Genetics - Lecture 9: DNA, RNA, Replication, and Transcription

Genetic material must…

1. contain complex information

2. Replicate faithfully

3. Encode the phenotype

4. Have the capacity to vary

Early studies of DNA (1868-early 1900s)

1868 - Johann Friedrich Miescher

• Isolated ‘nuclein’ from cell nuclei, later renames nucleic acid

• nuclear material contained substance - slightly acidic/high in phosphorus

Late 1800s - Albrecht Kossel

• Isolated the nucleotide bases: adenine, cytosine, guanine, thymine and uracil

Early 1900s – Phoebus Aaron Levene

• Discovered DNA consists of nucleotides

Early studies of DNA (1928-1944)

1928 - Fred Griffith

• Demonstrates transforming principle

• Bacterial transformation

1944 – Avery, MacLeod, and McCarty

• The transforming principle is DNA

1948 - Erwin Chargaff

• Ratios of adenine (A) to thymine (T), and guanine (G) to cytosine (C) are equal

• Regularity of ratio of the bases

Early studies of DNA (1952-1956)

1952 - Hershey and Chase

• DNA is genetic material in bacteriophage

• DNA passes on to progeny phages

1953 – Watson, Crick, Franklin, and Wilkins

• Devise secondary structure for DNA

• Three-dimensional structure of DNA

1956 – Fraenkel-Conrat and Singer

• Some viruses use RNA as genetic material

DNA structure

two complementary and antiparelell nucleotide strands that form a double helix

DNA structure (primary)

DNA’s nucleotide structure and how the nucleotides join together

• Pentose sugars (5 carbons)

  • RNA - ribose (hydroxyl group)

  • DNA - deoxyribose (hydrogen group)

DNA structure (secondary)

DNA’s stable three-dimensional configuration

• double helix

• hydrogen bond and base-pairing

• Antiparallel complementary DNA strands

DNA structure (Tertiary)

Complex packing arrangements of dsDNA in chromosomes

• Higher-order folding that allows DNA to be packed into the small space of a cell

  • Ex: Supercoiling

Nucleotide structure

• 3 parts

  • phosphate

  • Nitrogenous base

  • Sugar

• 1' carbon linked to nitrogenous base

• 5' carbon linked to phosphate group

• 3' carbon links to a hydroxyl (-OH) group

Nitrogenous bases

• purines

  • Two-ringed, adenine and guanine

• Pyrimidines

  • one-ring, cytosine, thymine, and uracil

A/T = two hydrogen bonds

G/C = three hydrogen bonds

Phosphate group

• Phosphorus atom bonded to four oxygen atoms

• Bonded to 5′-carbon of sugar

• Negative charge

• Forms structural backbone

Phosphodiester Bonds

sugar-phosphate-sugar bond that creates the backbone of the DNA and RNA molecules

• strong covalent linkage, connects 3’ carbon atom of one deoxyribose sugar to 5’ carbon atom of another via a phosphate group

Nucleotide

Repeating unit of DNA or RNA made up of a sugar, a phosphate, and a nitrogenous base

• The Four bases in DNA = four DNA nucleotides.

• DNA nucleotides have hydrogen on 2’ carbon

• RNA nucleotides have hydroxyl group on 2’ carbon

• Ex: dAMP, dGMP, dTMP, dCMP (deoxy+cytosine 5′-monophosphate, and same goes for all the others)

Deoxyribonucleotide

Basic building block of DNA, consisting of deoxyribose, a phosphate group, and a nitrogenous base

Ribonucleotide

Basic building block of RNA, consisting of ribose, a phosphate group, and a nitrogenous base

Nucleoside

Ribose or deoxyribose bonded to a nitrogenous base

Polynucleotide Strands

Series of linked nucleotides

Phosphodiester bonds/linkages

Nucleotides connectedly covalent bonds

Backbone of strand

alternating sugars and phosphate groups (sugar-phosphate backbone)

Polarity

5’ end (free phosphate group at 5’ carbon) and 3’ end (free hydroxyl group at 3’ carbon)

Double helix

Two polynucleotide strands wound around each other

3 dimensional configuration

• helical structure

• Variety of configurations, depend on base sequence and environmental conditions

Complementray strand

• The nitrogenous bases project into middle  – complementary base pairing

• A’s bind T’s, two hydrogen bonds

• C’s bind G’s, three hydrogen bonds

RNA Structure

• single stranded

• A, C, G, U (no T)

• Sugars = ribose (not deoxyribose)

B-DNA

• another secondary structure

  • most structurally stable

  • Sugar-phosphate backbone smooth and continuous

• Discovered by Watson and Crick

• Right-handed helical structure of DNA that exists when water is abundant

• The 2° structure described by Watson and Crick and the most common DNA structure in cells

• Consists of ~10 bases per 360° turn

• The base pairs are 0.34 nanometers (nm) apart, so each complete rotation of the molecule encompasses 3.4nm

• Diameter of the helix is 2nm.

A-DNA

• the form DNA assumes when little water is present

• Right-handed like B-DNA, but shorter and wider

Z-DNA

• forms a left-handed helix

• Sugar-phosphate backbone zig-zags back and forth

• Stretches of alternating G and C result in this conformation

• Can result if the molecule contains particular base sequences

Supercoiling

Higher-order folding that allows DNA to be packed into the small space of a cell

• E. coli

  • 4.6 million base pairs.

  • 1000x longer than cell

• Human Cells

  • > 6 billion base pairs

  • 6 feet long

Positive supercoiling

Tertiary structure that forms when strain is placed on a DNA helix by over-rotating

Negative supercoiling

Tertiary structure that forms when strain is placed on a DNA helix by under-rotating

Topoisomerase

Enzyme that adds or removes turns in a DNA helix by temporarily breaking nucleotide strands; controls the degree of DNA supercoiling

The bacterial chromosome

• Most bacterial genomes consist of a single circular DNA molecule

• Bacterial DNA highly folded into a series of twisted loop

• Loop ends stabilized by proteins.

• Supercoiling takes place within the loops

Eukaryotic chromosomes

• Each eukaryotic chromosome consists of a single extremely long linear molecule of DNA

• The packing of eukaryotic DNA (its 3° chromosomal structure) is not static but changes regularly in response to cellular processes

  • changes locally during replication and transcription

  • Over cell cycle, level of DNA packing changes.

  • Chromosomes progress from highly packed - to extreme condensation.

Chromatin

Material found in the eukaryotic nucleus; consists of DNA and histone proteins

• Chromatin condenses to form a thicker filament that forms loops, then loops are compressed into a thicker filament which then make up the chromatid of the chromosomes

Euchromatin

Chromatin that undergoes the normal process of condensation and de-condensation during the cell cycle

• Where most of the transcription takes place

Heterochromatin

Chromatin that remains in a highly condensed state throughout the cell cycle; found at the centromeres and telomeres of most chromosomes

Histone

Low molecular weight (positively charged) protein found in eukaryotes that associates closely with DNA to form chromosomes

Nucleosome

Basic repeating unit of chromatin, consisting of a core of eight histone proteins and ~146 bp of DNA wrapped around the core 1.65x

• Each histone protein making up nucleosome core particle has a flexible “tail”.

• Positively charged amino acids in the tails interact with the negative charges of the phosphates on the DNA, keeping the DNA and histones tightly associated

• Tails of one nucleosome may also interact with neighboring nucleosomes.

Chromatin structure

• double-stranded DNA wrapped ~ two times around octamer of eight histone proteins.

• Wrapped DNA and histones = nucleosomes - one unit of chromatin