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Biochemistry > DNA & BioTechnology > Flashcards

DNA & BioTechnology Flashcards

1
Q

Types of Eukaryotic Nucleic Acids

A
  1. Deoxyribonucleic Acid (DNA)—Double stranded

2. Ribonucleic Acid (RNA)———–Single stranded

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2
Q

Location of DNA Storage in Eukaryotic Cells

A
  1. Nucleus
  2. Mitochondria
  3. Chloroplast
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3
Q

Nucleic Acid Nomenclature

A
  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
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4
Q

Classifying Category of Nucleic Acids

A

Type of pentose

       1. if ribose-------------------->RNA----w/ OH
       2. if deoxyribose---------->DNA----w/ H
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5
Q

Types of Nitrogenous Bases in Nucleic Acids

A 
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

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6
Q

Types of Nucleosides

A
  1. Adenosine/Deoxyadenosine
  2. Guanosine/Deoxyguanosine
  3. Cytidine/Deoxycytidine
  4. Uridine/Deoxyuridine
  5. Deoxythymidine
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7
Q

Types of Nucleotides

A
  1. AMP/ADP/ATP
  2. GMP/GDP/GTP
  3. CMP/CDP/CTP
  4. UMP/UDP/UTP
  5. dTMP/dTDP/dTTP
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8
Q

Nucleic Acid Backbone Properties:

A
  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’
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9
Q

Model Deduced to Describe Structure of DNA

A 
1. Name
         I. Watson-Crick Model 
2. Date of Development
         I. 1953
3. Founding Figures
         I. James Watson 
        II. Francis Crick
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10
Q

Chargaff’s Rules

A

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

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11
Q

DNA Types

A
  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
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12
Q

Major & Minor Grooves

A

Sites of protein binding on DNA molecules

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13
Q

Denaturation & Reannealing

A
  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
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14
Q

Probe DNA

A

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

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15
Q

Chromosomal Terminology

A
  1. Chromosome [
  2. Nucleosome vs Chromatin [Histones + DNA Strands]
  3. Heterochromatin vs Euchromatin
  4. teomere
  5. Telomerase
  6. Centromere
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16
Q

Chromosome

A

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

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17
Q

Chromatin Vs. Nucleosome

A

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

18
Q

Histones

A
  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
Q

Nucleoproteins

A

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

20
Q

Heterochromatin Vs. Euchromatin

A

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
Q

Telomere & Telomerase

A

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
Q

Centromere

A

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
Q

DNA

A

Biological macromolecule that

  1. serves as blueprint for life
  2. provides info about evolutionary past
24
Q

DNA replication

A

Process of DNA copy making that is integral to

  1. Cell-division
  2. Reproduction
25
Q

DNA Replication Process

A
  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
Q

Replisome Complexes

A

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

27
Q

Replication Forks

A

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

28
Q

DNA Strand Separation Process

A

1, Helicase unwinds DNA strands at the replication origin

  1. Topoisomerase moves ahead of the helicase and prevents unwinded strands from supercoiling by nicking and resealing single strands, releasing its torsional strain
  2. 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
Q

DNA Daughter Strand Synthesis Process

A
  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
Q

DNA Daughter Strand Synthesis Terminology

A
  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
Q

DNA Polymerase Types

A
  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
Q

DNA Repair

A

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
Q

DNA Repair Types

A
  1. Antioncogenes
  2. Proofreading
  3. Mismatch Repair
  4. Nucleotide Excision Repair
  5. Base-Excision Repair
34
Q

Anti-Oncogenes

A

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
Q

Proofreading

A

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
Q

Mismatch Repair

A

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
Q

Nucleotide Excision Repair

A

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
Q

Base Excision Repair

A

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
Q

Recombination DNA

A
  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
Q

PCR

A

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

Biochemistry (12 decks)

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