Question 1: What is the genetic material?

Key points:
1. DNA is the genetic material in living beings and viruses
2. There are exceptions in some viruses and unusual agents

Griffith Experiment:
• Transformation
o Transforming factor, resulting in a phenotypic change
o What is its nature?

Avery, Macleod, and McCarty (1940s)

• Treated mixture of live R & dead S with protease and DNase, only the mice with
protease treated mixture died (So DNA was responsible for transformation)

Hershey and Chase (1952)

• Examined nature of genetic material in T2 bacteriophage (virus of a bacteria)

Cell Theory:
• Composed of cells
• Unit of structure/function
• Cells come from preexisting cells

Life cycle of T2 bacteriophage

1. Virus sits on bacterium
2. Injects genetic material
3. Bacterium produces viral components
4. Components are assembled into viral bodies
5. Viruses leave to repeat the process

Hershey Chase
• Labeled DNA and protein in bacteriophages (separately)
i. Allowed them to determine which component was entering the
cell, it was DNA

DNA STRUCTURE
Deoxyribonucleic Acid
Hydroxyl: OH
Phosphate: PO4

pH scale
relative concentration of hydrogen ions

Critical parameters of the Genetic Material

• Information storage
• Transmission (replication)

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 Key Points:
1. nucleotides form the repeating units of DNA
2. nucleotides are linked to form a strand
3. two strands are connected, making a double helix

Nucleotide components
1. 5 carbon (pentose) sugar
2. nitrogenous bases (ATCG)
3. Phosphate group

• Deoxyribose is missing a sugar from a hydroxyl

4 types of nitrogenous bases:

• Purines:
o Guanine (G)
o Adenine (A)
 Each has two rings of carbon/nitrogen
• Pyrimidines
o Cytosine (C)
o Thymine (T)
 Each has one ring of carbon/nitrogen

Phosphate group is what makes it Acid

Nucleotides link to form strands, with a sugar-phosphate backbone

• Sugar and phosphate groups are linked by a phosphodiester bond

Nucleotide strands
• Covalently linked together with a phosphodiester bond, 5’ carbon linked to 3’
• Strands have directionality
o 5’ end=free phosphate
o 3’ end= hydroxyl group

Nucleotide: sugar, phosphate, base

DNA polymerase: enzyme that makes DNA strands

Chargaff’s Experiment
• hypothesis: an analysis of the base composition of DNA in different species may
reveal important features of the genetic material
• studied base content in DNA of a variety of organisms
o percentages of ATCG
o AT and CG tend to be closely related
• Chargaff’s Rule:
o Levels of adenine=thymine
o Levels of cytosine=guanine

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 Watson and Crick: Double Helix
• Double stranded, helical (twisted structure)
• Antiparallel (top strand is 5’-3’, bottom is 3’-5’
• Sugar-phosphate backbone with bases inside
• ~10 basepairs per turn
• bonding keeps helices intact
o fairly weak bonds
• bonding is specific
o A-T, C-G
• Bases attach in middle by hydrogen bonds
o Hold double helix together, but are fairly weak
• Complementary
o Strands are opposite:
o 5’GATT3’
o 3’CTAA5’

RNA Biology
• ribonucleic acid
• has numerous roles in expression of the genetic material
• less stable than DNA
• RNA & DNA are differentiated within the cell:
o RNA is only one strand
o The sugar has all of its oxygens
o Uracil (U) replaces Thymine (T) in RNA

DNA Packaging
• Too much DNA, too little space
• DNA is highly condensed in order to fit into the nucleus
• Histone proteins and other proteins play an important role
• Final product: chromosome

Question 2: How does genetic material function?

GENES
• Sequences in the DNA that are the instructions for protein synthesis (information)
• The information is dictated by the order of bases
• Most genes contain information for building specific proteins

T. brucei: DNA Methylase Gene

How do genes work?

The Central Dogma of Molecular Biology

Replication->DNA->Transcription-> RNA

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 All occurs within the nucleus
RNA leaves nucleus and enters the cytoplasm, and is then translated into protein

Transcription: the process of synthesizing a messenger RNA (mRNA)

• If the genetic material is the information for protein synthesis, where do the other
molecules come from?
o Intake: sugar through the diet, etc.
o Enzymes can make molecules
 DNA contains the information to make the enzymes that can build
most other molecules (enzymes are mostly proteins
• Why is transcription (mRNA) production required?
o DNA can’t leave the nucleus, but mRNA can so it can get to the protein-
building organelles
o mRNA is an unstable molecule, so the cell can adjust which specific
molecules are made, because it can easily adjust the mRNA levels
o if DNA was directly translated, these levels would not be adjustable

Some poisonous mushrooms inhibit transcription

Transcriptional inhibitors are antibiotics
Transcriptional inhibitors are antitumor agents
Mutations in transcription factors can result in disease
P 53 mutations can result in Li-Fraumeni syndrom which involves many cancers:
breast, ovarian, leukemia

Mechanism of transcription
• DNA template
• RNA polymerase: enzyme that synthesizes RNA from DNA template
• Ribonucleoside triphosphates: nucleotides of RNA
• Accesory factors

Key Points:
• Catalyzed by RNA polymerase
• Sequences in DNA/RNA control initiation and termination (Binding proteins)
• End result: single-stranded RNA with codons

Promoters: sequences in the DNA that tell the RNA polymerase all the requisite
information
Accessory Factors: help RNA polymerase find promoter (TATA Binding protein)
Transcription factors: regulate the amount of transcription

Transcription elongation: RNA polymerase makes complement of template strand

Transcription Termination: RNA Polymerase exits the DNA

Strand with gene: DNA Coding Strand

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 GENETIC CODE & TRANSLATION
How does the genetic material function?
• Central Dogma of Molecular Biology

Key Points:
• Genes in DNA have instructions for protein building
• mRNA is a copy of the instructions, but is modified first

Deamination: C->U, changes C into U in DNA; if a U gets into DNA, it can distinguish
and remove it

Preparing RNA for Translation:

• cap and poly (A) tail addition
• Cap: helmet for mRNA
o Makes it more stable
o Added by enzymes in nucleus
o Facilitates delivery
• Tail or Track
o Over 300 A’s
o Facilitates translation and export
• These are called “processing reactions”
• Splicing
o Only occurs in 75% of human RNA
o Certain pieces of RNA are removed before translation
 Exon and intron are the two parts of RNA, introns get removed
 Exon remains, because it holds the needed information
 Specific exons can be left, and in different orders, while some are
removed
 Placing them in different orders can make a variety of proteins,
since the information is dependent on order

TRANSLATION
• Synthesis of a protein using the information within the mRNA (codons)
• Proteins are polymers of amino acids
• There are 20 standard amino acids

Amino Acids
• Amino group: NH2
• Central Carbon
• Carboxyl group

Translation joins amino acids as per the instructions in the mRNA

• Peptide bonds join the amino acids

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 o Fairly strong, but can still be broken
• Protein= polypeptide= long chains containing hundreds of amino acids

The Genetic Code

• System to convert information present in the mRNA to amino acids in protein

Cracking the Code

• Which codons specify which amino acids?
o Information in RNA codes for them
 Groups of 3= codon
• Read as 3 RNA bases (codon) in 5’ to 3’ direction
• Non overlapping
• Start codon: AUG, stop codon: UAA, UAG, UGA
• Genetic code is universal, so it allows for gene splicing
• Degenerate: more than one codon can specify a single amino acid (64
combinations of bases)

Final Product of Translation: polypeptide (protein)

Every protein has methionine (Met:AUG) at the beginning

How is information in the mRNA converted to amino acids?

Key Players:
1. mRNA: contains the information
2. tRNA: contains amino acids and recognizes mRNA codons
3. Ribosomes: RNA/protein structure that catalyzes amino acid addition

tRNA:
• Short, structured RNA
• Carries amino acids (charged tRNA)
• Recognizes codons in mRNA
• Transfer RNA Structure:
• Enzymes decide which amino acid is needed based on the anticodon at the
binding side

tRNA:mRNA interaction
• Amino acid found on a tRNA is related to the codon and anticodon

Ribosomes
• Recognize the mRNA
• Stabilize the mRNA/tRNA interaction
• Provide enzymatic activity that links amino acids
• Ribosome Structure:
o Large subunit: 5080 RNA bases (in 2-3 molecules), around 49 proteins
o Small subunit: 1900 RNA bases (in a single molecule) around 33 proteins

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 Translation overview
• Initiation: ribosome recognizes mRNA and initiator binds to the start codon
• Elongation: tRNAs bind to A site, and peptide bond is formed between the amino
acids
• Termination: release factor binds to stop codon, components disassemble

1. Translation Initiation
o Small subunit of ribosome recognizes mRNA by finding the cap
o Initiator tRNA binds to AUG (start codon) of mRNA
2. Translation Elongation
o Second amino acid joins initiation complex with second tRNA
o P site: peptide bond
o A site: new tRNA binds (except initiator)
 Sites are on large ribosomal subunit which is now on mRNA
o First peptide bond forms as new amino acid arrives
 When bond is formed, ribosome moves down and old A site
becomes P site
o This process continues, with tRNA attaching to mRNA and peptide bonds
forming between amino acids
3. Translation Termination
o Ribosome reaches stop codon
 No tRNA can bind to the stop codon
 Protein called “release factor” binds to stop codon
o Components disassemble because of the release factor

Multiple ribosomes translate mRNA simultaneously

Translates from 5’ to 3’

Translation: common target for antimicrobial drugs

Tetracyclines: b lock protein synthesis in bacteria and some eukaryotes

Used to treat numerous infections and found in animal feed
Streptomycin: blocks protein synthesis
First drug to successfully treat tuberculosis

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