BIOL3060 #2 Foundations of Genetics: Structure, Replication

Why is it called DNA (Deoxyribonucleic Acid)?

Deoxy → Missing an oxygen atom at the 2′ carbon of the • deoxy- "without oxygen."

Ribo → The sugar is based on ribose.

Nucleic → Found in the cell nucleus

Acid → Because of the negatively charged phosphate groups, DNA is an acid

Why is it called RNA (Ribonucleic acid)?

Ribo- → comes from the sugar ribose, which is part of each RNA nucleotide. •

Nucleic → because it's a nucleic acid (like DNA)

Acid → due to the negatively charged phosphate groups, which make the molecule acidic.

Nucleotides

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

Nitrogenous bases in DNA

Adenine, Thymine, Cytosine, Guanine

Nitrogenous bases in RNA

Adenine, Uracil, Cytosine, Guanine

purines

Adenine and Guanine (2 rings)

Pyrimidines

cytosine, thymine, uracil (single ring)

Nucleotides link via

phosphodiester bonds

how do phosphodiester bonds form?

Condensation reaction: these bonds form through a dehydration synthesis (water is removed)

DNA strand direction

5' to 3'

Nucleotides are always added to the ___ end of a growing chain.

3′

5′ prime end

phosphate attached to the 5th carbon of the ribose

3′ prime end

free hydroxyl group (-OH) on the 3rd carbon of the sugar.

Where do phosphodiester bonds form?

5' phosphate group of one nucleotide and 3' OH group of another

DeoxyRibonucleoside triphosphates (dNTPs)

A monomer used by DNA polymerase to polymerize DNA. Consists of the sugar deoxyribose, a base (A, T, G, or C), and three phosphate groups.

DNA vs RNA replication

DNA replicates in the nucleus, RNA replicates in the cytoplasm

Prokaryotic vs eukaryotic replication

SIMILARITIES

- both bi-directional processes

- both require primers to start the process

- both have leading and lagging

- DNA polymerase enzymes work from the direction of '5-'3 so new nucleotides are added to the '3 end of a primer.

DIFFERENCES

prokaryotes have only one site of replication

leading strand

The new continuous complementary DNA strand synthesized along the template strand in the mandatory 5' to 3' direction towards the fork

lagging strand

A discontinuously synthesized DNA strand that elongates by means of Okazaki fragments, each synthesized in a 5' to 3' direction away from the replication fork.

parent strand

original strand of DNA

daughter strand

the newly made stand in DNA replication

DNA polymerase III

adding bases to the new DNA chain; proofreading the chain for mistakes

Helicase

An enzyme that untwists the double helix of DNA at the replication forks.

Topoisomerase

releases torsional strains due to unwinding of DNA

dna ligase

enzyme that chemically links DNA fragments together

when does replication happen?

S phase Interphase

Primease

creates rna primer so polymerase knows where to start

DNA polymerase I

removes the RNA primer and replaces it with DNA

A-T have how many bonds

2 hydrogen bonds

C-G have how many bonds

3 hydrogen bonds

Denaturation

- Breaks hydrogen bonds

- Heat provides energy to overcome the hydrogen bonds between base pairs

- creates single stranded dna

Gregor Mendel

- Father of genetics

- Principles of Heredity

- 1866

Rosalind Franklin (1920-1958)

- British chemist and X-ray crystallographer

- She took Photo 51, an X-ray diffraction image of DNA that clearly showed the helical structure. (1953)

- She died young (age 37) from ovarian cancer

- Franklin's work was critical to discovering the double helix

James Watson & Francis Crick

The scientists credited with building the first correct model of the structure of DNA

- noble prize awarded in 1962

Human Genome Project

An international collaborative effort to map and sequence the DNA of the entire human genome.

1990 - 2003

Gene Expression

the process by which the information encoded in a gene is turned into a function

genome

complete set of genetic instructions for any organism

Even though every cell has the same DNA, only a _____ of genes is active in each cell type.

subset, This allows cells to perform specialized functions for the organism.

Human Genome

20,000 protein-coding genes.

A typical human cell expresses about 2,000 of those genes (~10%).

housekeeping genes

genes expressed in almost all cells

(i.e genes involved in glycolysis, because all cells need energy from glucose)

Locus

a position on a chromosome where a specific gene is located

beta globin locus

a stretch of DNA on chromosome 11 that contains the genes for several beta-like globin proteins, which are part of hemoglobin

Beta Globin Locus: Locus Control Region (LCR)

powerful regulatory element located far upstream of the gene cluster

- these sequences determine whether the protein-coding parts of the gene are turned on or off

Beta Globin Locus: Exons

Coding regions that make the protein

Beta Globin Locus: Intron

Non-coding sequences between exons

Beta Globin Locus: 3′ control region

Downstream regulatory sequences that can also influence gene expression.

- increase or decrease the production of that protein

Beta Globin Locus: 5′ control region

At the Upstream "start" end of the gene, contains regulatory sequences.

Beta Globin Locus: Core promoter

TATA box, where the general transcription machinery (like RNA polymerase) binds to start transcription

Beta Globin Locus: transcription factors

Collection of proteins that mediate the binding of RNA polymerase and the initiation of transcription. proteins that bind DNA to turn gene on or off

Beta Globin Locus: Regulatory promoter

DNA sequence located immediately upstream of the eukaryotic core promoter; contains consensus sequences to which transcription factors bind.