Ferguson Review (exam 1)

Question 1

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

Answer 1

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

Question 2

How is DNA packaged?

Answer 2

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

Question 3

What are the different levels of DNA packaging?

Answer 3

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

Question 4

What are the components of chromatin?

Answer 4

Nuclear DNA and proteins

Question 5

Describe Chromatin remodeling complexes

Answer 5

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

Question 6

Describe nucleosome packaging

Answer 6

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

Question 7

What are the requirements of a chromosome?

Answer 7

ORI

Centromere

Telomeres

Question 8

Describe what a single nucleotide is made up of

Answer 8

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

Question 9

What are phylogenetics?

Answer 9

the study of evolution

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

Question 10

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

Answer 10

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

Question 11

What can cause gene duplication?

Answer 11

little selective pressure to remain mutation free

Question 12

Define a pseudogene

Answer 12

a duplicated gene that has been irreversibly inactivated

Question 13

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

Answer 13

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

Question 14

What are the requirements for DNA replication?

Answer 14

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

Question 15

How does DNA synthesis work?

Answer 15

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

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

Question 16

describe how proofreading occurs during DNA replication

Answer 16

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

Question 17

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

Answer 17

Sliding clamp and clamp loader

Question 18

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

Answer 18

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

Question 19

List the types of DNA damage that occur

Answer 19

spontaneous deaminations (C to U is the most common)

spontaneous depurination

free radical exposure

UV radiation damage cause pyrimidine dimers

Question 20

Describe base excision repair

Answer 20

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

Question 21

Describe Nucleotide Excision Repair

Answer 21

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

Question 22

Compare Homologous recombination and Homologous end joining repair

Answer 22

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

Question 23

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

Answer 23

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.

Question 24

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

Answer 24

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

Question 25

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

Answer 25

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/

Question 26

Explain the difference between Transposons and Conservative site specific recombination.

Answer 26

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.

Question 27

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

Answer 27

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

Question 28

What is bacteriophage lambda?

Answer 28

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.

Question 29

What is Cre-lox recombination?

Answer 29

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.

Question 30

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

Answer 30

Yes

Question 31

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

Answer 31

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.

Question 32

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

Answer 32

Sertoli (Male) ; Follicle (female)

Question 33

Sertoli cells secrete ______ which _______

Answer 33

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

Question 34

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

Answer 34

the genital ridge becomes an ovary

PGC’s become egg cells

Question 35

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

Answer 35

Follicle cells = support

Theca cells = estrogen production

Question 36

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

Answer 36

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

Question 37

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

Answer 37

hyaluronic acid

Question 38

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

Answer 38

hyaluronidase

Question 39

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

Answer 39

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

Question 40

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

Answer 40

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.