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Genetics test#2

translation, DNA mutation repair, gene regulation prokaryotes & eukaryotes

Question	Answer
What is the biological polymerization of amino acids into polypeptide chains?	Translation
What materials are required for translation?	amino acids, mRNA, ribosomes, tRNA
What is one difference between eukaryotic and prokaryotic ribosomes?	Eukaryotic ribosomes are bigger and consist of more nucleotides
rRNA genes are____ repetitive and ___ repeated	moderately; tandemly
tRNAs	adapter molecules that have anticodons that base pair with mRNA codons and carry a corresponding amino acid on their 3' end
tRNAs contain	post-transcriptionally modified bases which enhance H-bonding efficiency during translation.(about 10% of nucleotides in tRNA are modified)
Aminoacyl tRNA synthetase charges (activates)	tRNAs with the appropriate amino acid
20 synthetases; 1 for each type of	amino acid
Initiation of translation requires	the small and large ribosomal subunits GTP charged initiator tRNA Mg2+ initiation factors
Initiation of translation in bacteria requires this sequence that procedes the AUG start codon. This sequence pairs with the 16S rRNA of the 30S small ribosomal subunit	Shine-Dalgarno
Elongation requires both ribosomal subunits assembled with the mRNA in order to form these two sites	peptidyl and aminoacyl sites
GTP-dependent release factors cleave the	polypeptide chain from the tRNA and release it from the translation complex
termination is signaled by a	stop codon: UAG, UGA, UAA in the aminoacyl site
mRNAs with several ribosomes translating at once	Polysomes (or polyribosomes)
The eukaryotic equivalent of the Shine-Dalgarno sequence	Kozak sequence
Is protein folding co-translational?	yes
post-translational modification consists of:	1)N-terminal amino acid removed/modified 2)individul amino acid residues sometimes modified 3)carbohydrate side chains may be attached 4)polypeptide chains may be trimmed 5)signal sequences are removed 6)polypeptide chains often complexed with metals
Functional domains	impart different functional capabilities based on folding; exons are proposed to encode these domains; one or more present in proteins
Spontaneous mutation	happens naturally; low rates; vary from species to species and gene to gene
Induced mutations	result from the influence of an extraneous factor
somatic mutations	occur in any cell except germ cells; nontransferable
germ-line mutations	occur in gametes, thus making them transferable
autosomal mutations	occur within the genes located on autosomes
x-linked mutations	occur within genes located on the X chromosome
point mutations	one base pair is altered
missense mutation	change a codon;change amino acid
nonsense mutation	changes a codon into a stop codon causing premature termination of translation
silent mutation	alter a codon; no amino acid change
transition	pyrimidine altered to another pyrimidine or purine altered to another purine
transversion	pyrimidine altered to a purine or vice versa
frameshift mutations	insertions or deletions of a base pair
neutral mutations	(vast majority of all mutations) occur in genes or portions of the genome that don't contain genes; have no effect on gene products
"slippage" leads to	small insertions or deletions
tautomeric shifts(spontaneous, transient repositioning of hydrogen atom)	can result in mutations due to anomalous base pairing
DNA damage by ___ and __ are the most common cause of spontaneous mutation	depurination; deamination
depurination	loss of a purine base
deamination	amino group in cytosine or adenine is converted to uracil and adenine is converted to hypoxanthine
transposons act as	naturally occurring mutagens
alkylating agents donate alkyl groups to amino or keto groups resulting in	transition mutations
intercalating agents	cause frameshift mutations by inserting between purines and pyrimidines; causes distortions which lead to replication errors
UV radiation creates	pyrimidine dimers which distort the DNA conformation causing replication errors
ionizing radiation(gamma rays,xrays,cosmic rays)	mutagenic; transform stable molecules into free radicals
most human genetic diseases are	polygenic but there are some monogenic diseases
trinucleotide repeats	normal: <30; affected >200
CAG repeats	found in coding regions like the polyglutamic tract or in non coding regions like toxic RNAs that sequester regulatory proteins
individuals with type O blood	lack glycosyltransferase activity
DNA proofreading	DNA polymerase III is able to recognize and correct errors in replication; catches 99% of errors
Mismatch repair	corrects errors that remain after proofreading
post replication repair	DNA replication skips over a lesion and requires homologous recombination mediated by the RecA protein
SOS repair system in E.Coli	allows DNA synthesis to become error-prone
photoreactivation repair	in E.coli removes thymine dimers caused by UV light; depends on the activity of the photoreactivation enzyme(PRE)
Two types of excision repair	1)Base excision repair(BER) 2)Nucleotide excision repair (NER)
Excision repair requires three steps	1)removal of mutation(nuclease) 2)gap filling(DNA polymerase) 3)sealing of the nick (DNA ligase)
Base excision repair (BER)	DNA glysolyase enzymes recognize specific bases; enzyme cleaves the glycosyl bond that connects a particular recognized base to the back bone sugar, removing it from the DNA
Nucleotide excision repair (NER)	multienzyme complex scans the DNA for distortions
DNA double strand break repair in eukaryotes	activated when both strands are cleaved; nonhomologous end joining & homologous recombinational repair are the two types
Homologous recombinational repair	digest back the 5' ends of the broken helix; 3' ends interact with a region of undamaged sister chromatid; DNA polymerase copies the undamaged DNA sequence into the damaged strand
The Ames test	uses strains of Salmonella typhimurium with increased sensitivity to mutagens to reveal the presence of specific types of mutations
Inducing mutations can involve these processes	1)ionizing radiation 2)Chemicals-ethylmethanesulfonate(EMS), nitrosoguanidine 3)Transposons
transposons	insert into a gene coding or regulatory region
Chemicals - ethyl methane sulfonate (EMS), nitrosoguanidine	single base pair changes, deletions, insertions
ionizing radiation	chromosomal breaks, deletions, translocations
genetic screen	visual or biochemical examination of large numbers of mutagenized organisms
Bacteria often respond to environmental change by	regulating transcription
Jacob and Monod's operon model	a group of genes is regulated and expressed together as a unit
The structural genes of the lac operon are transcribed as a	polycistronic mRNA
operon	a cluster of functionally related genes undeer coordinated control by a single on-off "switch"
Three parts of the operon	1)operator: stretch of DNA that acts as a regulatory "switch"-usually within the promoter 2)promoter 3)genes that they control
lactose metabolism in E.coli is regulated by an ___ _____	inducible system
lac Z gene	encodes for beta galactosidase which converts lactose into glucose and galactose
lac Y gene	encodes for permease which transports lactose into the bacterial cell
lac A gene	encodes for transacetylase which may be involved in the removal of toxic by-products of lactose digestion from the cell
in the absence of lactose, the lac operon	is bound by the lac repressor molecule at the operator, which blocks transcription of the lac genes
lac I	regulates transcription of the structural genes by producing a repressor molecule
regulatory elements are almost always located____	upstream of the gene cluster they control; cis-acting
molecules that bind cis-acting sites are ______ ____	trans-acting elements
analysis of lac expression in the absence or presence of lactose in ____ ___ ___ was used to prove the operon model for the lac operon	partial diploid merozygotes
if glucose and lactose are both present which does the cell prefer to use?	glucose, because it requires one less step of metabolism
maximal expression requires	no repressor bound at the operator and CAP must be bound at the CAP-binding site
catabolite-activating protein(CAP)	exerts positive control of lac operon; binds the CAP-binding site and facilitates the binding of RNA polymerase at the promoter
Can glucose inhibit CAP? if so how?	yes. cAMP is required for CAP binding. glucose represses the expression of adenylyl cyclase, which catalyzes the production of cAMP
___ ___ analysis of repressor complexes has confirmed the operon model	crystal structure analysis
binding of repressor to operators O1 and O3 creates ___ __ which prevents access of RNA polymerase to promoter	repression loop
binding of the ___ ___ ___ at a cis-acting site can regulate the gene cluster both positively and negatively	trans-acting element
positive regulation	turns on transcription
negative regulation	turns off transcription
Trp operon operator is bound by the repressor in the _______ of tryptophan	presence; the trp operon is a catabolic pathway
the binding of tryptophan to its repressor causes	a conformation change in the repressor allowing it to bind to the operator of the trp operon
attenuator	a regulatory sequence on a leader sequence that precedes trp structural genes
Attenuation	1)when tryptophan is present: transciption of leader regions still occurs but is abruptly halted before the operon genes are transcribed 2)when tryptophan is absent: transciption proceeds through the entire operon
leader sequence can form two conformations depending on the presence or absence of tryptophan	1) 1&2 + 3&4: transcription termination conformation 2) 2&3: non terminating conformation
trp present: _____ structures formed act as a transcriptional terminator	hairpin
trp absent: a different hairpin forms and act as as an ____ and transcription proceeds	antiterminator
other operons that utilize attenuation include	threonine, histidine, leucine, and phenylalanine
B. subtilis utilizes _____ instead of the ribosome stalling mechanism of attenuation	TRAP (trp RNA-binding attenuation protein)
a fully saturated TRAP can bind to 5' leader sequence to form ___ ____ and prevemt the formation of the ___ ____	terminator hairpin; antiterminator hairpin
uncharged tRNAtrp induces expression of the _____ gene, which sends the signal that trp is scarce	anti-TRAP (AT)
The AT protein	associates with TRAP in the tryptophan activated state and inhibits binding to the target leader RNA sequence
trypanosome vsg genes are ___ regulated	temporally. in multicellular eukaryotes these genes are also spatially regulated
prokaryotes ____ and ___; eukaryotes ____ and ____	grow; divide; develop; differentiate;
Gene regulation in eukaryotes is ___ ___ than it is in prokaryotes	more complex. regulation can occur at any one of the steps leading from DNA to protein product
humoral immunity	B-cells produce immunoglobins that bind antigens; each B-cell produces only one type of immunoglobulin; variable regions allow recognition of a specific antigen
___ __ in B-cells contribute to antibody diversity	DNA rearrangement
random recombination: how many different LV and J regions?	30-50 different functional LV regions/ 5 different J regions
two other mechanisms that increase antibody diversity are:	1) imprecise recombination between any pair of LV and J regions 2) high hypermutation(random somatic mutation)
chromatin modification can	regulate gene expression
changes to nucleosomes:	1)histone variants 2)Histone modification 3)chromatin remodeling
histone modification	chemical modification of histone tails alters the structure of chromatin, making genes accessible or inaccessible for transcription
types of histone modification:	1) acetylation by histone acetyltransferase(HAT) opens up chromatin 2)removal of acetyl groups by histone deacetylase(HDAC) closes the configuration 3)phosphorylation 4)methylation
histone code	sum of complex patterns and interactions of histone modifications that change chromatin organization and gene expression
chromatin remodeling	repositioning of nucleosomes lets different chromosomal region become accessible to transcription proteins. an example is SWI/SNF
chromatin remodeling complexes may alter nucleosome structure in several ways including	1)altering contacts between DNA and histones 2)altering the path of the DNA around the nucleosome 3)altering the structure of the nucleosome core itself
DNA methylation	is associated with decreased gene expression. the addtion of methyl groups catalyzed by methyltransferase. occurs most often on the cytosine of CpG dinucleotides; clustered regions called CpG islands
CpG islands	located in and near promoter sequences and adjacent to genes
epigenetic trait	a stable, mitotically and meotically heritable phenotype that results from changes in gene expression without alterations in the DNA sequence
three major epigenetic mechanisms	1)DNA methylation 2)histone modification 3)RNA interference
whether methylation is beneficial or detrimental depends on	the particular gene and on the environment
transcriptionally inert regions are often found to be	hypermethylated
methylation patterns are ____ and ___	tissue-specific; heritable
the incorporation of base analog that cannot be methylated causes what?	a change in the pattern of gene expression by inducing the expression of normally silent genes
histone modification and DNA methylation interact to determine availability for transcription	1)ope n config.=DNA is unmethylated and histones are acetylated, allowing genes to be transcribed 2)closed config.=DNA methylatted at CpG islands and histones are deacetylated. genes can't be transcribed

Created by: ESPOLADE

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Chapters 1-5

translation, DNA mutation repair, gene regulation prokaryotes & eukaryotes

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