BIOL 2153 Final LSU Daniel Powell

T/F Mitochondria and chloroplasts are organelles with their own genomes

True

How are mitochondria and chloroplast inherited?

maternally

Endosymbiont theory

mitochondria and chloroplasts are descended from bacteria that fused with nucleated cells

Why is mtDNA better to use in forensic analysis when the biological sample is low or very old?

Each cell has many mitochondria but only one nucleus, so there is more of it in every sample

What are the main reasons mitochondria and chloroplast can only function inside the cell?

Organelle gene incorporated into nuclear genome, organelle copy of the gene becomes redundant, changes may make it non-functional

What does homoplasmic mean?

contain only one type of organelle genome

What does heteroplasmic mean?

contain a mixture or organelle genomes

Why is the nervous system more susceptible to mitochondrial dysfunction?

Tissues with higher energy requirements are less tolerant of mutant mitochondria

What are transgenes?

gene transferred by a scientist into an organism's genome (can be inserted into random locations)

What are transgenic organisms?

a plant or animal whose genome contains a transgene transferred into the organism

What are the different ways to introduce transgenes into organisms?

Pronuclear injection, transposon vectors, retroviral vectors, T-DNA vectors

How does P-element transformations work?

A transformation plasmid is constructed to contain the P element inverted repeats surrounding a transgene and a visible marker

a helper plasmid contains the transposase gene

both are injected into the embryo resulting in mosaic offspring

What are the different uses for transgenic organisms?

Can clarify which gene causes a mutant phenotype

transgene reporter constructs can tell us where and when genes or proteins act

serve to produce proteins needed for human health

used to model gain-of-function genetic diseases in humans

What is the basic process of organismal cloning?

Extract nucleus from donor egg cell

take nucleus from somatic cell of the organism to be clones and transfer to donor egg

grow the hybrid embryo in vitro

implant into surrogate

What is the basic process of human gene therapy?

Introduce a therapeutic gene into the somatic cells of patients

Why are organismal clones not completely identical clones?

The mitochondria is different

If you wanted to make a mouse model of a human disease that's caused by a gain of function mutation, would you make a knock-out or knock-in?

Knock-ins are used to make models of human disease

What is the purpose of the helper plasmid in P-element transformations?

It contains the transposase gene

What is in vivo?

therapy delivered to somatic cells in the body

What is ex vivo

cells removed from body, treated, then put back in

What are the advantages and disadvantages of the retroviral gene delivery method for human patients?

integrate into the genome, but can cause mutations

What are the advantages and disadvantages of the AAV vector gene delivery method for human patients?

doesn't integrate into the genome but therapeutic vector eventually degrades

What is the mechanism of RNAi based gene silencing

transcriptional gene silencing (mRNA is never made)

post-transcriptional gene silencing (mRNA is made, but degraded before it can be used to make protein

What does Dicer recognize?

Cleaves dsRNA into smaller pieces

What is in the RISC complex?

Assembles and cleaves target mRNA

What is the target that gets degraded?

mRNA of endogenous gene is degraded

What determines the gene specificity?

Guide RNA

What are the major advantages and disadvantages of RNAi?

Benefits: does not require genome editing and delivery is easy (direct injections or can sometimes just feed small RNAs to animals

Disadvantages: cannot directly activate genes or make specific mutations

Why does the guide sequence need to be unique?

If not there will be off target effects

How does CRISPRi inhibit gene expression?

Express a small RNA that will be processed through the RNAi pathway, single stranded RNA will bind to complementary mRNA of interest and cause destruction of the mRNA target

What are growth factors?

(go signals) nitrogen's are growth factors that stimulate cell proliferation

What are receptors

found on the surface of the cell; bind growth factors; initiate signal transduction cascade; ultimately activates synthesis of transcription factors

What are transcription factors?

regulate genes whose protein products cause cells to divide or stop dividing

What are the ways cancer cells evade normal controls?

Produce ectopic cell division signals (autocrine stimulation)

Lose contact inhibition

Avoid programmed cell death

How do oncogenes drive cancer progression and how do they act?

dominant gain of function mutations drive cancer, results in increased proliferation

How do tumor suppressors drive cancer progression and how do they act?

recessive loss of function mutations drive cancer

What is the relationship between telomeres and replicative lifespan?

Telomere length dictates replicative lifespan

What are driver mutations?

cause cancer phenotypes

What are passenger mutations?

occur due to increased mutation rate of cancer cells, do not contribute to disease

What is the evidence that cancer cells arise from a single cell (are clonal)?

Cancer is a disease of old age: supports the idea that cancer involves the accumulation of mutations in the clonal descendants of a somatic cell, successive mutations confer the properties of cancer to a clone of cells

How do cell-cycle checkpoints safeguard against genomic stability?

Point mutations, Translocations, and

Gene amplification

What are proto-oncogenes?

normal allele that has the potential to become an oncogene

What is the normal function of proto-oncogenes?

Often encode proteins needed for cell cycle progression (accelerators)

What kinds of mutations cause a proto-oncogene to become an oncogene?

Deletion or point mutation in coding sequence, regulatory mutation, gene amplification, and chromosome rearrangement

How do tumor suppressors act? What is the normal function of tumor suppressors?

Loss-of-function mutations in both gene copies results in increased proliferation

How do allele frequencies change over time for populations in H-W equilibrium?

the population has an infinite number of individuals, individuals mate at random, no new mutations appear, no migration into or out of the population, genotypes have no effect on fitness-ability to survive and transmit alleles to the next generation

How does small population sizes affect allele frequences of existing genetic variation and new mutations?

population bottlenecks, founder effects and genetic drift

Population bottlenecks

large proportion of individuals die (for example from environmental disturbances)

Founder effects

a few individuals separate from a larger populations and establish new population

Genetic drift

change in allele frequencies as a consequence of randomness in inheritance due to sampling error from one generation to the next

How does natural selection promote the loss, spread, or maintenance of an allele in a population?

the process that progressively eliminates individuals whose fitness is lower

Individuals whose fitness is higher become the parents of the next generation

What is the concept of Most Recent Common Ancestor and how it supports the origin of modern humans in Africa?

an unbroken line of descent connects the MRCA with all modern humans,

the modern sequences are not identical, because mutations occur along lineages

Humans share a MRCA mtDNA from Eve, 200,000 ago in Africa

What is the evidence for interbreeding between modern humans and archaic humans like Neanderthals and Denisovans?

Current DNA variants show markers of interbreeding

non-African humans have Neanderthal SNP

humans indigenous to Africa have ancestral SNP

How is heritability estimated?

Broad sense and narrow sense

What is broad sense variance and how is it calculated?

It is the proportion of phenotypic variance that is ascribable to genetic variation

measured only when comparing identical twins

What is narrow sense variation and how is it calculated?

the proportion of variance due to variance of the additive genetic component

How are Quantitative Trait Loci (QTL) identified?

specific genes that contribute to complex traits

identified based on correlation with phenotype

What is the importance of linkage disequilibrium (LD) for association mapping in humans?

variants of two loci are correlated and sequence at site 1 suggests the sequence at site 2

T/F Heritability of a trait determines it's potential to evolve

True

How does QTL mapping extend linkage analysis?

by using many more genetic markers and statistical tests for correlations between alleles and trait values.

T/F Mendel's law of independent assortment states that the alleles of two or more different genes get sorted into gametes independently of one another

True

T/F Mendel's law of segregation states that dominant alleles segregate to gametes and recessive alleles segregate to somatic cells

False

The two alleles for each trait separate during gamete formation

T/F Gametes contain half the amount of DNA as somatic cells

True

T/F if two recessive mutants with same phenotype are crossed a produce a wild type phenotype, this indicates that the mutations are in different genes

true

In the common daisy, genes A and B control flower color. Both genes have a dominant allele (A or B) and a recessive allele (a or b). At least one copy of each dominant allele is required for flowers to be colorful instead of white.

what type of gene interaction is described here?

a) additivity

b) recessive epistasis

c) reciprocal recessive epistasis

d)

dominant epistasis

C

In the common daisy, genes A and B control flower color. Both genes have a dominant allele (A or B) and a recessive allele (a or b). At least one copy of each dominant allele is required for flowers to be colorful instead of white.

Predict the genotype and phenotype of the F1 progeny of a cross between two white-flowered plants: AA bb x aa BB

a) AA bb, white

b) aa BB, white

c) Aa Bb, colorful

d) Aa Bb, white

e) aa bb, colorful

c

If phenotype is controlled by the genotypes at two different loci, a possible interaction between alleles of these genes can be called

a) epistasis

b) epigenetics

c) dominance

d) codominance

a

Which will produce a 1:1:1:1 genotypic ratio?

A) AA BB x aa bb'

B) Aa Bb x Aa Bb

C) Aa Bb x aa bb

D) Aa BB x aa BB

c

ABO blood type demonstrates which of the following inheritance patterns?

A) complete dominance

B) incomplete dominance

C) codominance

D) A and C

E) B and C

D

Albinism is a recessive disorder in which hair and skin lack pigmentation. Two albino parents have 3 children who all have colored skin. Which of the following genetic interactions can explain this?

a) incomplete dominance

b) modifier gene

c) complementation

d) epistasis

C

What is the outcome of crossing pure-breading plants with antagonistic traits?

a) only one of the traits will be seen in the progeny

b) both traits will be seen in the progeny

c) both traits will be seen in the progeny in a 3:1 ratio

d) only one trait will be seen and it will be the trait of the female

a

T/F a gene that affects more that one trait is called polygenic

False

pleitropy

T/F a test cross for a single gene that produces a 1:1 phenotypic ratio indicates the unknown genotype is heterozygous

True

T/F dominant mutations generally produce non-functional proteins

False

T/F Mutations are the source of new alleles

true

T/F gametes contain half the amount of DNA as somatic cells

True

T/F Chromosome duplication occurs between meiosis I and meiosis II

false

S phase

T/F Double stranded DNA contains both covalent and hydrogen bonds

true

T/F daughter cells produced during meiosis are genetically identical

False

Meiosis produces gametes that contain half the number of chromosomes found in other cells

T/F crossing over allows the reassortment of linked genes

true

T/F A single replication fork departs from each origin of replication

false

T/F homologous chromosomes contain the exact same DNA sequence

False

contain the same size, shape, and banding but different DNA

T/F crossing over occurs during prophase I of meiosis

True

What is the protein that progressively unwinds DNA ahead of each replication fork?

a) primase

b) helicase

c) topoisomerase

d) ligase

B

Cells in the G2 stage of the cell cycle have ___________ as cells of the same species in the G1 stage

a) twice as many crossovers

b) twice as many chromatids

c) half as many chromatids

d) the same number as chromatids

b

Males with one copy of an x-linked gene are said to be _______ for that gene

a) homozygous

b) heterozygous

c) hemizygous

d) deficient

c

Recombination occurs between

a) homologous non sister chromatids

b) non homologous non-sister chromatids

A

Which of the following is a diploid cell destined for a specialized role in the production of gametes?

a) somatic cell

b) germ cell

c) sperm

d) ovum

B

T/F a mutation that causes increased expression of a gene is a hypomorphic mutation

false

hypomorphic : gene product has weak, but detectable activity

T/F a transcription factor is a trans acting element that often binds to gene promoters and enhancers

True

Which of the following codons could be recognized by the following anticodon: 5'-GGC-3'

a) 5'-GCU-3'

b) 5'-GGC-3'

c) 5'-CCG-3'

d) 5'-CCG-3'

e) both c and d

a

Epigenetic marks at imprinting control regions are rest

a) every other generation

b) during DNA replication of Meiosis I

c) During DNA replication of mitosis

d) randomly

B

What is the order of effect on phenotype for mutation types from most to least deleterious

nonsense>frameshift>nonconservative missense> conservative missense> silent

A crossover event in the inversion loop of a pericentric inversion between two homologous non-sister chromatids may result in

a) gene duplication

b) gene deletion

c) semi sterility

d) all of the above

d

In positional cloning, to determine linkage between a SNP and a disease locus, the matings that are most informative are between

a) a double homozygote and a double heterozygote

b) two double heterozygotes

c) two double homozygotes

A

3:1

Aa x Aa phenotypic ratio

1:2:1

Aa x Aa genotypic ratio

1:1

Aa x aa genotypic ratio

1:0

AA x _ _ or aa x aa phenotypic ratio

(all are the same)

9:3:3:1

Aa Bb x Aa Bb phenotypic ratio in a dihybrid cross