All terms in this list:

Griffith Experiment: Smooth bateria=lethalRough bacteria=harmless1)Injection with smooth bateria=dead mice2)Infection with with rough bacteria=no dead mice3)Injection with heat killed-smooth bacteria=no deadmice4)Injection with live rough bacteria mix

Transformation: Shows that information containing molecules have been introduced into the bacteria

Info containing molecule: Must be:
easily replicated
stable
not active
common for all organisms
compact
transferable
code, language-smaller units that can be placed in various sequence.

4 Types of macromolecule: Protein
lipids
nucleic acid
carbohydrates

Lipid: make up cell membrane and energy storage molecule making it unlikely to be the genetic material.

Carbohydrate: Burn for energy unlikely to be genetic material.

Nucleic acid: Function unknown, simple composition which people think it was possible to be the genetic material (true)

Protein: have many functions, complex
composition, leading contender but turned out to not be the genetic material.

The Avery, Macleod, and McCarthy experiment: Killed the smooth/deadly bacteria, then extract the lysate cells, then treated them with protease then ribonucleasea and last deoxyribonucleose to see that causes tranformation. Until the DNA was destroyed, transformation occurred.

The Hershey-Chase Experiment: Used E. coli and one of its infected bacteriophage, T2.
marked the phage protein with 35S and 32P.
for the labeled DNA phage, ghost phage resulted and bacteria became labeled.
For labeled protein, phages are labeled, unlabeled bacteria result

What was known about DNA?: Certain chemical properties:
– Very hydrophilic
– Composed of sugars,
phosphate, and nitrogenous
bases.
– negative charged (due to the
phosphate groups)
– DNA was likely a very long
molecules, perhaps a
polymer.

DNA composition: Adenine, Cytosine, Guanine, Thymine

Ratios of Nucleotides: Ratio of A and T always the same
Ration of G and C always the same

DNA bases: A and G are purines
T and C are pyrimidines

Linus Pauling: His model:
3 strands
Bases go on the outside
INCORRECT!

Watson & Crick (Franklin): DNA consists of two strands
wrapped around each other in a
double helix
– Sugar-phosphate backbones are
on the outside and nitrogenous
bases on the inside
– Each base pairs with a
complementary partner
• A with T, and

Base “pairing” by hydrogen bonds: A – T 2 hydrogen bonds
G – C 3 hydrogen bonds

Properties of an information storage molecule: Code – order of bases in DNA is how
information is stored
• Universal structure – DNA has same
structure in all organisms
• Stable – DNA strands held together by
many hydrogen bonds
• Able to be packaged into small volu

“Central Dogma”: DNA to RNA to proteins

A gene: • Genes consist of DNA sequences that encode proteins
and regulatory sequences. Regulatory sequences include
promoters and enhancers that control where and when a
gene is transcribed.
• In eukaryotes, genes will include exons (tran

Transcription: RNA polymerase requires:
• DNA template (but no primer from primase is necessary)
• NTPs (not dNTPs) – ATP, CTP, GTP, UTP
• Uracil (U) instead of thymine (T)
• NTPs are added one at a time, and the energy for the reaction

Messenger RNA processing (only in eukaryotes): Splicing – removal of introns from mRNA

ribosomes: Ribosomes carry out translation to
make proteins

Origin of replication: site on chromosome or
plasmid where DNA replication begins

Replication fork: site at which replication is
currently occurring

Leading strand: strand of DNA replicated
continuously

Lagging strand: strand of DNA replicated in
Okazaki fragments

RNA primers: short pieces of RNA placed by
primase to make double-stranded sites for DNA
polymerase to bind

DNA helicase: separates strands of template DNA
molecule by breaking hydrogen bonds between bases

Primase: places RNA primers on template DNA

DNA polymerase: catalyzes addition of nucleotides to a
new strand of DNA using hydrogen bonding of
complementary bases on template
– New strand is synthesized in the 5’à3’ direction
– Uses the hydrolysis of nucleotide triphosphates to
release

DNA ligase: catalyzes phosphodiester bond formation
between Okazaki fragments

Annotation: identi]ication of sequences of interest
–protein-coding regions
–regulatory regions
–many others (alternative splice sites, repeating
elements)

Eukaryotic Chromosomes: • Chromosome - single
DNA molecule
• Associated with
proteins – histones
• More compact = less
accessible to proteins
• Less compact (more
‘open’) = more
accessible to protein

Chromatin Immunoprecipitation (ChIP): used to identify DNA sequences bound by specific proteins
4. Identify DNA sequences stuck to proteins
(various methods)
1. Form covalent bonds between
proteins and DNA
2. Break up DNA into small pieces
3. Use antibodies to isolate

Polymerase Chain Reaction–DNA replication in vitro: Step 1 Denaturation
95 °C
Step 2 annealing
55-65 °C

Step 3 elongation
72 °C

Why is helicase not needed for the polymerase chain reaction?: The activity catalyzed by helicase is accomplishedby
heating in PCR

Reverse transcriptase: allows the synthesis of
DNA from an RNA template

Plasmids: allow the manipulation of genes
Gene (or part of a gene) “cloned” when it is incorporated into a plasmid

Restriction endonucleases (REs): Bacterial enzymes that
restrict or prevent viral
infection by degrading the
invading viral DNA.
• REs recognize a speciQic
4-8 bp nucleotide motif,
and cut both strands of the
DNA within that sequence.

Molecular hybridization: allows the identification of DNA
or RNA molecules by base sequence

Dideoxy sequencing (Sanger): Each new DNA molecule
ends with a ddNTP
Therefore, each nucleotide
base may be determined

Bacterial transcription: Transcription occurs in three phases:
1. Initiation
2. Elongation
3. Termination

transcription initiation: Sigma factor mediates binding to promoter
Different sigma factors bind to different promoters
RNA polymerase unwinds short section of DNA

transcription elongation: RNA polymerase synthesizes RNA from NTPs
catalyzes phosphodiester bond formation using
energy released from NTP hydrolysis
At some point sigma factor dissociates

Transcription termination (2 types): 1)Intrinsic terminators
RNA ‘hairpin’ forms and
causes termination
2)Rho-dependent
Rho protein binds mRNA
and knocks off RNA
polymerase when it pauses

Eukaryotic transcription: RNA polymerase doesn’t bind to promoters directly, but
recognizes speciVic TFs bound to promoters.
• Control elements are more diverse, and interact w/ each
other in a more complex manner.
• mRNA processing is required before tra

Alternative splicing: generates protein diversity

The Genetic Code: Unambiguous
– codon à 1 amino acid
• Degenerate
– amino acids à multiple
codons
• Non-overlapping
• no
“
commas
”
• Universal
– all organisms

Transfer RNAs (tRNAs): have specific amino acids attached to the 3’ end and an
anticodon complementary to a specific codon in mRNA

Classes of DNA/Effect on DNA sequence: Silent(s)Missense(s)Nonsense(s)Frameshift(indels)

Cause of mutation: • Spontaneous mutations
– no known outside cause
• Induced mutations
– caused by source
outside organism

Type of Substitutions: Transition - base changed
to another of the same
chemical class
(purine---purine)

(pyrimidine---pyrimidine)
• Transversion - base changed
to another of a different
chemical class

Effect on protein activity: Loss-of-function
– null – complete loss of function
– hypomorph – reduced function
• Gain-of-function
– hypermorph – ‘increased’ function
– neomorph – new function

Effect on phenotype of organism: neutral – no measurable effect on fitness
beneficial – positive effect on fitness
deleterious – negative effect on fitness
lethal – causes death or non-development of organism
conditional – effects on organism depend upon
env

Tautomers of bases: structural isomers that exist in equilibrium
standard base-pairing (C-G)
anomalous base-pairing (C-A)

Deamination: produces ‘unnatural’ DNA bases that can change base-pairing .
-Adenine deaminated to Hypoxanthine
Hypoxanthine pairs with Cytosine
-Cytosine deaminated to Uracil
Uracil pairs with Adenine

Chemical mutations – base analogs: 5-bromouracil
• resembles thymine and
will be incorporated into
deoxyribonucleotides
• pairs mostly with A
• has a high rate of
tautomerization, during
which it will pair with G

Chemical mutagens – alkylating agents: add alkyl groups (CH3-, CH3-CH2-, etc.) to nucleotide bases à
changes how they pair
Examples: Ethyl methanesulfonate (EMS), mustard gas

UV radiation causes covalent bonds to form between pyrimidines: TT dimers usually OK
CC dimers pair with AA
during DNA replication
to cause mutations

Genetic screens of mutants can be used to study genes (‘Forward’ genetic approach): 1)Obtain population withmutants and/orpromote mutagenesisin a population 2)Study population of
organisms to
identify mutants3)Conduct furtheranalysis to identifygene responsiblef