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315 terms

Genetics EXAM 2

Chapter 8.6-17.3 plus lab terms
STUDY
PLAY
Transformation
genetic recombination with DNA
bacteriophage
a virus that infects bacteria
transduction
genetic recombination after phage infection
lysogeny
virus repressed and incorporated into the bacterial chromosome
prophage
the viral DNA that integrates into the chromosome
temperate
viruses that can either lyse cells or act as a prophage
virulent
viruses that only lyse cells
lysogenic
a bacterium with a prophage
DNA and RNA nucleotides
consist of a sugar, a base, and a phosphate group
x-ray diffraction of DNA
the experimental evidence of DNA structure
Gel electrophoresis
separating DNA fragments by size
Avery, MacLeod, and McCarty's experiment
DNA is the 'transforming principle'; used ribonuclease, DNAase, protease.
Hershey/Chase experiment
DNA directs the reproduction of bacteriophages; labeled protein coat and labeled DNA
Meselson-Stahl experiment
evidence that DNA replication is semiconservative in bacteria; used nitrogen isotopes.
semiconservative replication of DNA
one old, one new
replicon
length of DNA replicated from one origin
gyrase
a DNA topoisomerase that relaxes supercoiling downstream by making cuts that undo twists and knots
RNA primer
synthesized under direction of an RNA polymerase called a primase
Primase
RNA polymerase
Fluorescent in situ hybridization (FISH)
can be used to detect chromosomal translocations
chromosome painting
combination of probes produce a unique color pattern for each pair of homologous chromosomes
single stranded binding proteins
help keep the replication bubble open
DNA synthesis
removing the RNA primers and filling the gaps
telomeres
protect chromosomes from fusion or degradation
Tetrahymena
telomerase was discovered by Blackburn and Greider in _________; a single-celled eukaryote.
telomerase
only found in cells that undergo extensive proliferation (embryonic cells, germ cells, stem cells)
reverse transcription
DNA transcribed from RNA
synapsis
pairing of homologous chromosomes during meiosis
degenerate
most amino acids can be specified by more than one codon
frameshift mutation
an insertion of one nucleotide shifts
Wobble rules
only minimum of 30 different tRNAs needed to specify 61 triplets
promoter
specific DNA sequences upstream of a gene
introns
eukaryotic RNA transcripts contain nucleotide segments that are not found in final mRNA product
Snurps
small nuclear RNAs (snRNAs) complexed with proteins
amino acids
subunits of proteins
radical groups
gives tRNAs their chemical identity
Beadle and Tatum
induced and isolated Neurospora mutants that showed auxotrophic growth
protein secondary structures
arrangement of amino acids within certain sections of protein
quaternary level
for proteins made up of more than one subunit that are associated through non covalent bonds
point mutation
single nucleotide substitution that can be a missense, nonsense, or silent mutation
missense mutation
codon now encodes a different amino acid
nonsense mutation
stop codon inserted instead
silent mutation
same amino acid due to 3rd position wobble
Spontaneous mutations
arise from replication errors or tautomer shifts or depurination and deamination
replication errors
wrong nucleotide inserted, slippage in repeat regions
tautomer shifts
(T, G keto to enol; A, C amino to imino) cause anomalous base-pairing
induced mutagens
arise from chemical mutagens, UV light, ionizing radiation
xeroderma pigmentosum
recessive disorder than predisposes individuals to UV-induced DNA damage and skin cancer; mutations in at least 7 genes involved in nucleotide excision repair can cause this disorder
proofreading
DNA polymerase III (bacteria) can also act as 3' to 5' nuclease
mismatch repair
repair enzyme recognizes mismatch in newly synthesized strand
RecA protein
directs recombinational exchange
Ames test
screens compounds for their mutagenicity in Salmonella bacteria
ethylmethane sulfonate (EMS)
introduces point mutations by changing G to A
attenuator
section of mRNA transcribed from the leader sequence with domains that can form hairpins and that has two codons for Tryptophan
terminator
specific mRNA hairpin that forms from domains 3 and 4 in the attenuator sequence
prokaryotic genes
primary level = transcription
chromatic remodeling
an important level of eukaryotic gene regulation
histone acetylation
loosens histones from DNA (decreases attraction between basic histone and acidic DNA)
promoter
necessary for transcription initiation at basal level; located immediately upstream of genes often in standard positions, specify transcriptional start site AND direction of transcription (orientation matters), include TATA, GC, and CAAT boxes
enhancers
necessary for maximum level of transcription; time and tissue-specific gene expression, position is NOT fixed, orientation of element doesn't matter
silencers
repress level of transcription initiation; control gene expression in tissue- or temporal-specific ways
high level of expression
induced when cells expose to heavy metals and steroid hormones
transcription factors
bound to enhancers (or silencers) interact with RNA polymerase II and other basal/general transcription factors
isoforms
different proteins produced from same gene; usually tissue-specific and can be found at different stages of development
Dscam gene (flies)
encodes axon guidance receptors that controls neuronal wiring; has most alternative splicing combinations
jumping genes
can move within or between chromosomes causing mutations where they insert
inducible
a product whose production must be stimulated (usually by a particular molecule)
constitutive
a product that is constantly produced
repressible
production that can be turned off (usually by presence of molecule that system is producing)
cis-acting site
regulatory region adjacent to gene whose expression it controls
trans-acting molecules
molecules that binds to cis-acting sites to regulate expression
lacZ
encodes enzyme that converts lactose to usable glucose
lacY
encoded permease needed for transport of lactose into the cell
lacA
encodes enzyme that might play a role in detoxification
operator-binding site
active site
lactose binding site
regulatory site
regulatory site
reversible interaction with lactose controls activity of LacI protein
Catabolite-activating protein (CAP)
• allows lactose metabolism to also be regulated by glucose
• activates expression of lac operon in the absence of glucose
• inhibits expression of lac operon when glucose is present
attentuation
when an RNA hairpin can stop transcription; discovered by Charles Yanofsky looking at tcp operon
cell proliferation
abnormal cell growth and division
metastasis
ability to invade other parts of body
multiple mutations
needed to convert a normal somatic cell into a malignant cell
genomic instability
duplication, loss, and translocation of whole or part of chromosomes
E6
a proto-oncogene; if viral, inactivates human p53 tumor suppressor
RB1
a tumor suppressor; cell-cycle checkpoints, binds E2F; mutation, deletion, inactivation by viral E7; leads to retinoblastoma, osteosarcoma and many other types of cancers;
retinoblastoma
tumor that develops in the retina due to mutations in both copies of the RB1 tumor suppressor gene; is a major cause of blindness
RB
controls the G1 to S cell cycle checkpoint
unphosphorylated RB
inhibits the E2F transcription factor
E2F
induce expression of >30 genes that control G1 to S transition
oncogene
mutant version of a proto-oncogene
ras proto-oncogenes
mutated in 30% of cancers
human E6/E7 proteins
inactivate two human tumor suppressor proteins p53 and RB at specific times during cell cycle
viral E6/E7 proteins
act as gain-of-function oncogenes; they inactivate human p53 and RB all the time, leading to unregulated progression of cell cycle
TS genes
control cell-cycle checkpoints
cellular apoptosis
cell suicide (if chromosomal defects detected)
ras proto-oncogenes
normal function to transmit signals from cell surface to nucleus that tell cell to divide
gain of function mutants
prevent Ras protein from reverting from active to inactive state ras oncogenes
human papilloma virus (HPV)
a human oncogenic DNA virus; many strains cause warts
p53 tumor suppressor gene
is mutated in more than 50% of human cancers
p53 transcription factor
stops cell cycle until DNA repaired and activates genes leading to apoptosis
plasmid DNA preps
can use E. coli to harvest many copies of recombinant DNA plasmids
restriction enzymes
isolated from bacteria (they use to protect against viral infection); recognize a specific ds DNA sequence (many are palindromic)
plasmid vectors
vehicle for carrying and replicating DNA; replicated independently from host chromosome; has set of restriction sites for inserting gene of interest
selection strategies
antibiotic selection or color selection
antibiotic selection
can use antibiotics to selectively grow E. coli cells with particular plasmid
color selection
some plasmids have this to visualize which do (white) and don't (blue) have gene insertions
lacZ gene
is used for blue/white color selection of recombinant plasmids
X-gal
a lactose analog
lactose analog
produces galactose and a blue compound when cleaved by beta-galactosidase
plasmid DNA
a small circular piece of DNA endogenous to bacteria; independent of the main bacterial chromosome and are independently replicated within the bacterial cell
cDNA
copy DNA; exon sequences only
exons
the DNA segments of a gene that contain the sequences that, through transcription and translation, are eventually represented in the final polypeptide product
introns
An intervening sequence of DNA that lies between coding regions in a gene. Are transcribed but are spliced out of the RNA product and are not represented in the polypeptide encoded by the gene
recombinant DNA
contains cDNA of your favorite gene and can be amplified after it has been transformed into a bacterial cell
restriction enzymes/endonucleases
specialized proteins that recognize specific DNA base pair sequences and cut the DNA at those sites by breaking the phosphodiester bonds in the DNA backbone
recognition sites/sequence
specific DNA base pair sequences
sticky ends
unpaired bases after palindromic sequences are cleaved where the cDNA insert is pasted into a digest plasmid vector using the enzyme DNA ligase
DNA ligase
the enzyme used to paste cDNA insert into a digested plasmid vector; uses energy from the hydrolysis of ATP to make the new phosphodiester bonds, resulting in a circular recombinant plasmid DNA
vector
Vehicle for carrying and replicating DNA
purpose of genetic cloning
to produce multiple copies of your favorite gene in order to study the structure and expression of that gene
multiple cloning site (MCS)
a region that most plasmids used for cloning have been genetically engineered to have
lacZ gene
codes for a protein that converts the colorless artificial substrate, X-gal, to a blue colored derivative; the presence of this gene in the plasmid allows for the selection of transformed bacterial cells that have taken up recombinant plasmid as opposed to plasmid only
PolA1
strongly reduces ability to repair DNA; mutation
I, II, III
Polymerase _______ exhibit 5' to 3' polymerization
I, II, III
Polymerase _______ exhibit 3' to 5' exonuclease activity
I
Polymerase _______ exhibit 5' to 3' exonuclease activity
3' to 5'
_______ exonuclease activity used in proofreading
III
Polymerase _______ carries out main task of DNA replication
I
Polymerase _______ is the most present
5' to 3'
elongation of DNA is ______
polymerase
_______ fills in gaps of DNA
ligase
_______ connects pieces of DNA
telomerase
_______ fills in gaps of DNA by 3' end
telomerase
discovered by Blackburn and Greider
endonuclease
________ introduces nicks before and during recombination
heteroduplex
double stranded molecule of DNA produced from genetic recombination
Holliday structure
________ forms during recombination
ligation
________ creates recombinant duplexes
19000-73000 microns
length of one human chromosome
2 meters
length of combined DNA in one cell
5-10 microns
diameter of nucleus
positively
histone is _______ charged.
nucleosome
DNA wrapped around histone proteins
heterochromatin
silent (condensed) chromatin
euchromatin
active chromatin
Acetylated
_______ histones are associated with open form of chromatin
Deacetylated
________ histones are associated with a closed form of chromatin
methylation
________ correlates with genes being switched off; silencing genes
20
number of amino acids
universal
genetic code is __________
locally
insertion of 3 nucleotides shifts the frame ______
degeneracy
the ability of elements that are structurally different to perform the same function or yield the same output
triple binding assay
__________ reveal degeneracy of the genetic code
wobble hypothesis
pattern of degeneracy of genetic code led to _______
sigma
RNA polymerase _____ subunit recognizes promoter (specific DNA sequences upstream)
transcription
the process of creating a complementary RNA copy of a sequence of DNA
reverse transcription
telomerase fills in gaps through _______
polycistronic mRNA
a large mRNA (or clusters of bacterial genes) that encodes more than one protein
poly-A tail
added to mRNA after transcription; multiple adenosine monophosphates
tetrahymena
capable of excising their own introns
spliceosomes
complex of snRNA (snurps) and protein subunits that removes introns
cis-elements
region of DNA or RNA that regulates the expression of genes located on that same molecule of DNA
TATA box
DNA sequence (cis-regulatory element) found in the promoter region; 35 bases upstream
CAAT box
distinct pattern of nucleotides with GGCCAATCT consensus sequence that occur upstream by 75-80 bases to the initial transcription site
enhancer
short region of DNA that can be bound with proteins to enhance transcription levels of genes; can be upstream, downstream, or within a gene; optimizes transcription
poly-A tail
Eukaryotic mRNAs without a _____ are rapidly degraded
N-terminus
start of a protein or polypeptide terminated by an amino acid; amino end
C-terminus
the end of an amino acid chain terminated by a free carboxyl group; carboxyl end
3'
amino acid is bound to ________ side in tRNA
Cloverleaf model
model for tRNA
5' to 3'
mRNA is translated ______' to ______'
EF-Tu
mediates the entry of the aminoacyl-tRNA into a free site of the ribosome
Aminoacyl-tRNA
tRNA to which an amino acid is adhered
EF-G
catalyzes the translocation of the tRNA and mRNA down the ribosome at the end of each round of polypeptide elongation
PKU
rare condition in which a baby is born without the ability to properly break down an amino acid called phenylalanine.
Beadle and Tatum
created one gene, one enzyme hypothesis
depurination
Base is removed and DNA polymerase doesn't know which nucleotide
thymine dimers
_________ are specifically induced by UV light; inhibit normal DNA replication
nucleotide excision repair
repair of UV-induced thymine dimers
28
______ nucleotides are excised in eukaryotes during nucleotide excision repair
methylated parent strand
how do repair enzymes recognize the newly synthesized strand from the parent strand in Mismatch Repair?
mutagenicity
rate at which revertants induce mutations compared to spontaneous mutations
double-stranded break
lead to chromosome rearrangements, cell death or cancer; very bad
Homologous recombination DNA repair
sister chromatid serves as template since both DNA parental strands are damaged; in response to ionizing radiation
transposable elements
another source of spontaneous mutations; jumping genes
Barbara McClintock
discovered transposable elements
ds
________ movement dependent on presence of association (ac)
ac
________ movement is autonomous
ac
in the absence of ____, ds is not transposable
ds
in the presence of ac, ___ may be transposed.
transposons
transposable elements
trans-acting
LacI inducer is _________ factor
lactose binding site
If _________ region of LacI repressor is defective, transcription of lac operon will never occur
constitutive
If region of LacI protein that binds operator is defective, _________ transcription of lac operon occurs
lactose
______ induces lactose
lactose
In the presence of ______, the LacI repressor does not prevent transciption of lac operon
prevents
In the absence of lactose, the LacI repressor ______
transcription of lac operon
active site
site on lac1 that binds to operator and shuts it down
regulatory site
lactose binding site of lac1
inducible
lactose metabolism is an ________ system
lactose
important form of energy if glucose is not present
galactosidase
enzyme induced by lactose
transposase
creates breaks in chromosomes, allows transposons to insert themselves
allosteric
can reversibly react with a molecule
cAMP
binds to CAP in the absence of glucose
transcription
prokaryotic genes are regulated at _______ or primary level
histone acetylation
loosens histones from DNA (decreases attraction between basic histone and acidic DNA)
alteration of DNA-histone contact
sliding chromatin exposes DNA
alteration of DNA path
DNA pulled off chromatin
remodeling of nucleosome core particle
nucleosome dimer forms
eukaryotic
______ genes regulated at many levels. (memorize steps)
Alternative splicing
process by which the exons of the RNA produced by transcription of a geneare reconnected in multiple ways during RNA splicing; The resulting different mRNAs may be translated into different protein isoforms; thus, a single gene may code for multiple proteins
primary tumor
uncontrolled cell proliferation leads to formation of a ___________ which is usually not the cause of death
secondary tumors
when cells begin to metastasize, _______ can form which are malignant
age-related
mutations accumulate over time: cancer is often ______
carcinogens
________ induce cancer
proto-oncogenes
promotes cell cycle, gain of function
tumor suppressor
loss of function, restricts movement through the cell cycle
cellular apoptosis
cell suicide
tumor suppressor
both copies of gene must be nonfunctional to cause cancer
tumor suppressor
initiate cellular apoptosis if chromosomal defects detected
tumor suppressor
control cell-cycle checkpoints
Cell cycle checkpoints
___________ prevent uncontrolled cell division and growth
apoptosis
if DNA or chromosomal damage is so severe that repair is impossible, cells initiate _______
spontaneous
cancer is usually _________
one
______ (number) mutation needed in proto-oncogenes to cause cancer
Gain-of-function
___________ mutations in proto-oncogenes cause cancer
ras proto-oncogenes
transmit signals from cell surface to nucleus for cell to divide
human papilloma virus
can lead to cervical, anal, penile, vaginal, and oral cancer
e6 and e7
viral ________ act like oncogenes
e7
viral ______ inactivates RB tumor suppressor
rb
controls g1 to s cycle checkpoint
p53
crucial in multicellular organisms, where it regulates the cell cycle and, thus, functions as a tumor suppressor that is involved in preventing cancer
p53
Activates genes that halt cell cycle. Allows for genes to correct.
Reverse transcriptase
Which enzyme makes DNA from an RNA template?
thymine
______ is the same as 5-methyl uracil.
T
T or F
In forming a nucleotide, phosphate is most often attached to the nucleoside at the C-5' position of the sugar.
C-3' and C-5'
To which positions in the sugar of a deoxyribonucleotide can a phosphate be esterified?
F
T or F
Both DNA and RNA follow Chargaff's rules of base pairing.
FISH
Which technique can be used to identify the location of genes on a chromosome?
F
T or F
The two replication forks move in the same direction.
conservative
In the Meselson-Stahl experiment, which mode of replication was ELIMINATED based on data derived after one generation of replication?
III
Which DNA polymerase is mainly responsible for genome replication in E. coli?
gyrase
Which enzyme in E. coli is responsible for relieving the tension ahead of the fork that results when the DNA is unwound to form the replication bubble or eye?
OH
RNA primer is considered essential for DNA synthesis by DNA polymerase III because the enzyme requires a free 3'-___ group to initiate synthesis.
OH or PO4
T
T or F
Okazaki fragments are short fragments of DNA joined by DNA ligase.
3' to 5' exonuclease
Which activity of E. coli DNA polymerase I is responsible for proofreading the newly synthesized DNA?
T
T or F
Telomeres are only a component of linear chromosomes.
T
T or F
DNA synthesis is continuous on the leading strand and discontinuous on the lagging strand.
F
T or F
DNA synthesis is discontinuous on the leading strand.
F
T or F
DNA synthesis is conservative on the leading strand and semiconservative on the lagging strand.
discontinuous
The discovery of Okazaki fragments suggested that DNA synthesis is _______.
I
Which DNA polymerase is responsible for the removal of the RNA primers at the origin and at the 5' ends of the Okazaki fragments in E. coli?
F
T or F
The direction of DNA synthesis by DNA polymerases is sometimes 5' to 3' and sometimes 3' to 5', depending on whether the organism is a prokaryote or a eukaryote.
F
T or F
The data obtained from the Meselson-Stahl experiment after one generation of replication eliminated the dispersive model of DNA replication.
DNA polymerase
Which enzyme catalyzes the addition of nucleotides to a growing DNA chain?
homologous recombination
Crossing over in prophase I is an example of _______.
T
T or F
The process that determines the length of heteroduplex DNA on the chromatids is called branch migration.
Chromatids
Which structures can be involved in homologous recombination?
__________ of homologous chromosomes
gene conversion
In a Neurospora cross of a strain with the d allele to one with the wild-type allele, some asci were found with a ratio of three d spores and one + spore. This result may be due to _______.
gene conversion
Which event is the consequence of a mismatch in the heteroduplex that forms during general recombination?
Double-stranded branched DNA
Which forms of DNA has NOT been observed as a chromosome of viruses?
F
T or F
The entire genome of the ancestral bacteria has been preserved in present-day mitochondria and chloroplasts.
F
T or F
The majority of proteins that function in mitochondria are encoded by mitochondrial genes.
F
T or F
Mitochondrial genes closely resemble eukaryotic nuclear genes.
F
T or F
Introns are found only in nuclear genes.
F
T or F
Mitochondrial DNAs are similar among all eukaryotes.
T
T or F
Chromosomal DNA is associated with both histone and nonhistone proteins.
Two tetramers of histone proteins
What makes up the protein component of a nucleosome?
Coiling around nucleosomes
What is the first order of chromatin packing?
F
T or F
The diameter of the chromatin fiber is 25 nm.
T
T or F
The diameter of a DNA double helix is 20 Angstroms.
F
T or F
The second order of chromatin packing occurs when nucleosomes coil together to form a fiber that is 300 nm in diameter.
T
T or F
The second order of chromatin packing occurs when nucleosomes coil together to form a solenoid fiber that is 30 nm in diameter.
T
T or F
Euchromatin is replicated earlier than heterochromatin.
H1
Which histone protein attaches to DNA strands between nucleosomes?
F
T or F
Heterochromatin replicates early in S phase.
T
T or F
Heterochromatin replicates late in S phase.
F
T or F
Telomerase DNA is an example of repetitive DNA.
F
T or F
rRNA genes are found within satellite DNA.
F
T or F
The eukaryotic genome is composed primarily of functional genes with little excess DNA.
T
T or F
Mitochondria and chloroplasts arose independently from free-living bacteria.
T
T or F
Eukaryotic cells engulfed the ancestral bacteria from which mitochondria and chloroplasts are derived, and the two entities formed a symbiotic relationship.
T
T or F
The ancestral bacteria from which mitochondria and chloroplasts are derived were capable of photosynthesis and aerobic respiration.
T
T or F
Telomeres are organized into heterochromatin.
F
T or F
Telomeres are organized as euchromatin.
T
T or F
Telomeres are composed of short tandem repeats.
T
T or F
Telomeres are highly conserved in evolution.
II
Which RNA polymerase transcribes protein-coding genes into mRNA in eukaryotes?
5'
The addition of a 7-mG cap at the ____ end
3'
the addition of a poly-A sequence at the _____ end
degenerate
Both the codons UUU and UUC specify for the amino acid phenylalanine. What is the term for this phenomenon?
T
T or F
The genetic code is unambiguous, meaning that a codon specifies only a single amino acid.
F
T or F
The genetic code varies by organism and must be determined for each.
T
T or F
Although nearly all enzymes are proteins,not all proteins are enzymes.
F
T or F
Hemoglobin is a covalently bound tetramere made up of 4 proteins: 2 alpha subunits and 2 beta subunits.
beta subunit
What is affected in sickle cell anemia?
T
T or F
As wavelength decreases, energy increases.
solenoid
A set of 6 nucleosomes is called a __________.
F
T or F
When referring to tumor suppressor gene, cancer loss of heterozygosity is likely to suppress cancer formation.
Griffith's experiment
At the end of this experiment the person mixed living IIR(avirulent) and heat-killed IIIS(before heat killed is virulent) and the mouse died....and it turned out that living IIIS was recovered.
F
T or F
The purine Uracil is RNA-specific
T
T or F
The pyrimidine Thymine is DNA specific
F
T or F
The lagging strand has to have an RNA primer, but the leading strand does not.
T
T or F
When tryptophan is present..... the repressor binds to tryptophan and then they both bind to the operator preventing transcription.
ITR
part of the transposable element that shows transposase where to cut
Postreplication repair
fixing replication errors that weren't corrected by normal proofreading and mismatch repair
trp
_______ operon is a repressible system
P site
At the beginning, in which site does the initiator tRNA(fmet) bind to mRNA codon
peptidyl transferase
Peptide bond formation is catalyzed by_________.
uncharged
When tRNA is in the E site is it charged or uncharged?
fragile X and Huntingtons
2 diseases that effect nucleotide repeats
NO
If you were to study the molecular structure of an amino acid chain and knew the amino acids that are used in making the specific protein, could you find out the sequence of DNA for that protein.
F
T or F
RecA is the only protein required for bacterial recombination.
RNA polymerase II
Which RNA polymerase transcribes protein-coding genes into mRNA in eukaryotes?