DNA Structure and Function

Question 1

Is DNA positively or negatively charged? How does this affect stability?

Answer 1

Negative

Enhances stability

Question 2

How many H bonds between C and G?

Answer 2

3

Question 3

How many H bonds between A and T?

Answer 3

2

Question 4

Which carbon on a ribose contains the hydroxyl group?

Answer 4

C2

Question 5

What are the purines?

Answer 5

Adenine

Guanine

Question 6

Describe the appearance of guanine

Answer 6

Bulky, carbonyl

Question 7

Describe the appearance of adenine

Answer 7

Bulky, amine

Question 8

Describe the appearance of cytosine

Answer 8

Not bulky, amine

Question 9

Describe the appearance of thymine

Answer 9

Not bulky, carbonyl

Question 10

You always read a DNA sequence __’ to __’

Answer 10

5’ to 3’

Question 11

How does the A form helix appear?

Answer 11

Bases appear twisted and larger/stretched

Question 12

What are the stabilizing factors of DNA?

Answer 12

H bonds between bases

Van der Waals forces

Positively charged ions

Question 13

Does single or double stranded DNA absorb light better?

Answer 13

Single stranded due to openness/exposure of bases

Question 14

What is the melting temperature of DNA?

Answer 14

When 50% of the DNA is separated

Question 15

Does AT-rich or GC-rich DNA require higher melting temps?

Answer 15

GC-rich

Question 16

What are nucleoside reverse transcriptase inhibitors (NRTIs)?

Answer 16

Block HIV RNA from being reverse transcribed

lacks a 3’ hydroxyl

Question 17

What is AZT?

Answer 17

an NRTI to fight HIV

Question 18

What is acyclovir?

Answer 18

An anti-HIV drug that is converted by (virus-encoded) thymidine kinase into a nucleoside (gGTP) analog similar to AZT

(lacks a 3’ OH)

Question 19

What is ciprofloxacin?

Answer 19

A quinolone (fluoroquinolone)

Used to treat a wide variety of infections agents (gram-negative AND gram-positive)

Question 20

How does ciprofloxacin work?

Answer 20

Binds to DNA gyrase topoisomerase II (or IB) via a water metal ion (Mg2+) bridge

Inhibits the topoisomerase ligase activity leading to DNA fragmentation

Question 21

Does DNA have to be cut and re-ligated to be supercoiled?

Answer 21

Yes

Question 22

Type I topoisomerases can only work on DNA that is ______.

Answer 22

Strained

Question 23

Do type II topoisomerases require ATP?

Answer 23

Yes

Question 24

Does type I topoisomerase require ATP?

Answer 24

No, uses the energy of the strained DNA

Question 25

What type of organisms use type II topoisomerases?

Answer 25

Bacteria, which is why Cipro only attacks bacterial not human DNA!

Question 26

What are Type I topoisomerases used for?

Answer 26

Ovarian, colorectal, cancer (since type I will attack human DNA, this is the only useful purpose)

Question 27

Which four histones make up the nucleosome core?

Answer 27

H2A, H2B, H3, H4

Question 28

What is the function of H1 histone?

Answer 28

Holds the tertiary structure of the nucleosome together by binding to the linker DNA

Question 29

Histones are ______ charged.

Answer 29

Positively

Question 30

What is a solenoid?

Answer 30

6 nucleosomes per turn coiled with DNA to form a long fiber

Question 31

mRNA is created based off the ______ strand and is thus the ___' to ___' strand.

Answer 31

Template 3' to 5'

Question 32

What type of mRNA/DNA is colinear? Why?

Answer 32

Prokaryotic mRNA/DNA because there are no introns/exons and thus the sequences are nearly identical

Question 33

What are 3 traits of prokaryotic genes?

Answer 33

1. DNA and protein are colinear 2. Gene sequences are unique/not repeated 3. Size of genome corresponds to number of genes

Question 34

What are 3 traits of eukaryotic genes?

Answer 34

1. Size of genome does not correspond to number of genes 2. Most eukaryotic DNA is non functional or not unique 3. About 10% of genome codes for proteins

Question 35

How many repeats must genes have be to be considered a "highly repetitive sequence"?

Answer 35

> 300,000 copies/genome

Question 36

What are some attributes of highly repetitive sequence?

Answer 36

Not transcribed Usually short tandem AT rich repeats Make up 10% or less of the genome

Question 37

What is a prime example of a highly repetitive sequence?

Answer 37

Telomeres!

Question 38

What are some attributes of moderately repetitive sequences?

Answer 38

Derived from transposons Usually transcribed usually not translated Make up 25%-45% genome Code for highly used genes such as histones, rRNA, tRNA but mostly nonfunctional Separates highly transcribed single copy DNA (i.e. LINES and SINES)

Question 39

How many repeats are "moderately repeated sequences"?

Answer 39

2-300,000

Question 40

What are unique or single copy sequences?

Answer 40

Make up 40-60% of genome - coding and noncoding Only 1% of the genome is made into protein in any one cell Some unique sequences can be related/grouped after a duplication and divergence (e.g. globulins, tubulins, actins) These are often tissue or developmentally regulated and can be clustered or dispersed

Question 41

What are housekeeping genes?

Answer 41

Universally required genes

Question 42

What are pseudogenes?

Answer 42

Non-functional unique sequences that arise by gene duplication

Question 43

What is myotonic dystrophy type 1?

Answer 43

An autosomal dominant trinucleotide (CTG) repeat in which increased repeat-element copy number results in increased severity. Age at onset decreases and the severity increases in successive generations (anticipation)

Question 44

Trinucleotide repeats _____ than 49 are ______.

Answer 44

less than 49 = asymptomatic

Question 45

What mistake leads to trinucleotide repeats?

Answer 45

Slippage during replication

Question 46

What are some triplet repeat diseases?

Answer 46

Fragile X Friedrichs Ataxia Huntingtons Myotonic dystrophy