BIOL 202 Final Exam

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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

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


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