Genetics Final exam 4

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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is pretty outdated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