BIOL 202 Final Exam
What is the outcome of telophase 2
4 unique haploid daughter cells
AFTER REPLICATION A human female has ___ autosomes, ____ chromatids, and _____ sex chromosomes
44; 88; four x (92 chromatids total)
AFTER REPLICATION A human male has ___ autosomes, ____ chromatids, and _____ sex chromosomes
44; 88; two x and two y (92 chromatids total)
At the beginning of meoisis, a human cell has ____ chromosomes and ____ chromatids in the form of ______________________
46; 92; homologous pairs
How many form of DNA polymerase are in eukaryotes
5
What are the 3 components of a single nucleotide
5 carbon sugar, nitrogenous base, phosphate group
Transcription termination region is on the ____ end of the template strand
5'
Which side of the mRNA is the start codon on
5'
What DNA sequence does an ORF begin with
5' - ATG - 3'
What are the three sequences an ORF could end with
5' - TAA - 3' 5' - TAG - 3' 5' - TGA - 3'
What is attached to 4' carbon in deoxy/ribose
5' carbon
Forward primer has identical sequence to ______________ strand
5' to 3'
If the coding strand is 5' to 3' then the mRNA strand would be __________
5' to 3'
Ribosome reads RNA during translation in the __________________ direction
5' to 3'
Transposons compose approximately ____% of the human genome
50
if 35% of mutant flies show wild type appearance, mutant gene has penetrance of
65%
Hexaploidy number
6n
How long of a cells life is spent in interphase
90%
With no gene interactions, what is the mendelian ratio for a dihybrid cross
9:3:3:1
recessive epistasis ratio
9:3:4
inducible expression
Expression of genes that encode products only when they are needed by the cell.
Down Syndrome (Trisomy 21)
Extra chromosome 21 (2n +1) in some or all cells
What is considered high triglyceride levels
200+
Can CAP bind to the lac operon in the absence of cAMP?
No, cAMP-CAP complex is only active if glucose, and therefore cAMP, is present
Do all cells have the same set of transcription factors expressed?
No, they are expressed when they are needed such as in response to developmental cues or environmental stimuli
apurinic site
a site in DNA that is missing a purine base
Consensus sequences are (cis/trans)
cis
Describe the role of gyrase in DNA replication
corrects DNA supercoiling, relieving tension and allowing replication to continue
mutations are only heritable if they take place in ______________ cells
germ-line (gametes)
Ex.) n = 6 means that a cell is __________ and has ___ chromosomes and __________ homologous pairs
haploid; 6; 0
what is the function of repetitive DNA
often nothing
What is an intron
sequence of DNA that is not involved in coding for a protein; separates exons
Describe the difference between sex-limited and sex-influenced disorders
sex-limited can ONLY appear in one sex but sex-influenced is just MORE LIKELY to appear in one over the other
Repeat sequences (CRISPR)
short, palindromic, interspersed DNA sequences
In eukaryotes, Repressors bind to
silencers
What happens when the repressor is bound to the operator
It inhibits the action of RNA polymerase, effectively repressing the transcription of the structural genes
Describe the structure of chromatin
"Beads" of nucleosomes
Formula for calculating m.u. from the number of parental and recombinant gametes
# of recombinant gametes ------------------------------- x 100 = __________m.u. # of parental gametes
# of Barr bodies =
(# of X chromosomes) - 1
crRNA
(CRISPR RNA) Complementary to phage DNA and tells Cas9 where to cut
gRNA
(Guide RNA) chimera (crRNA and tracrRNA combined)
tracrRNA
(Trans Activating Crispr RNA) recruits Cas9 and holds crRNA in place
Why is blood type genetics a polymorphism
It is a case of multiple alleles
In a pedigree, what does a blank circle mean
unaffected female
In a pedigree, what does a blank rectangle mean
unaffected male
When does cAMP bind to CAP site
under high levels of glucose
How does the Iˢ mutation affects the lac operon
uninducible (always off) because the repressor is always bound to the operator, regardless of if lactose is present
What effect does the P⁻ mutation have on the lac operon
uninducible expression of structural genes - if the RNAP cannot bind to the promoter, transcription will never occur
If the lac operon has the genotype of (I⁺O⁺Z⁻Y⁺), describe the regulation for the Z and Y structural genes
uninducible for Z, inducible for Y
If the lac operon has the genotype of (Iˢ O⁺Z⁺Y⁺), describe the regulation for the Z and Y structural genes
uninducible for both
What is the purpose of telomeres
Prevents the ends of DNA from accidentally attaching to each other or the loss of genes
snRNA (small nuclear RNA)
RNA molecule of around 200 nucleotides that participates in RNA splicing
Describe the role of primase in DNA replication
RNA polymerase which creates RNA primers for DNA polymerase to begin replication of DNA from
What forms RNA primers
RNA primase
Is I⁻ recessive or dominant to I⁺
Recessive
Describe the density of euchromatin
Relatively uncoiled compared to heterochromatin
What is the phenotype of the Iˢ mutation
Repressor cannot bind to lactose
What is the negative regulation of the lac operon
Repressor will block transcription unless removed by lactose
What are the two CAS proteins
Restriction endonuclease and helicase
Describe Rho-dependent termination
Rho protein binds to G-C rich regions and displays helicase activity separating the RNA strand from the DNA template strand.
What is the most abundant type of RNA
Ribosomal RNA (rRNA) (~80%)
Describe genomic imprinting
The offspring only expresses an allele from one parent
Penetrance
The percentage of individuals with a particular genotype that actually displays the phenotype associated with the genotype.
After performing a chi-squared tests, a p value less than 0.05 means...
The differences between the expected and experimental are NOT due to chance
After performing a chi-squared tests, a p value more than or equal to 0.05 means...
The differences between the expected and experimental are due to chance
How does electrophoresis work?
The gel box has an electric field with a positive and negative end. DNA is negatively charged so it migrates to the positive end.
map unit (m.u.)
Unit of measure for distances on a genetic map; distance between genes which one product of meiosis out of 100 is recombinant
What does helicase do?
Unzips DNA
Nirenberg and Leder used the triplet binding assay to determine specific codon assignments. A complex of which of the following components was trapped in the nitrocellulose filter?
charged tRNA, RNA triplet, and ribosome
How can you tell birth order from a pedigree
children furthest to the left are the oldest, new children are added to the right
in a complementation test, you will ALWAYS cross __________________________________ mutants that are mutant for only one gene
homozygous recessive
Are cis-acting regulatory elements present in prokaryotes or eukaryotes
both, but eukaryotes have many more
Is DNA content halved in meiosis 1 or 2
both, goes from diploid to haploid in 1 and remains haploid in 2
Describe the positive regulation of the lac operon in the presence of glucose
cAMP-CAP overrides transcription of the lac operon in the presence of glucose
What type of DNA has no introns
cDNA
What type of DNA does recombinant DNA require for the coding region. Why?
cDNA because normal DNA will have introns which cannot be spliced out by bacteria, resulting into longer, nonfunctional protein chains
What are some common sources of carbon for bacteria
carbohydrates (ex. glucose, galactose, lactose)
loss of function mutation
causes a complete or partial loss of function
gain of function mutation
causes the appearance of a new trait or function or causes the appearance of a trait in inappropriate tissue or at an inappropriate time
Transcription factors are ____-specific
cell; only the cells that need a gene expressed will have the TF's necessary to express it
Why do bacteria need a source of carbon
cellular respiration and synthesis of new molecules
# of chromosomes = # of _____________________
centromeres
How could you epigenetically change expression of a protein
change methylation acetylation pattern
broadly, complementation tests are used to determine...
how many different genes are involved in a phenotype
Forked line method
https://www.youtube.com/watch?v=1rh7im3NNm4
What bonds do tRNA and rRNA interact with
hydrogen bonds
What does β-gal do
hydrolyzes lactose to glucose and galactose
What attaches at the 3' Carbon?
hydroxyl (OH) group to form a phosphodiester bond with the 5' carbon on next phosphate group in the nucleotide chain
What causes gigantism?
hypersecretion of GH
What causes dwarfism?
hyposecretion of GH
Describe the analogy for codominance
if A = red and a = blue, incomplete dominance is Aa = blue and red spotted
Describe the analogy for incomplete dominance phenotypes
if A = red and a = blue, incomplete dominance is Aa = purple
How could a woman be affected by an x-linked recessive disorder
if her dad is affected and her mom is a carrier
What two things could prevent the repressor from binding to the lac operon operator
if lactose binds to the repressor first or if the operator binding site is mutated
When does cAMP not bind to CAP site
if little/no glucose is present
How can a genetic disorder be classified as sex-linked
if some ones sex has literally anything to do with the transmission on the disorder
is a functional lacZ gene after transformation a success or failure? Why?
if the gene is functional, it was not interrupted by the insertion of a cloned gene, so cloning vector re-annealed before it was added
is a non-functional lacZ gene after transformation a success or failure? Why?
if the gene is non-functional, it was interrupted by the successful insertion of a cloned gene
How could two linked genes result in a 1:1:1:1 ratio
if they were far enough apart for enough recombination to occur
in vivo
in a cell in the body
How is the lac operon inducible
it requires the presence of lactose to spark production.
Describe the role of ligase in DNA replication
joins okazaki fragments (created by discontinuous synthesis on the lagging strand) together into a continuous strand bridged by telomeres
What do superscript numbers mean on alleles
just different alleles of the same gene, not necessarily dominant or recessive
How does the presence of glucose affect the lac operon
lac genes will not be expressed, bacteria prefer glucose so if it is present, the cell will not want to metabolize lactose
What is the third structural gene on the lac operon you do not need to know anything about
lacA
What is the gene upstream from the lac operon that codes for the repressor
lacI
What genes codes for permease
lacY
What structural gene codes for β-gal
lacZ
Under what environmental conditions is the lac operon maximally activated
lactose is present and glucose is absent
What problem did BT corn solve
larvae killing corn
more linked genes means (more/less) recombinant gametes
less
complete linkage
linkage between genes that are located close together on the same chromosome with no crossing over between them
The real ORF is determined by which one is...
longest
What is the best strategy for solving questions surrounding independent assortment
look at one trait at a time
Euchromatin has ________ levels of methylation and _________ levels of acetylation
low; high
What is the operon state if there is lactose present
operon is expressed due to lactose binding to repressor leaving the operator open and allowing RNAP to transcribe structural genes
repressible enzymes
normally produced by the cell but its synthesis is turned off when it is not needed
Sliding increases access to DNA by changing _______________
nucleosomes
How many times would the restriction enzyme typically cut the plasmid pre-transformation
once, to make it linear
What is the operon state is there is no lactose present
operon is repressed due to repressor binding to operator and blocking transcription
Related genes are often in clusters called _____________
operons
If two linked genes are far enough apart and the result is a 1:1:1:1 ratio (50% parental and 50% recombinant) this would be indistinguishable from what?
the transmission of 2 unlinked independently assorting genes
What is the one rule all X-linked disorders obey
there can never be father to son transmission
If recombination frequency is less than 50% what does this mean
there is gene linkage
If two homozygous recessive white sweet peas are crossed, what would all purple offspring mean for the complementation test results (White --A/A--> White --B/B--> Purple)
there was complementation to produce wildtype phenotype because mutations are in different genes
If two homozygous recessive white sweet peas are crossed, what would all white offspring mean (White --A/A--> White --B/B--> Purple)
there was no complementation and the mutations are in the same gene
What does it mean if the lac operon is inducible
there will only be transcription in the presence of lactose
What does it mean for two genes to be linked
they are part of the same chromosome
in a complementation test, if two homozygous recessive mutants do not complement...
they must be mutations in the SAME gene
What do spliceosomes do?
they take out introns and splice the exons together
If two homozygous recessive white sweet peas are crossed, what would complementation to produce the wildtype phenotype mean for the offspring (White --A/A--> White --B/B--> Purple)
they would all be purple
How many hydrogen bonds between G and C?
three
What is the purpose of the siRNA pathway
to destroy double-stranded RNA from viruses
why would you do a complementation test
to determine whether 2 mutations are alleles of the same gene or if they are mutations of separate genes
What is the main reason humans have melanin
to protect folate from being broken down
When designing recombinant PRIMERS, where is the restriction enzyme added
to the 5' ends
On the leading strand, daughter strand elongates (toward/away from) the replication fork
toward
Are transcription factors cis or trans
trans
activators are _________-acting elements
trans
are repressors cis or trans
trans
repressors are _________-acting elements
trans
Are the Iˢ and I⁻ genes cis or trans
trans, can affect all structural genes regardless of what chromosome they are on
Is the I repressor cis or trans
trans, can bind to different operators on different strands
In prokaryotes, what is the critical step in gene regulation
transcription, specifically, the binding of RNA polymerase to the promoter
After plating the transformed bacteria, why might a plate be empty
transformation did not work because the plasmids cannot resist the antibiotics on the plate
Where do women get their X chromosomes
one of moms X and dad's only X
What is the phenotype of the Oᶜ mutation
operator sequence wont bind to repressor
True or False: structural genes on the lac operon are alternatively spliced
true
How many hydrogen bonds are between A and T?
two
How many hydrogen bonds are between A and U?
two
How many alleles does each locus have?
two (one from each parent)
When confirming transformation, after DNA is isolated from white/blue screen and digested with restriction enzyme, what does success look like on a gel
two bands
Circular chromosomes are found in ____________ and contain _____ exons and _____ introns per gene
prokaryotes/mitochondria/chloroplasts and contain 1 exon and no introns
Recombinant DNA uses _____________________ promoters and ____________________ genes
prokaryotic promoters and eukaryotic genes
What is the phenotype of the P⁻ mutation
promoter does not bind to RNA polymerase
Template locations for genes are determined by the location of ___________
promoters
In what phase of mitosis does chromatin coil into chromosomes
prophase
In what phase of mitosis does the nuclear envelope dissolve
prophase
transition mutation
purine to purine or pyrimidine to pyrimidine
transversion mutation
purine to pyrimidine or vice versa
Ribosomes are composed of
rRNA and proteins
The types of tandem repeats are
rRNA genes, VNTRs, and STRs
How is the x chromosome to be inactivated chosen
randomly
autosomal recessive disorders are (rare/not rare) and why?
rare, it would be very difficult for two recessive genes in two parents to persist long enough to find each other in a kid
What two things does the process of making recombinant DNA need to start
reaction enzymes and DNA cloning vectors
Most loss of function mutations are (recessive/dominant)
recessive
complementation tests only work for...
recessive mutants, you will ALWAYS cross homozygous recessive mutants that are mutant for only one gene
What is the purpose of the sigma subunit in RNA polymerase
recognizes DNA binding site for initiation of transcription
multiple cloning site
region in cloning vector (plasmid) that has been engineered to contain recognition sites of a number of restriction enzymes
cis elements
regions of non-coding DNA which regulate the transcription of nearby genes
cis acting sites
regulatory sites that regulate genes on the same strand
A stop codon is recognized by...
release factors
What are the two types of CRISPR DNA sequences
repeats and spaces
Where does helicase bind
replication fork
What binds to the operator
repressor
What does lacI code for
repressor
What is the phenotype of the I⁻ mutation
repressor cannot bind to the operator
What is the role of rRNA in ribosomes
responsible for all catalytic translation functions
What effect does the I⁻ mutation have on the lac operon
results in constitutive expression due to the operator always being open
Describe the job of telomerase
reverse transcribes DNA from RNA to extend telomeres
What is rRNA and what does it do?
ribosomal RNA; it makes up the structure of the ribosome
What problem did the golden papaya solve
ringspot virus mutilates the fruit and keeps it from reproducing
What separate during anaphase in mitosis
sister chromatids
hypermorphic mutation
slightly new function (gain of function)
What makes up spliceosomes and what are their functions
snRNA, recognizes the introns and proteins splice them out of the sequence
What RNA is responsible for RNA induced gene silencing and what are its two sub categories
sncRNAs which include small interfering RNAs (siRNAs) and micro RNAs (miRNAs)
In the Ames Test, the appearance of his+ revertants in the presence of a non-mutagenic control compound indicates that ...
some of the reversion mutations are not caused by the mutagen being tested
Enhancers/silencers have ______________ transcription factors they bind to
specific
Melanin
substance that shield nuclei from overexposure to UV light (mutagen)
Is the repressor synthesized or from the environment
synthesized (lacI)
In what phase of mitosis do daughter nuclei appear
telophase
In what phase of meiosis do spindle fibers retract
telophase 1 and 2
Promoter is on the __________ strand
template
What must be present for DNA polymerase III to replicate DNA
template strand
how would you verify mutations are homozygous recessive so a complementation test could be run?
test cross to a true breeding
in vitro
test tube
What is tRNA charging?
the attachment of a tRNA to its appropriate amino acid (3' end of tRNA)
After plating the transformed bacteria, what does a plate with cultures mean
the cells were PROBABLY transformed (all that you know is that they got the abx resistance, they may still not have the cloned gene inserted)
Define cytokinesis
the cytoplasmic division of a cell at the end of mitosis or meiosis, bringing about the separation into two daughter cells.
Cellularly, how can someone be a carrier for a genetic disorder but not exhibit severe symptoms?
the disorder is haplosufficient, the other wildtype gene is sufficient to exude the wildtype phenotype
Proteome
the entire set of proteins expressed by a given cell or group of cells
recombination frequency for two genes is proportional to...
the length of DNA between them on the chromosome
Depurination
the loss of a purine base from a nucleotide, forming an apurinic site
visible mutations
the new allele produces a detectable phenotypic effect
Sum law
the probability of obtaining any single outcome, where that outcome can be achieved by two or more events, is equal to the sum of the individual probabilities of all such events
Product law
the probability of two independent random events both occurring is the product of the individual probabilities of the events
Methylation of DNA
the process by which the methyl groups are added to certain nucleotides in genomic DNA
Plasmid Transformation
the process of introducing a plasmid into the bacterium such that it is "transformed" to a new phenotype
RNA polymerase binds to ___________
the promoter
Variable expressivity
the range of expression of a given phenotype (the degree or intensity)
How can the PCR product insert into the cloning vector
the sticky ends of them correspond to each other due to having used the same restriction enzymes
Epigenetics
the study of environmental influences on gene expression that occur without a DNA change
Can autosomal dominant disorders skip generations
no
How long is a polynucleotide
Longer than an oligonucleotide
Lack of Xist gene expression means...
No X chromosome inactivation
No Xist =
No X chromosome inactivation
In what phase of mitosis does the cell begin to elongate
anaphase
In what phase of meiosis are homologous pairs separated
anaphase 1
In meiosis, when do sister chromatids separate
anaphase 2
In what phase of meiosis do spindle fibers pull single chromatids
anaphase 2
What do inducers do in prokaryotes
block repressors
Are promoters present in prokaryotes or eukaryotes
both
Are repressors present in prokaryotes or eukaryotes
both
are males or females affected by X-linked dominant disorders
both
If the lac operon has the genotype of (I⁺O⁺Z⁺Y⁺), describe the regulation for the Z and Y structural genes
both are inducible
2n means a cell is ______________
diploid
Ex.) 2n = 6 means that a cell is __________ and has ___ chromosomes and __________ homologous pairs
diploid; 6; 3
if two mutants with the same phenotype are crossed and their offspring are wild-type, they (do/do not) complement each other
do
in a complementation test, if two mutants produce wild-type offspring, they (do/do not) complement each other
do
Linked SNPs
do not reside within genes and do not affect protein function
Is Oᶜ recessive or dominant to O⁺
dominant
Is cDNA double or single stranded?
double
What is a phosphate group besides the two oxygens forming bonds to C5'
double bonded oxygen, negative oxygen
Describe first step of PCR
double-stranded DNA is heated to ~95 degrees Celsius to separate the strands so they are accessible
At the 3' end, UTRs are (downstream/upstream) from exons
downstream
Where is the transcription termination located on the gene
downstream from the exons
Describe how the codon chart is degenerate
each amino acid can be coded for by by more than 1 codon
Describe how the codon chart is non-overlapping
each individual ribonucleotide is a part of only 1 codon
How do restriction enzymes differ
each recognizes a specific restriction site
Describe how the codon chart is unambiguous
each specific codon only codes for one amino acid
XIST gene
encodes a non-coding RNA that coats and inactivates the X chromosome
Where are telomeres located
ends of eukaryotic chromosomes
activators bind to
enhancers
what kind of molecules do the three structural genes in the lac operon code for
enzymes
Are enhancers present in prokaryotes or eukaryotes
eukaryotes
Are epigenetic marks present in prokaryotes or eukaryotes
eukaryotes
Are higher order transcriptional complexes present in prokaryotes or eukaryotes
eukaryotes
Are nucleosomes present in prokaryotes or eukaryotes
eukaryotes
Are silencers present in prokaryotes or eukaryotes
eukaryotes
is chromatin-remodeling activity present in prokaryotes or eukaryotes
eukaryotes
What are the two types of melanin
eumelanin and pheomelanin
Is the lac operon and the repressor an example of positive or negative control
negative
What charge does DNA have? Why?
negative because of the negative phosphate group
Gut microbes can synthesize....
neurochemicals
Are transcription factors a post-transcriptional regulatory mechanism?
no
Is chromatin remodeling a post-transcriptional regulatory mechanism?
no
do X-linked dominant disorders skip generations
no
Describe how the codon chart is commaless
no punctuation, codons read without breaks
Three types of DNA test for prenatal babies
Carrier, prenatal, preimplantation
True/False: RNAP is a regulatory factor
False
What do SSBP's prevent
H-bonds between
Autoploidy
Polyploid organism with multiple chromosome sets all from the same species.
Which side of a polypeptide is the C-Terminus
Stop codon
DNA stop codons (5' to 3')
TAA, TAG, TGA
mRNA stop codons
UGA, UAA, UAG
describe with A & B how trans linkage appears
aB/Ab
Spacer sequences (CRISPR)
unique DNA sequences that are complementary (match) to phage DNA
origin of replication (recombinant DNA)
(oriC) Where DNA replication begins enabling the plasmid to reproduce itself
What is separated in anaphase 2
(sister chromatids) x-shaped chromosomes separated into two identical chromatids
Promoter ends at the _____ site
+1
RNA coding region begins at the ___ site on DNA
+1
Transcription begins at the ______ site
+1
Can DNA polymerase initiate the synthesis of DNA on its own?
No, an RNA primer must be present
Are SNP's typically found inside genes
No, but they can be
If there are two genes linked on one chromosome and there is a crossover between two non-sister chromatids. How many combinations are possible?
4
how many Barr bodies do males typically have
0, unless they have a genetic condition giving them more than their normal 1 X chromosome
A haploid human cell has ___ homologous pairs and ___ chromosomes
0; 23
How many chromosomes in a prokaryote
1
If the recombination frequency is 1%, there genes are _____ map units apart
1
Pyrimidines have _ ring(s)
1 ring
1 m.u. is equal to what recombination frequency
1%
When two genes on two different chromosomes independently assort, how many combinations are possible
4
how many Barr bodies do females typically have
1, unless they have a genetic condition giving them more/less than their normal 2 X chromosomes
Triploidy number
3n
dominant epistasis ratio
12:3:1
Variable number tandem repeats (VNTRs)
15-100 BP tandem repeats throughout genome
How many telomeres are on an x-shaped chromosome (2 chromatids)
4
What is the phenotypic ratio for codominance
1:2:1
What is the phenotypic ratio for incomplete dominance
1:2:1
How many alleles does one diploid organism have for a gene for the ABO blood type
2
How many subunits make up a ribosome?
2 (large and small)
About how many genes in the human microbiome
2 million
purines have _ ring(s)
2 rings
What is the outcome of telophase 1
2 unique haploid daughter cells
when two genes are on one chromosome and there is no crossing over, how many combinations are possible
2, its complete linkage
Short tandem repeats (STRs)
2-9 BP tandem repeats throughout genome
How many different kinds of aminoacyl tRNA synthase enzymes are there and why
20 different kinds, one for each amino acid as they are specific to each
BEFORE REPLICATION A human female has ___ autosomes, ____ chromatids, and _____ sex chromosomes
22; 44; two X (46 chromatids total)
BEFORE REPLICATION A human male has ___ autosomes, ____ chromatids, and _____ sex chromosomes
22; 44; x and y (46 chromatids total)
A diploid human cell has ___ homologous pairs and ____ chromosomes
23; 46
Disomy diploid number
2n
Trisomy diploid number
2n + 1
Tetrasomy diploid number
2n + 2
Octosomy diploid number
2n + 6
Monosomy diploid number
2n - 1
How many form of DNA polymerase are in prokaryotes
3
How many alleles exist in the population for a gene for the ABO blood type? What are they?
3 IA, IB, i
How long is a trinucleotide
3 nucleotides
In which direction does the exosome complex degrade mRNA?
3' -> 5'
Where are phosphodiester bonds
3' C --- P --- 5' C (Connects sugar to phosphate group to next sugar)
Where on DNA does DNA polymerase add nucleotides to
3' end (OH group)
What direction must primers be pointing relative to target DNA
3' end of primer must be pointed toward target DNA
If the coding strand is 5' to 3' then the template strand would be __________
3' to 5'
Enhancers
A DNA sequence that recognizes certain transcription factors that can stimulate transcription of nearby genes.
Haplotype
A group of alleles of different genes on a single chromosome that are closely enough linked to be inherited usually as a unit (one from each parent)
expression vector
A cloning vector that contains the requisite prokaryotic promoter where a eukaryotic gene can be inserted and only cDNA not mRNA
Cloned DNA
A fragment of recombinant DNA that can be replicated in host cells
silent mutation
A mutation that changes a single nucleotide, but does not change the amino acid created.
nonsense mutation
A mutation that changes an amino acid codon to one of the three stop codons, resulting in a shorter and usually nonfunctional protein.
neutral mutation
A mutation that has no effect on the organism
Ames test
A procedure using bacteria to identify mutagens and their potential severity
Repressors
A transcription factor that suppresses the transcription of a gene.
In the Griffith experiment, when the heat-killed S and normal R were combined, what occurred
A transforming factor from the heat-killed S made the R virulent and the mice died
Epistasis
A type of gene interaction in which one gene masks or modifies the phenotypic effects of another gene that is independently inherited.
describe with A & B how independent assortment
A/a ; B/b
What four gametes can be made from a dihybrid that is AB on one chromosomes and ab on the other if there is a single crossover between non sister chromatids
AB, Ab, aB, ab
Describe with A & B how cis linkage appears
AB/ab
What mutation keeps triglyceride levels low
APOC3
DNA start codon (5' to 3')
ATG
mRNA start codon
AUG
tRNA wobble
Accurate base pairing is required only in the first 2 nucleotide positions of an mRNA codon, so codons differing in the 3rd "wobble" position may pair with differing mRNA
Euchromatin is generally (inactive/active)
Active
What are the two ways chromatin could be remodeled
Adding functional groups to N-terminus tail of histone proteins or acting on H2.A.Z
How do we designate wildtype alleles in drosophila
Adding superscript positives to denote the wildtype
Acetylation
Addition of an acetyl group to a histone
What are the two purines
Adenine (A) and Guanine (G)
Start codon comes (before/after) the +1 site
After
When confirming transformation, when does two bands mean success
After transformed DNA is isolated and digested with restriction enzyme, a band will show for the desired gene and a band will show for the original cloning vector (restriction enzyme separates them)
When would PCR be used in making recombinant DNA
After transforming agrobacteria to confirm gene insertion and after transforming target organism to confirm vector insertion
What is the purpose of the regulatory region
Aka the Promoter, contains information on where and when a gene will be transcribed
What is the tautomer pair for A and C
Amino - imino
What is the A site of a ribosome?
Aminoacyl site, where each new charged tRNA delivers its amino acid
What is an exon?
An expressed sequence of DNA; codes for a protein
Draw a branch diagram for (R/r; F/f x R/r; F/f)
Answer in camera roll but should be 9:3:3:1
proximal promoter elements
Any regulatory sequence in eukaryotic DNA that is located close to (within 200 base pairs) a promoter and binds a specific protein thereby modulating transcription of the associated protein coding gene
When plating hopeful lacZ-transformed cells on x-gal, what result suggests failure
BLUE. If lacZ is functional, b-gal will be present, which turns x-gal blue. A functional lacZ gene means it was not interrupted by the insertion of a cloned gene
Which replicates first, heterochromatin or euchromatin
Euchromatin
What attaches to the 1' carbon in DNA/RNA?
Bases A to T and G to C
Is prokaryotic DNA replication unidirectional or bidirectional
Bidirectional beginning at Ori C origin
artificial selection
Breeding organisms with specific traits in order to produce offspring with identical traits.
Stop codon side of the polypeptide is the ___ terminus
C
Which is stronger, C-G or A-T and why
C---G forms 3 hydrogen bonds (A--T is 2) due to having an extra ring
consensus sequence
Comprises the most commonly encountered nucleotides found at each specific nucleotide in DNA or RNA
Heterochromatin is found in (eukaryotes/prokaryotes)
Eukaryotes
crRNA fits into __________
Cas9
Describe the Avery, MacLeod, and McCarty experiment
Centrifuged cells to separate different macromolecules and removed one at a time to see which removal would not contain any genetic material; discovered genes were in DNA
cDNA
Complementary DNA. DNA produced synthetically by reverse trascribing mRNA. Because of eukaryotic mRNA splicing, cDNA contains no introns.
Describe semi-conservative replication
DNA double strand separate and act as templates, producing 2 identical copies of the DNA, each has half the original strand and half the new strand
Viral chromosomes are (circular/linear) and DNA is (double/single) stranded
Circular or linear and double or single
Bacterial chromosomes are (circular/linear) and DNA is (double/single) stranded
Circular; single
Are the Oᶜ and P⁻ mutations cis or trans
Cis
Promoters are cis or trans acting?
Cis acting: because it only affects adjacent genes.
Describe the shape of tRNA
Cloverleaf, with an anticodon area to read the mRNA's codon
transcription factors
Collection of proteins that mediate the binding of RNA polymerase and the initiation of transcription.
The same gene in different cells with have the same _______, including all its ________________________________
DNA; regulatory elements
What is the third step of transforming bacteria (recombinant DNA)
Confirming transformation
The TATA box is an example of a...
Core promoter element
What does a restriction enzyme do to DNA structure?
Cuts both strands of DNA within recognition sequence
What does restriction endonuclease do?
Cuts up DNA at a specific recognition site (molecular scissors)
What are the three pyrimidines?
Cytosine (C) Thymine (T) Uracil (U)
Methylation reduces expression by modifying ________
DNA
What kind of primer is used for PCR replication
DNA
What are the two binding sites on the repressor
DNA binding domains and inducer binding domains
If cis elements are the same...
DNA in all cells are is identical
What causes leading and lagging strands of DNA
DNA is antiparrallel, DNA polymerase can only replicate 5' to 3' , leading strand replicated normally, lagging strand loops to temporarily make it the correct direction and, with a new primer each time, polymerase makes discontinuous okazaki fragments to later be joined by ligase
If enhancers or silencers are far from the promoter, how do they interact with the complex of proteins that initiate transcription?
DNA loops bring distant enhancers and silencers into close physical proximity with the promoter regions of the genes that they regulate
What removes RNA primers form the lagging strand and replaces them with DNA?
DNA polymerase I
What removes RNA primers?
DNA polymerase I
Why can telomerase add telomeres but DNA polymerase III cannot
DNA polymerase can only add nucleotides in the 5' -> 3' direction, telomeres are required to be added to the 5' ends of Okazaki fragments (3' -> 5' direction of DNA)
Recombinant DNA
DNA produced by combining DNA from different sources
Transposons (jumping genes)
DNA segments that spontaneously move to new location on same/different chromosome
What is a palindromic sequence?
DNA sequence that is the same when read either 5' to 3' or 3' to 5'
cis elements take the form of _______________________________
DNA sequences
What are the two CRISPR components
DNA sequences (repeats and spacers) and CAS genes/proteins (Restriction endonuclease and helicase)
trans-acting elements
DNA sequences that code for elements which binds to cis elements on other DNA molecules (RNAP is trans-acting and bind to promoter which is cis)
What is a nucleosome
DNA wrapped around histone proteins
What molecule was isolated to be the transforming factor responsible for making R virulent again and who isolated it
DNA, isolated by Avery, McCleod, and McCarthy
If CRISPR is being used to REPLACE a gene, which DSB repair method is used
HDR
Why do people have geographically-grouped skin tones
Darker skin (more melanin) for hot areas to prevent overexposure to UV, lighter skin (less melanin) for cooler areas to allow sufficient vitamin D
Briefly describe Griffith's experiments
Discovered recombinant DNA by injecting a rat with a dead virus and alive molecule similar to the virus and observed the virus transform the molecule into an alive version of the virus
A cell's life consists of interphase and _______________
Division (mitosis/meiosis)
2nd step of CRISPR
Double stranded DNA is unwound and Cas9 site-specifically cleaves it
3rd step of CRISPR
Double stranded break is repaired but a mutation is introduced
After s phase, chromatid count ___________________ and chromosome count ______________________
Doubles; remains the same
Describe the second step of transcription
Elongation: elongation of the RNA sequence in the 5' to 3' direction (RNAP adds to the 3' end of the growing RNA)
Describe the second step of translation
Elongation: polypeptide is elongated as charged tRNAs bring corresponding amino acids to ribosomes (5' to 3')
Mendel's Law of Independent Assortment
Equal segregation of one allele pair is independent of equal segregation of other allele pair during gamete formation
Describe the role of SSBP's (single stranded binding proteins) in replication
Essentially wedges to hold DNA strands apart so it can be replicated
How does the half-life of eukaryotic mRNA compare to prokaryotic mRNA
Eukaryotic has a much longer lifespan
Why do expression vectors require a prokaryotic promoter
Eukaryotic promoters require transcription factors, which prokaryotes do not have
How are SNPs different from single point mutations?
Even when SNPs only change one BP (they can change multiple) they do it in similar ways for a large chunk of the population
What is the E site of a ribosome?
Exit site, where discharged tRNAs leave the ribosome
What causes poly-A tails to shorten (mRNA decay)
Exosome complexes brought to AU-rich sequences in the 3' untranslated region (3' UTR)
True or False: DNA is separated by the same thing in PCR as it is in vivo
False, in vivo DNA is separated by helicase, PCR uses heat
True or False: cDNA contains a promoter
False, only exons
True or False: crossing over occur in prophase 1 and 2
False, only prophase 1
Turner Syndrome
Females with XO (1 missing X chromosome)
What is the possible lifespan if mRNAs
Few minutes to a few days
Describe the first step of transcription
Initiation: RNA polymerase finds genes, accesses template strand, makes a short RNA of build off
Forward primer goes _' to _', while reverse primers go _' to _'
Forward is 5' to 3' and reverse is 3' to 5'
What are the sub-phases of interphase
G1, S, G2
Give an example of a DNA palindrome
GGATCC
epigenetic vs genetic
Genetic changes alter the DNA sequence, epigenetic changes alter the access to the DNA
Describe the first step of translation
Initiation: ribosome/mRNA complex forms, 1st tRNA is charged
On a cellular level, how are plants resistant to herbicides (specifically referring to superweeds)
Genetically modifying the DNA to produce more EPSPS enzymes than the herbicide can bind to and deactivate
Describe how a cell transitions from metabolizing glucose to lactose if both are initially present
Glucose is finally depleted, cAMP levels go up, cAMP binds CAP and the CAP-cAMP complex binds the CAP binding site and promotes transcription of the structural genes.
What inhibits the adenyl cyclase and what is the effect?
Glucose; no cAMP-CAP complex because adenyl cyclase produces cAMP
What are superweeds
Glyphosate (herbicide) resistant weeds which rob crops of nutrients/water/sunlight
Why were codons theorized to be in sets of 3
Groups of 2 would not be enough combinations for 20 amino acids and groups of 4 would be way too many
What do SSBP's prevent
H-bonds between bases
Where do men get their X chromosome
HAS to be from their mother, their father gives them their Y
What are the possible outcomes of a homologous pair going through nondisjunction in meiosis 1
Holologs fail to separate, leading to Trisomy or Monosomy (50/50)
What connects annealed DNA fragmets
Hydrogen bonds
The FUT1 allele is epistatic to the IA/IB which are hypostatic to the FUT1. What does this mean?
IA/IB is dependent on FUT1
Which DNA polymerase is primarily responsible for adding new nucleotides to extend the chain in replication
III (3)
Why might a transformed bacteria produce too long an mRNA strand
If it was transformed with DNA and not cDNA, it still had intron which cannot be spliced out by bacteria so are still translated
In what situation can a eukaryotic promoter be used in recombinant DNA
If the eventual host is a eukaryote
What was the drawback with aqua-advantaged salmon
If their DNA got out it could destroy ecosystems
Why are dominant lethal alleles so rare in a population?
If they are present and able to be passed on, they are also present and able to kill so they must be passed on quickly
Why are DNA primers used for PCR rather than RNA primers
If you used RNA primers, you would have to remove them after replication. This would lead to a shortening of the fragments
Heterochromatin is generally (inactive/active)
Inactive
Is the lac operon inducible or repressible?
Inducible
What is the first step of transforming bacteria (recombinant DNA)
Isolating desired gene with PCR and engineering correct restriction sites with primers
Why is heterochromatin generally inactive
It is too tightly coiled for its DNA to be accessible
What mutation is known as the super repressor
Iˢ
What gene codes for a mutated repressor in the lac operon
I⁻
What repressor mutation results in the repressor being unable to bind to the operator
I⁻
What is the tautomer pair for T and G
Ketone - enol
if an SNP is located very far from a disease-causing gene, why would it be bad at predicting disease
Less effective than if closer because there is more of a chance the SNP and disease causing gene would be separated by crossing over
short interspersed elements (SINEs)
Less than 500 BP interspersed repeats
What occurs after the PCR product is annealed to plasmid
Ligase seals up the DNA backbone
What is the second step of transforming bacteria (recombinant DNA)
Ligating desired gene into multiple cloning site to hybridize cloning vector
Pheomelanin
Lighter pigmentation
How could an "off" gene be turned on in a cell no possessing the correct transcription factors
Linking the coding region to another promoter for a gene that IS expressed
Why are liver extracts used in the Ames test?
Liver enzymes may activate some innocuous compounds, making them mutagenic
What problem did aqua-advantaged salmon solve
Low salmon supply
how do mosaics arise
MITOTIC errors during THEIR early development
What is PGD
Preimplantation genetic diagnosis, isolating embryo and selecting those which you want
Describe the Chase and Hershey Experiment
Marked bacteria with radioactive phosphorus and sulfur (components of DNA and proteins, respectively), bred new generation, found DNA to be radioactive and not protein, confirming inheritable material was in DNA
What is mRNA and what does it do?
Messenger RNA; transcribes instructions on how to make specific proteins from DNA and delivers to ribosomes
How effective do you think a SNP at predicting disease if a SNP is located very close to a disease-causing gene
More effective than if further away because there is less of a chance the SNP and disease causing gene would be separated by crossing over
Where must enhancers be located in relation to a target gene in order to work
Most anywhere on the same chromosome, could be on the same gene, some distance, or thousands of BP's away
Where must silencers be located in relation to a target gene in order to work
Most anywhere on the same chromosome, could be the same gene, some distance, or thousands of BP's away
What is the difference in ingredients for non-homologous end joining (NHEJ) vs. homology-directed repair (HDR)
NHEJ has no repair template so repair mutations are random
Can an O⁺ 'save' a cell with Oᶜ mutation
No, an O⁺ region must be located immediately adjacent to the structural genes because it is a cis element
Start codon side of the polypeptide is the ___ terminus
N
If CRISPR is being used to DELETE a gene, which DSB repair method is used
NHEJ
Tautomers
Nitrogenous base variations that can interconvert by exchanging the location of a proton.
What are the two options for repairing a double-stranded break in CRISPR
Non-homologous end joining (NHEJ) or homology-directed repair (HDR)
What attaches to the 2' carbon in RNA (ribose)
OH group
Out of mitosis, meiosis 1, and meiosis 2, when do homologs pair up
ONLY meiosis 1
Describe dispersive replication
Old and new strands are mixed together in hybrid strands
Describe conservative replication
Old strand pairs with old strand. New strand pairs with new strand
Alternative Splicing of mRNA
One gene can code for more than one protein due to exons being spliced together differently into a variety of different mRNAs
Why are homologous chromosomes paired
One is from the mother and one is from the father and they contain different alleles for the same genes
How many promoters are needed for a recombinant vector
One per gene that needs to be expressed (one for cloned gene, antibiotic/herbicide resistance gene, etc.
Approximately what fraction of genes in the human genome undergo alternative splicing?
Over 95%
heterogeneous nuclear RNA (hnRNA)
Preprocessed mRNA; converted to mRNA by adding a 3' poly-A tail and 5' cap and splicing out introns
Once the cloning vector is combined with the PCR product, how are those few vectors replicated
PCR
What occurs after the cloning vector is cut open
PCR product is annealed to plasmid
If a dihybrid is crossed with a tester and the progeny are 30% AB/ab; 30% ab/ab; 20% Ab/ab; 20% aB/ab What is the dihybrids genotype
Parentals are more common so since the most common outputs are AB and ab, the parental dihybrid must be AB/ab (punnet square of tester (ab) with AB (AB/ab 30% P) with ab (ab/ab 30% P) with Ab (Ab/ab 20% R) with aB (aB/ab 20% R)
What is the P site of a ribosome?
Peptidyl site, where the growing polypeptide still attached to tRNA is located during translation.
If attempting to transform a bacterium with a lacZ plasmid, how can you confirm it was properly inserted
Plate the bacteria on x-gal and see if it shows and white or blue color to determine the presence of b-gal
What is the regulatory region also called
Promoter
In what phase of meiosis do tetrads form
Prophase 1
In what phase of meiosis does crossing over occur?
Prophase 1
Where was genetic information thought to be before its discovery in DNA
Proteins
Transcription factors (TFs)
Proteins that bind promoters and are functional in transcription.
What kind of primer is used for in vivo replication
RNA
What is sncRNA used for
RNA interference (RNAi) to silence specific sequences of mRNAs
The types of interspersed retrotransposons are
SINEs and LINEs
What gene is mutated in most cases of familial ALS?
SOD1
The only type of highly repetitive DNA is
Satellite DNA
Is DNA replication conservative, dispersive, or semi-conservative?
Semi-conservative
What part of RNA polymerase binds to and recognizes DNA transcription site
Sigma subunit
If no polarities for an antiparallel sequence are given, the start codon denotes the ____ end. Why?
Since translation goes 5' to 3' the start codon denotes the 5' end
What is the physical state of DNA after being denatured by heat?
Single stranded
What are the possible outcomes of a homologous pair going through nondisjunction in meiosis 2
Sister chromatids fail to separate, leading to Trisomy (25%), Normal (50%) or Monosomy (25%)
The types of middle repetitive DNA are
Tandem repeats and interspersed retrotranspons
What MUST a sequence have to be an ORF
Start and stop codons
Which side of a polypeptide is the N-Terminus
Start codon
Describe the third step of translation
Stop codon signals release factors and complex dissociates
Both melanin and surfactant genes are present in all cells. Explain why melanin is not expressed in a lung cell.
Surfactant genes have cis-acting regulatory elements that are recognized by transcription factors in lung cells, but those same TF's are not present in skin (where melanin would be)
Complementary siRNA inhibits __________
TRANSLATION, not transcription
What is the 5' -> 3' sequence of a telomere
TTAGGG
What type of DNA is most likely to mutate as a result of DNA polymerase mistakes
Tandem
Describe the difference between interspersed and tandem DNA
Tandem is consecutive groups of repetitive DNA, interspersed is groups of repetitive DNA with spaces between them
Describe intrinsic hairpin termination
Termination sequence "folds" into hairpin shape held together by strong G---C hydrogen bonds to stop transcription by overpowering weaker A--U hydrogen bonds in DNA/RNA complex
Describe the third phase of transcription
Termination: the RNA, RNAP, and DNA dissociate through either Rho-Dependent or Intrinsic hairpin termination
Describe the second step of PCR
The DNA is annealed by lowering the temperature to 50-65 degrees, which allows the left and right primers to find and bind complementary base pairs to the single stranded DNA.
Describe the third step of PCR
The DNA is heated to 72 degrees , which allows taq polymerase to attach to each priming site and synthesize the new strand.
Why is Taq polymerase used in PCR?
The DNA polymerase must be thermostable as PCR involves cycles of heating.
Describe 3' to 5' exonuclease activity.
The ability of DNA polymerase to polymerize in the correct 5' to 3' direction, but if a mistake is made, it can reverse direction to repair the mistake and move on
Pleiotropy
The ability of a single gene to have multiple effects.
How do we designate mutant alleles in drosophila
The absence of a superscript positive
allosteric
The binding of a regulatory molecule to a protein at one site that affects the function of the protein at a different site.
allosteric regulation
The binding of a regulatory molecule to a protein at one site that affects the function of the protein at a different site.
How would a transformed bacteria resist the antibiotics but still not have the cloned (PCR) gene
The cut plasmid sticky ends could have re-annealed before the lacZ (PCR) product was inserted
Why is plating on antibiotics not sufficient for checking if (PCR) cloned gene was inserted into the bacteria
The cut plasmid sticky ends could have re-annealed before the lacZ (PCR) product was inserted and while the bacteria acquired the plasmid, it would be with the abx resistance and NOT the lacZ (PCR) gene
Why are most affected individuals with an autosomal dominant disease usually heterozygotes (Aa) and not homozygotes (AA)
The progeny would need to inherit the same dominant gene from both parents
Reverse primer sequence is _________________
The reverse compliment sequence to the forward primer
What would be predicted for a cell in which the repressor could not bind the inducer?
The structural genes are permanently repressed (opposite of I-) because the mutant repressors cannot interact with the inducer (lactose) Thus, repressors would always bind to the operator sequence
Why is ligase not needed in PCR
There is no lagging strand and therefore no okazaki fragments to join
In an Ames test, why is it important to include control plates that are not treated with the potential mutagen
There will be some spontaneous mutation - you want to use the control plate as a baseline for this. If the plates treated with the potential mutagen have about the same number of revertant colonies as the control, it is likely the result of spontaneous mutations rather than ones induced by the test compound
What are the four ways to categorize mutations
Type of molecular change, effect on function, phenotypic effect, location
Why is it theorized mitochondria/chloroplasts evolved from prokaryotes
They contain DNA similar to bacteria
You can finally answer this. What caused genes to be "off" in certain cells
They do not have the necessary transcription factors to express that gene. TF's are only present in cells where they are needed
Why do indigenous peoples in the arctic have dark skin
They get enough vitamin D from fish-heavy diets so their skin can have maximum UV protection
Describe Nirenberg and Matthaei experiment.
They radioactively labels amino acids to see which codons resulted in them. Radioactive tRNA, RNA triplets, and ribosomes were passed through a filter and if radioactivity WAS retained on the filter then the amino acid WAS coded for by that codon (this had to be done 20 times for every possible codon)
What do farmers want to be resistant to glyphosphate
They want crops to be resistant but weeds not so that they can spray the whole field and not kill any crops
What happens when an individual is homozygous dominant for familial hypercholesterolemia?
They will have a heart attack before 20, sometimes before 5 (no LDL receptors)
Describe the density of heterochromatin
Tightly condensed compared to euchromatin
Why would you ligate a fragment of DNA into a cloning vector?
To replicate the DNA fragment
What were the purpose of Nirenberg's ribonucleotide homopolymers?
To see which amino acids were produced which AAA, UUU, CCC, and GGG
Why would you perform a chi-squared analysis
To test whether deviation form the expected result (null hypothesis) was due to purely chance or not
Why does UV light lead to skin cancer
UV light is a mutagen that, when given access to DNA, can mutate it to be cancerous
Transcribed CRISPR DNA recognizes ______________ via ________________________________________ and the ____________________ cleaves it
Transcribed CRISPR DNA recognizes viral DNA via base pairing and the restriction endonuclease cleaves it
Does RNA polymerase function during transcription or translation
Transcription
Which encompasses a larger sequence, transcription region or translated region
Transcription
In the video, why is pitX normally expressed in a pituitary cell and not an eye cell
Transcription factors are present in the pituitary cells that interact with specific enhancers of pitX (they are not present in an eye cell)
Activators
Transcription factors that turn operons on by binding to enhancers in DNA
What is tRNA and what does it do?
Transfer RNA; carries a specific anticodon that matches with the codon of the mRNA; this provides tRNA with the instructions of what amino acid to bring to protein synthesis in the ribosomes.
What is considered low triglyceride levels
Under 100
In the cake analogy aneuploidy is similar to ________________
Tripling only one ingredient
In the cake analogy euploidy is similar to ________________
Tripling the entire recipe
True or False: Tetrads only form during meiosis because mitosis does not require crossing over
True
True or False: The DNA to be cloned and the plasmid it is to be inserted into are cut with the same restriction enzyme
True
True or False: The lac operon has both positive and negative regulation
True
True or False: The x chromosome chosen to be inactivated will be the same one composing Barr bodies for the rest of that person's life
True
True or False: I⁻ and Oᶜ mutations have the same effect on the lac operon
True, both are constitutive for both Y and Z
True or False: All somatic cells have identical DNA
True, some cells simply express different genes
Describe Lyte's experiments
Trying to transplant microbes to improve mood - found that mice given bacteria known to result in anxiety increased the anxiety of the mice
What is "setting up a digest"
Using a restriction enzyme to cut the DNA into specific sequences
How is genomic imprinting maintained
Using methane, the DNA blocks info from being transmitted to genes.
what problem did golden rice solve
Vitamin A deficiency in people eating rice commonly
When plating hopefully transformed lacZ cells on x-gal, what result suggests success and why?
WHITE. If lacZ is nonfunctional, b-gal will not be present, won't affect x-gal color. A nonfunctional lacZ gene means it was interrupted by the insertion of a cloned gene
When dsRNA is introduced, it ________________ the gene's __________ via _____________ leading to ______________________________
When dsRNA is introduced, it silences the gene's mRNA via RNAi leading to mRNA degradation
How does Acetylation affect transcription
When histones are acetylated, transcription increases because the positive charge on histone decreases which in turn decreases their attractive to negative phosphate groups and makes an opening in the chromatin
Why is Agrobacterium used to make recombinant DNA?
When infecting other cells, it inserts its DNA into them and makes part of the hosts DNA, the agrobacterium's DNA
____ sex chromosome is essential for development
X (X0 is viable, 0Y is not)
Genetic maleness is determined by the presence of .....
Y chromosome
Are epigenetic changes heritable?
Yes
Is DNA methylation heritable?
Yes
Is Iˢ or I⁺ dominant over the other
Yes, Iˢ is dominant
what is the mutated form of lacY
Y⁻
what is the mutated gene for permease
Y⁻
What is the effect of the Y⁻ mutation on the lac operon
Z is normal (inducible) and Y is constitutive
What is the effect of the Z⁻ mutation on the lac operon
Z is uninducible and Y is normal (inducible)
What is the mutated gene for β-gal
Z⁻
Silencers
a DNA sequence capable of binding transcription regulation factors, called repressors, to induce a negative effect on the transcription of its particular gene
lethal mutation
a gene or chromosomal mutation that influences the development of an organism in such a way that the organism cannot survive
lac operon
a gene system whose operator gene and three structural genes control lactose metabolism in E. coli
What performs tRNA charging
aminoacyl tRNA synthase enzyme
What attaches to the 2' carbon in DNA (deoxyribose)
a hydrogen
heterogeneous trait
a mutation at any one of a number of genes can give rise to the same phenotype
null mutation
a mutation that results in complete absence of function for the gene
missense mutation
a nucleotide-pair substitution that results in a codon that codes for a different amino acid
open reading frame (ORF)
a sequence of DNA or RNA that could be translated to give a polypeptide
SNP (single nucleotide polymorphism)
a single base-pair site where variation is found in at least 1% of the population
tautomeric shift
a spontaneous mutation that involves a temporary change in a base structure to occur at the moment DNA polymerase is passing through this specific base. pyrimidines are usually in the keto form (and switch to enol), while purines are usually in amino form (and switch to imino). this creates AG and CT base pairings.
merozygote (partial diploid)
a strain of bacteria containing an extra piece of DNA (ex. extra lac operon) (partial diploid)
With X-linked dominant disorders, describe the transmission for daughters
an affected MALE will pass it to ALL his daughters (they will all be affected)
sticky ends
an end of a DNA double helix at which a few unpaired nucleotides of one strand extend beyond the other.
Cas9
an enzyme that cuts DNA
In what phase of mitosis are sister chromatids pulled to poles
anaphase
How long is an oligonucleotide
about 20 nucleotides
What are the two kinds of transcription factors
activators and repressors
What three things turn hnRNA into mature RNA
adding a 3' poly-A tail, adding a 5' cap, and splicing out introns
Purpose of RNA polymerase
adds nucleotides to growing mRNA strand during transcription
regulatory mutation
affect regulation of gene expression
Causative SNPs
affect the way a protein functions, correlating with a disease or influencing a person's response to medication
where do SSBP's bind
after replication fork
Where does topoisomerase bind?
ahead of the replication fork
What is a complementation group
all mutations present in any single gene
If two homozygous recessive white sweet peas are crossed, what would no complementation mean for the offspring (White --A/A--> White --B/B--> Purple)
all offspring would be white
dominance
allele expresses phenotypic trait in heterozygotes (only 1 copy needed)
recessive
allele expresses phenotypic trait in homozygotes (2 copies needed)
Lactose is a(n) ______________ effector of the repressor
allosteric
cAMP is a(n) _________________ effector of CAP
allosteric
Fertility (F') factor genes
allows genes to be transferred from one bacterium carrying the factor to another bacterium lacking the factor by conjugation
In what phase of mitosis do centromeres break
anaphase
What are the two important sites on tRNA
anti-codon and amino acid binding site
how many alleles for a locus in a population
as many as have been retained from when they originally formed (mutated)
On the lagging strand, daughter strand elongates (toward/away from) the replication fork
away from
When confirming transformation, after DNA is isolated, digested with restriction enzyme, and replicated with primers for desired gene in PCR, what does success look like on a gel
band present at all, if the desired gene was never transformed, this PCR's primers would have nothing to bind to since the gene wouldn't be there
By what metric does electrophoresis separate DNA
base pair length (shorter chains go further through the gel)
cAMP-CAP complex
binding of cAMP activator to CAP enhancer, increases the rate of transcription (like all enhancers)
Different genes will have different __________ regulatory elements
cis
Identical genes will have the same __________ regulatory elements
cis
are enhancers cis or trans
cis
are silencers cis or trans
cis
operators are _________-acting elements
cis
Reverse primer hybridizes to the _____________ strand
coding
The forward primer has the same sequence as the...
coding strand in the same direction
___________ strand is typically given as the consensus sequence. Why?
coding; less work to convert to mRNA
Blood types are (codominant/incompletely dominant)
codominant
gRNA function
combined functions of tracrRNA and crRNA
amorphic (null) mutation
complete loss of function
neomorphic mutation
completely new function (gain of function)
Polyploidy
condition in which an organism has extra WHOLE sets of chromosomes
If the lac operon has the genotype of (I⁻O⁺Z⁺Y⁺), describe the regulation for the Z and Y structural genes
constitutive
What is the effect of the Oᶜ mutation on the lac operon
constitutive expression due to the operator always being open
Describe the expression/regulation of the Z and Y genes with the following genotype: (I⁺OᶜZ⁻Y⁺ / I⁺O⁺Z⁺Y⁺)
constitutive for both
Describe the expression/regulation of the Z and Y genes with the following genotype: (I⁺O⁺Z⁻Y⁺ / I⁺Oᶜ Z⁺Y⁺)
constitutive for both
If the lac operon has the genotype of (Iˢ Oᶜ Z⁺Y⁻), describe the regulation for the Z and Y structural genes
constitutive for both
If the lac operon has the genotype of (I⁺Oᶜ Z⁺Y⁻), describe the regulation for the Z and Y structural genes
constitutive for both
Describe the expression/regulation of the Z and Y genes with the following genotype: (IˢOᶜZ⁻Y⁺ / I⁺Oᶜ Z⁺Y⁺)
constitutive for both (no repressor binding)
Describe the expression/regulation of the Z and Y genes with the following genotype: (I⁻O⁺Z⁺Y⁻ / I⁻O⁺Z⁺Y⁺)
constitutive for both (no repressor binding)
constitutive expression
continuously expressed regardless of environmental conditions
All bonds in DNA are ____________ bonds except those between ___________ which are ______________ bonds
covalent; base pairs; hydrogen
When are recombinant gametes created
crossing over in prophase 1
Linear chromosomes are found in _______________ and contain ________ introns and _________ exons
eukaryotes; more than 1
Eumelanin
darker pigmentation
Describe the purpose of dosage compensation
deactivates one X chromosome in individuals with more than 1 to prevent over-expression of X-linked genes
What reaction occurs to bind two peptides together
dehydration synthesis forms new covalent bond
3 steps of PCR
denaturation, annealing, extension
haplosufficient
describes a gene that, in a diploid cell, can promote wild-type phenotype with only one copy
haploinsufficient
describes a gene that, in a diploid cell, cannot promote wild-type phenotype with only one copy
Describe the effects of localized transcription factors
different cell and protein productions due to....(garland)
What do semi-colons represent in (A/a; B/b x a/a; b/b)
different chromosomes
Exons can be spliced with differing ________________, resulting in different _________________
different expressions result in different proteins (Ex. for a gene with exons 1, 2, and 3, there are 7 possible proteins (1, 2, 3, 123, 12, 13, 23)
trans-acting factors take the form of __________________
diffusible molecules
difference between a dihybrid and a dibybrid cross
dihybrid (AaBb) dihybrid cross (AaBb x Aabb)
how are superweeds created
evolution
What is the coding region of a gene called
exon
How is expressivity different than penetrance
expressivity describes individual variability, not statistical variability among a population of genotypes
Individuals with Turner Syndrome are phenotypically ___________
female (mostly)
How many carbons in DNA sugar
five (pentose)
what are tetrads
found during meiosis - made up of pairs of homologous chromosomes (4 chromatids)
blunt ends
fragment ends of a DNA molecule that are fully base paired, resulting from cleavage by a restriction enzyme
rRNA genes are (functional/nonfunctional)
functional
1st step of CRISPR
gRNA recruits Cas9 to gene of interest
What type of mutation is APOC3
gain of function
Hypostatic
gene being masked
positive gene regulation
gene expression will be off unless a regulatory molecule specifically turns it on
negative gene expression
gene expression will occur unless otherwise shut off by a regulatory molecules
trans acting molecules
gene product (protein or RNA typically) that acts to regulate expression of a target gene on a different strand
selectable marker gene
genes carried by cloning vector (plasmids) for confirmation of vector uptake, often antibiotic resistance, bioluminescence, etc.
If recombination frequency is = 50% what does this mean
genes independently assorted (either far apart on the same chromosome or on different chromosomes)
What are the two ways in which meiotic recombination can occur
genes on different chromosomes (or far apart on the same chromosome (independent assortment) genes near each other on the same chromosome (linked) (crossing over between non-sister homologous chromatids)
epistatic
genes that mask the expression of other genes
Barr bodies are composed of...
heterochromatin
Repetitive DNA composes
heterochromatin
Telomeres and centromeres are composed of
heterochromatin
Heterochromatin has ________ levels of methylation and _________ levels of acetylation
high; low
Which bacteria grow on the agar plate if the Ames test is positive?
his+ prototrophs
explain the connection between the ability to cause reversions in his- bacteria and the ability to cause cancer in humans
his- bacteria need histidine supplemented since they have a mutation that prevents them from synthesizing it themselves. Reversions in his- bacteria colonies are caused by a mutation that reverses the original mutations. If a compound can cause a reversion, that means it must cause mutations. Mutations can lead to cancer in humans.
What do HIS- bacteria need to grow
histidine
Acetylation increases access to DNA through modifying ____________
histones
A cell becomes haploid once ______________________ seperate
homologous chromosomes
Nondisjunction occurs when
homologous chromosomes fail to separate in meiosis 1 or sister chromatids fail to separate in meiosis 2
what is separated in anaphase 1 of meiosis
homologous pairs, sister chromatids are still bound by centromeres in x-shaped chromosomes
true breeding means
homozygous
Are telomeres sequences in tandem or interspersed
in tandem
Barr bodies
inactivated X chromosomes
Blocking the 3'UTR from shortening would lead to...
increased mRNA stability
As the distance between two linked genes increases, recombinant frequency....
increases
Mosaics
individuals whose somatic cells display two different karyotypes (different chromosomal numbers)
In regard to the lac operon, lactose is the ______________
inducer
In the lactose metabolism, lactose is the _____________
inducer
What regulates inducible expression in prokaryotes
inducers
If the lac operon has the genotype of (I⁺O⁺Z⁺Y⁻), describe the regulation for the Z and Y structural genes
inducible for Z, constitutive for Y
Describe the expression/regulation of the Z and Y genes with the following genotype: (I⁺O⁺Z⁺Y⁺ / I⁻O⁺Z⁺Y⁺)
inducible for both
Describe the expression/regulation of the Z and Y genes with the following genotype: (I⁻O⁺Z⁺Y⁺ / I⁺O⁺Z⁻Y⁻)
inducible for both
What is the purpose of the miRNA pathway
inhibits translation
Why do bacteria regulate gene expression
it allows bacteria to respond to changes in their environment
Why is the human microbiome like an organ?
it has a function that is carries out consistently
Individuals with Kleinfelter syndrom are phenotypically __________
male (mostly)
are males or females affected more from X-linked recessive disorders
males
Kleinfelter's Syndrome
males with XXY
Consensus sequences are found in _____________
many organisms due to being evolutionarily conserved
Where is melanin found?
melanocytes
Mendel's Law of Segregation
members of gene pairs (alleles) separate equally into each gamete (Ex. Heterozygote has half A gametes and half a gametes)
In what phase of meiosis do spindle fibers attach to kinetochores
metaphase
In what phase of mitosis do chromosomes line up
metaphase
In what phase of mitosis do spindle fibers form
metaphase
In what phase of meiosis do tetrads align in the middle of the cell
metaphase 1
complementation test
method of discovering whether two mutations are in the same or separate genes
What are the three ways DNA can be made more accessible for transcription
methylation, acetylation, sliding
This aneuploidy typically leads to death
monosomy
more linked genes means (more/less) parental gametes
more
How does methylation affect gene expression
more methylation results in less gene expression
wildtype allele
most common allele in a population
Describe how the codon chart is universal
most organisms use the same codon dictionary
How could you GENETICALLY change expression of a protein
mutate it, add/take genes, alter or add enhancers or silencers
What are the two processes responsible for genetic variation
mutation and meiotic recombination
frameshift mutation
mutation that involves the insertion or deletion of a nucleotide in the DNA sequence, shifting all codons afterward to be different
Transcription factors are only present in DNA molecules which....
need to be expressed
a linked SNP is located...
outside the gene
Between parental gametes and recombinant gametes, which are generally more common
parental
hypomorphic (leaky) mutation
partial loss of function
What enzyme brings lactose into prokaryotes
permease
What is the phenotype of the Y⁻ mutation in the lac operon
permease does not let lactose enter the cell
What attaches to the 5' carbon in deoxy/ribose
phosphate group of same nucleotide
What specifically do restriction enzymes cut when cleaving DNA
phosphodiester backbone
In the video, how is pitX expression different in a spineless vs. spined stickleback
pitX enhancer that interacts with pelvis-specific transcription factors is deleted in spineless fish = no pitX expression
lactose ______________ regulates operon
positively
Are histones positively or negatively charged
positively charged
What are histones
positively charged proteins with DNA coiled around them
Polymorphism
presence of two or more variant forms of a specific DNA sequence that can occur at the same loci
Polymorphism
presence of two variant forms of a DNA sequence among individuals/populations (Ex. SNPs)
gene induction
process s to induce or increase gene expression
gene repression
process s to reduce or prevent gene expression
Are operators present in prokaryotes or eukaryotes
prokaryotes
Are operons present in prokaryotes or eukaryotes
prokaryotes
Which cells contain a lac operon
prokaryotes
Describe the expression/regulation of the Z and Y genes with the following genotype: (IˢOᶜZ⁻Y⁻ / I⁺O⁺Z⁺Y⁺)
uninducible for both (would be constitutive, but the super repressor prevents ALL transcription of the lac operon)
What are UTRs?
untranslated regions: parts of mRNA that won't be translated to protein but have functions like ribosome binding. located at the 5' and 3' ends.
Describe the role of helicase in DNA replication
unzips DNA near replication fork so single template strands are accessible for replication
At the 5' end, UTRs are (downstream/upstream) from exons
upstream
Promoter is (upstream/downstream) of the coding region
upstream
Where is the regulatory region
upstream from exon(s)
How is cDNA made?
using reverse transcriptase, an enzyme isolated from retroviruses that converts RNA to DNA
recessive epistasis
when the recessive allele of one gene masks the effects of either allele of the second gene (bb will suppress A regardless of its dominance)
Are introns within genes or in-between genes
within
What lines up in the middle of the cell during metaphase 2
x-shaped chromosomes (chromatid pairs)
are X-linked dominant disorders rare
yes
are X-linked recessive disorders rare
yes
are autosomal recessive disorders are equal in prevalence between men and women
yes
can autosomal recessive disorders skip generations
yes
can parents unaffected by X-linked recessive disorders have affected children
yes
do autosomal recessive disorders become more common with inbreeding
yes
do people affected with autosomal dominant disorders have to have an affected parent
yes
with autosomal recessive disorders, can unaffected individuals have affected children
yes
Transcription and translation can occur simultaneously in __________________ but not in _________________
yes in prokaryotes, not in eukaryotes
long interspersed elements (LINEs)
~6000 BP interspersed repeats
What enzyme hydrolyzes lactose to glucose and galactose
β-gal
What is the phenotype of the Z⁻ in the lac operon
β-gal does not break down lactose
