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Flashcards in Genetic Material Deck (38):
1

DNA compostion

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

2

nucleotides

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

3

nucleoside

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

4

DNTP's

deoxynucleoside 5' triphosphates
activated precursor in the synthesis of DNA

5

primary structure of DNA

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

6

oligonucleotides/primers

small groups 5-50 of nucleotides linked via phosphodiester bonds

7

denotations of the 5' and 3' ends

5' = phosphate
3' = hydroxyl

8

Watson and Crick Double helix:
directionality
structure
bonding

-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

9

Features of the structure of DNA

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

10

supercoiling of DNA

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

11

topoisomerases

enzymes that catalze change in the supercoiling of DNA

12

Topoisomerase 1 and 2:
reaction catalyzed
cancer

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

13

camptothecin

inactivates topo1

14

mAMSA

inhibits topo2

15

Doxorubicin

indirectly inhibits topo2

16

Z DNA

-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

17

DNA Bending

-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

18

Triplex DNA structure

-polypurine/polypyrimidine tracts can form this (H-DNA)
-biological consequences unknown

19

DNA Melting

-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)
-

20

Reannealing

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

21

Functional Genes

-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

22

lost genes

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

23

additional gene elements, "junk DNA"

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

24

Pseudogenes

-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.)

25

processed pseudogenes

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

26

proviruses

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

27

repetitive DNA sequences

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

28

transposable elements:
definition
classes

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)

29

SINE's

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

30

LINES's

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

31

Simple Sequence Repeats (SSR's)

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

32

microsatellites

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

33

Minisatellites

-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

34

Genetic Marker:
terms of common and rare variations

-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

35

Satellite Sequences:
description
composition
location

-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)

36

Telomeres:
location
composition
function
role in cell division
tumors

-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

37

telomerase:
function
class
somatic cells vs tumor cells

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

38

Histones:
function
types
Nucleosome

-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