Section 1.1 DNA Structure and Genome Organization

Central dogma of molecular biology (FIRST QUESTION OF EXAM 4)

Hypothesis which describes the flow of genetic information in the cell

DNA (replicable) → Transcription → RNA → Translation → Protein

Actual central dogma is much more _____

Complex; Every step can more or less self regulate or regulate a previous step

Where is genetic information stored in prokaryotes? Eukaryotes? Why is this important

Prokaryotes: Cytoplasm (Nucleoid); We typically use E. coli as an example

Eukaryotes: Nucleus; Transcription and RNA processing inside, translation in cytoplasm

This is important because we can utilize the differences in our central dogma to create therapies for diseases

(Oswald) Avery’s Experiment: What bacteria were used? What strains? What phenomenon was utilized? What is a cell-free extract?

Determined what molecule contains genetic information in the cell

Used the bacteria Streptococcus pneumoniae

Used two strains:

• Smooth (S) cells: Produced polysaccharide capsule (Pathogenic)

• Rough (R) cells: Did not produce a capsule; Meaning it did not contain the genetic information required to make it (Non-Pathogenic)

Bacterial transformation: External DNA is taken up by the bacterial cell and utilized to change its morphology or physiology

Cell-free extract: Everything inside a cell, DNA, RNA, proteins, lipids, carbs, in a solution (The cell is not alive)

Essentially, Avery took the cell-free extract (And modified it to remove one type of macromolecule, e.g., a protease to degrade proteins) from a smooth cell and combined it with rough cells; If recombination and cell division do not result in an S cell, then that macromolecule is what contains genetic information

Proteinase, RNase, and DNase were used one at a time. DNase was the only enzyme that resulted in no transformation

Nucleotides Vs. Nucleosides

Major purine bases

Major pyrimidine bases

Nucleotides have a nitrogenous base, a pentose, and 1+ phosphate; they make up DNA

Nucleosides have everything except a phosphate group

Purines: Adenine and Guanine

Pyrimidines: Thymine, Cytosine, and Uracil

What structure is this? Purine or Pyrimidine?

Adenine; Purine

What structure is this? Purine or Pyrimidine?

Guanine; Purine

What structure is this? Purine or Pyrimidine?

Thymine: Pyrimidine

What structure is this? Purine or Pyrimidine?

Cytosine: Pyrimidine

What structure is this? Purine or Pyrimidine?

Uracil: Pyrimidine

Polynucleotide; How is DNA/RNA written

Polymer of many nucleotides (Can be DNA or RNA); DNA and RNA are written via bases (ATGCU) from 5’ → 3’ end (Phospho group to hydroxy group)

Oligonucleotide: Polymer of several nucleotides

Phosphodiester linkage

Connects the 3’ of one base to the 5’ phosphate of another base

(Erwin) Chargaff’s Rules

1. DNA has a concentration in which A=T and G=C

2. Base composition percentages varies between species

3. Base composition is the same in different cells types within an individual organism

4. Base composition does NOT change with age, nutrition, or environment

Photo 51

X-rays bend/diffract in different directions based on the location of atoms in a macromolecule

Showed DNA is helical; each turn is 34 Å (3.4nm), 10 bases (Close to actual measurements)

An X-ray diffraction image of hydrated DNA (Dehydrated had been done already, but hydrated was necessary to infer structure because DNA is hydrated in cells)

Rosalind Franklin collected a large portion of the data in Crick and Wilkins DNA structure proposal.

Chemical Structure of DNA

Repeating units of 2’-deoxyribonucleoside 5’-monophosphate (dNMP)

DNA contains two unbranched polynucleotide chains in an antiparallel orientation

The chains interact via H-bonds (Weak interactions allow separation for certain processes)

Based on “Watson-Crick-Franklin” base pairing: AT(U) & GC

Backbone made of the sugar and phosphate portion of nucleotides

Denaturing/annealing, T_m, how do specific base pairings affect it

This process is called denaturing; 50% denaturation occurs at T_m (melting temperature)

Complementary single strands of DNA anneal to each other via base pairing

GC-rich sequences have higher T_m because they contain 3 H-bonds

AT pairing only has 2 H-bonds

What conformation is DNA typically in

DNA is a long, flexible molecule, typically in the B-DNA conformation

Right-handed helix, 10.5bp per turn, bp is flat and perpendicular to backbone, hydrophobic portion is on the inside (Occurs via hydrophobic and base-stacking interactions)

Bps are exposed in major and minor grooves, where other things can interact with DNA

Alternate DNA conformation

A-DNA: Conformation of dehydrated DNA; Good structural model of double-stranded RNA and RNA-DNA hybrid molecules; Right-handed

Z-DNA: <1% of cellular DNA; Seen in areas of high G-C content; Left-handed

Other forms: Cruciform, triplex, and quadruplex

RNA structure

RNA (ribonucleic acid): Usually a linear, single-stranded polynucleotide chain

Contains a ribose sugar-phosphate backbone; uracil (U) instead of thymine (T); still reads 5’ → 3’

Still helical due to base-stacking interactions

RNA can pair with complementary RNA/DNA; resembles A-DNA; still antiparallel; G-U base pairing can occur when RNA base pairs with itself or another RNA molecule

RNA molecules can also form

Secondary and tertiary structures; Similar to how protein is organized

Occurs as a result of internal base pairing

Primary structure is the linear form

Gene vs Genome

Gene: DNA encoding a functional RNA or proteins as well as the regulatory elements controlling its expression

Genome: Complete set of genetic material present in a cell/organism

Ex. E. coli has a singular circular chromosome (DNA molecule that encodes genes)

Gene positions are fixed in a species

The Human Genome

Human cells contain 46 linear chromosomes; Eukaryotes have proteins bound to chromosomal DNA