Genetics Final exam 4

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The most important model organism

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136 Terms

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The most important model organism

mus musculus

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one gene-one enzyme hypothesis

is pretty outdated

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operon

a group of genes that operate together

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Most all cells in your body have the

EXACT same code. Differentiation is due to differences in gene expression

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world simplest animal

Trichoplax

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Cellular differentiation

the process in which a stem cell alters from one type to a differentiated one

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in eukaryotes, each gene has its own

promoter

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Promoters

can have binding sites for both activator and repressor proteins

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Enhancers

are distal regulatory elements that stimulate gene transcription

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Insulators

can block the effect of enhancers

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Core promoter

similar in every gene; Transcription factors bind

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Regulatory Promoters

mix combos of regulatory elements bounds by activator proteins; Transcriptional activators bind

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Distal promotor

the distal sequence upstream of the gene that may contain additional regulatory elements, often with a weaker influence than the proximal promoter

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Cell signaling

The ability of a cell to receive, process, and transmit signals with its environment and with itself

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Signaling cascade

is a series of chemical reactions that occur within a biological cell when initiated by a stimulus

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histone

protein molecule around which DNA is tightly coiled in chromatin

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primary protein structure

sequence of a chain of amino acids

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secondary protein structure

alpha helix and beta pleated sheet

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tertiary protein structure

3D folding pattern of a protein due to side chain interactions

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quaternary protein structure

multiple protein subunits

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domains

(distinct regions made up of specific amino acid sequences) are associated with unique functions in proteins

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DNA binding motif

Specific activity of proteins which bind DNA and can interact with DNA to turn genes off or on

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Zinc fingers

represent the majority of the DNA-binding motifs in eukaryotes, are involved in several processes

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Leucine zipper:

the Helix-loop-helix (HLH) dimer, is shown bound to DNA fragment — each alpha helix represents a monomer

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Replication protein A

is the major protein that binds to single-stranded DNA in eukaryotic cells.

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SSB proteins

have motifs which favor SSDNA

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proximal promoter elements

modulate the efficiency of basal levels of transcription

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activators

act at core promoter

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co-activator

protein binding

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Regulatory regions

Carry consensus sequences to assist in gene regulation

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Activators

increase transcription initiation

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repressors

decrease transcription initiation

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TFIID

the first general transcription factor to bind the promoter, binds to the TATA box through the TATA binding protein

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Bacterial small regulator RNAs (sRNAs)

small bacterial RNAs that regulate gene expression

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Riboswitch

(prokaryotic)A catalytic RNA whose activity responds to a small ligand

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miRNAs

(eukaryotic) Small noncoding RNA gene that regulate gene expression

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RNA interference (RNAi)

(eukaryotic) introduction of double-stranded RNA into a cell to inhibit gene expression

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RNA silencing

The ability of a dsRNA to suppress expression of the corresponding gene systemically in plants

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siRNA

(eukaryotic) Small interfering RNAs (21-24 nt typically) from a variety of sources that act to suppress gene expression

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Cosuppression

The ability of a tansgene (usually in plants) to inhibit expression of the corresponding endogenous gene (requires sequence similarities)

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RISC

A protein complex containing an Argonaute family protein with endonuclease activity

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RITS

a form of RNA interference by which short RNA molecules trigger the downregulation of transcription of a particular gene or genomic region

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DICER

facilitates the activation of RISC, which is essential for RNA interference

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DNA methylation

adding a methyl group to DNA; deregulates

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Chromatin Remodeling

ATP-dependent movement of nucleosomes relative to the DNA

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Argonaute

common theme in eukaryotic RNA-directed chromatin modification is that small RNAs bound to Argonaute family proteins

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Ubiquitination

Downregulates DNA transcription; reversible and does not result in destruction of histones

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Phosphorylation

Upregulates gene expression associated with cell growth and division

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CpG sites

regions of DNA where a cytosine nucleotide is followed by a guanine nucleotide in the linear sequence of bases along its 5' → 3' direction

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CpG islands

CpG sites occur with high frequency in genomic regions

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DNA methyltransferases

Enzymes that add a methyl group

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Housekeeping genes

constitutive genes that are required for the maintenance of basic cellular function, and are expressed in all cells of an organism under normal circumstances

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RNA-induced transcriptional silencing is mediated by what type of molecule?

Short RNA

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Transcriptional silencing of TE elements was carried out by what type of protein and what type of RNA?

Argonaute and SiRNA(or piRNA)

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Does acetylation of chromatin upregulate or downregulate gene expression?

Upregulate

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What activity do housekeeping genes have?

Essential metabolic activities

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leading cause of death in the West

Cancer

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Cancer

a genetic disease at the somatic level, characterized by gene products derived from mutated or abnormally expressed genes

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Cancer RARELY arises from single gene mutation but instead from

the accumulation of mutations in many genes

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proliferation

Abnormal cell growth and division results in tumors

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metastasis

Defects in normal restraints that prevent cells from spreading

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Benign tumors

result from unregulated cell growth forming a multicellular mass that can be removed by surgery, causing no serious harm. (primary tumors)

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Malignant tumors

result from cells that break loose and form secondary tumors

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clonal

(both primary and secondary) originated from a common ancestral cell

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Cancer stem cell hypothesis

Tumor cells that proliferate give rise to cancer stem cells that have the capacity for self- renewal

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Cancer cells show higher than normal rates of

-Mutation -Chromosomal abnormalities -Genomic instability

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Chronic myelogenous leukemia (CML)

The C-ABL gene on chromosome 9 is translocated into the BCR gene on chromosome 22 (Philadelphia chromosome)

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G1/S checkpoints

monitor cell size and determine whether DNA damage has occured

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G2/M checkpoint

physiological conditions are checked (once G1/S are passed) prior to mitosis

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M

The formation of the spindle-fiber system and the attachment of spindle fibers to the kinetochores associated with the centromeres are monitored

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cyclins and cyclin-dependent kinases (Cdks)

Two types of regulatory proteins are involved in cell cycle control

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apoptosis

programmed cell death

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Proto-oncogenes

genes whose products promote cell growth and division

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oncogene

(a cancer-causing gene) is a mutated or aberrantly expressed proto-oncogene, a gain-of-function alteration

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Tumor-suppressor genes

regulate cell-cycle checkpoints or initiate the process of apoptosis

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ras genes

are mutated in more than 30 percent of human tumors and encode signal transduction molecules that are associated with the cell membrane and regulate cell growth and division

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ras is a

proto-oncogene

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p53 tumor-suppressor gene

mutated in more than 50 percent of all cancers, encodes a nuclear protein that acts as a transcription factor repressing or stimulating transcription of more than 50 different genes (a lot p53=low levels of mutation)

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The p53 protein becomes more stable and transcriptionally active in response to

chemical DNA damage, ionizing radiation , UV light

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p53 protein two responses

Arrest cell cycle followed by DNA repair, or Apoptosis

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RB1 (retinoblastoma 1) tumor-suppressor gene

Loss or mutation of both alleles of this gene contributes to the development of many cancers due to unregulated progression through the cell cycle

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retinoblastoma protein (pRB)

a tumor-suppressor protein that controls the G1/S cell-cycle checkpoint by preventing passage into the S phase

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Retroviruses

can contribute to the development of cancer in animals and humans

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carcinogen examples

aflatoxin, nitrosamines, synthetic Pestides, or abestos

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natural metabolism causes

oxidative products

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E. coli

bacteria model organism

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H. pylori

causes stomach acid

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Recombinant DNA

used to copy or clone DNA, which allowed scientists to isolate and study specific DNA sequences

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Restriction Enzymes

Cut DNA at Specific Recognition Sequences

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Type II restriction enzymes

cleave within or at short specific distances from recognition site; most require magnesium (endonuclease)

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endonucleases

cleaves nucleic acid strand at the middle

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exonucleases

cleaves nucleic acid strands from the ends

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EcoRI

is a type II restriction endonuclease enzyme isolated from species E. coli

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plasmid

an extrachromosomal ds-DNA molecule that replicates independently from the chromosomes within bacterial cells, can be multiple copies per cell

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blue colonies

empty vectors

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white colonies

vectors with insert

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Selection

usually "selects for" one type of cell (the desired cell type) - typically by killing all the others

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Screening

usually refers to a method to distinguish/discriminate between (not live vs. dead) the desired and undesired cell type

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Library screening

used to sort through a library and isolate specific genes of interest

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probe

any DNA or RNA sequence that is complementary to the target gene of sequence to be identified

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