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Molecular Diagnostics > Lecture 4: Errors, Repair, SNP COPY > Flashcards

Lecture 4: Errors, Repair, SNP COPY Flashcards

1
Q

Types of DNA damage

A
  • Single strand breaks
  • Double strand breaks
  • Pyrimidine Dimer
  • Nucleotide base oxidation
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2
Q

Cause of DNA damage

Exogenous

A

Thermal disruption
UV light exposure
Ionizing radiation
Exposure to mutagens, carcinogens, and viruses

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3
Q

Cause of DNA damage

Endogenous

A

Cellular metabolism
Hydrolysis
Nuclease Digestion

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4
Q

AGENTS THAT DAMAGE DNA

Certain wavelengths of radiation

A
  • ionizing radiation such as gamma rays and X-rays
  • ultraviolet rays, especially the UV-C rays (~260 nm) that are absorbed strongly by
    DNA but also the longer-wavelength UV-B that penetrates the ozone shield.
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5
Q

AGENTS THAT DAMAGE DNA

Chemicals in the environment

A
  • many hydrocarbons, including some found in cigarette smoke
  • some plant and microbial products, e.g. the aflatoxins produced in moldy peanuts
  • Chemicals used in chemotherapy, especially chemotherapy of cancers
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6
Q

AGENTS THAT DAMAGE DNA

Intrinsic Spontaneous mutation

Most of the errors during dna replication occur by

MMR enzyme mutation causes

High reactive oxygen causes

A
  • most error during DNA replication by error of polymerase 3’ to 5’ exonuclease activity
  • MMR enzyme mutation caused mismatch repair failure
  • Highly-reactive oxygen radicals produced during normal cellular respiration as well as
    by other biochemical pathways.
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7
Q

REPAIRING DAMAGED BASES

The recent publication of the human genome has revealed _________ genes whose
products participate in DNA repair. More is expected to be discovered

A

130

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8
Q

REPAIRING DAMAGED BASES

  • Damaged or inappropriate bases can be repaired by several mechanisms:
A
  • Direct chemical reversal of the damage
  • Excision Repair, in which the damaged base or bases are removed and then replaced with
    the correct ones in a localized burst of DNA synthesis. There are three modes of excision
    repair, each of which employs specialized sets of enzymes.
  • Base Excision Repair (BER)
  • Nucleotide Excision Repair (NER)
  • Mismatch Repair (MMR)
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9
Q

REPAIRING DAMAGED BASES

Excision Repair

A

In which the damaged base or bases are removed and then replaced with
the correct ones in a localized burst of DNA synthesis. There are three modes of excision
repair, each of which employs specialized sets of enzymes.

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10
Q

REPAIRING DAMAGED BASES

The 2015 Nobel Prize in chemistry was shared by three researchers for their
pioneering work in DNA repair: Tomas Lindahl (BER), Aziz Sancar (NER), and
Paul Modrich (MMR).

A
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11
Q

DIRECT REPAIR GENES

DNA photolyase

A
  • Natural repair system for pyrimidine dimers caused by UV damage
  • Directly reverse cyclobutane pyrimidine dimer (CPD) via photochemical reactions
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12
Q

DIRECT REPAIR GENES

O6-methylguanine-DNA methyltransferase (MGMT)

Naturally occurring mutagenic DNA lesion _________

Prevents what

The _______ state of the ________ gene promoter determines

A
  • naturally occurring mutagenic DNA lesion O6-methylguanine back to guanine
  • prevents mismatch and errors during DNA replication and transcription
  • the methylation state of the MGMT gene promotor determined whether tumor cells
    would be responsive to temozolomide drug therapy
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13
Q

BASE EXCISION REPAIR (BER)

The damaged base estimated to occur some _______ times a day in each cell in
our body!

A

20,000

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14
Q

BASE EXCISION REPAIR (BER)

Remove it by a __________. There are at least 8 genes encoding different
DNA glycosylases:

A

Remove it by a DNA glycosylase. There are at least 8 genes encoding different
DNA glycosylases

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15
Q

BASE EXCISION REPAIR (BER)

There are at least 8 genes encoding different
DNA glycosylases.

Each enzyme responsible for

Two genes encoding enzymes (________________) function to remove deoxyribose phosphate in where

A
  • Each enzyme responsible for identifying and removing a specific kind of base damage.
  • Two genes encoding enzymes (AP endonuclease and DNA Exonuclease) function to
    removal deoxyribose phosphate in the backbone, producing a gap
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16
Q

BASE EXCISION REPAIR (BER)

Replacement with the correct nucleotide. This relies on DNA polymerase _________, one of at least _____ DNA polymerases encoded by our genes

A

Replacement with the correct nucleotide. This relies on DNA polymerase
beta, one of at least 11 DNA polymerases encoded by our genes

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17
Q

BASE EXCISION REPAIR (BER)

______ of the break in the strand. Two enzymes are known that can do this;
both require ______ to provide the needed energy.

A

Ligation of the break in the strand. Two enzymes are known that can do this;
both require ATP to provide the needed energy.

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18
Q

BASE EXCISION REPAIR

One stand of DNA contains __________
base, such as _________

A

One stand of DNA contains deaminated
base, such as Uracil

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19
Q

BASE EXCISION REPAIR

DNA glycosylases scans _______

A

the DNA and
removes Uracil, leaving AP site

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20
Q

BASE EXCISION REPAIR

AP endonuclease locates _________

A

AP site and nicks backbone

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21
Q

BASE EXCISION REPAIR

DNA Exonuclease removes

A

nucleotides near the nick, leaving gap

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22
Q

BASE EXCISION REPAIR

DNA Polymerase synthesizes to _______

A

fill in gap

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23
Q
A
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24
Q

BASE EXCISION REPAIR

DNA Ligase seals the

A

backbone

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25
Q

NUCLEOTIDE EXCISION REPAIR (NER)

NER differs from BER in several ways:

A
  • It uses different enzymes (XP products).
  • Even “though there may be only a single “bad” base to correct, NER removes a large “patch around
    the damage such as to removes DNA damage induced by ultraviolet light (UV), such as thymine dimer.
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26
Q

NUCLEOTIDE EXCISION REPAIR (NER)

The steps and some key players:

The damage is recognized by ______________, also functions in normal transcription) and
may be more protein factors that assemble at the location.

A

Transcription Factor IIH, (TFIIH)

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27
Q

NUCLEOTIDE EXCISION REPAIR (NER)

The steps and some key players:

The DNA is unwound producing a “bubble”. The enzyme system (Numerous proteins, including _____
products (____________), may cut both the ___’ side and the _____’ side of the damaged area so the
tract containing the damage can be removed.

A

XP ( XPA, XPB, XPF, XPG)

3’

5’

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28
Q

NUCLEOTIDE EXCISION REPAIR (NER)

The steps and some key players:

A fresh burst of DNA synthesis — using the intact (opposite) strand as a template — fills in the correct
nucleotides with ___________

A

A fresh burst of DNA synthesis — using the intact (opposite) strand as a template — fills in the correct
nucleotides with DNA polymerase delta and epsilon

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29
Q

XERODERMA PIGMENTOSUM (XP)

Type of disease

Effects what pathway

A

A rare inherited autosomal recessive
disease of humans in which a deficiency of
excinuclease XPa and other XP products occurs

Effects the NER pathway

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30
Q

XERODERMA PIGMENTOSUM (XP)

XP can be caused by

A

XP can be caused by mutations in any one
of several genes (XPA, XPB, XPF, XPG), all
of which have roles to play in NER

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31
Q

XP resulting in

A
  • XP resulting in skin discolouration and
    multiple tumours on exposure to UV light.
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32
Q

XP unprepared __________ in humans may lead to ___________

A
  • Unrepaired pyrimidine dimers in humans
    may lead to melanoma
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33
Q

MISMATCH REPAIR (MMR)

  • DNA mismatch repair is a system for recognizing and repairing erroneous insertion,
    deletion, and mis-incorporation of bases that can arise during ____________________, as well as repairing some forms of ____________
A
  • DNA mismatch repair is a system for recognizing and repairing erroneous insertion,
    deletion, and mis-incorporation of bases that can arise during DNA replication and
    recombination, as well as repairing some forms of DNA damage
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34
Q

MISMATCH REPAIR (MMR)

Mismatch repair deals with correcting mismatches of the __________; that is, failures to
maintain normal ________ base pairing (AT, CG)

A

Mismatch repair deals with correcting mismatches of the normal bases; that is, failures to
maintain normal Watson-Crick base pairing (AT, CG)

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35
Q

MISMATCH REPAIR (MMR)

It can enlist the aid of enzymes involved in both ______________ and ____________ as well as using enzymes specialized for this function.

A

It can enlist the aid of enzymes involved in both base-excision repair (BER) and nucleotide-
excision repair (NER) as well as using enzymes specialized for this function.

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36
Q

MISMATCH REPAIR (MMR)

  • Recognition of a mismatch requires several different proteins including one encoded by
    __________ known as ________________, a caretaker gene
A
  • Recognition of a mismatch requires several different proteins including one encoded by
    MSH2 known as MutS protein homolog 2, a caretaker gene
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37
Q

MISMATCH REPAIR (MMR)

Cutting the mismatch out also requires several proteins, including one encoded by ______
known as ______ homologs. It forms a complex with _____ and _______, increasing the _______
footprint on the DNA.

A

Cutting the mismatch out also requires several proteins, including one encoded by MLH1
known as MutL homologs. It forms a complex with MutS and MutH, increasing the MutS
footprint on the DNA.

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38
Q

MISMATCH REPAIR (MMR)

Mutations in either of these genes predisposes the person to an inherited form of colon
cancer. So these genes qualify as _____________

A

Tumor suppressor genes

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39
Q

Mismatch Repair in Prokaryotes and Eukaryotes

Mut S recognizes

A

and binds mismatch

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40
Q

Mismatch Repair in Prokaryotes and Eukaryotes

Mut L links

A

S to H

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41
Q

Mismatch Repair in Prokaryotes and Eukaryotes

Mut H recognizes the

A

CH3-parental strand and makes nick on daughter strand

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42
Q

Mismatch Repair in Prokaryotes and Eukaryotes

In human: MutS =

MutL=

MutH=

A

hMSH (1-6); MutL = hMLH1 and hPMS2; MutH = GTBP

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43
Q

REPAIRING STRAND BREAKS

Single-Strand Breaks (SSBs)

A
  • Breaks in a single strand of the DNA molecule are repaired using the
    same enzyme systems that are used in Base-Excision Repair (BER).
  • BER, NER and MMR are all strand specific SSB repairing system
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44
Q

REPAIRING STRAND BREAKS

Double-Strand Breaks (DSBs)

There are two mechanisms by which the cell attempts to repair a
complete break in a DNA molecule:

A
  • Direct joining of the broken ends. This requires proteins that recognize and bind
    to the exposed ends and bring them together for ligating. They would prefer to
    see some complementary nucleotides but can proceed without them so this
    type of joining is also called Nonhomologous End-Joining (NHEJ).
  • Homologous Recombination (next page)
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45
Q

Direct joining of the broken ends

A

Direct joining of the broken ends. This requires proteins that recognize and bind
to the exposed ends and bring them together for ligating. They would prefer to
see some complementary nucleotides but can proceed without them so this
type of joining is also called Nonhomologous End-Joining (NHEJ)

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46
Q

REPAIRING OF DOUBLE STRAND BREAKS

Homologous Recombination (also known as Homology-
Directed Repair HDR).

Sister chromatids available In

A

available in G2 after chromosome duplication

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47
Q

REPAIRING OF DOUBLE STRAND BREAKS

Homologous Recombination (also known as Homology-
Directed Repair HDR).

Homologous chromosome

In what stage of the cell cycle

This requires what

A

(in G1; that is, before each chromosome
has been duplicated). This requires searching around in the nucleus
for the homolog - a task sufficiently uncertain that G1 cells usually
prefer to mend their DSBs by NHEJ.

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48
Q

REPAIRING OF DOUBLE STRAND BREAKS

Homologous Recombination (also known as Homology-
Directed Repair HDR).

Same chromosome

If there are duplicate copies of the gene blank

A

if there are duplicate copies of the gene on the
chromosome oriented in opposite directions (head-to-head or back-to-
back).

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49
Q

REPAIRING OF DOUBLE STRAND BREAKS

Homologous Recombination (also known as Homology-
Directed Repair HDR).

Two of the proteins used in homologous recombination are encoded by
the genes _______ and _______. Inherited mutations in these genes
predispose women to ______ and _________ cancers

A

Two of the proteins used in homologous recombination are encoded by
the genes BRCA1 and BRCA2. Inherited mutations in these genes
predispose women to breast and ovarian cancers

50
Q

Gap O G0

A

quiescent/ Senescent
Gap 0 G0
A resting phase where the cell has left the cycle and has stopped
dividing

51
Q

Interphase

Gap 1

A

Gap 1 G1
Cells increase in size in Gap 1. The G1 checkpoint control
mechanism ensures that everything is ready for DNA synthesis.

52
Q

Interphase

Synthesis or s phase

A

Synthesis S DNA replication occurs during this phase.

53
Q

Interphase

Gap 2 or G2

A

Gap 2 G2
During the gap between DNA synthesis and mitosis, the cell will
continue to grow. The G2 checkpoint control mechanism ensures that
everything is ready to enter the M (mitosis) phase and divide.

54
Q

Cell
division

M mitosis

A

-Cell
division
-Mitosis M
Cell growth stops at this stage and cellular energy is focused on the
orderly division into two daughter cells. A checkpoint in the middle
of mitosis (Metaphase Checkpoint) ensures that the cell is ready to
complete cell division.

55
Q

MAJOR PROTEINS THAT CONTROL CELL CYCLE

Control Proteins

A
  • Cyclin-dependent protein kinases (Cdks)
  • Cyclins
56
Q

MAJOR PROTEINS THAT CONTROL CELL CYCLE

Complexes: Cdk-cyclin

A
  • ability of Cdk to “P” target is dependent on the cyclin that it forms a
    complex with
57
Q

CELL CYCLE CHECKPOINT PROTEINS

G1 checkpoint

Activates what in the nucleus

Unphosphyrylated Rb acts as an

Activated what also prevents G1-S phase transcription

A
  • Active cyclin D-cdk4 complexes phosphorylate retinoblastoma protein (pRb) in the
    nucleus. Unphosphorylated Rb acts as an inhibitor of G1 by preventing E2F-mediated
    transcription.
  • Activated P53-p21 interaction also prevent G1 to S phase transition

Activated what interaction also prevents G1 to S phase transition

58
Q

CELL CYCLE CHECKPOINT PROTEINS

G2 checkpoint

Mechanisms

A
  • DNA damage in the G2 phase initiate a signaling cascade that regulates wee1 and
    cdc25 activity, therefore controlling mitotic entry via cyclin B-cdK2 can delay in
    mitotic entry
59
Q

CELL CYCLE CHECKPOINT PROTEINS

Mitotic checkpoint

A
  • Spindle assembly checkpoint (SAC), through P53-cdK2-GADD45 cascade, to ensure
    chromosome segregation is correct.
  • prevents anaphase onset until all chromosomes are properly attached to the spindle.
60
Q

APOPTOSIS

The process of programmed cell death that may occur in _______________

A

The process of programmed cell death that may occur in multicellular
organisms

61
Q

APOPTOSIS

Biochemical events lead to characteristic cell changes (morphology) and death
(different from necrotic or autophagic cell death):

A
  • blebbing, cell shrinkage, nuclear fragmentation, chromatin condensation, chromosomal
    DNA fragmentation, and global mRNA decay
62
Q

APOPTOSIS

  • Highly _________ and ____________ process that confers advantages during an
    organism’s lifecycle.
A
  • Highly regulated and controlled process that confers advantages during an
    organism’s lifecycle.
63
Q

APOPTOSIS

Apoptotic Genes

BCL2 and TP53

A
  • AIFM2, BAK1, BBC3, BCL2, BCL2L1 (BCL-X), BID, BNIP3, CDKN2A (p16INK4), DNM1L, MPV17, PMAIP1
    (NOXA), SFN (14-3-3s), SH3GLB1, SOD2, TP53.
64
Q

NECROSIS VS APOPTOSIS

Necrosis

A
  • Increase in cell volume
  • Loss of plasma membrane integrity
  • Leakage of cellular contents

cells die accidentally due to injury,
trauma (ex. a poisonous spider bite),
or lack of nutrients (ex. lack of blood
supply)

65
Q

NECROSIS VS APOPTOSIS

Apoptosis

When do cells commit suicide

A
  • cell shrinkage
  • plasma membrane blebbing
  • formation of apoptotic bodies

Cells commit suicide when lacking any
incoming survival, or severe viral infection.
or when they detect extensive DNA
damage in their own nucleus. Cells will
murder other cells to clear out unneeded
cells or to eliminate potentially self-attacking
immune cells.

66
Q

THE UBIQUITIN-PROTEASOME SYSTEM

Proteasome, a complex inside all

A

Proteosome, a complexes inside all eukaryotes and archaea, and in some
bacteria.

67
Q

THE UBIQUITIN-PROTEASOME SYSTEM

Proteosome main function

A

Main function is to degrade unneeded or damaged proteins by proteolysis, a
chemical reaction that breaks peptide bonds

68
Q

THE UBIQUITIN-PROTEASOME SYSTEM

Proteasomes are located both in the

A

nucleus and in the cytoplasm

69
Q

THE UBIQUITIN-PROTEASOME SYSTEM

The proteasomal degradation pathway is essential for many

A

Cellular processes,
including the cell cycle, the regulation of gene expression, and responses to
oxidative stress.

70
Q

THE UBIQUITIN-PROTEASOME SYSTEM

Protein degradation during

A

anaphase of mitosis of cell cycle.

71
Q

THE UBIQUITIN-PROTEASOME SYSTEM

The importance of proteolytic degradation inside cells and the role of ubiquitin
in proteolytic pathways (UPP) was acknowledged in the award of the 2004
Nobel Prize in Chemistry to Aaron Ciechanover, Avram Hershko and Irwin Rose

A
72
Q

HUMAN GENOME PROJECT

Launched in

A

1989 -expected to take 15 years

73
Q

HUMAN GENOME PROJECT

Competing Celera project launched in

A

1998

74
Q

HUMAN GENOME PROJECT

Genome estimated to be ______ complete
* 1st Draft released in _____
* “Complete” genome released in _____
* Sequence of last chromosome published in _____

A

Genome estimated to be 92% complete
* 1st Draft released in 2000
* “Complete” genome released in 2003
* Sequence of last chromosome published in 2006

75
Q

HUMAN GENOME PROJECT

cost:
Celera:

A
  • Cost: rv $3 billion
  • Celera: rv $300 million
76
Q

THE HUMAN GENOME:

All humans share _____ of the same genetic sequence

A

99.9%

77
Q

THE HUMAN GENOME:

____ of human genome variation comes from Single Nucleotide
Polymorphisms (SNPs)

A

90%

78
Q

THE HUMAN GENOME:

The most common sources of variation between humans are

A

The most common sources of variation between humans are single
nucleotide polymorphisms (SNPs)—single base differences between
genomic sequences.

79
Q

GENOME SEQUENCING PROJECT FINDS SNPS

The Human Genome Project involves sequencing

The Celera sequence comes from

A

DNA cloned from a number of
different people.[The Celera sequence comes from 5 people]

80
Q

GENOME SEQUENCING PROJECT FINDS SNPS

_____ occur normally throughout a person’s DNA.

A

SNPs

81
Q

GENOME SEQUENCING PROJECT FINDS SNPS

It occur almost once in every _______ nucleotides on average, which means
there are roughly 2-10 million SNPs in a person’s genome.

A

1,000

82
Q

GENOME SEQUENCING PROJECT FINDS SNPS

This inevitably leads to the discovery of any sequence difference-_____ is the most
common one.

A

SNPs

83
Q

GENOME SEQUENCING PROJECT FINDS SNPS

SNP can act as biological markers, helping scientists locate

A

that are
associated with disease

84
Q

GENOME SEQUENCING PROJECT FINDS SNPS

When SNPs occur within a gene or in a regulatory region near a gene, they
may play a more direct role in ______________

A

disease by affecting the gene’s function

85
Q

POLYMORPHISMS

Most disease-causing gene mutations are uncommon in the
______________.

A

Most disease-causing gene mutations are uncommon in the
general population.

86
Q

POLYMORPHISMS

Polymorphisms definition

Genetic alteration that occur in

A

Genetic alterations that occur in more than 1 percent of the
population are called polymorphisms.

87
Q

POLYMORPHISMS

They are common enough to be considered a normal variation in the

A

DNA

88
Q

POLYMORPHISMS

Polymorphisms are responsible for many

A

of the normal differences
between people such as eye color, hair color, and blood type.

89
Q

POLYMORPHISMS

Although many polymorphisms have no negative effects on a person’s
health, some of these variations may influence

A

he risk of developing
certain disorders.

90
Q

Human Genetic Variation

what disease are caused by dysfunctional alleles

A

genetic diseases such as cystic fibrosis or Huntington’s disease are caused
by dysfunctional alleles

91
Q

Human Genetic Variation

But there are different forms of each gene - known as

A

Alleles

blue vs. brown eyes (or purple vs white flowers

92
Q
A
93
Q

LIFE CYCLE OF SNP
(LONG WAY FROM MUTATION TO SNP)

A

1.) Appearance of
new variant
by mutation
2.) Survival of rare allele
3.) Increase in allele frequency
after population expand
4.) New allele is fixed
in population as novel polymorphism

94
Q

SEQUENCE VARIATION AND SNP DISTRIBUTION

types of regions

A
  • Non-Coding region (2/3)
  • Regulatory region
  • Coding region (1/3)
95
Q

SEQUENCE VARIATION AND SNP DISTRIBUTION

coding region can be what or what

A
  • Synonymous
  • Non-Synonymous
96
Q

SEQUENCE VARIATION AND SNP DISTRIBUTION

  • Non-Synonymous
A
  • missense
    • Conservative
  • Non-Conservative
    • nonsense
97
Q

SEQUENCE VARIATION AND SNP DISTRIBUTION

  • One half of all coding sequence SNPs result in
A

non-synonymous
codon changes.

98
Q

LEARNING FROM OUR DIFFERENCES

Many common diseases and many drug responses ____________

Studying what can improve our understanding and treatment of diseases

A
  • Most common diseases and many drug responses have been
    shown to be influenced by inherited differences in our genes
  • Studying genetic variances can improve our understanding
    and treatment of disease
99
Q

3 billion genes but only how many coding region genes

A

20,000

100
Q

Polymorphisms dont really cause any changes to your

A

Body

101
Q

Endogenous

A

In the body mutations

Cellular metabolism
Hydrolysis
Nuclease Digestion

102
Q

Types of DNA damage

A

Single strand DNA damage
Double stranded DNA damage
Pyrimidine dimer such as Thymidine can cause sun mutations

103
Q

DNA glycosylase

Generated at the blank site add the what

A

Generated at the AP site and add the correct base back at the 3’prime end and then DNA ligase can correct short strand

104
Q

Thymidine dimer is what type of correction

A

NER

105
Q

XP proteins cut from the _______ end and then polymerase ___________ and ___________ fix it

A

5’ end

Delta and Epsilon fix it

106
Q

Mismatch repair

If what didn’t find the wrong one

A

If polymerase didn’t find wrong one

107
Q

Muts and mutsH are associated with

A

Lower organisms systems

108
Q

If enzymes are not corrected then certain diseases can occur such as

A

Xeroderma pigmentoserum
Fanconi anemia
Blood syndrome
Ataxia telangietasia

109
Q

BRCA1 is a what repairing enzyme

A

Homologenous double stranded repairing enzyme

110
Q

BRCA2 is a

A

Suppressor gene that can lead to brest cancer and ovarian cancers

111
Q

The cell cycle check phases

A

G1, G2, metaphase

112
Q

Cyclin is activated by

A

Phosphorylation

113
Q

P53 is a

A

Tumor suppressor gene

114
Q

BCL2 is a

A

Mitochondrial protein and has regulatory functions

115
Q

When the nucleus becomes fragmented what proteins are produced

A

uPP proteins and bind to and conjugate then go to proteasome so that degradation can occur

116
Q

Inactivation of CDK by

A

Ubq is conjugated to it then cyclin- CDK will be broken and cyclin will go through apoptosis

117
Q

90% of all human variation comes from

A

Single nucleotide polymorphisms

118
Q

almost every 1000 bases you will find one different ________

A

SNP( variant) or different forms of each gene alleles such as hair and eye color

119
Q

You can have two alleles but maybe only one ________

A

gene different per trait on a chromonsome

120
Q

Human Genetic Variation

Every human has essentially the same set of

A

Genes

Molecular Diagnostics (12 decks)

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