Ferguson Review (exam 1) Flashcards by Kole Hale

Describe the structure of DNA? how many turns per base pairs?

Composed of nucleotides arranged in complementary, antiparallel strands in a double helix

5 carbon sugar and phosphate backbone (5’ phosphoryl end and 3’ hydroxyl end)

1 turn every 10 base pairs

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How is DNA packaged?

Around histones composed of octamers (H2A, H2B, H3, and H4)

H1 linker histones help stack nucleosomes and occur in a 1:1 ratio with nucleosomes

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What are the different levels of DNA packaging?

in nucleosomes

zig-zag stacking with the help of H1 to form chromatin

all forms of packaging are a dynamic structure and histone modifications changes the structure as well

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What are the components of chromatin?

Nuclear DNA and proteins

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Describe Chromatin remodeling complexes

big complex that rearranges nucleosomes, and puts newly synthesized DNA on histones to form nucleosomes

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Describe nucleosome packaging

each nucleosome (200 nucleotide pairs) of DNA wrapped around histones and “linker DNA”

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What are the requirements of a chromosome?

ORI

Centromere

Telomeres

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Describe what a single nucleotide is made up of

5-carbon sugar and a nitrogenous base linked via a glycosidic bond

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What are phylogenetics?

the study of evolution

commonly use phylogenetic tree diagrams to compare and contrast the genetic makeup of different organisms

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Explain how modifications to the N-terminal tails of histones affect the genetic expression of the genes on that particular histone.

Methylation silences the gene

Acetylation: loosens the gene so that it can be expressed

Phosphorylation: generally activates the gene

it is more about the overall code for the gene; sometimes methylated and acetylated genes will become more genetically active

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What can cause gene duplication?

little selective pressure to remain mutation free

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Define a pseudogene

a duplicated gene that has been irreversibly inactivated

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What does it mean when there is a gene that duplicates and diverges over time?

both copies of a gene remain functional and basically create their own species based on their different expressions

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What are the requirements for DNA replication?

a sufficiently large supply of nucleotides

New histones

the separation of the 2 parent strands

dATP, dGTP, dCTP, and dTTP

a primer with a free OH on the 3’ end

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How does DNA synthesis work?

DNA polymerase synthesizes DNA in the 5’ to 3’ direction

leading strand (continuous) and lagging strand (okazaki fragments) are simultaneously created from the template

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describe how proofreading occurs during DNA replication

DNA polymerase conducts 3’ to 5’ exonuclease activity (squeezing) to proofread

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What proteins are involved at the replication fork during DNA synthesis?

Sliding clamp and clamp loader

What is tautemerization? it occurs as what type of failed proofreading step?

the wrong base gets added to the new DNA strand when DNA polymerase exonuclease proofreading step messes up

List the types of DNA damage that occur

spontaneous deaminations (C to U is the most common)

spontaneous depurination

free radical exposure

UV radiation damage cause pyrimidine dimers

Describe base excision repair

fixes 1 base

Glycosylase flips through and ID’s incorrect bases

Endonuclease and phosphodiesterase cut it out

DNA polymerase makes new base

DNA ligase seals the new base in

Describe Nucleotide Excision Repair

fixes anything that creates torque on the helix ex. pyrimidine dimers

Excision Nuclease cuts out the issue

DNA helicase pulls it out

DNA polymerase and DNA ligase make a new sequence end seal it in

Compare Homologous recombination and Homologous end joining repair

Recombination: occurs on paired homologous chromosomes in order to create genetic diversity; RecA type strand exchange occurs, double Holliday junction forms, crossover usually doesn’t occur but can

Repair: enzyme chews back the ends that are not “flush” and then sticks them back together “as is”; most common repair for ds breaks and causes mutations

Describe the structure, enzyme used, and mechanism of Transposition for DNA-only Transposons

S: Short, inverted repeats

E: Transposase

M: transposase binds to the short inverted repeats on either side of the transposon to form a central DNA intermediate; moves either by “cut and paste” or replicative pathways.

Describe the structure, enzyme used, and mechanism of Transposition for Retroviral-like retrotransposons.

S: Long terminal repeats (LTR’s) at each end

E: Reverse Transcriptase and Integrase

M: Moves as an RNA intermediate driven by a promoter in the LTR

Integrase cuts one strand at each end of the viral DNA, exposing the 3’ OH head. the 3’ OH head attacks the phosphodiester bond of target DNA and is then ligated into the DNA sequence

Describe the structure, enzyme used, and mechanism of Transposition for Nonretroviral-like retrotransposons.

S: dsDNA copy of L1 is directly inserted into the target DNA E: Reverse Transcriptase and Endonuclease M: moves as an RNA intermediate that is synthesized by a neighboring promoter endonuclease nicks target DNA at insertion point which leaves an exposed 3' OH to serve as a primer for RT to work. ssDNA copy of L1 is linked to target DNA and a dsDNA copy is then made with L1 now present in DNA/

Explain the difference between Transposons and Conservative site specific recombination.

conservative site-specific recombination requires a sequence in the DNA that is "jumping" and in the DNA that will be the destination. Transposons do not form protein/DNA intermediates , while conservative site specific recombination does.

During conservative site-specific recombination, what occurs if the sites are in the same orientation? what if they are inverted in orientation?

DNA sequence can be integrated or excised ; DNA sequence is inverted INSTEAD of excised.

What is bacteriophage lambda?

the first mobile genetic element to be fully understood a viral life cycle that puts it's genetic code in a host DNA and either stays latent or activates and goes through the lytic pathway.

What is Cre-lox recombination?

can be used to delete/translocate specific genes. This may affect genes that are only expressed in certain tissues. basically, a cre lox gene will be silenced in regular tissues, but will become activated when in specific tissues.

Can crossing over and gene conversion occur on the same chromosome?

Yes

Compare and contrast gene conversion and crossing over. How are they related to Holliday junctions?

gene conversion is when the genetic contribution to the offspring is not even from each parent; "mostly mom or dad DNA" Crossing over is when portions of paternal and maternal DNA "switch" chromosomes ; "chromosome ends/sections switch" both serve to create genetic diversity and can be the end result of Holliday junctions.

The presence of Sry in somatic cells directs cells to differentiate into ________ cells instead of _________ cells.

Sertoli (Male) ; Follicle (female)

Sertoli cells secrete ______ which _______

anti-mullerian hormone ; suppresses female development by causing the mullerian duct to regress

What occurs in the absence of Sry in terms of the end products of the genital ridge and the Primordial Germ Cells (PGC's)?

the genital ridge becomes an ovary PGC's become egg cells

_________ are the female gamete support cells, and ________ are the estrogen producing cells.

Follicle cells = support Theca cells = estrogen production

How many rounds of DNA synthesis and rounds of cell divisions occur in meiosis?

1 round of DNA synthesis and 2 rounds of cell divisions to produce haploid gametes.

The extracellular matrix of an egg cells is rich in what?

hyaluronic acid

What enzyme to capacitated sperm use to penetrate the granulosa cells of the egg?

hyaluronidase

When sperm contacts the zona pellucida of an egg, what happens? explain

an acrosomal reaction occurs which consists of the acrosomal cap of the sperm using exocytosis to release hydrolytic enzymes to burrow through the zona pellucida

once the sperm reaches the egg's plasma membrane, what occurs to prevent polyspermy? how does this happen?

a cortical reaction occurs that induces the cortical granules of the egg to release their contents and block all other sperm from entering the egg. increased Ca2+ levels in the cytosol that inactivates ZP3 and cleaves ZP2.