Genetics Exam 1 MSU Denver Melvin

Central Dogma of Molecular Biology

DNA --transcription--> RNA --translation--> polypeptides/proteins

What did Hershey and Chase discover?

DNA = genetic material
Bacteriophage = viruses that infect bacteria
DNA has phosphate
Proteins have sulfur

What did Friedrich Miescher do?

Coined the term "nuclein"

What did Griffith and Avery do?

Discovered that the "transforming factor" is made of DNA through Griffith's experiments with virulence of strep's R and S strains in mice
Avery tried to disprove his findings but was unsuccesful

Components of DNA

Nucleotides (nitrogen base)
Phosphate group
Pentose sugar ring

Pyrimidines

T, U, C
(C)ing (T)(U)t PYRamids

Purines

A, G
PURe (A)(G)ony

What did Wilkins and Franklin discover?

DNA is helical and repetitive
Phosphate is on the outside

What did Watson and Crick discover?

Built a physical model of B-DNA

What links nucleotides to backbone?

Phosphodiester bond (covalent)

What joins nucleotides ?

Weak hydrogen bonds that are easily broken

G+C form __ hydrogen bonds

3 hydrogen bons

A+T form __ hydrogen bonds

2 hydrogen bonds

DNA strands run....

Antiparallel to each other

How many phosphates do free nucleotides have?

Three phosphate groups

Somatic cells are...

Diploid
Body cells

Gametes are....

Haploid
Sex cells

% G equals

% C

Humans have ___ chromosomes

46 chromosomes
(23 PAIRS of chromosomes)

Bacterial genomes are...

Haploid
Chromosomes circular
High coding to non-coding ratio

Eukaryotic genomes are...

Diploid
Linear chromosomes
Bi-parental inheritance

Horizontal Gene Transfer (HGT)

When a virus/outside source infects the cell and injects DNA

Vertical Gene Transfer (VGT)

Passing of genes from one generation to the next (parent to daughter cell)

Genome Equivalence

The concept that all cells of an organism carry the same genome (but use it differently depending on the cell type)

DNA is compact through....

Supercoiling

What is bacterial DNA organized by?

Proteins

Components of chromatin

DNA and proteins

Eukaryotic chromatin proteins

Histones

Histones

H1, H2A, H23, H3, H4

Histones have ____ charged tails

Positively (+)

Functions of chromatin

Package DNA
Regulate gene expression
Protects DNA from physical damage during replication and translation

Can conclusions about genome be determined by number of chromosomes?

NO

What is the function of H1?

Keeps the DNA attached

What is the function os H2-4?

Create 10nm fiber along with DNA

Features of chromosomes

Single strand of DNA wound around proteins
Haploid

Features of sister chromatid

Only seen during meiosis/mitosis
2 pieces of DNA
Diploid

Karyotype

Isolating and pairing all the chromosomes from a cell ---> in METAPHASE

Function of karyotyping

Used to study chromosomal abnormalities and find out gender.

In karyotyping, chromosomes are sorted based on.....

Size
Centromere position
Chromosome banding

Giesma staining

Dark and light bands
Heterochromatin and euchromatin
Cells cultured/synchronized during metaphase
ENTIRE GENOME

FISH

Fluorescent in situ hybridization
Cultured and synchronized during metaphase
ONE SPECIFIC GENE

Metacentric

Centromere in middle

Submetacentric

Centromere slightly off center
Short upper arms, long lower arms

Acrocentric

Describes a chromosome whose centromere is placed very close to, but not at, one end

Telocentric

No upper arms

DARKER staining in Giesma

A+T rich
HETEROchromatin

LIGHTER staining in Giesma

G+C rich
EUchromatin

Syntenic

When genes of the same chromosome are physically connected

Diploid Genome of Humans

~6 billion base pairs of DNA
46 chromosomes
~20,000 genes

Autosomes

Any chromosome that is not a sex chromosome

Allele

Different version of a gene

Mutation

ANY change in the DNA sequence
Evolution's daddy
Can be neutral, harmful, or beneficial

SNPs

(single nucleotide polymorphisms) a single base pair site where variation is found in at least 1% of the population
Ex: lactose intolerance

Haplotype

A group of SNPs inherited from a parent

VNTR

Variable Number of Tandem Repeats
Short sequences of nucleotides that are repeated (different # of times in different individuals)
Used for DNA fingerprinting and forensics

CNVs

Copy number variations
About 12% of genome

Transpones, SINES, LINES

Self-replicating sequences
Constitute a large portion of the human genome

Semiconvervative model

Used by ALL organisms

Steps of DNA Replication

1. Initiation
2. Unwinding
3. Priming
4. Replication/Elongation

1. Initiation (Eukaryotic)

Starts at "ori"- point of origin (A+T rich so easier to break)
"TTAT" popular for OriC
Starts at specific DNA sequences

2. Unwinding (eukaryotic)

DNAa, DNAb, DNAc, SSB, Topoisomerase, DNA polymerase I

DnaA

Binds to "9-mer" or ori and causes slight openign at 13-mer to bend DNA
Breaks H-bonds between base pairs at 13-mer

DnaB

Carried by DnaC
Bind to 13-mer of ori
Locally unwinds DNA
Breaks H-bonds between base pairs ---> helicase activity

DnaC

Carries DnaB to the ori
ESSENTIAL

Single-stranded DNA binding proteins (SSB)

Prevents re-annealing/binding of the DNA

Topoisomerase

Enzyme that rotates and removes coils in a controlled manor
Nicks phosphodiester bond to remove tension and then rejoins
W/O DNA cannot be separated or it will break beyond repair

DNA Polymerase

Replicates DNA using parental template
5' ---> 3' direction

A cell in the epithelium that lines your lung is....

A diploid somatic cell

The genome of the lung epithelial cell (somatic)...

Contains all the DNA sequences of a complete human genome

Gametes are haploid cells and...

Contain half the amount of DNA of a somatic cell
Contain all the DNA sequences of a human genome

How many autosomes are there in the human genome?

22 pairs, 44 individual

Sister chromatids are...

Exact replicas of each other
Products of DNA replication

DNA replication occurs in...

Interphase

If the sequence below is the template for replication, what direction will the DNA polymerase proceed to copy this strand?

5'-ACGTAGAGTGCTC-3'

Right to left

Which protein relaxes coils in DNA caused by unwinding of the DNA helix?

Topoisomerase

Which protein catalyzes the last phosphodiester bond formation between Okazaki fragments?

Ligase

Which protein has 5'--> 3' endonuclease activity?

DNA polymerase I
DNA polymerase III
Primase

Which protein has 5'-->3' exonuclease activity?

DNA polymerase I

Which protein has 3'-->5' exonuclease activity?

DNA polymerase I
DNA polymerase III

Which histone protein is not part of the core nucleosome structure?

H1

A mutation that affects only somatic cells of a parent will...

will have no effect on the offspring

What part of the nucleotide is "labelled" with 15N?

Base

After DNA replication, the resulting DNA molecules contain one strand of the original parental DNA and one newly synthesized DNA strand. What is the explanation for this phenomenon?

DNA replication is semiconservative

Replication uses a template that serves to direct the sequence of newly synthesized DNA. What is the template?

One strand of the DNA molecule

In their famous experiment, which of the following would Meselson and Stahl have observed after one cycle of replication in 14N medium if DNA replication were conservative?

DNA molecules containing two 14N-DNA strands only

Which of the following represents the correct order of phases in the cell cycle?

G1-S-G2-M

Sister chromatids are present in all or part of the following phases?

S
G2
Beginning of M-phase (prophase --> metaphase)

What do DNA polymerase I and III do in terms of proofreading?

Identify mutant base pairs and correct them before continuing transcription
3' ---> 5' EXOnuclease activity

5' ---> 3' ENDOnuclease activity

DNA polymerase I (adding nucleotides)
DNA polymerase III (elongating)

5' ---> 3' EXOnuclease activity

DNA polymerase I (removes RNA primer)

3' ---> 5' EXOnuclease activity

DNA polymerase I and DNA polymerase III (proofreading)

Hayflick limit

The number of times a cell can divide before senescence (the end of replication)

Telomeric sequences

Repeated, non-coding sequence repeated 250-1000 times at the end of sequences

Telomerase

a DNA polymerase expressed in gametes and stem cells that MAINTAINS and EXTENDS telomere sequences
Extends at 3' end
Only active in GERM and STEM cells, NOT somatic cells (if present in somatic cells it will create cancer cells)

In Eukarya, during replication DNA is...

repackaged into chromatin

Polymerase Chain Reaction (PCR)

Exponentially produces DNA fragments of interest through in nitro DNA replication

Reaction components of PCR

1. Template DNA
2. DNA primers (flank region of interest and provide free 3'-OH)
3. Nucleotides (dNTPs in triphosphate form)
4. Enzyme (Taq: heat stable DNA polymerase that will survive PCR)
5. Buffers (pH, salts, etc)

Steps of thermocycling

1. Denature DNA (95 C)
2. Primer annealing (45 - 68 C, depending on A/T + G/C content)
3. Extension (72 C, when DNA is made)

PCR is used for....

Genetic testing
Identification of disease (ID pathogens)
Forensic analysis (crime scene samples, identification of remains)
Amplification of DNA samples from anthropological specimen

STR

Short Tandem Repeating (region of a DNA molecule that contains short segments consisting of three to seven repeating base pairs)