· Central Dogma - Describes how information in the genetic code (DNA) in converted into usable forms (RNA and protein). Protein information results in enzymes that make us look and function they way we do.
o We inherit our "genes" in the form of DNA - ½ came from Mom and ½ came from Dad.
o All cellular containing organisms (from bacteria to plants and animals) use DNA as the chemical that this genetic information is stored in.
o Since viruses are non-cellular they do not follow this rule.
o Some viruses use DNA (just like our cells do), some use RNA only, and some use bizarre combinations of both (HIV and HBV).

· DNA - Structure
o composed of nucleotides (sugar + base + phosphate). Sugar is deoxyribose.
o 4 different kinds of bases used in DNA = adenine and guanine (purines), thymine and cytosine (pyrimidines)
o These nucleotides are hooked together in a 5' to 3' orientation (based on the carbons in the sugar). They are hooked by a phosphodiester bond.
o DNA is usually double stranded (in all cellular organisms and in most of the viruses that use DNA). The second strand is runs anti-parallel to the first (3' to 5') and the bases are complementary.
o The base pairing rules state that A binds to T and G binds to C between the two strands.

· Replication - the production of two identical copies of DNA
o When cell replicate to make two new daughter cells, each one gets an identical copy of the DNA.
o The DNA strand is split and each strand has a new daughter strand synthesized following the base pairing rules.
o Mistakes or changes in the sequence is called a mutation and may affect the RNA or protein made from that stretch of DNA sequence.

· RNA - an intermediary between DNA sequence and protein
o Very similar to DNA in structure with the following changes:
§ the sugar is ribose instead of deoxyribose (missing an oxygen from 2' position)
§ the bases are adenine, guanine, uracil and thymine.
§ usually single stranded (except in those odd viruses that use double-stranded RNA)
o Three functional forms of RNA used in cellular organisms
§ messenger RNA (mRNA) - carries the code to make a new protein
§ ribosomal RNA (rRNA) - is part of the cellular machine that makes a new protein
§ transfer RNA (tRNA) - is the decoder between nucleotide language (DNA/RNA) and amino acid language (protein). Brings the appropriate amino acid to the ribosome.

· Transcription - the process of making RNA from DNA
o Is a highly regulated and intricate process where only certain regions of the DNA are read by an enzyme (RNA polymerase) and converted to RNA sequence. The same base pairing rules apply in the interactions between DNA and RNA except A binds to U instead of T.
o Determines which regions of DNA in a particular cell will be converted into protein.
o A region of DNA (called a promoter) immediate in front of the gene determines the frequency that that particular gene will be transcribed. The promoter is recognized by proteins called transcription factors that direct the RNA polymerase enzyme to transcribe that gene.
o We will see later that HIV does something called reverse transcription - which is a process by which RNA information is converted into DNA information (backwards of regular transcription).

· Translation - process by which RNA information is converted into amino acid information
o Requires an mRNA (code for the protein), ribosome (RNA and protein containing machine), and tRNAs (bring amino acids to ribosome and convert RNA code into amino acid information).
o Since there are only 4 bases in RNA and there are 20 amino acids, it takes more than one base to code for a particular amino acid.
o Every three bases (called a codon) is a code for one amino acid. The code is read without bases skipped or used for more than one codon.
o There are three potential reading frames for each RNA. These are shown in the example below.

1. THE FAT CAT ATE ONE BIG FAT RAT XXX
2. XXT HEF ATC ATA TEO NEB IGF ATR ATX
3. XTH EFA TCA TAT EON EBI GFA TRA TXX

o As you can see, only one of the reading frames makes sense. Adding or removing a base from DNA or RNA can change the reading frame of a gene and make a completely non-sense protein, which either will terminate early or be degraded.
o The Genetic Code tells us which triplets code for which amino acids. Most amino acids have more than one codon that will code for them.

· Splicing - only occurs in eukaryotic organisms
o In bacteria (prokaryotic) each gene in the DNA is one complete protein coding region without any breaks or inserts. The RNA produced from each gene does not have to be edited before the ribosomes can convert the sequence into protein.
o In fungi, plants and animals (eukaryotic) cells, there are inserts in the protein coding region of the DNA. These inserts are non-sense sequence and are called introns. The protein coding sequence regions are called exons.
o In a eukaryotic cell, the introns have to be removed and the exons connected together to make a single open reading frame (a region of DNA or RNA sequence with no inserts or stop codons).
o This process occurs in the nucleus by machines called spliceosomes.
o There can be variability in the way the exons are connected together and slightly different mRNAs, that will produce different proteins, can be produces from the same precursor mRNA. This process is called alternative splicing.
o Once the splicing has been completed, the mRNA travels out of the nucleus to the cytoplasm where the ribosomes are and can be translated into a protein.