(WIP) Chapter 9 – The Information of Life: DNA and RNA Structure, DNA Replication, and Chromosome Structure

Bio 190A

Four criteria necessary for the genetic material

1. Information

2. Replication

3. Transmission

4. Variation

Information

must contain information necessary to construct entire organism

Replication

must be accurately copied

Transmission

must be passed from parent offspring and from cell to cell during cell division

Variation

be able to account for differences between individuals and species

A ___ ___ __ ___ was postulated in the late 1800s

biochemical basis of heredity

Smooth (S)

strains secrete capsules; are typically deadly

Rough (R)

strains do not secrete capsules; are typically survivable

A surprising result occurred when a mix of live type R and heat-killed type S bacteria was injected

The mouse died and living type S bacteria were isolated from the blood

Griffith postulated that a substance (genetic material) from the dead type S cells had

transformed the type R cells into type S

In the 1940s, Avery, MacLeod, and McCarty used Griffith’s observations as a part of an experimental strategy to

biochemically identify the genetic material

Initial experiments indicated that only purified DNA could convert R to S; however, purified DNA might still contain traces of contamination that may be the

transforming principle

Enzymes that break down DNA, RNA, or protein were used to

degrade potential contaminants

DNA and RNA are

nucleic acids, polymers of nucleotides that are responsible for th storage, expression, and transmission of genetic information

The structure of DNA can be considered at different levels of complexity:

1. Nucleotides

2. Strand

3. Double helix

4. Chromosomes

5. Genome

Nucleotides

the building blocks

Strand

a linear polymer

Double helix

the two strand twisted tigether

Chromosomes

DNA associated with different proteins

Genome

the complete complement of genetic material in an organism

A nucleotide had 3 components:

a pentose sugar, a phosphate group, and a nitogen-containing base

A strand is formed when

nucleotides are covalently attached

Key structural features of a DNA strand

• Covalent bonds, called phosphodiester bonds, link nucleotides together

• A sugar in one nucleotide is linked to a phosphate group in the next nucleotide, forming a sugar-phosphate backbone

  • Bases project away form the backbone

• Stands have directionality, based on orientation of the sugar molecules

• The 5’ end has a free phosphate group, and the 3’ strand has a free hydroxyl group

Important features of DNA:

• Double-stranded helix

• AT/CG Rule

• Strands are complimentary to each other

• Strand are antiparallel

  • Contains major groove and minor groove; the major groove provides a binging site for many proteins

X-ray diffraction

a key experimental tool that led to the discovery of the DNA double helix structure

Rosalind Franklin

In the 1950s, analyzed DNA diffraction patterns which indicated

• a helical structure

• a uniform diameter (~2nm)

• diameter too big to be a single strand

Erwin Chargaff

In 1950, analyzed the base composition of DNA that was isolated from many different species and found a pattern

James Watson and Francis Crick

synthesized the work of others to discover the structure of DNA

In the 1950s, 3 different models for DNA replication had been proposed:

• Semiconservative mechanism

• Conservative mechanism

• Dispersive mechanism

Original strands are ___ strands and newly-made strands are ___ stands

parent; daughter

E. Coli grew in an environment with ______ (existing parent strands were formed with ___ __), then the bacteria were ______ (any newly made daughter strands would be formed with ___ __)

¹⁵N to label DNA; heavy ¹⁵N; switched to an environment with ¹⁴N; light ¹⁴N)

Meselson and Stahl experiment results were constant with

the semiconservative mechanism

During replication, the 2 parental strands are separated and serve as ___ ___ for the synthesis of daughter strands

template strands

Origin of replecation

a site within a chromosome hat serves as a starting point for DNA replication

Replication bubble

an opening formed when DNA stands are unwound

Replication proceeds outwards from ___ ___ in both directions (bidirectional replication)

the replication forks

Eukaryotic chromosomes are ___ and have a ___ structure with ___ origin(s) of replication

larger; linear; multiple

DNA helicase, DNA topoisomerase, and single-stranded binding proteins are responsible for

fork formation an movements

Two enzymes are needed to synthesize DNA strand during replication:

DNA polymerase and DNA primase

DNA polymerase

covalently links nucleotides together

DNA polymerase had 2 important functional constraints:

1. Cannot begin synthesis on a bare template strand; it can only extend a pre-existing strand

2. Synthesizes DNA in a 5’ to 3’ direction

DNA primase

makes a complimentary primer of RNA (10 to 12 nucleotides in length) that can be extended by DNA polyemrase

Daughter strands are synthesized differently at the replication fork:

• The leading strand is made continuously, extending in the same direction tat the replication fork is moving

• The lagging strand is made as a series of Okazaki fragments, extending in the opposite direction as the replication fork

Permanent mistake in DNA repication are

extraordinarily rare

DNA replication has high fidelity due to:

1. Hydrogen bond between A/T and C/G are more stable than between mismatched pairs

2. DNA polymerase is unlikely to catalyze bonds between nucleotides if a mismatched base pair occurs

3. DNA polymerase can proofread to remove mismatched pairs

A typical eukaryotic chromosome can be ______ of base pairs in length and must fit in the ___, meaning chromosomes must be ___ and ___

hundreds of millions; nucleus; folded and compacted

Chromosome vs chromatin

describes a discrete unit of genetic material vs. refers to the complex of DNA and proteins that make up eukaryotic chromosomes

Eukaryotic DNA is first compacted by wrapping around a group of proteins called ___, which forms structures called ___

histones; nucleosomes

Nucleosomes interact with each other to form

more compact structures

The zigzag model

proposes that nucleosomes zigzag back and forth, connected by straight linker regions of DNAA third level

Loop domains

structure formed when a third level of compaction occurs as segments of nucleosomes are folded into loops

Dimer

a chemical structure or macromolecule formed by the union of two simpler sub-units called monomers

SMC proteins

form a dimer and initially form a small loop

SMC stands for

structural maintenance of chromosomes

CTCF proteins

bind a specific DNA sequence; when they bind together, loop growth stops

CTCF stands for

CCCTC binding factor

Topologically associating domains (TADS)

Chromatin organized into loop domains

TAD structural organization is though to

facilitate proper gene regulation

During interphase (the time when a cell is not dividing)

the compaction level along each chromosome varies

Heterochromatin

describes highly compacted regions; genes in the regions are typically transcriptionally inactive

Euchomatin