Hereditary material, and set of instructions for protein synthesis.

two types: deoxyribonucleic and ribonucleic acids (DNA and RNA).

Ribose vs deoxyribose (differ only in the presence of a single O atom

nitrogenous bases: 5 types, in two classes

• purines: adenine, guanine (bigger, 2 rings)
• pyrimidines: cytosine, thymine, uracil (smaller, 1 ring)

DNA is the genetic material

1928 Griffith, transforming principle

1940’s Avery showed that the transforming chemical was DNA. Not too many convinced.

1950’s Hershey and Chase expt. to choose between protein and DNA as transforming chemical (source of heredity).

Structure of DNA leads to understanding of function

• One important function of DNA is that it must be able to replicate
• = make an exact copy vital for heredity

Watson and Crick (1954)

• double helix structure
• each strand with a sugar-phosphate backbone, and the N-base
• DNA made up of two chains (held together by H-bonds)
• chains are anti-parallel

Look at nucleotide in detail (numbers of the C’s in the sugar)

Chargaff’s rules allow prediction of one strand from sequence of other.

5’-CATTCGCAATCGG-3’

3’-GTAAGCGTTAGCC-5’

strands are complementary -- provides a mechanism for replication.

• Each strand can act as template to control the synthesis of its complement.
• End product is two identical double-stranded DNA molecules, each with the exact same sequence of bases on each strand.

Details of DNA replication (complicated by the anti-parallel nature of the strands)

Main enzyme is DNA polymerase

adds new neucleotides to a growing chain

only adds new nucleotides at the 3’ end of an existing, partly double-stranded

The short piece is called a primer, un-primed DNA can’t replicate.

RNA can also prime DNA (differ only in the type of sugar, can have same base pairing, except U for T)

many other enzymes play a role in replication:

• helicase (unwinds the double helix - uses energy (1 ATP per base pair)
• single-strand binding proteins (keep the two strands apart)
• primase (adds a short RNA primer onto a single-stranded DNA)
• DNA polymerase (extends primer (5’->3’)
• Exonuclease remove primer (5’->3’)
• DNA ligase (sews up gaps in DNA)

• leading strand -- continuous synthesis (since fork is opening up in the 5’-3’ direction)
• lagging strand -- new DNA made in short pieces (about 200 bases long) called Okazaki fragments), need new primer (RNA sequences), old primers are removed by exonuclease

Protein synthesis is directed by DNA, and mediated by RNA.

• This sequence is copied into temporary RNA molecules (messenger RNA) in a process called transcription.
• The sequence is used to direct the synthesis of a polypeptide in a process called translation

Flow of information (Central Dogma of Molecular Biology)

DNA --(transcription)--> mRNA --(translation)--> protein

Transcription: production of messenger RNA

• Not all of DNA is transcribed at one time. Only active genes are transcribed.
• Ends of transcription unit are determined by special sequences in the DNA
• RNA polymerase unwinds the DNA at the region of the promoter (TATA box), and begins to copy using the opposite strand as the template.
• Termination: RNA polymerase stops transcribing when encounters AATAAA (and some other special sequences).
• Other DNA binding proteins (transcription factors) also influence whether the RNA polymerase can bind.

Genetic code:

• to translate sequence of nucleotides into sequence of amino acid
• is a triplet code, there are more codons than there are AA’s -- redundant

Code is universal -- same code used by almost all organisms from bacteria to mammals

How know where to start? AUG (met) is also the "start" codon.

How know where to stop? UAA, UGA, UAG all are "stop" codons

Mechanics of translation

Is a multi-step process, with many other proteins and nucleic acids playing a part.

• Transfer RNA’s -- tRNA
• ribosomes -- made of many proteins and RNA’s

• has a region of un-paired bases at one end called the anti-codon -- complementary to the 3-base codon sequence of genetic code on mRNA
• Has a site at the 3’ end to which an amino acid is attached. The specific AA is the one that corresponds to the proper codon.
• There is a special enzyme (one for each tRNA) that recognizes the tRNA
• It is this set of enzymes that "knows the code."

Steps in protein synthesis:

• Initiation: mRNA, met-tRNA, ribosomes come together
• Elongation: new tRNA’s bring amino acids to the growing polypeptide chain
• Termination: stop codon binds release factor, that releases polypeptide and dissociates ribosome.

Exons = the DNA sequence that is expressed (kept in the mRNA)

Introns = the DNA sequence that is not expressed (intervening).

Splicing is done by snRNPs, they assemble into a spliceosome. Sequences in the snRNP recognize specific sequences in the pre-mRNA (splice junctions) and cut and paste the exons together to make a mature mRNA

• Note: procaryote mRNA does not get spliced.

• The catalyst that did the splicing was not a protein.
• Some RNA’s can splice themselves.
• Autocatalytic RNA called ribozymes.

Now several other types of ribozymes have been found (rRNA in ribosome catalyzes parts of protein synthesis). May be a common feature. May have been the first catalysts in the evolution of life (RNA world).