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MMSC491 Exam 1

Terms in this set (64)

Epigenetic
Changes in phenotype
Heritable
Not due to changes in DNA sequence
DNA methylation or histone modification
Collective term for all different DNA molecules within a cell or organism
Genome
DNA protein complex
Chromosome
How many DNA molecules does a male have? female have?
Male 25
Female 24
Single ring based on carbon and nitrogen atoms

C,T
Pyrimidine
Double ring structure

A, G
Purine
How many bonds holds together G-C
3 hydrogen bonds
How many bonds hold together A-T
2 hydrogen bonds
DNA replication
In preparation for new DNA synthesis before cell division each strand unwinds with helicase
Both strands become available as templates for making complementary DNA strands that are synthesized 5' to 3' direction
Semi-conservative
One new strand (leading strand) can be synthesized continuously
The lagging strand is synthesized in pieces known as Okzaki fragments
Classical DNA dependent DNA polymerase
Standard DNA replication
RNA dependent DNA polymerase
Genome evolution and telomere function
Use 1 of 2 DNA strands as a template for synthesizing an RNA copy
Transcription
Sugars in DNA and RNA
Both are 5 carbon atoms

Hydroxyl group at C2 in ribose

H atom replaces hydroxyl group in deoxyribose
ssDNA structure
Sugar phosphate backbone is asymmetrical because phosphate groups connect with carbon at 5' and a sugar with carbon at 3 hydroxyl group on the 3' end
Protein- DNA complex (aids in fitting large DNA molecules in nucleus within confines of this organelle)
Chromatin
Histones
Basic proteins found in chromatin

React with negatively charged phosphate backbone of DNA molecules
Average sized chromosome
4.8 cm long with 140 million base pairs
What does chromatin do
Organizing feature

Supports rapid DNA replication

Aids in proper segregation of replicated DNA during cell division

Aids in transcriptional regulation
What are the special units of chromosome function
Replication origins
Centromeres
Telomeres
Centromeres
Specific sequence of DNA location at midsection of chromosome
Bound to kinetochore (bound by spindle fibers-microtubules, aid in moving chromosome from 1 side of cell to other) during DNA segregation
Essential for proper segregation of chromosomes during cell division
Replication origins
Specific sequences of DNA required for replication
Chromosomal replication
Multiple origins are necessary in higher eukaryotes
Not conserved throughout nature
Certain proteins bind to origins and recruit replication machinery to the site
Telomeres
Specialized sequences at ends of chromosomes
Become degraded, leads to chromosome being unstable and recombination or fusion can happen so the end won't be exposed; if it is exposed nucleosomes degrade the chromosome
Highly conserved sequence throughout nature
Polyploid
DNA undergo multiple rounds of replication without division
Origination from cell fusion to give rise to cells with multiple nuclei

Hallmark of cancer cells
Mitochondrial copy number
Can vary from 100s to many thousands
Human egg and sperm show different mitochondrial DNA copies
Gametes
Autosomes
X,Y sex chromosomes
S phase
DNA replication
M phase
Cell division
Exons vs. Introns
Exons:
protein coding segments of our genome
show moderate variation in size

Introns:
non-coding sequences that separate exons of a gene
show extraordinary size variation
Open reading frame
Initiation codon open reading frame
Reading frame
3 possible forward reading frames for any mRNA
The right way is due to correct recognition of AUG initiation codon
If 1 or 2 nucleotides are deleted from coding sequence, produces a frame shift resulting in a nonsense translation
Alternative splicing
Common- increasing variety of gene products
Aids in genome evolution
1 gene can give ride to many different proteins
Splice sites important in genetic diseases
GU splice donor site
AU splice acceptor site
Carry of the process of RNA splicing
Spliceosomes
snRNA
3 phases of translation
initiation, elongation, termination
Start codon
AUG
Stop codon
UAA, UAG, UGA
Post-translational modification
Mature protein
What side of tRNA binds amino acid
3' through covalent bonding
Contains peptidyl transferase activity that forms peptide bonds
rRNA
Post translational processing
Chemical modification
Protein folding
Cleavage and transport
Joining of multi polypeptide chains
Disulfide bonds between cysteine residues
RNA involved in RNA maturation
snRNA
snoRNA
RNA enzymes-ribozymes
Cleave tRNA and RNA precursors
What RNA causes genetic disorders and cancer
ncRNA
Secondary structure in RNA
Basic motifs= stem loop structure
When RNA folds back on itself, 2 short regions pair
GU base pairs form RNA in addition to GC and AU base pairs
Projects undertaken to understand the human genome
HGP- Human Genome Project

ENCODE- how much of genome is actually functionally significant (found that most is)
General organization of the human genome
Mitochondrial vs. genomic DNA
Heterochromatin vs. euchromatin
Repetitive DNA
Gene families
Pseudogenes
Euchromatin vs. Heterochromatin
Euchromatin:
relaxed/extended
transcriptionally active

Heterochromatin:
highly condensed
PCR
Polymerase Chain Reaction
Lab technique
Takes very small sample of DNA and amplifies it
Lag phase
Exponential phase
Saturation phase
DNA cloning
Fractionating and purifying DNA by transforming cells with recombinant DNA

Cloning vectors:
plasmid
bacterial artificial chromosome
yeast artificial chromosome
Nucleic acid hybridization probe
A single type of cloned DNA
High stringency nucleic acid hybridization
High temp
Low salt concentration

Short probe allows to discriminate alleles that differ at nucleotide position
Low stringency nucleic acid hybridization
Identify nucleic acid sequences that are distantly related from given probe
DNA clone from human gene and use that to identify a mouse gene
Reduced stringency and long DNA probe allow stable heteroduplexes to form even though there may be base mismatches
Two fundamental classes of hybridization assays
1. labeled probe, unlabeled test sample

2. unlabeled probe, labeled test sample.
Microarray hybridization
Unlabeled DNA that have been fixed to glass, high density grid formate
Constitutional DNA sequence variation vs. Inherited
Somatic mutations:
UV radiation, changes in DNA of skin cells (not present constitutionally throughout body)
Endogenous errors in chromosome and DNA function
DNA replication error
Chromosome segregation and recombination errors
Exposure to endogenous and exogenous sources
Chemicals
Replication slippage
Occurs within regions of short tandem repeats
Ex: 30 nucleotide sequence with 15 sequential repeats, increases chance of mistake
What diseases does an altered number of chromosomes cause
Down syndrome
Cancer
Single strand vs. Double strand breaks
Double strand breaks are more damaging to the cell

Single strand breaks are easily repaired (breakage of phosphodiester bond)
Hydrolytic DNA damage
Hydrolysis is inevitable in aqueous environment of cells
Cleave base from sugar to produce an a-basic site, loss of purine bases (de-purination is common)
Hydrolysis can strip amino groups from bases, deamination, base is left with carbonyl group
Reactive oxygen species (ROS) DNA damage
Incomplete 1 electron reduction of oxygen
Superoxide anions (hydrogen peroxide and hydroxide radical)
Roles in intra and extracellular signaling pathways
Originated in mitochondria where electrons can prematurely reduce oxygen
Attack covalent bonds and sugars, causing DNA strands to break
Can attack bases
Ionizing radiation causing DNA damage
ROS that break sugar-phosphate backbone that cleave DNA strands

X-rays, gamma rays
Non-ionizing radiation causing DNA damage
Covalent bonding between adjacent pyrimidine bases- thymine dimers

UV
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