# AP Biology/Gene Expression and Regulation

Introduces how hereditary information passes from parent to offspring and how those traits are expressed.

## Objectives and Skills

Topics may include:
* The roles and functions of DNA and RNA
* The mechanisms of gene expression
* How genotype affects phenotype
* Mutations, genetic diversity, and natural selection
* Genetic engineering and biotechnology

## Study Notes

* DNA Polymerase - Enzyme that can replicate DNA.
* Leading Strand - NEW DNA Strand that grows continuously in the 5' to 3' direction [bottom].
* Lagging Strand - NEW DNA Strand that grows continuously in the 3' to 5' direction [top].
* Replication Fork - During DNA Replication, an open section of DNA in which a DNA polymerase can replicate DNA (DNA is separated into single strands and where new DNA is synthesized). Helicase unwinds the DNA double-helix at these replication forks.
* Okazaki Fragments - Short sections of DNA that are synthesized on the lagging strand of the replicating DNA.
* Daughter DNA - New DNA strands that aren't equal.

### Remember

* The 3' end has a sugar while the 5' end has a P group.
* Each new DNA strand is made from one parental strand and one newly synthesized strand = semi-conservative.

## History

Thomas Morgan worked with drosophila (fruit flies). Specific genes for specific traits. "Transforming Factor" by Frederick Griffith. He worked with streptococcus pneumonia Bacteria to find a cure for pneumonia.

## Central Dogma
### DNA

* DNA
* mRNA [tRNA to bring AA (amino acids)]
* Ribosome (rRNA proteins)
* Proteins

### RNA

Retroviruses (RNA virus) follow different pattern.
* RNA
* DNA
* host DNA
* mRNA

## Protein Synthesis

* Transcription [of DNA] - Nucleus
* Translation [of DNA] - Ribosome

### DNA Replication

Copying of double-stranded DNA and is needed for cell reproduction before cell divsion.
* Semi-Conservative process of DNA - Two resulting DNA copies each have one strand of parental DNA and one newly constructed strand.

#### Proteins

* Helicase - Unwinds DNA double helix into 2 strands.
* SSB proteins - Coat the DNA strands to prevent re-annealing.
* RNA polymerase - Synthesizes the short DNA primes in order to get the process of DNA replication started (can only extend a DNA strand, not create one).
* DNA polymerase - Strings nucleotides (DNA) together to make a new strand.
* Sliding Clamp - Holds the DNA polymerase to the DNA strand during replication.
* RNASE lt - Removes the RNA polymerase by hydrolyzing its phosphodiester bonds [DNA polymerase creates DNA strands in the places of the removed RNA primes].
* Ligase - Links short DNA strands together to value a long DNA strand.

### Transcription and Translation

* Transcription - Synthesis of RNA using info in the DNA. DNA is used as a template to make a complimentary RNA strand. This becomes mRNA. Takes place in the nucleus.
* Translation - Synthesis of a polypeptide using mRNA. Must create an Amino Acid sequence. Takes place in the ribosome.

#### Transcription

* Initiation - RNA polymerase binds to the promoter, DNA strands are unwinded and the polymerase begins RNA synthesis.
* Elongation - Polymerase creates RNA strand in teh 5' to 3' direction.
* Termination - The RNA transcript is removed and the poylmerase is removed from the DNA
RNA polymerase attatches to a promoter, specific nucleotide sequence in the DNA of a gene, and the sequence that signals the end of transcription is the terminator.

#### Translation

After transcription, RNA splicing, and translation, the mRNA is ready for translation.
A cell reads a series of codons along an mRNA molecule, and the translator is called a tRNA (return amino acids from the cytoplasmic pool of amino acids). The anticodons on the tRNA are the opposite of the codons on the mRNA (pairs with an mRNA codon).

### RNA processing

Before translation,, the pre-mRNA strand is modified before going to the cytoplasm for translation. The...
* 5' cap end - A 5'cap modified form of G nucleotide.
* Poly-A tail - On the 3' prime end made up of 30-200 nucelotides.
* Riboenzymes - RNA enzymes that catalyze their own splicing.
* Wobble - U at the 5' end of the tRNA anticodon can pair with either an A or 6 in the 3' end of the mRNA codon.
These are added to the untranslated regions of the pre-mRNA. These ends do not come for any protein.

### RNA splicing

Caps are added (5' cap first then the A nucleotide is added). In between, the introns are cut out, leaving the exons in (exons express while introns are intervening sequences and are removed from the primary transcript.

### Gel electrophoresis

Used to separate mixtures of DNA, RNA, or proteins according to molecular size.
The molecules are separated and passed to an electric field through a gel that contains small pores. The layer DNAs travel the slowest vs. vice versa.

### tRNA

* Aminoacyl-tRNA synthetases - Correct matching up of tRNA and amino acid is carried out by the enzymes.