Genetic Material

Question 1

DNA compostion

Answer 1

polymer of nitrogenous bases (purines and pyrimidines) linked together by a backbone of an alternating series of sugars (5 carbon pentose) and phosphate residues

Question 2

nucleotides

Answer 2

consists of a nitrogenous base, a pentose and one or more phosphate group

Question 3

nucleoside

Answer 3

a nitrogenous base with a pentose. so it is a nucleotide without and phosphates.

Question 4

DNTP’s

Answer 4

deoxynucleoside 5’ triphosphates

activated precursor in the synthesis of DNA

Question 5

primary structure of DNA

Answer 5

• linear polymer of deoxyribonucleotides connected 3’-5’ phosphodiester linkages.
• polymer consists of a pentose phosphate backbone with N base on each link

Question 6

oligonucleotides/primers

Answer 6

small groups 5-50 of nucleotides linked via phosphodiester bonds

Question 7

denotations of the 5’ and 3’ ends

Answer 7

5' = phosphate
3' = hydroxyl

Question 8

Watson and Crick Double helix:
directionality
structure
bonding

Answer 8

• right handed
• two polynucleotide chains wound around one another
• antiparallel = 5’ end of one strand is paired with the 3’ stand of the other
• sugar phosphate backbones are on the outside and the nitrogenous bases faces inward towards their complementary base (hydrophobic)
• helix held together via hydrogen bonds
• stacked 3.4A apart
• 10 BP per turn

Question 9

Features of the structure of DNA

Answer 9

• can store vast amounts of charge at phys pH
• complimentary structure suggested a mode of replicaion
• structure prevents information loss when dmage occurs

Question 10

supercoiling of DNA

Answer 10

can be positively supercoiled or negatively supercoiled
supercoiling confers energy into the molecule which can later be used for seperation of the strands.
Coiling is directly correlated to regulation of gene expression

Question 11

topoisomerases

Answer 11

enzymes that catalze change in the supercoiling of DNA

Question 12

Topoisomerase 1 and 2:
reaction catalyzed
cancer

Answer 12

catalyze a 3 step reaction to change the conformation of DNA:
1. Cleavage of one (topo1) or both (topo2) strands of DNA
2. passage of DNA around the breaks
3. resealing of the DNA breaks
cancer drugs inhibit these enzymes

Question 13

camptothecin

Answer 13

inactivates topo1

Question 14

mAMSA

Answer 14

inhibits topo2

Question 15

Doxorubicin

Answer 15

indirectly inhibits topo2

Question 16

Z DNA

Answer 16

• this is a left handed helix of DNA
• alternating purines and pyrimidines are more likely to adopt this structure
• adopted in response to negative supercoiling
• purpose unclear, may be in recombination/regulation of expression

Question 17

DNA Bending

Answer 17

• some sequences are inherently bent
• adenine repeats are prone to bending
• may be a result of protein-DNA interactions
• examples: bending DNA around histones
• may bring distant sequences closer together

Question 18

Triplex DNA structure

Answer 18

• polypurine/polypyrimidine tracts can form this (H-DNA)

- biological consequences unknown

Question 19

DNA Melting

Answer 19

-results in disruption of the duplex structure and -seperation of the strands.
-narrow range of temps
-varies with ion conc and sequence comp (G and C more stable, has 3 H bonds vs 2 in A-T)
-

Question 20

Reannealing

Answer 20

• Hybridization (reassociation) of the 2 strand just below the Tm
• highly specific, must be complimentary
• important in the use of probes

Question 21

Functional Genes

Answer 21

• only accounts for 1-2% of the human genome
• range in size from 1-100kb
• genes involved in similar systems are located together (color vision genes are together). have the same “domain”
• families in the same domain reflects that a genes arose from a common ancestral gene
• may have multiple repeating copies of commonly used genes

Question 22

lost genes

Answer 22

could be because the gene product is readily attainable in our food supply

Question 23

additional gene elements, “junk DNA”

Answer 23

some of it has regulatory roles but much of it is said not to be used

Question 24

Pseudogenes

Answer 24

• closely related to functional genes and arose in the same duplication process that give rise to gene families.
• they do not code for normal gene products (deletions, point mutations, insertions, etc.)

Question 25

processed pseudogenes

Answer 25

formed when DNA copies of RNA (reverse transcripts) are inserted back into the genome. large amount of these can sometimes be found

Question 26

proviruses

Answer 26

- DNA copies of retroviruses inserted into chromosomes | - all species carry them in their chromosomes

Question 27

repetitive DNA sequences

Answer 27

- can be complex patterns or simple nucleotide repeats | - includes transposable elements, simple sequence repeats, and satellite DNA

Question 28

transposable elements: definition classes

Answer 28

sequences capable of inserting copies of themselves into new genomic locations. 1. elements that transpose through reinsertion of the products of reverse transcription (proviruses, SINE and LINE, and processed pseudogenes) 2. transpose directly through DNA copies and encode their own transposase (little evidence for this in humans)

Question 29

SINE's

Answer 29

- Short Interspersed Repeat Elements | - among the most abundant sequences in the human genome

Question 30

LINES's

Answer 30

- long intersperse repeat elements - atleast 500nt in leangth - full length LINE elements encode a reverse transcriptase

Question 31

Simple Sequence Repeats (SSR's)

Answer 31

-about 3% of the human genome. one ever 2kb

Question 32

microsatellites

Answer 32

- 2 to 5 bp repeats, occur in averagely sequences of 100 - present at thousands of loci - the number of repeats is denotaed as subscript

Question 33

Minisatellites

Answer 33

- 14 to 15 bp in length - also called variable number tandem repeats - repeated in less than 10 to over 100 - scattered throughout the genome - not transcribed into RNA

Question 34

Genetic Marker: | terms of common and rare variations

Answer 34

- Any site in the genome where there is variation - if the difference is a rare one, then it is termed a mutation - If it is common, it is called polymorphism

Question 35

Satellite Sequences: description composition location

Answer 35

- highly repeptitive short DNa sequences (5-100bp) - have a different density than bulk DNA (seperat differently from genomic DNA) - organized as megabases on nontranscribed regions (centromeres, the y chromosome, or telomeres)

Question 36

``` Telomeres: location composition function role in cell division tumors ```

Answer 36

- found at the end of chromosomes - hexameric TTAGGG repeat, 1000-1700 copies - chromosome protection and replication - chromosome lose 50 to 200 nucleotides of this with every division. acts as a mitotic clock (short = signal for senescence) - tumor cells do not lose their telomeres

Question 37

telomerase: function class somatic cells vs tumor cells

Answer 37

- enzyme that synthesizes telomeres - is a reverse transcriptase - repressed in normal human somatic tissue - reactivated in tumor cells

Question 38

Histones: function types Nucleosome

Answer 38

- what DNA is wrapped around to be condensed - 4 types: H2A, H2B, H3, and H4 - there are two of each type in each core group, or Nucleosome (octomer) - nucleosomes are further ordered into chromatin fibers