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
 * 1) The 3' end has a sugar while the 5' end has a P group.
 * 2) 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
Retroviruses (RNA virus) follow different pattern.
 * DNA
 * DNA
 * 1) mRNA [tRNA to bring AA (amino acids)]
 * 2) Ribosome (rRNA proteins)
 * 3) Proteins
 * RNA
 * RNA
 * DNA
 * 1) host DNA
 * 2) 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

 * 1) Helicase - Unwinds DNA double helix into 2 strands.
 * 2) SSB proteins - Coat the DNA strands to prevent re-annealing.
 * 3) 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).
 * 4) DNA polymerase - Strings nucleotides (DNA) together to make a new strand.
 * 5) Sliding Clamp - Holds the DNA polymerase to the DNA strand during replication.
 * 6) RNASE lt - Removes the RNA polymerase by hydrolyzing its phosphodiester bonds [DNA polymerase creates DNA strands in the places of the removed RNA primes].
 * 7) 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.