AP Biology -- Gene Expression (Unit 6)

Transformation

a change in genotype and phenotype due to assimilation of foreign DNA

bacteriophages

viruses that infect bacteria. Bacteriophages consist only of proteins and DNA.

DNA is the genetic material

polymer of nucleotides, DNA composition varies from one species to the next, A and T bases are equal and the number of G and C bases are equal

nucleotides

a nitrogenous base, a sugar, and a phosphate group

Purine

A/G, 2 organic rings, 2X the size, 2 hydrogen bonds

Pyrimidine

C/T, single ring, X size, 3 hydrogen bonds

Why do purine and pyrimidines bases always pair together?

because of the number of *hydrogen bonds* they are able to form

origins of replication

The site where replication occurs where the two DNA strands are separated, opening up a replication "bubble".

DNA polymerase

adds nucleotides to the 3' end of the growing DNA sequence. It needs a primer. It can only go in one direction and extend on an existing DNA molecule

RNA Primase

In DNA replication, RNA primase adds temporary RNA nucleotides for DNA polymerase to work from and add nucleotides to

replication fork

a Y-shaped region where new DNA strands are elongating that is located at the end of the replication bubble.

Single-strand binding proteins

bind to and stabilize single-stranded DNA

Helicases

enzymes that untwist the double helix at the replication forks.

Topoisomerase

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

leading strand

the template strand of DNA where replication happens continuously toward the replication fork because it is aligned properly

lagging strand

the template strand of DNA where DNA polymerase must work in the direction away from the replication fork

Other functions of DNA polymerases

proof reading by replacing any incorrect nucleotides

Okazaki fragments

The fragments that are going by DNA ligase to compose the lagging strand. They are short replicated fragments on the lagging strand that are formed 5-3. The spaces between the fragments are filled via DNA ligase to make a continuous DNA strand.

mismatch repair

repair enzymes that correct errors in base pairing

nucleotide excision repair

a *nuclease* cuts out and replaces damaged stretches of DNA

Telomeres

non-coding DNA at the ends of chromosomes.

Telomerase adds "junk" repeats to leading strands... Polymerase is able to copy lagging strand...

Now the unreplicated lagging overhang is unimportant "junk" (BUT telomerase can only be found in cancerous tissues)

bacterial chromosome

double-stranded, circular, few

eukaryotic chromosome

linear, large amount of protein

Chromatin

a complex of DNA and protein, is found in the nucleus of eukaryotic cells

euchromatin

Loosely packed chromatin

heterochromatin

densely pack chromatin

What is a gene?

protein

How is a gene transcribed?

RNA polymerase

How is transcript processed?

RNA splicing

What is the language of DNA/RNA?

genetic code

How is RNA read?

tRNA

How is protein produced?

ribosomes

Transcription

the synthesis of RNA using information in DNA

Transcription produces messenger RNA (mRNA)

Translation

the synthesis of a polypeptide, using information in the mRNA

Codon/triplet nucleotides

The genetic code must be written in triplets because they are the smallest unit of uniform length that can code for all the amino acids. There are 20 amino acids. This will allow for 64 possible codes, with repetition.

Gentic code in universal

Reading frame

the sequence of the DNA that is between the start codon and the end codon (with triplet sequences in between). They can be altered/changes when there are insertions and deletions.

Ribosomes

the sites of translation (in eukaryotes, the nuclear envelop separates transcription)

primary transcript

initial RNA transcript from any gene prior to processing

central dogma

he concept that cells are governed by a cellular chain of command: DNA to RNA to protein

RNA polymerase

The Starter of RNA synthesis. It pries the DNA strands apart and hooks together the RNA nucleotides

terminator

in bacteria, the sequence signaling the end of transcription

promoter

The DNA sequence where RNA polymerase attaches to start transcription.

transcription unit

The stretch of DNA that is transcribed

The three stages of transcription

Initiation, Elongation, Termination

transcription initiation complex

The completed assembly of transcription factors and RNA polymerase II bound to a promoter

Transcription factors

mediate the binding of RNA polymerase and the initiation of transcription

Transcription factors guide the blind polymerase

TATA box

The promotor that crews the initial complex in eukaryotes

introns

These noncoding regions are called intervening sequences

Initiation of translation

Small subunit of the ribosome attaches to the cap and moves to the translation initial site. TrNA anticodons attach to the codon that had MET (the amino acid for the start codon). The large subs unit attaches to make the P and the A site.

Elongation of translation

MET is transferred to the A site amino acid and the tRNA moves along to the next site. The amino acids attach on the tRNA in the a site. The ribosome moves along the mRNA.

Termination of translation

A release favor comes in (the stop codon) and the chain stops building on the polypeptide. The protein is then released.

exons

they are eventually expressed, usually translated into amino acid sequences

RNA splicing

removes introns and joins exons, creating an mRNA molecule with a continuous coding sequence

domains

Proteins often have a modular architecture consisting of discrete regions

Ribozymes

catalytic RNA molecules that function as enzymes and can splice RNA

RNA

It can form a three-dimensional structure because of its ability to base-pair with itself

Some bases in RNA contain functional groups that may participate in catalysis

RNA may hydrogen-bond with other nucleic acid molecules

How is protein synthesized?

Requires all three major types of RNA...

• mRNA - "Recipe"

the coding sequence of the gene

• aminoacyl tRNAs - "Cook"

read codon, carry appropriate amino

acid (translation!)

• rRNA - "Cookware"

forms the core of the ribosome which

forms peptide bonds between amino acids

tRNAs

transfer amino acids to the growing polypeptide in a ribosome

anticodon

the anticodon base-pairs with a complementary codon on mRNA

wobble

Flexible pairing at the third base of a codon that allows some tRNAs to bind to more than one codon

Ribosomes

Ribosomes facilitate specific coupling of tRNA anticodons with mRNA codons in protein synthesis

P site

holds the tRNA that carries the growing polypeptide chain

POINT MUTATIONS

single base changed

FRAMESHIFTS:

any insertion or deletion NOT divisible by 3 will shift the reading frame...

causing extense missense (wrong amino acid coding)

Silent mutations

have no effect

missense

have the wrong amino acid

nonsense

have an early stop!

operator

Aclusteroffunctionallyrelatedgenescanbeundercoordinated control by a single "on-off switch"

repressor

can switch the operon off/on by preventing gene transcription by binding to the

operator and blocking RNA polymerase

operon

the entire stretch of DNA that includes the operator, the promoter, and the genes that they control

How gene expression is controlled in bacteria

they are only in prokaryotes

corepressor

a molecule that cooperates with a repressor protein to switch an operon off (tryp)

REPRESSIBLE OPERON:

repressor is NOT bound; operon is usually on

• for enzymes that ARE normally needed

• can be turned OFF if not needed (repressor

is made active by excess product of the pathway)

tryp

***anabolic pathways; their synthesis is repressed by high levels of the end product