Genetics Final Study Set 1

Telophase

Nuclear membrane begins to reform around each separated chromosome Chromosomes begin to condense Cleavage furrow forms

Prometaphase

Nuclear membrane fully breaks apart into vesicles Centrosomes move to opposite ends of cell Spindle apparatus fully formed Kinetochore microtubules begin to form and capture sister chromatids

Metaphase

Sister chromatids align along the metaphase plate Kinetochore microtubules are attached to each dyad on opposite poles

Anaphase

Sister chromatids are pulled apart towards opposite poles of cell Chromatids become individual chromosomes Kinetochore microtubules shorten, which move the chromosomes to opposite ends of the cell Polar microtubules lengthen to elongate the cell

Prophase

Sister chromatids condense Microtubules begin to form the spindle apparatus Centrosomes begin to move apart Nuclear membrane begins to break

Okazaki Fragments

Small fragments of DNA produced on the lagging strand during DNA replication, joined later by DNA ligase to form a complete strand.

Transcription Initiation

RNA polymerase binds to promoter

Iron Regulatory Protein

RNA-binding protein that influences the two mRNAs that encode ferritin and the transferrin receptor

Chargaff's Rule

% adenine = % thymine; % cytosine = % guanine

rho-Independent Termination

1. Stem-loop causes RNA polymerase to pause 2. During this pause, the weakly bound U-rich sequence is not able to hold the RNA-DNA hybrid together, causing termination

rho-Dependent Termination

1. rho protein binds to the rut site in RNA and moves towards the 3' end 2. RNA polymerase transcribes a region that forms a stem-loop and then proceeds to the terminator 3. Stem-loop causes RNA polymerase to pause 4. During this pause, the rho protein proceeds to the open complex and separates the RNA-DNA hybrid

Complete Turn of Helix =

10 bp and 3.4nm

5' Cap

7-methylguanosine cap structure is recognized by cap-binding proteins

Telomerase

An enzyme that catalyzes the lengthening of telomeres in eukaryotic germ cells

Operator

DNA element at one end of the operon that is the binding site for the repressor, which regulates expression by controlling access of RNA polymerase to the promoter

Hemimethylation

DNA sequence with one methylated strand and one unmethylated strand

Promoters

DNA sequences that direct the exact location for initiation of transcription as well as specifies the direction of transcription

Cis-Acting Elements

DNA sequences that only affect a particular nearby gene on the strand that they are on TATA Box Enhancers Silencers

Combination Control

Describes the way in which groups of transcription regulators work together to regulate the expression of a single gene One or more activator proteins One or more repressor proteins

Positive Control Conditions for lac Operon

Glubose Absent, Lactose Present

Negative Control Conditions for lac Operon

Glucose Present, Lactose Absent Glucose Present, Lactose Present

I+ Z- Y+ / F' I- Z+ Y+

I+ is dominant to I-

I+ Z+ Y+

I+ is inducible

I- Z- Y+ / F' I+ Z+ Y-

I+ is trans-acting

I- Z+ Y+

I- is constitutive

Coding Strand

The strand of DNA that is not used as a template during transcription; also called the sense strand.

Stop Codons (Translation Termination)

UAG UAA UGA

O+ Z+ Y+ / F' O+ Z- Y+

Z+ is dominant to Z- (synthesis of both enzymes is induced)

Pachytene (Prophase 1)

a bivalent has formed and crossing over has occurred

Iron Response Element

a cis sequence found in certain mRNAs whose stability or translation is regulated by cellular iron concentration

Basal Transcription

a low level of transcription resulting from just the core promoter

Genomic Imprinting

a marking process that occurs during gametogenesis in which an offspring expresses a gene that is inherited from one parent but not both

Enzyme Adaptation

a particular enzyme only appears in the cell after the cell has been exposed to the enzyme's substrate

Trans-Acting Factors

a regulatory protein that binds to a regulatory element in the DNA and modifies its expression

Transformation

a segment of DNA from a dead bacterium is absorbed by a living bacterial cell and incorporated into the bacterial chromosome

A Site

accepts incoming aminoacyl-tRNA (charged-tRNA)

Gram-Positive

acteria that have a thick peptidoglycan layer that stains purple when Gram stain is used

CpG Islands - CpG Sites

adjacent C-G base pairs

Small Effector Molecules (Allosteric Effectors)

affect transcription regulation by binding to regulatory proteins (repressors/activators)

Translation Elongation

amino acids are added to the polypeptide chain one at a time

Antisense RNA

an RNA strand that is complementary to mRNA, which when synthesized will regulate translation

preRC

assembly of this structure begins eukaryotic replication

Auxotrophs

bacteria that are unable to synthesize essential nutrients

Gram-Negative

bacteria that have a thin peptidoglycan layer that stains pink when Gram stain is used (more dangerous)

Conjugation

bacterial DNA is transferred from one to another through direct contact

Coupling

bacterial mRNA transcription and translation occurs at the same time in the cytoplasm

oriC

bacterial origin of replication

Specialized Transduction

bacteriophage genetic material can cut itself out (excise) of the host chromosome, which could imprecisely cut out some of the host chromosome with it

Corepressors

bind to repressors and cause them to bind to DNA

MCM Helicase

binding of this protein complete DNA replication licensing

H3K9me3

binds to heterochromatin protein 1 (HP1) to direct histone deacetylation and DNA methylation, resulting in repression

GAL80

blocks GAL4 from activating transcription

Full Methylation

both DNA strands are methylated

Proteolytic Cleavage

breaking of bonds between amino acids in proteins

DNA Helicase

breaks hydrogen bonds between DNA strands

Catabolite Repression

caused by presence of glucose, lactose will break down into glucose and galactose, which will stop lac operon expression via CAP

G2 Phase

check to make sure that cell has all materials needed for cell division

Exonucleases

cleave a covalent bond between two nucleotide at one end of a strand

Endonucleases

cleave bonds within a strand

Swi2-Snf2

coactivator of transcription: repositions the nucleosome and exposes the promoter

Exporter

complex of 10 to 15 proteins encoded by the F factor that pumps DNA/relaxase into the recipient cell during conjugation

trp mRNA Leader Sequence

contains an attenuator region and two tryptophan codons

Mediator

controls the switch to the elongation phase in eukaryotic transcription

G1 Phase

copies of organelles are made, checks that materials needed for DNA replication are present, and checks for any present mutations

H2A, H2B, H3, H4

core histones, form an octamer through a pair of each

DNA Methyltransferase

covalently attaches methyl groups to DNA, inhibiting eukaryotic transcription by inhibiting the binding of an activator protein

DNA Ligase

covalently links the DNA backbones in Okazaki fragments together

Avery, Macleod, and McCarty

discovered that DNA was the genetic material by purifying each macromolecule, only treatment with DNase eliminated transformation

Watson and Crick

discovered the double helix structure of DNA based on the work of other scientists

Barbara McClintock

discovered transposable elements by studying corn

AG-GU Rule

each intron is cut at each end and these intron ends almost always have GU at the 5' end and AG at the 3' end

GAL1, GAL2, GAL7, and GAL10

encode enzymes that catalyze steps in the biochemical pathway that converts galactose into glucose

trpL

encodes a short peptide called the leader peptide

lacl Gene

encodes the lac repressor protein

trpR

encodes the trp repressor protein

Transcription Termination

end of RNA synthesis occurs when the short RNA-DNA hybrid of the open complex is forced to separate, which releases the newly made RNA as well as the RNA polymerase

DNA Replication Licensing

ensures that DNA replication is initiated only once per cell cycle and prevents genetics material that could lead to instability or disease from being replicated

Aminoacyl-tRNA Synthetase

enzyme that attaches an amino acid to specific tRNAs There are 20 of these enzymes, one for each amino acid

Phosphatase

enzyme that removes phosphate group from another enzyme

Shine-Dalgarno Sequence

facilitates the binding of mRNA to the 30S subunit in prokaryotes

F+

formed after a bacterial cell with F factor conjugates with an F- cell do not transfer any of their chromosome to recipient cell

cAMP

formed from ATP in the presence of low glucose

Hfr Strain

formed when an F factor integrates into the bacterial chromosome, then transferring a portion of the bacterial chromosome to a recipient cell during conjugation

Heterogamous

gametes are morphologically different

Isogamous

gametes are morphologically similar

Generalized Transduction

genes picked up by the phage can come from any part of the bacterial genome

Operon

group of genes operating together

Housekeeping Genes

groups of genes that express a relatively constant level of expression in most cells and tissues of an organism

Naturally Competent Bacteria

have the ability to freely absorb DNA from the environment

Enhanceosomes

help recruit transcriptional machinery

Sex-Influenced Traits

heterozygous males and females have different phenotypes

Heterochromatin

highly condensed chromatin

P Site

holds the tRNA that is linked to the growing polypeptide chain

Upstream Activator Sequences (UAS)

if deleted, genes are silent

X-Inactivation

in females, compensates for the single X chromosome in males by inactivating extra X chromosomes to turn them into Barr bodies, which is maintained throughout somatic cell division

Inducer

increases transcription by binding to either regulatory protein Binding to a repressor will cause stop it from inhibiting transcription Binding to an activator will cause it to bind to DNA

Allolactose

inducer molecule that binds to lac repressor and prevents it from binding to DNA strand

GCN5

interacts with histones using acetyltransferase to activate genes

Ferritin

iron storage protein

Single-Stranded Binding Proteins

keep the strands of DNA separate during replication

GAL4

key regulator of pathway with 2 domains: Activation domain required for regulatory activity DNA-binding domain associates with UAS

H1

linker histone binds to DNA linker region helps organize adjacent nucleosomes

ter Sequences (only found in prokaryotes)

locate on the opposite side of the oriC

Euchromatin

loosely packed chromatin

Attenuation

mechanism by which an operon transcribes some but not all of its products

Torpedo Model

model for eukaryotic termination: 1. An exonuclease binds to the 5' end of the RNA that is still being transcribed and degrades it in the 5' to 3' direction 2. Exonuclease catches up to RNA pol II and causes termination

Allosteric Model

model for eukaryotic termination: RNA polymerase II is destabilized and dissociated from the DNA after transcribing the polyA signal sequence

Conservative Model

model where both parental strands stay together after replication

Semiconservative Model

model where double-stranded DNA contains one parental and one daughter strand after replication

Dispersive Model

model where parental and daughter DNA segments are interspersed in both strands after replication

Polycistronic mRNA

molecules of mRNA that code for multiple proteins

Translational Repressors

most common translational regulatory protein, inhibiting translation

polyA Tail

most mature mRNAs have a string of adenine nucleotides at their 3' ends that is enzymatically added after the gene is transcribed

Transposon

moved to a new target site in DNA turing simple transposition

Retrotransposon

moved via an RNA intermediate during retrotransposition

Transcription Elongation

new nucleotides are added to RNA strand

Maternal Effect

non-Mendelian inheritance pattern where the genotype of the mother directly affects the phenotype of the offspring

Diakinesis (Prophase 1)

nuclear membrane breaks apart and prophase 1 ends

Epigenetics

occur when a modification of a gene or chromosome affects gene expression, but the modification is not permanent over many generations

Incomplete Penetrance

occurs when a dominant trait is not expressed in and individual that carries it

Incomplete Dominance

occurs when a heterozygote has an intermediate phenotype between its parental phenotypes

Variable Expressivity

occurs when individuals have the same genetic composition but express a spectrum of traits

Material Inheritance

occurs when organelles, such as mitochondria or chloroplasts, are transmitted via the egg

Epistasis

occurs when the alleles of one gene mask the phenotypic expression of the alleles of a different gene

Codominance

occurs when the heterozygote expresses both alleles at the same time without having an intermediate phenotype

Overdominance

occurs when the heterozygote has an advantage and greater reproductive success over homozygotes

Complementation

occurs when two individuals with similar recessive phenotypes produce offspring with a wild-type phenotype

O+ Z- Y+ / F' Oc Z+ Y

operator is cis-acting

Oc Z+ Y+

operator is constitutive (lac operon is always expressed regardless of lactose presence)

O+ Z+ Y+

operator is inducible (synthesis of both enzymes is induced)

Synapsis

pairing of two chromosomes that occurs during meiosis

Enhancer-Blocking Insulators

prevent enhancer activation

Operon Components

promoter, operator, structural genes

GAL3

promotes GAL operon expression Both a sensor and inducer

Archibald Garrod

proposed that there was a relationship between genes and protein production through study of homogentisic acid oxidase

Relaxosome

protein complex that recognizes origin of transfer (DNA sequence) and makes a cut in the DNA during conjugation

tus

protein that binds to ter sequences, stopping the movement of the replication fork

Transferrin

protein that transports iron in the blood

Transcription Factors

proteins that bind to regulatory elements and influence the rate of transcription

Meiosis 2

reduces the 2 daughter cells from meiosis 1 from diploid to haploid (2n→1n, two sets of chromosomes to one) starts with half the genetic content seen in mitosis

Regulatory Transcription Factors

regulate the rate of transcription of target genes by influencing the ability of RNA polymerase to begin transcription of a gene

Xic

regulates X-inactivation

Repressors

regulatory protein that binds to cis-acting regulatory DNA element, such as a promoter or enhancer, to inhibit transcription (negative control)

Activators

regulatory protein that binds to cis-acting regulatory DNA elements to increase or activate transcription of an adjacent promoter (positive control)

Silencers

regulatory sequences that inhibit transcription

Enhancers

regulatory sequences that stimulate transcription

Core Promoter

relatively short DNA sequence within eukaryotic genes necessary for determining the precise start point of transcription

Induction

relief of repression of a gene/genes under negative control

Topoisomerase II (DNA Gyrase)

removes positive supercoiling ahead of the replication fork

DNA Polymerase I

removes the RNA primer and replaces it with DNA

DNA Pol II, IV, and V

repair and replicate damaged DNA

Nucleosome

repeating structural unit of eukaryotic chromatin

Sister Chromatids

replica of eukaryotic chromosomes formed before cell division

Leptotene (Prophase 1)

replicated chromosomes condense

S Phase

replication of chromosomes

General Transcription Factors (GTFs)

required for binding of RNA polymerase to core promoter

Regulatory Elements

short DNA sequences that affect the ability of RNA polymerase to bind to the core promoter (often found in the -50 to -100 region)

AraC Protein

singular binding protein in the arabinose operon that is an: activator in the presence of arabinose repressor without arabinose present

Allosteric Site

site on a protein that binds to a small effector molecule, modifying the activity of its active site

DnaA Boxes

sites for the binding of DnaA protein

GATC Methylation Sites

sites that help to regulate DNA replication

AT-Rich Regions

sites where the DNA strands separate

ORC

six subunit complex that acts as the first initiator in eukaryotic DNA replication

RNA Interference

small RNAs called microRNA (miRNAs) and short, interfering RNA (siRNAs) silence the translation of mRNA

Inhibitors

small effector molecule that binds to activators and prevent them from binding to DNA

Methionine

start codon in eukaryotes

Formylmethionine

start codon in prokaryotes

Senescent

state of cells when their telomeres are too short, causing them to lose their ability to divide

lacY

structural gene that codes for permease which transport lactose into the cell

lacZ

structural gene that modifies lactose into allolactose and cleaves the lactose molecule in order to yield glucose and galactose

Frederick Griffith

studied Streptococcus pneumoniae to discover transformation

Jacob and Monod

studied enzyme adaptation by analyzing lactose metabolism in E. coli

40S, 60S

subunits of eukaryotic ribosomes

30S, 50S

subunits of prokaryotic ribosomes

Is

super-repressor mutation that prevents expression even in the presence of an inducer

Zygotene (Prophase 1)

synapsis begins and the synaptonemal complex begins to form

Diplotene (Prophase 1)

synaptonemal complex dissociates

Primase

synthesizes RNA primer

DNA Polymerase III

synthesizes new DNA only in the 5' to 3' direction

E SIte

tRNA that has given up its amino acid is let go by the ribosome at this site

Ubiquitination

targets a protein for degradation using ubiquitin

Template Strand

the DNA strand that is transcribed

DNA Pol III Holoenzyme

the complex of all 10 subunits of DNA pol III

Feedback Inhibition

the final product in a pathway inhibits an enzyme that acts early in the pathway

Law of Segregation

the two copies of a parental gene separate into individual copies, with one from each parent being passed down to offspring

Sex-Limited Traits

traits expressed only in one sex, causing sexual dimorphism

X-Linked Inheritance

traits found on X chromosome are more common in males than females unless the trait is dominant

Blending Hypothesis

traits from each parent blend together to form an intermediate offspring

Spermatogenesis

two cells produced, one stays a spermatogonial cell while the other becomes a primary spermatocyte (which goes through both stages of meiosis)

Heterogametic

two different types of gametes

Law of Independent Assortment

two genes will randomly sort their alleles during meiosis

Sporophyte

undergoes meiosis to produce haploid spores, which then divide by mitosis to produce the gametophyte

Meselson and Stahl

used light and heavy nitrogen to distinguish daughter and parental strands in bacterial DNA replication

Hershey and Chase

used radioactive phosphorus to label DNA and radioactive sulfur to label proteins in T2 phages (transduction)

Testcross

used to map distance between two or more linked genes done by breeding an individual heterozygous for 2+ genes with an individual that is homozygous recessive for the same genes

Positive-Effect Variegation (PEV)

when genes are relocated to heterochromatic regions, causing genes to be silenced

G0

when no cell division occurs and the cell is only maintaining homeostasis

Synteny

when two or more genes are located on the same chromosome and are linked

Isoacceptor tRNAs

when two or more tRNAs that differ at the wobble base are able to recognize the same codon

Prototrophs

wild-type bacteria that grow on minimal media