Gene Expression and Regulation

Rosalind Franklin

performed X-Ray Crystallography of DNA, revealing its regular and repetitive helical shape

Erwin Chargaff

Analyzed the base content of DNA and found that the amount of adenine equaled and amount of thymine and the amount of guanine equals the amount of cytosine.

Watson and Crick -

created the first 3D, double helix model of DNA

3 components of nucleotide structure

pentose sugar, phosphate group, and nitrogenous base

Pyrimidines

cytosine, thymine, uracil (single ring structure)

Purines

adenine and guanine (double ring structure)

bonds connecting nitrogenous base pairs

hydrogen bonds

hydrogen bonds between adenine and thymine

2 hydrogen bonds

hydrogen bonds between cytosine and guanine

3 hydrogen bonds

deoxyribose

pentose sugar found in DNA

ribose

pentose sugar found in RNA

components of DNA backbone

sugar and phosphate

phosphodiester linkage

covalent bonds that join adjacent nucleotides between the -OH group of the 3' carbon of one nucleotide and the phosphate on the 5' carbon of the next

antiparallel

One strand runs 5' to 3', other strand runs in opposite, upside-down direction 3' to 5'

5' end

free phosphate group

3' end

free hydroxyl group

uracil

a nitrogen-containing base found in RNA (but not in DNA)

(center) rungs of DNA nitrogenous bases

nitrogenous bases

nucleoid region

The region in a prokaryotic cell consisting of a concentrated mass of DNA.

shape of prokaryotic DNA

circular

Shape of eukaryotic DNA

linear

location of eukaryotic DNA

nucleus

plasmids

Small, circular DNA molecules that are separate from the chromosomal DNA (mostly found in prokaryotes)

recombinant plasmid DNA

a gene of interest is inserted into a plasmid genome

conservative model of DNA replication

The parental strands direct synthesis of an entirely new double stranded molecule; The parental strands are fully "conserved"

semi-conservative model of DNA replication

The two parental strands each make a copy of itself; After one round of replication the two daughter molecules each have one parental and one new strand

dispersive model of DNA replication

The material in the two parental strands is dispersed randomly between the two daughter molecules; After one round of replication the daughter molecules contain a random mix of parental and new DNA

Meselson-Stahl Experiment

Used isotope of nitrogen to change the weight of DNA N15 & N14, demonstrated that the semi-conservative model is the best description of replication.

origins of replication

Site where the replication of a DNA molecule begins

replication fork

A Y-shaped region on a replicating DNA molecule where new strands are growing.

helicase

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

single strand binding proteins

bind to the DNA to keep it open and stabilize it until it can be used as a template

Topoisomerase

prevents strain and corrects "overwinding" ahead of replication forks by breaking, swiveling, and rejoining DNA strands

primase

initiates replication by adding short segments of RNA, called primers, to the parental DNA strand

DNA Polymerase III

adding bases to the new DNA chain; proofreading the chain for mistakes (moves along the parental strand in a 3' to 5' direction and adds nucleotides on the new strand in a 5' to 3' direction)

leading strand

only requires one primary to synthesize a continuous complementary DNA strand synthesized along the template strand in the mandatory 5' to 3' direction.

lagging strand

The strand that is synthesized in fragments using individual sections called Okazaki fragments; requires many primers

Okazaki fragments

Small fragments of DNA produced on the lagging strand during DNA replication, joined later by DNA ligase to form a complete strand.

DNA ligase

enzyme that joins the okazaki fragments forming a continuous DNA strand

telomeres

repeating units of short nucleotide sequences that do not code for genes and form a cap at the end of DNA to help postpone erosion

mismatch repair

The cellular process that uses specific enzymes to remove and replace incorrectly paired nucleotides.

nuclease

An enzyme that cuts DNA or RNA, removing one or a few bases