, dnaZ, dnaG, dnaB

slow stop mutants

dnaA, dnaC

dnaE

alpha subunit of DNA polymerase 3, synthesizes DNA

dnaX

T subunit of DNA polymerase 3, part of the clamp loader complex, promotes the dimerization of two DNA polymerase 3 proteins together at the replication fork

dnaN

Y subunit of DNA polymerase 3, helps the B subunit bind to the DNA

dnaG

primase, needed to make RNA primers

dnaB

helicase, needed to unwind the DNA strands during replication

dnaA

DnaA protein that recognizes the DnaA boxes at the origin

dnaC

DnaC protein that recruits DNA helicase to the origin

methylation before replication

full methylated parental strands, replication initiated well

methylation immediately after replication

hemi-methylated, replication poorly initiated

trombone model

lagging strand must loop to invert the physical, but not biological direction of synthesis

topoisomerase

separates catenanes (decatenation)

eukaryotic alpha polymerase

initiates DNA replication in conjunction with primase

eukaryotic epsilon polymerase

replication of the leading strand

eukaryotic delta polymerase

replication of the lagging strand

eukaryotic gamma polymerase

replication of mitochondrial DNA

eukaryotic beta polymerase

DNA repair and other functions

polymerase switching

pol a is replaced by polymerase delta and polymerase epsilon for elongation

bacterial RNA polymerase holoenzyme

recognizes promoter DNA

bacterial RNA polymerase B, B'

enzymatic

bacterial RNA polymerase w

structural

bacterial RNA polymerase a

2x, DNA and transcription factor binding, CTD recognizes UP-elements

bacterial RNA polymerase sigma factor

promoter recognition, initiation only (not elongation or replication), can recognize promoter elements

core RNAP

synthesizes RNA with B, B', w, a (x2)

intrinsic termination

no protein is required to physically remove the RNA from the DNA

nusA

stabilizes the RNA pol pausing

RNA polymerase 1

transcribes most rRNA (ribosomal) genes

RNA polymerase 2

all protein-coding genes, miRNA genes, genes for non-coding RNA

RNA polymerase 3

tRNA (transfer RNA), 5S rRNA (ribosomal), small RNAs

TFIID

transcription factor for RNA polymerase 2, binds to the TATA box, a complex of proteins that includes TATA-binding protein (TBP) and several TBP-associated factors

TFIIB

binds to TFIID, promotes the binding of RNA polymerase 2 to the core promoter

TFIIF

bound to RNA polymerase 2

TFIIE and TFIIH

bind to RNA polymerase 2 to form a preinitiation or closed complex

TFIIH

acts as a helicase to form an open complex, phosphorylates the CTD of RNA polymerase 2, which breaks the contact between RNA polymerase 2 and TFIIB

TFIIB, TFIIE, TFIIH

released after the open complex is formed

CTD

c-terminal domain

NTD

n-terminal domain