BIO 340 Exam 4

matastasis

the spread of cancer cells from one part of the body to another - invade normal tissues and travel to new locations, forming new tumors;

mRNA in trpL

the termination stem loop, which halts RNA polymerase progress along the DNA within the leader region

paralogs

homologous genes in the same species

Major predictions of operon model

- lacL gene produces diffusible product (trans-acting) - lacO region involved in regulation - lacO gene region must be adjacent to structural genes to regulate transcription

histone acetyltransferase (HAT)

- recruited by activators and add acetyl(COCH3) groups - These add acetyl groups to positively charged residues in the N-terminal histone tails; the acetylation neutralizes the positive charge and relaxes the histone/DNA interaction - Acetyl groups are removed by histone deacetylases (HDACs), which are recruited by repressors

attenuation of trp operon

- second mechanism controlling trp operon by trpL region

Bases are forced apart to accommodate intercalating agents:

- Ethidium bromide - Acridine orange - Actinomycin D - SYBR® Safe

GAL genes are inducible:

- Transcription is regulated by presence or absence of substrate (galactose) - Absence of galactose: GAL structural genes not transcribed - Galactose added to medium: Transcription begins immediately

autoinducer function

- binds to a regulatory molecule, which in the case of A. fischeri is LuxR. - The LuxR-autoinducer complex then activates transcription of the luciferase target genes that confer bioluminescence.

normal cells

- highly specialized - confined to boundaries of tissue type and contact inhibition

additional control of the lac operon

- inducer: repressor complex alone yields only basal transcription with only a small number of polycistronic mRNAs - Basal transcription is not sufficient to generate enough copies of the lac operon mRNA for metabolism of lactose - Positive control of the lac operon occurs at the CAP-cAMP binding region of the lac promoter - The site attracts the CAP-cAMP complex composed of the catabolic activator protein (CAP) and cyclic adenosine monophosphate (cAMP)

GAL 1 and GAL 10 genes

- transcription of both genes are positively regulated - controlled by central control region UASg (upstream activating sequence of GAL genes) - contain four binding sites for Gal4 protein (Gal4p)

Transcription Control

- under control of a single regulatory region 1. Genes coding for enzymes with regulatory functions are organized in clusters 2. Regulatory regions usually located upstream of gene cluster they control 3. Cis-acting site / domain - regulatory region on same strand 4. Trans-acting elements - molecules that bind cis-acting sites

cAMP (cyclic adenosine monophosphate)

-To bind to promoter, CAP must be bound to cyclic adenosine monophosphate (cAMP) -Glycolysis inhibits activity of adenylyl cyclase, which catalyzes conversion of ATP to little cAMP -when glucose is present, almost no CAP-cAMP can form

Cancer cells share two fundamental properties

-abnormal cell growth and division: unregulated cell proliferation -metastatic spread

cancer cells

-dedifferentiated (look and behave more like primordial cells) - higher rate of proliferation than normal cells - larger with larger nuclei than normal cells - poor organization as they grow

bacterial innate immunity

-express endonucleases (restriction enzymes) which cleave specific dna sequences -restriction enzymes destroy foreign bacteriophage dna, while the bacterium protects its own dna by methylating it -block phage absorption -block phage dna insertion -induce suicide in infected cells

modulation

-mRNA translation - protein processing - modification - degradation

repressible operons in anabolic pathways

-operate through activity of the end product to block transcription of the operon - Certain repressible operons have a second regulatory capability called attenuation which fine-tune transcription to match the immediate needs of the cell

SWR1 complex

-responsible for replacing common histone H2A protein with a variant form (H2AZ)

double helix distortion

-very dynamic structure, flexible

natural circular plasmids range in size from _______. They behave as additional genetic units which are inherited and ________ of the bacterial chromosome, but rely on the _____ and ____ for transcription and replication

1 to > 200 kb replicate independently host enzymes proteins

apoptosis steps:

1. Fragmentation of nuclear envelope 2. Disruption of internal cellular structures 3. Dissolution of cell into small, spherical apoptotic bodies 4. Engulfing of apoptotic bodies by phagocytic cells

selection of transformants

1. LacZ gene codes for the enzyme called β-galactosidase 2. β-galactosidase metabolizes lactose producing galactose and glucose. 3. β-galactosidase converts X-Gal into a blue colored product 4. To activate LacZ gene transcription the activator called IPTG is required

Lac Operon Function and Mechanism:

1. Lactose permease allows the entry of lactose into the E. coli cell from a growth medium. 2. Lactose has its galactoside linkage cleaved by beta galactosidase. 3. Beta galactosidase converts lactose to allolactose. 4. Excess allolactose is cleaved by beta galactosidase into galactose and glucose.

lac (lactose) operon have three features:

1. Regulator 2. Control locus 3. Structural locus

The chromatin modifications alter the strength of the nucleosome-DNA associations, and can cause chromatin structure to either:

1. Relax: forming open promoters 2. condense: leading to closed promoter structures

3 mechanisms which trans-acting proteins access target DNA sequences

1. Some regulatory sequences are not tightly bound by histones, so that regulatory proteins can easily access the DNA sequences 2. Change the distribution or composition of histones by chromatin remodelers 3. Enzymatic modification of histones by addition or removal of acetyl or methyl groups to particular lysine residues

open promoter function

1. The poly A/T tract of open promoters contains binding sequences (BS) that attract transcriptional activators (ACT) 2. The binding region is flanked by sequences that help position one nucleosome upstream and one downstream (called the +1 nucleosome) of the NDR 3. The downstream nucleosome contains a variant histone H2A, called H2AZ, that is easily removed from the transcription start site

Adenomatous polyposis coli (APC)

A tumor suppressor gene. If mutated, it no longer has function. - common in colorectal (colon) cancer.

polymerase chain reaction (PCR) steps

1. Thermostable DNA polymerase 2. Template 3. Primers (short oligonucleotides 18-40 nts) 4. Nucleotides (dNTPs) 5. Buffer (with mono and divalent cations)

low levels of tryptophan

1. Translation stalls at codons 10 and 11 2. The ribosome obscures region 1, allowing regions 2 and 3 to pair 3. Antitermination conformation continued transcription of genes needed for production of tryptophan

when galactose is present:

1. galactose and Gal3 bind to Gal80 2. Gal80 releases Gal4, freeing the DNA-binding domain of Gal4 to recognize and bind to the UASG sites 3. Transcriptional activation domain activates transcription of GAL genes

requirements for vectors:

1. origin of replication 2. selectable marker 3. multicoloning site / polylinker: site that allows gene to be cloned to be placed into the plasmid vector

trp operon contains:

1. regulatory region with promoter (trpP) 2. operator (trpO) 3. leader region (trpL) containing attenuator region 4. structural genes for tryptophan synthesis: trpE, D, C, B, A 5. Gene (trpR) outside operon that encodes repressor protein (trpR) that is activated when bound to tryptophan

enhancers

A DNA sequence that recognizes certain transcription factors that can stimulate transcription of nearby genes. Located on either side of gene, some distance from gene, or even within gene - Important in reaching maximum level of transcription

Similarity searches

A genome sequence statistically similar to gene with known function likely encodes for protein with similar function

metastatic spread

A process by which cells detach from the primary tumor and move to other sites in the body, forming new malignant tumors The ability to invade new tissues results from new mutations in cancer cells

repressors

A protein that suppresses the transcription of a gene, silence element, silence transcription initiation

pair end sequencing

A sequence is generated from both ends of DNA fragments of known size

MicroRNA

A small, noncoding RNA molecule, typically about 21-25 nucleotides long, that binds to mRNA to inhibit its translation. - transcribed by RNA polymerase II and produce transcripts that foldback upon themselves to produce dsRNA -Precursor transcripts are synthesized in the nucleus and processed into miRNAs by Dicer activity

mutations in ras genes lead to production of _____ and ______

hyperactive ras protein, increased cell division

trans-activating domain

Activates or represses transcription by binding to other transcription factors or RNA polymerase

positive control

Activator protein must be present to turn on gene transcription

Human Genome Project (HGP)

An international collaborative effort to map and sequence the DNA of the entire human genome. - clone by clone approach

omics

Areas of biological research having an "omics" connection are continually developing Proteomics Metabolomics Glycomics Toxicogenomics, etc

Enhancer and silencer sequences

At greater distances from the core promoter are the enhancer and silencer sequences (or enhancers and silencers)

Inducible enzymes

Bacteria adapt to environment by producing inducible enzymes only when specific substrates are present

DNA binding domain

Binds to specific DNA sequences in the cis-acting regulatory site

RISC

Binds to the 21-25 bp andseparates the strands to create miRNAs

DNase I hypersensitivity

Hypersensitivity occurs in the immediate vicinity of transcribed genes and surrounding promoters, enhancers, and other transcription-regulating sequences

sporadic cancer

Cancer caused by accumulation of a number of mutations in somatic cells; 90-95% associated Mutation occurs in a single somatic cell

How can a virus cause cancer?

Carry an oncogene into cell and insert it into host genome Altered cell regulation due to changes in kinase activity or production of regulatory proteins Insertion of promoter or enhancer next to cellular oncogene

metastasis enters blood or lymphatic system, and is controlled by large number of gene products:

Cell-adhesion molecules, cytoskeleton regulators, and proteolytic enzymes

chemical

Chilling cells in the presence of divalent cations such as Ca2+ (in CaCl2) renders the cell walls more permeable to plasmid DNA

DNase I hypersensitive sites

Chromatin region that becomes sensitive to digestion by the enzyme DNase I

GAL gene system in yeast (saccharomyces cerevisiae)

Composed of four structural genes and three regulatory genes Products of structural genes transport galactose into cell for metabolism CHECK slide for photo

repressible operons

Contain genes coding for anabolic enzymes - Several genes in a series are turned off (repressed) by the product synthesized by the enzyme

ISWI complex

Contains remodelers that mainly control placement of nucleosomes into a position that silences transcription

Mechanisms of posttranscriptional gene regulation

Control of alternative splicing mRNA stability Translation RNA silencing

operon

Coordinated set of genes regulated as a single unit - Found only in bacteria and archaea - cap site, lac promoter, operator, lacZ, Y, A, lac terminator

Two types of regulatory proteins are involved in cell cycle control are what?

Cyclins Cyclin-dependent kinases (Cdks)

transcription regulatory proteins

DNA binding domain trans-activating domain

epigenetic modifications

DNA methylation Histone acetylation and phosphorylation

CRISPR- Cas

Defenses are part of "adaptive" immunity if the defense mechanism uses past exposure to a pathogen to stimulate improved defense against future exposure to the same pathogen

non specific interactions

Deoxyribonuclease I (Dnase I) binds electrostatically to DNA at the minor grove

computer automated DNA sequencers

Designed for high-throughput sequencing Made genomics possible Essential for Human Genome Project Sequences contained multiple capillary gels Generated over 2 million bp per day

Tryptophan is absent from the cell:

the repressor protein cannot bind the operator thus allowing for transcription of the operon

transformation: eukaryotes

Electroporation Transfection Microinjection Biolistic (gene gun) Ti plasmid - tumor-inducing plasmid of Agrobacterium radiobacter

lacZ (b-galactosidase)

Enzyme that converts disaccharide lactose to monosaccharides glucose and galactose - Conversion is necessary for lactose to serve as primary energy source in glycolysis

LacY (Lactose Permease)

Enzyme that facilitates entry (PERmits) of lactose into bacterial cell

lacA (galactoside transacetylase)

Enzyme that may be involved in removal of by-products of lactose digestion from the cell

constitutive enzyme

Enzymes are continuously produced regardless of chemical makeup of environment

qPCR- TaqMan probe

Fluorescence-labeled oligonucleotides - 5' to 3' exonuclease activity of the polymerase cleaves the probe, releasing the fluorophore into solution, where it is allowed to fluoresce

whole-genome shotgun sequencing (WGS)

Focuses on sequencing all of the DNA in an organism's genome by cutting the DNA into many small, easily sequenced sections then uses computer algorithms to align overlapping segments to assemble the entire genome.

Phases of the cell cycle

G1, S, G2, M Three important checkpoints: G1, G2, and M phases - G1 checkpoint is most important

orthologs

Genes from different species thought to have descended from common ancestor

oncogenes

Genes that induce or continue uncontrolled cell proliferation

proto-oncogenes

Genes that initiate or maintain cell division May become cancer genes (oncogenes) bymutation

IPTG - isopropylthiogalactoside

Gratuitous inducers are analogs of lactose

familial retinoblastoma

Individuals inherit one mutant copy of RB1 gene • 85% to 95% chance of developing the disease

inherited cancer

Inherited genes cause a predisposition to cancer; 5% associated with germ line mutations Mutations are carried in all cells

coactivators

Interact with proteins and enable activators to make contact with promoter-bound factors ; form complex enhanceosome

RNAi is widespread in eukaryotes

It is thought that it evolved by helping organisms protect their genomes against mutational effects of transposable genetic elements

recombinant DNA

Joining of DNA molecules - Produced by artificially joining DNA from different biological sources not found together in nature

absence of lactose

LacI binds as a tetramer to the operator region. It represses the lac operon by preventing open complex formation by RNA polymerase. NO lactose = Enzymes are not needed and expression of genes encoding enzymes is repressed, lac operon and transcription is blocked

____ stimulates transcription of lac operon and induces synthesis of enzymes

Lactose

RB1 tumor suppressor gene

Loss or mutation of RB1 gene contributes to development of cancers due to unregulated progression through cell cycle Originally identified via studies on retinoblastoma: rare retinal cancer

chemical modification of chromatin

Lysine is frequently targeted for methylation Methylation plays a role in converting open chromatin to closed chromatin Demethylation is carried out by histone demethylases (HDMTs)

eukaryotic gene regulation

More complex than that in prokaryotes - Large amount of DNA is associated with histones and other proteins - mRNAs must be spliced, capped and polyadenylated prior to transport from nucleus• - Genes on numerous chromosomes

Methyl (CH3) groups are added to _____ by _______

N terminal histone tails, histone methyltransferases (HMTs)

inducible operon

Operons encoding enzymes that act in catabolism• - Operon is turned on (induced) by substrate(s) for which the structural genes encode - Enzymes needed to metabolize a nutrient are only present when that nutrient is present in the environment

tumor inducing plasmid (Ti plasmid)

Part of the plasmid —transfer DNA (T-DNA) is transferred from the bacterium to plant cell nuclei upon infection - Once inside the plant cell, T-DNA integrates into random locations of the plant genome

transformation: prokaryotes

Plasmids are introduced into bacteria via transformation and hosts are engineered to lack restriction enzymes and recA

CAP (Catabolite-activating protein)

Positive control of the lac operon occurs at the CAP binding site of the lac promoter - The site attracts the CAP-cAMP complex composed of the catabolic activator protein (CAP) and cyclic AMP (cAMP) - Binds to CAP-binding site, facilitating RNA polymerase binding at promoter and facilitating transcription

polymerase chain reaction (PCR)

Process of increasing small quantities (amplifying) of DNA for analysis - Used for diagnostic tests for genetic diseases and detecting pathogens - Reverse-transcription PCR (RT-PCR) uses mRNA as template

control locus

Promoter: recognized by RNA polymerase Operator: acts as an on/off switch for transcription

caspases

Proteases responsible for initiating apoptosis and digesting intracellular components

readers

Proteins that recognize modified histones

activators

Proteins that turn operons on by binding to DNA; enhancer element, enhance transcription initiation

Sporadic retinoblastoma

RB1 gene mutation on chromosome 13

clones

Recovered copies of recombinant DNA molecule - Used to study structure and orientation of DNA

tumor repressor proteins

Repair damaged DNA Control cell adhesion Act in cell-signaling pathways that inhibit the cell cycle

silencers

Repress the level of transcription initiation

catabolite repression

Without CAP-cAMP bound to the lac promoter region, lac gene transcription is very inefficient

because double helix are flexible aromatic macrocyclic flat _____ composed of fused, heterocyclic rings, can ____ between the _____ pairs of bases

hydrophobic molecules, slip, stacked

trpL

Short polypeptide with two back-to-back codons for tryptophan - "sensors" for the availability of tryptophan in the cell Encodes a short polypeptide called the Leader peptide contains four sequences regions (1,2,3,4) and the mRNA produced can form loop structures

Human genomic sequence is 99.9% same with most genetic differences resulting from:

Single nucleotide polymorphisms (SNPs) Copy number variations (CNVs)

genomic alternations associated with cancer include:

Single-nucleotide substitutions Chromosomal rearrangements Deletions

SWI/SNF complex

Slides and relocates nucleosomes. Also functions to open chromatin structure by displacing or ejecting nucleosomes.

epigenetics

Study of factors that affect gene expression but do not alter nucleotide sequence of DNA

co-suppression

Suppressed expression of both endogenous gene and transgene

tumor-suppressor genes

Suppression of the cell cycle can be important in the case of damage to a cell'sDNA - p53 prevents a cell from passing on mutations due to DNA damage - Mutations in the p53 gene prevent suppression of the cell cycle - p53 is the most frequently mutated gene in cancers (50% of all cancers)

microsynteny

Synteny at the level of just a few genes

core promoter region

The core promoter region containing the TATA box and other sequences. -It is immediately adjacent to the start of transcription -It is the sequence to which RNA polymerase II and its associated transcription factors bind

loops in enhanceosomes

The loops allow enhanceosome proteins to interact with RNAP II and transcription factors at the core promoter and proximal promoter elements Loops may be small or large based on the distance between the enhancer sequence and the gene it regulates

sequence specific interactions

The major groove is more accessible for highly specific interactions

lac repressor function

The three segments of the operator share a conserved 21-bp inverted repeat around a central G-C base pair - The tetrameric repressor binds to O1 and O3 and induces DNA loop formation that brings O1 and O3 close together - The loop structure includes part of the promoter and blocks access by RNA polymerase

proto-oncogenes can be converted to oncogenes by:

Translocation gene duplication point mutations

RNAi can silence gene expression transcriptionally and posttranscriptionally T/F?

True

writers and erasers are recruited to specific chromatin locations by DNA binding proteins to modify histone tails, T/F?

True

enhancer element is called the upstream activator sequence (UAS or UASg) T/F?

True - each UASg contains two 17 bp repeat sequences that are binding sites for Gal4

_____ acts as a correpressor by binding to the trp repressor and activating it

Tryptophan

BLAST searches

Used to screen databases and compare a sequence to a known sequence

Single nucleotide polymorphisms (SNPs)

Variations in the DNA sequence due to the change of a single base in genome

cloning vectors

a DNA molecule that can accept foreign DNA, be transferred to a host cell, and get replicated in it - plasmids - phases and viruses - cosmids - artificial chromosomes

electroporation

a brief electrical pulse applied to a solution containing cells creates temporary pores in their plasma membranes, through which DNA can enter

transformation

a normal cell converted to a cancerous cell

autoinducer

a small signal molecule that takes part in quorum sensing

Taq DNA polymerase

a thermostable polymerase used in polymerase chain reaction isolated from Thermus aquaticus - half life is 40 mins at 95 celsius - Low replication fidelity because it lacks a 3' → 5' exonuclease proofreading mechanism

gene regulation

ability of an organism to control which genes are transcribed in response to the environment/ turning on and off genes

Conversion of a proto-oncogene to anoncogene can lead to ____ of the cell cycle

abnormal stimulation

dysplasia

abnormal/disorganized fast development or growth of cells, tissues, or organs -progress to neoplasia

_____ binds to trpO and prevents transcription of the operon

activated repressor

writer enzymes

add chemical groups to chromatin

Principal chemical modifications are _____ and removal of ______ and ______ groups

addition, acetyl , methyl

restriction endonucleases (restriction enzymes)

an enzyme produced by certain bacteria, having the property of cleaving both strands of DNA molecules at or near a specific sequence of nucleotides.

enhanceosomes

are protein complexes that assemble at enhancers to facilitate transcription. - direct DNA bending into loops

presence of lactose

b-galactosidase (LacZ), when at low levels, cleaves and rearranges lactose to make the inducer allolactose. Allolactose binds to LacI, reducing its affinity to the operator and thus allowing induction of the operon. Lactose present: Indirectly induces activation of genes by binding repressor

negative control

binding of a repressor protein to a regulatory DNA sequence and preventing transcription of a gene or gene cluster

Transcription negative control:

binding of a repressor protein to a regulatory DNA sequence and preventing transcription of a gene or gene cluster - Some repressor proteins undergo inactivation - Some repressors undergo activation

positive control

binding of an activator protein to regulatory DNA and initiating gene transcription

Transcription positive control:

binding of an activator protein to regulatory DNA and initiating gene transcription -Allosteric effector compound binding induces a conformational change that activates the DNA-binding domain -Activator proteins have a DNA-binding domain that is converted to in active conformation by binding of an inhibitor to the allosteric domain

repressor has: Allosteric domain

binds a molecule or protein and cause a change in conformation of the DNA-binding domain - allostery

in plants, infection of a single leaf by a virus can generate RNAI response that _______

blocks viral replication and protects the rest of the plant from the infection

BRCA1 and BRCA2 genes increase susceptibility to _____ and ____ cancer

breast, ovarian - BRCA1 and BRCA2 are DNA damage repair genes

programmed cell death

called apoptosis - occurs when DNA /chromosome damage is too sever to repair so cells stop progressing in the cell cycle - prevents cancer - eliminates cells not contributing to final adult organism

cancer-causing agents

carcinogens; - any substance or event that damages DNA and causes mutationsto occur in proto-oncogenes or tumor-suppressor genes

open promoters

cause genes to be constitutively expressed - they have a nucleosome-depleted region (NDR) of 100-150 bp immediately upstream of the transcription start site

covered promoters

characterize genes whose transcription is regulated -transcription is blocked until nucleosomes are displaced or removed from the promoter - There is active competition between nucleosomes and transcription factors for binding

cloning into plasmids

check slides page 18

carcinogens are:

chemcials (natural of sythetic) radiation some viruses

chromatin modifier proteins

chemically alter histone proteins in the nucleosomes by adding or removing chemical groups

binding of repressor proteins to silencer sequences

cis-acting regulatory sequences that directly prevent enhancer-mediated transcription

regulator

composed of the gene that codes for the repressor (lacI) - a protein capable of repressing the operon

hallmarks of cancer

concepts of proto-oncogenes and tumor suppressor genes alone cannot fully describe genetic abnormalities driving cancer development and progression

Drosha enzyme complex

cuts the pri-miRNA near the middle of the stem and produces two segments

DNA ladders or markers

designed for sizing of double-stranded DNA made by restriction digestion of DNA with restriction enzymes

restriction map

diagram that shows the lengths of fragments between restriction sites in the strand of DNA - Provides information on length of cloned insert and location of restriction sites within clone - smallest fragments move farthest down the gel - fragments visualized on gel

fluorescence is _______ proportional to the amount of template at that time

directly

ras genes

encode signal transduction molecules that regulate cell growth and division in cell membrane; most frequently mutated genes in human tumors

activator protein binds at

enhancer element that favor formation of PIC and initiation of translation

transcription of genes in the galactose utilization pathway is carefully regulated by _____

enhancer-like sequences

Gene Silencing by double stranded RNA: Dicer

enzymes that cuts the dsRNA into 21-25 bp fragments of siRNA or miRNA that are bound by RNA-induced silencing complex(RISC), which denatures them

attenuation

fine-tune transcription to match the immediate needs of the cell

SYBR safe

fluorescent dye that is positively-charged and binds non-specifically to DNA predominantly via electrostatic interactions and groove binding

blunt ends:

fragments produced with double-stranded ends

Sticky ends (cohesive ends)

fragments produced with overhangs

GTFs

general transcription factors; trans-acting regulatory proteins, which can bind to their target sequences on any chromosome

homologous genes

genes that are evolutionarily related

the protein Mig1 is produced in the presence of ____ and binds ______ upstream of GAL genes

glucose, silencer sequences

tumor suppressor genes

help prevent uncontrolled cell growth

Most transposons in eukaryotes are located in ____

heterochromatin and are silent

Eukaryotic repressors _____ through different mechanisms than those seen in bacteria

inhibit transcription

pri-miRNA

initial transcript is called primary microRNA; forms double stranded stem of 65-70 nucleotides

defining feature of eukaryotic DNA is _____

its packing into chromatin

proximal elements

located near and upstream of the promoter, regulates genes

repressor has : DNA-binding domain

locates and binds operator or other target DNA sequences

structural locus

made up of three genes, each coding for a different enzyme needed to catabolize lactose 1. lacZ: b-galactosidase 2. lacY: lactose permease 3. lacA: galactoside transacetylase

divalent cations

magnesium or manganese ions - The divalent ions are co-factors of Taq DNA polymerase activity

alternative splicing

many genes code for multiple proteins - HGP found that number of genes is lower than number of predicted proteins

malignant tumors

metastasized cells invading other tissue and causing life-threatening problems

chromatin remodeling

modifications that reposition nucleosomes so as to open or close promoters and other regulatory sequences

codon bias

multiple codons for the same amino acid are not used equally; nonrandom - due to scarcity of some tRNAs - Organisms vary in the degree to which certain codons are used when there is more than one codon for a given amino acid

RISC (RNA-induced silencing complex)

multiprotein complex that contains aprotein in the Argonaute family

results from mutated gene products or abnormally expressed genes:

mutations continue to accumulate; mutations affect multiple cellular functions

delay between exposure to carcinogen and appearance of cancer is an indication of the _____

mutlistep process - ex: leukemia from radiation exposure has incubation period of 5-8 years

DNA and RNA is ____ charged DNA can be _____ and form using gel electrophoresis

negatively separated based on size

cancerous cell is characterized by at least one active _____ and mutation of _____

oncogene , tumor suppressor genes

dideoxynucleotide chain termination sequencing (sanger)

one strand of a DNA fragment is used as a template for synthesis of a nested set of complementary fragments

transgenic plants

plants are infected with bacteria whose plasmids usually cause tumors in plants. the tumor producing gene is inactivated and the bacterial plasmid instead only introduces the desired donor gene - The opine- and tumor-producing genes of T-DNA can be replaced by a gene of interest - The gene is inserted between the left and right borders of the T-DNA

Posttranscriptional regulation

plays an important role in regulating gene expression via alternative splicing

Regulation of inducible or repressible type transcription is under _____ or _____

positive control or negative control

monovalent cations

potassium, sodium and ammonium ions - Monovalent ions stimulate the activity of Taq DNA polymerase and shield the negatively charged phosphate backbone, thereby weakening the electro-repulsive forces between primer and target DNA

closed chromatin

produced by modifications that cause regulatory sites to be covered by nucleosomes, restricting access by regulatory proteins

Encyclopedia of DNA Elements (ENCODE)

project seeking to determine transcriptional start sites, promoters, enhancers, and functional elements in the human genome

Gal4

promoter and enhancer elements bind to regulatory activator protein Gal4 - continuously present in cells - interacts with Gal80 protein and keeps it inactive when galactose is absent

Burkitt's lymphoma

reciprocal translocation between chromo 8 and 2, 14, or 22 -over expression of MYC protein drives excessive cell division

Chronic Myelogenous Leukemia (CML)

reciprocal translocation between chromo 9 and 22 - both mature and immature granulocytes are overproduced in the marrow and blood

open chromatin

relaxed association between DNA and nucleosomes and allows for access by regulatory proteins

eraser enzymes

remove groups from chromatin

high tryptophan levels

ribosome moves to stop codon and region 1 binds to region 2, which leads to the binding of region 3 and region 4, causing termination of transcription prematurely by attenuation

Paradigm of the lactose operon

scientists Jacques Monod and François Jacob proposed the idea that genes could be regulated in E. coli, enzymes used to metabolize - Lactose were inducible - Glucose were constitutive -lactose utilization lacZYA operon of E. coli was the first gene regulatory system described

Copy number variations (CNVs)

segments of DNA that are duplicated or deleted

repressor proteins bind at the ________

silencer elements at a decrease rate of preinitiation complex (PIC) assembly and RNA II polymerase release

plasmids

small circular extrachromosomal double stranded DNA molecules that replicate independently from the bacterial chromosome

promoters

specific region of a gene where RNA polymerase can bind and begin transcription made up of DNA sequence elements: - initiator (Inr) - TATA box -TFIB recognition element (BRE) -Downstream promoter element (DPE) -Motif ten elment (MTE)

chromatin remodeling and modifying enzymes are recruited to

specific sites by trans-acting factors that bind target DNA sequences

SSU rRNA gene

standard method for identifying species

Metatranscriptomics

study of RNA transcripts obtained from an environmental community

functional genomics

study of gene function based on the mRNAs or possible proteins they encode as well as regulatory elements

Metaproteomics

study of protein data obtained from an environmental sample

metagenome

sum total of all DNA sequenced from an environmental sample

antibiotic selection

the process of culturing bacteria on antibiotic-containing medium, which only allows transformed bacteria to grow - To select recombinants / clones, most plasmids havean antibiotic resistance gene

quorum sensing

the process where bacterial cells work together at high density - discovered in Aliivibrio fischeri, a bioluminescent bacterium

multiple _____ factors bind to several different enhancer and promoter elements and fine tune the level of transcription initiation

transcription factors

cis-acting sequences

transcription regulation requires binding of many regulatory factors to specific DNA sequences: promoters, enhancers, silencers - located on same chromosome as gene that it regulates

pre-miRNA

transported to the cytoplasm where dicer removes the terminal loop

____ strains have ___ rates of operon transcription in the presence of tryptophan than trpR+ suggesting a second mechanism for trp operon regulation

trpR-, higher

trpR- cells should produce ______ constitutively as there is no repressor protein to inhibit transcription

tryptophan

retinoblastoma protein (pRB)

tumor-suppressor protein that controls the G1/S cell-cycle checkpoint - prevents passage into S phase - depends on phosphorylation state

Cancer cells not eliminated by the immune system form ____

tumors

synteny

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

benign tumors

unregulated cell growth that forms a multicellular mass, removed by surgery, no serious harm

RNAi plays protective role in response to _____

viral infection