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Flashcards in DNA & BioTechnology Deck (40):
1

Types of Eukaryotic Nucleic Acids

1. Deoxyribonucleic Acid (DNA)---Double stranded
2. Ribonucleic Acid (RNA)-----------Single stranded

2

Location of DNA Storage in Eukaryotic Cells

1. Nucleus
2. Mitochondria
3. Chloroplast

3

Nucleic Acid Nomenclature

1. Nucleosides: compounds composed of a pentose
connected through its C-1 to a
Nitrogenous base
2. Nucleotides: Nucleosides connected through their
C-5 to 1+ phosphate groups;
constituting compounds of DNA & RNA

4

Classifying Category of Nucleic Acids

Type of pentose
1. if ribose-------------------->RNA----w/ OH
2. if deoxyribose---------->DNA----w/ H

5

Types of Nitrogenous Bases in Nucleic Acids

I. Purines--2-ringed
1. Adenine
2. Guanine
II. Pyramidines--1-ringed
3. Cytosine
4. Uracil
5. Thymine


****U is found only in RNA
T is found only in DNA*************


Pg. 170

6

Types of Nucleosides

1. Adenosine/Deoxyadenosine
2. Guanosine/Deoxyguanosine
3. Cytidine/Deoxycytidine
4. Uridine/Deoxyuridine
5. Deoxythymidine

7

Types of Nucleotides

1. AMP/ADP/ATP
2. GMP/GDP/GTP
3. CMP/CDP/CTP
4. UMP/UDP/UTP
5. dTMP/dTDP/dTTP

8

Nucleic Acid Backbone Properties:

1. Composing elements:
I. Phosphate
II. Pentose
2. Overall charge:
I. Negative due to presence of phosphate
3. Reading & writing direction
I. 5-3
II. free phosphate on C-5 & free 3'OH on C-3
4. Formed by:
I. linkage of 5'C of on-coming pentose to 3'OH
or phosphate of the previous sugar
******Ex: 5'-A-p-G-p-T-3'****

9

Model Deduced to Describe Structure of DNA

1. Name
I. Watson-Crick Model
2. Date of Development
I. 1953
3. Founding Figures
I. James Watson
II. Francis Crick

10

Chargaff's Rules

Rules that define structure of DNA as part of
Watson-Crick-Model
1. Antiparallel DNA chains
2. Helical wounding of DNA strands around a
common axis---[right handed]
3. External placement of pentose-P backbone and
internal placement of nitrogenous bases in the
right sided double helix
4. Complementary base-pairing of nitrogenous
bases
I. A-------2H-bonds-------T
II. C-------3H-bonds-------G
5. Presence of H-bonds and hydrophobic
interactions b/c nitrogenous bases
6. Equal concentration of purines and pyramidines

11

DNA Types

1. B-DNA
1. Right handed helix
2. Makes a turn every 3.4 nm
3. Contains 10 bases per spin
4. Stable
2. Z-DNA
1. Left handed helix
2. Makes a turn every 4.6nm
3. Contains 12 bases per spin
4. Unstable/does not play a role in biology

12

Major & Minor Grooves

Sites of protein binding on DNA molecules

13

Denaturation & Reannealing

1. Definition:
I. Process of separating and rebinding composing
strands of DNA by manipulating
1. pH
2. T
3. Salinity
2. Importance:
II. Detection of gene of interest in a mixture using
laboratory techniques such as
1. Polymerase Chain Reaction [PCR]
2. Probe-DNA

14

Probe DNA

DNA strand with a particular sequence that can be used in a DNA mixture to target a gene of interest

15

Chromosomal Terminology

1. Chromosome [
2. Nucleosome vs Chromatin [Histones + DNA Strands]
3. Heterochromatin vs Euchromatin
7. teomere
8. Telomerase
9. Centromere

16

Chromosome

Molecules found in the cell nucleus that houses supercoiled DNA strand that is composed of billions of base-pairs

17

Chromatin Vs. Nucleosome

Chromosomal constituent composed of
Histone Complex [H2A+H2B+H3+H4] wrapped by
supercoiled DNA

18

Histones

1. Definition
I. Small nucleoproteins that make up part of
chromatins
2. Types:
I. H2A ]--------Combine to form a protein
II. H2B ] -------complex that gets wounded by
III. H3 ]--------200 N-bases to form a
IV. H4 ]---------nucleosome

V. H1 }---------provides stability for the
nucleosome by sealing off DNA
as it enters & leaves it

19

Nucleoproteins

Proteins that associate with DNA-
Types:
1. Histones
2. Acid-soluble nucleoproteins that stimulate
processes like transcription

20

Heterochromatin Vs. Euchromatin

DNA terminology used to refer to condensed/inaccessible/dark/highly repetitive DNA sequence [Heterochromatin] and to diffused/accessible/light DNA sequence [Euchromatin] during the S phase of interphase where cell undergoes DNA replication to initiate meiosis & mitosis

21

Telomere & Telomerase

Chromosomal terminology respectively referring to
1. the repetitive sequence of [TTAGGG] at the end of a chromosome that gets reduced in length with each round of DNA replication, contributing to aging
2. the enzyme that restores part of the lost telomere after each round of DNA replication



*****Telomere limits the number of cell cycle divisions

22

Centromere

The central part of a chromosome, mainly consisting of heterochromatin and GC content, that holds sister chromatids together prior to their separation during anaphase

23

DNA

Biological macromolecule that
1. serves as blueprint for life
2. provides info about evolutionary past

24

DNA replication

Process of DNA copy making that is integral to
1. Cell-division
2. Reproduction

25

DNA Replication Process

1. Strand Separation
I. DNA strands unwind at DNA's origin of
replication with assistance of
replisome/replication complexes
2. Daughter strand synthesis
I. Daughter strand synthesis follows at the
replication origin of DNA using replication forks
3. Telomere replication

26

Replisome Complexes

Specialized proteins that assist DNA polymerase in the process of DNA replication

27

Replication Forks

Mechanisms that participate in replicating a DNA molecule by moving in opposite directions at the DNA's replication origin

28

DNA Strand Separation Process

1, Helicase unwinds DNA strands at the replication origin
2. Topoisomerase moves ahead of the helicase and prevents unwinded strands from supercoiling by nicking and resealing single strands, releasing its torsional strain
3. The un-winded purines and pyramidines on the strands bind to single-stranded DNA-binding proteins to avoid potential chance of re-association and DNA degradation

29

DNA Daughter Strand Synthesis Process

1. Laying of RNA primer on both lagging and leading strands of DNA
2. Synthesis of 10 primary nucleotides by RNA primase in a 5' to 3' direction
3. Addition of 5' deoxyribonucleotide triphosphate [dATP, dGTP, dCTP, dTTP] to the daughter strand in a 5' to 3' direction by DNA polymerase III [in prokaryotes] and by DNA polymerase alpha & delta in eukaryotes
4. Release of a [PPi]/Pyrophosphate from the strand after formation of each phosphodiester bond
5. Removal of RNA from the daughter strand by DNA polymerase I [prokaryotes] or by RNase H [Eukaryotes]
6. DNA nucleotide replacement of gap resulting from RNA removal in the beginning of the daughter strand by DNA polymerase I in prokaryotes and by DNA polymerase delta in eukaryotes
7. Sealing of the new DNA strand's terminal using DNA ligase

30

DNA Daughter Strand Synthesis Terminology

1. DNA polymerase:
I. Enzyme that reads leading and lagging
strands of DNA in a 3' to 5' direction and
synthesizes the daughter strand in a 5' to 3'
direction
2. Leading Strand:
I. Separated DNA strand that is read in a 3'to5'
direction and replicated by DNA polymerase in
a 5'to3' direction using only 1 RNA primer
3. Lagging strand:
I. Separated DNA strand that is read in and
synthesized in multiple Okazaki fragments
using multiple RNA primases.
4. RNA Ligase:
I. Enzyme tha seals newly generated daughter
strand's terminal after substitution of the gap in
the strand created by removal of RNA primer
with DNA nucleotides
5. DNA Ligase:
I. Enzyme that closes the gap b/w okazaki
fragments

31

DNA Polymerase Types

1. Alpha
I. Synthesize leading and lagging strands
2. Beta
I. Participate in DNA repair process
3. Gamma
I. Replicates mitochondrial DNA
4. Delta
I. Synthesize leading and lagging strands
II. Fill gaps created from RNA primer removal
5. Epsilon
I. Participate in DNA process

32

DNA Repair

Process that prevents cancer progression and tumor formation by reversing DNA damage exerted through
I. exposure to chemicals & radiation
II. DNA polymerase imperfect replication
III. Spontaneous mutations of proto-oncogenes

33

DNA Repair Types

1. Antioncogenes
2. Proofreading
3. Mismatch Repair
4. Nucleotide Excision Repair
5. Base-Excision Repair

34

Anti-Oncogenes

One strategy for DNA repair in which genes like p53 and rb, DNA repair genes, encode proteins that suppress tumor growth and carcinogenic cell division

35

Proofreading

One form of DNA repair in which DNA polymerase detects unstable, incorrect base-pairings in semi-conservative DNA molecules and attempts to excises and replace the incorrect base with its correct complementary pair


***Bases are excised from the newly synthesized strand that is less methylated compareed to the parent strand****

36

Mismatch Repair

One form of DNA repair in which the mismatched replicated pairs gone unrecognized through cell cycle's s-phase become captured and removed during the cell cycle's G2 phase.

37

Nucleotide Excision Repair

AKA NER
DNA repair mechanism in G1 & G2 of cell division cycle in which bulges and lesions of DNA structure caused by thymine dimerization become recognized, excised by excision endonucleases, and replaced by newly synthesized DNA before being sealed off by DNA Ligase

****Dimerization of thymine is a DNA-damage-inducing process triggered by ultraviolate radiation****

38

Base Excision Repair

Type of DNA repair where the presence of an inappropriate base in a DNA molecule is recognized, removed by glycosylases, and cleaned by an AP endonuclease.

Required in cases where removal of an amine group due to excessive thermal levels converts one base to another [i.e. Cytosine to Uracil] that should not be present in the nucleic acid chain.

*****review pg. 189********

39

Recombination DNA

1. Recombinant DNA
I. Technology that enables multiplication of a
DNA fragment through either
1. DNA cloning
2. PCR [Polymerase Chain Rxn]
to achieve
1. gene alteration
2. protein analysis
3. Genetic testing for carrier detection
4. Prenatal dx for genetic diseases
5. Gene therapy

*****review 190*****

40

PCR

A DNA recombinant technique used for
1. determination of etiology of a disease
2. determination of blood relationships
& 3. identification of criminal suspects
by multiple cycles of
1. denaturation
2. replication
& 3. reannealing of DNA
until enough DNA is yielded for testing