Genetics Final Exam

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UAS (upstream activating sequence)

Back 1

increases transcription of a gene, enhancer

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GAL4

Back 2

activation domain that binds to UAS

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GAL80

Back 3

inhibitor for GAL4

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GAL3

Back 4

when bound to galactose binds GAL80 after allosteric conformational change and stops it binding GAL4

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HML

Back 5

can initiate change in yeast mating type

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MAT

Back 6

receives change of yeast mating type

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HO endonuclease

Back 7

cuts DNA internally to change yeast mating type

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enhanceosome

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bridge between enhancer and TATA box (DNA looping)

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enhancer

Back 9

stimulate transcription and can act far away from the genes they are regulating

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SWI-SNF

Back 10

large multi-unit protein complex that can reposition nucleosomes (GAL4 can bind and recruit), requires ATP

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methyltransferase

Back 11

adds methyl group

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demethylase

Back 12

removes methyl group

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acetyltransferase

Back 13

adds acetyl group

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deacetylase

Back 14

removes acetyl group

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kinase

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adds phosphate

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phosphatase

Back 16

removes phosphate

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histone code

Back 17

the information content stored in histone modification

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histone tails

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protruding amino terminal ends of histones

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core histones

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H2A, H2B, H3, H4

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histone variants

Back 20

replace core histones with ... ex: CENP-A replaces H3 and H2AZ replaces H2A

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CpG

Back 21

dinucleotides that can be methylated in mammals

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CpG islands

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unmethylated CG dinucleotides found in clusters near gene promoters

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SIR2 (silent information regulator)

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encodes a histone deacetylase = chromatin condensation

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euchromatin

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large area of active chromatin

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large area of inactive chromatin

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heterochromatin

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insulator

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physically separates enhancer from gene or stop spread of heterochromatin, can use DNA loops to separate enhancer from promoter

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Mig1

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represses transcription of GAL when galactose and glucose are present by recruiting tup1

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hyperacetylated

Back 28

histones associated with nucleosomes of active genes

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hypoacetylated

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histones associated with nucleosomes of inactive genes

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maternal imprinting

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copy of gene derived from mother is inactive

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paternal imprinting

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copy of gene derived from father is inactive

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CTCF

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binds to ICR if unmethylated and blocks transcription of Igf2 in maternal imprinting

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ICR (imprinting control region)

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bound by CTCF if unmethylated

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H19

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Only expressed in paternal imprinting

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Ifg2 (internal growth factor)

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only expressed in maternal imprinting

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dosage compensation

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deactivates genes in all but one X chromosome

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Barr body

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inactivated X chromosome in mammals

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Xic

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gene necessary and sufficient to cause X-inactivation

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homeotic mutations

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result in one body part resembling another body part

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hox genes

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affect the identity of body segments and their associated appendages

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homeobox gene

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very highly conserved DNA sequence with a helix-turn-helix structure, only found in higher eukaryotes

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IS (insertion-sequence) element

Back 42

simplest transposable element, encodes transposase, surrounded by small inverted terminal repeats

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prokaryotic composite transposon

Back 43

inverted IS elements on either side, contain new function like resistance

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prokaryotic simple transposon

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contain 2 IR, transposase, resolvase, new function like resistance

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R factor

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plasmids with genes that encode resistance from several antibiotics from many overlapped transposons

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replicative transposition

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increase copy number

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conservative transposition

Back 47

cut and paste

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pol

Back 48

transcribes reverse transcriptase, in all retrotransposons, only in euks

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gag

Back 49

maturation of RNA, in some retrotransposons/retroviruses

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LTR, long terminal repeat

Back 50

flank retrotransposons, retroviruses, in euks

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env

Back 51

viral envelope, in some retrotransposons

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Ac

Back 52

encodes transposase that can move transposons in the same family (Ac or Ds), autonomous

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Ds

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non-autonomous, can be transposed by transposase encoded by Ac

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LINEs

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autonomous, code for pol, long

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SINEs

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non-autonomous, short

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synonymous mutations

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altered codon specifies same amino acid

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missense mutation (conservative)

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altered codon specifies chemically similar amino acid

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missense mutation (nonconservative)

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altered codon specifies chemically dissimilar amino acid

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basic amino acids

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his, lys, arg

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acidic amino acids

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asp, glu

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causes insertion in DNA

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loop in new strand

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causes deletion in DNA

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loop in template strand

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depurination

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loss of a purine base

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CPD (cyclobutane pyrimidine dimer)

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binds to photodiner and splits, needs light

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DNA glycosylase

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cleaves base-sugar bond in base-excision repair, yields AP site

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AP endonuclease

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makes a nick in DNA during base-excision repair

Front 67

deoxyribophosphodiesterase (dRpase)

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removes stretch of DNA in base-excision repair

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GGR (global genomic repair)

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recognition of damaged base followed by NER

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NER (nuclear excision repair)

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repairs damage to more than one base or bulky adducts

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transcription-coupled NER

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RNA pol pauses at site of damage and recruits CSA and CSB

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CSA and CSB

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two proteins that recognize damaged DNA and recruit TFIIH

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XPB and XPD

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helicase subunits of TFIIF

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TFIIH

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protein involved in NER

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mismatch repair

Back 74

1) recognize mismatch, 2) determine correct nucleotide in mismatch, 3) excise incorrect nucleotide; repair

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MutS

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recognizes mismatched nucleotide pair in E. coli

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MutH

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recognizes methylated parents strand and nicks daughter strand in mismatched DNA of E. coli

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MutL and UvrD

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proteins involved in mismatch repair of E. coli

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error-prone repair/translesion/SOS system

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allows for the bypass of stalled replication forks by inserting nonspecific bases

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RecA

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binds to ssDNA in error-prone repair

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bypass polymerase

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tolerates large adducts, lacks 3'-5' proofreading, falls off DNA quickly

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Rad6 and Rad18

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adds ubiquitin monomer to PCNA at start of error-prone repair to recruit bypass polymerase, causes conformation change

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NHEJ (nonhomologous end joining)

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fix double strand breaks in DNA with XRCC4

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KU70 and KU80

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in NHEJ bind to DNA ends to prevent further damage

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SDSA (synthesis-dependent strand annealing)

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error-free repair of double strand break with sister chromatids

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Spo II

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asymmetrical nicking in meiotic recombination

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Rad51 and DmcI

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assist in meiotic recombination

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Ames test

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used to test for carcinogens

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oncogene mutations

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gain of function dominant mutations in genes that encode proteins activated in tumor cells, only one allele needs to be mutated

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proto-oncogene

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WT form of oncogene

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tumor suppressors mutations

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repressive loss of function mutations, need both alleles to be mutated

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Ras oncoprotein

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activated by GTP, cancer causing if blocked and signal remains on

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p53

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tumor suppressor gene that encodes a transcriptional regulator sequence in response to DNA damage

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C-value

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DNA content

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artificial chromosome

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like a plasmid but can accept much larger DNA fragments

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whole-gene shotgun sequencing

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traditional method of sequencing genomes with genomic library, sequencing individual clones and paired-end reads

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paired-end reads

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circular plasmids/artificial chromosomes used to connect contigs by filling in gaps in genome sequencing

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ORF (open reading frame)

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protein coding sequence beginning with an ATG start codon and ending with an in-frame stop codon

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EST (expressed sequence tags)

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short sequence of reads of cDNA from sequencing only the ends

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BLAST (basic local alignment search tool)

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computational tool for identifying nt or aa sequences

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synonymous codon

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multiple codons for a single AA

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codon bias

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certain synonymous codons are used preferentially within protein coding genes of an organism

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pseudogenes

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ORFs or partial ORFs that have accumulated enough mutations to be nonfunctional

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processed pseudogenes

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DNA sequences that have been reverse transcribed from RNA and randomly inserted into the genome

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orthologs

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related genes in similar organisms that usually share similar functions

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paralogs

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relates genes in the same organism that arise by gene duplication and may have different functions

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synteny

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order of genes within chromosomal region is the same as their order in the most recent common ancestor of two species

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CNV (copy number variation)

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variation in the number of copies of DNA sequence between individuals

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DNA microarray analysis

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method to determine gene expression on a genome-wide level

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high throughput seqencing

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alternative to DNA microarray analysis, sequence all cDNA by pyrosequencing for example

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yeast two-hybrid assay

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method to identify protein-protein interactions

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ChIP (chromatin immunoprecipitation)

Back 111

assess protein-DNA interactions, can couple with high throughput sequencing

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Tn10

Back 112

tetracycline resistance, composite, conservative

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Tn3

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amp resistance, simple, replicative

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Ty elements

Back 114

transposable elements in yeast with an RNA intermediate, have LTRs

Front 115

target-site duplication

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duplicate sequences at former overhangs of transposons, direct repeats

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retrovirus

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ssRNA virus that uses DNA intermediate for replication

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alu

Back 117

most abundant SINE in humans, target site for alu restriction enzyme

Front 118

thymidine glycol, 8-oxo-7-hydrodeoxyguanosine

Back 118

mutant bases resulting from oxidative damage

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tup1

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recruited by mig1 and contains a histone deacetylase

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Xi

Back 120

inactivated X chromosome

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Xist

Back 121

non-protein coding RNA from Xic, forms heterochromatin to inactivate one X chromosome

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MCM1 and a1

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proteins present in an a mating type yeast cell

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MCM1, alpha1, and alpha2

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proteins present in an alpha mating type yeast cell

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MCM1, a1, and alpha2

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proteins present in an a/alpha mating type yeast cell

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H3K4

Back 125

activates transcription whether methylated or acetylated

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class II/DNA transposons

Back 126

have short inverted repeats, no RNA intermediate