Midterm

Question 1

What are some of the biggest differences between prokaryotes and eukaryotes

Answer 1

eukaryotes:
* DNA in nucleus -highly organized, multiple linear chromosomes
* *replicate/transcription occurs in the nucleus, and the processed mRNA is transported to the cytoplasm for translation
* DNA is supercoiled around histone proteins to form chromatin //Negatively coiled
* Chromatin can be condensed or relaxed to regulate gene expression
* Condensing to chromosome occurs in M phase only
* in proliferation:G1/S/G2 phase:
** Euchromatin - some chromatin diffuse, lightly packed, active for expression
**Heterochromatin: dense, tightly packed, not active for expression

*Linker DNA connects neighboring nucleosomes
Histone 1: binds to nucleosome core, stabilize DNA strand that twists around octamer
H1 binds to linker DNA to stabilize chromosome structure

• High order DNA: 6 nucelosomes per turn in 30 nm fiber, w/ 30 nucelosomes per loop

prokaryotes:
* DNA in cytoplasm-lacks structure - single, circular
* Both transcription and translation in the cytoplasm
* Supercoiling important for DNA repl/RNA transcribe //Negatively coiled

• Supercoiled = Too condensed, no bio activity
• Type 2 prokaryotic topoisomerase = gyrase
• Prokaryotic genomes are generally smaller in size, typically containing a single, circular chromosome with limited non-coding regions.

Question 2

What is central dogma

Answer 2

nucleic acids carry genetic infrormation
1. nucelic acids are essential for prokaryotes, eukaryote, and virusses
2. 2 types: DNA and RNA
3. DNA contains genetic information used in development and funcitoning of all known living creatures
4. RNA is involved in transmission of genetic information

Question 3

What are telomeres and how do they function

Answer 3

• protection at end of the chromsomes, separate one chromosome from another
• consist of multiple tandem repeats of a short sequence
• carry a small segment of RNA complementary to the tendem repeat → telomerease recognize the telomere to add up new repeats

Question 4

What are the stages if DNA repllication?

Answer 4

1. Initiation
2. Elongation
3. Termination

Question 5

Do the stages of DNA replication differ between prokaryotes and eukaryotes, and if so, how

Answer 5

Initation:
- eukaryotes need a RNA-DNA primer; has multiple replication origins
- prokaryotes need an RNA primer; have topoisomerase and helicase to help unwind

Elongation:
- different polymerases
- eukaryotes replication moves i both directions

Termination:
- eukaryotes: teloomeres; nucelosome needss to reassemble; primer removal
- prokaryotes: repliation terminates at spcific sites

Question 6

What is the significance of polymerase in eukaryotes and prokaryotes

Answer 6

• pol-α: associates with prmase; mainly ivoled in initiation of synthesis of leading and lagging strand
• pol-δ: proofreads; mainly involved in the lagging strand synthesis
• pol-ε: proofreads; mainly involved in leading strand synthesis

Question 7

What is complementary base pairing

Answer 7

A = T
G = C

WRITE IN 5’ to 3’

Question 8

What are the different types of chromatin and how do they impact gene function

Question 9

Durign RNA processing, what are the essential peieces

Question 10

What makes transcription different from replication

Question 11

How does tRNA read the mRNA; what do codons mean?

Question 12

What are operons

Question 13

There are several processes for repressors and activators, how do they differ

Question 14

What is the difference between somatic and germline mutations

Question 15

What is the signficance of SNPs and mutations; are they interchangeable

Question 16

What types of SNPs are there

Question 17

What is the difference between a genotype and phenotype

Question 18

What are different ways of genetic diversity

Answer 18

• founder effect
• positive selection
• genetic drifts
• bottle neck effect

Question 19

Founder effect

Question 20

Positive selection

Answer 20

process by which new advantageous genetic variants sweep a population-

Question 21

Genetic drifts

Answer 21

variation in the relative frequency of different genotypes in a small population, owing to the chance disappearance of particular genes as individuals die or do not reproduce

Question 22

Bottle neck effect

Answer 22

an extreme example of genetic drift that happens when the size of a population is severely reduced

Question 23

What regulates gene transcription

Answer 23

Operons
Repressors
Activators

Question 24

Ethics vs. omics

Answer 24

Pharmacogenetics
* 1. Variation of one single gene influences response to a single drug
* 1. One to one
Pharmacogenomics
* Studies how genes or the genome can influence the response to drugs
* Many to one

Question 25

Difference between rs# and * alleles

Answer 25

RS# = reference identifier
* alleles = When a novel variant is identified
*# = identified significant variant

Question 26

Do the nomencalture stuff

Question 27

What are the overall differences between phase I and II enzymes

Answer 27

Phase 1: possible outcomes
* The drug becomes completely inactive.
* One or more of the metabolites are pharmacologically active, but less so than the original drug.
* The original substance is not pharmacologically active, but one of its metabolites is. The original substance is called a prodrug
Phase 2: outcomes
* Conjugated metabolites formed in phase 2 are unlikely to be pharmacologically active
UGT, SULT, NATs, COMT, etc

Question 28

What are transporters

Answer 28

Membrane proteins that carry either endogenous compounds or xenobiotics across biological membranes
Influx
* OAT, OCT
Efflux
* PGP, BCRP
Active/Secondary (ATP/SLC)

Question 29

What are some positives and negatives of DTC

Answer 29

GOOD
* Genetic information more accessible, convenient
* Gain insight for health conditions/genetic disorders
* Provide info about ancestry
* Lifestyle changes due to knowledge about genetic predispositions
BAD
* Lack professional counseling
* Accuracy may vary
* Can cause anxiety/stress
* Genetic markers can be missed
* FDA concerts with validity

Question 30

What is genealogy and how do you do this?

Answer 30

Study of families, hx, tracing of lineages
Interviews, historical records, genetic analysis

Question 31

What control does the FDA have in DTC tests

Answer 31

Assess
Analytical validity
If a test can accurately and reliably measure what it claims
Clinical validity
If measurements are predictive a certain state of health
Claims
What a company says about the test vs how well it works
If inaccurate → Cease+Desist

Question 32

What is the significance of single gene etics and why may it not be the big picture

Answer 32

combinatorial effects of multiple genes give the most accurate pharmacologic picture for a given medication (big picture)
Otherwise, the clinical effect may be muted creating mixed outcomes.

Question 33

What are teh stages of PCR

Answer 33

1. Denaturation
   70C - separate dsDNA into ssDNA
2. Annealing
   50C - allow primers to attach to DNA template
3. Elongation
   72C - DNA poly synthesizes new DNA strand complement to template

Question 34

Why is PCR important

Answer 34

it produces enough copies of a DNA sequence that we can see or manipulate that region of DNA

Question 35

What are microarays

Answer 35

a grid of DNA segments of known sequence that is used to test and map DNA fragments, antibodies, or proteins.

Question 36

What is the difference between microwarrays adn GWAs

Answer 36

Microarrays
*Looks at EXPRESSION - used in dx of disease
*Extent of genes turned on/off in cells/tissues
GWAS
*Looks at DNA
*Identify genomic variants that are statistically associated w/ risk for disease/trait

Question 37

What is the difference between common and rare variants

Answer 37

Common: low effect
Rare: high effect

Question 38

What types of plots are really important for GWAs and microarrays, how do you read them