Molecular Biology

I. History:Ground breaking discoveries T.H. Morgan Griffith, Avery and McCleod Hershey and Chase Watson and Crick (refer to your article for most of this!)

How do we know that DNA is the molecule that transfers info? T.H. Morgan showed that differences in chromosomes determined fly traits Think back: What are chromosomes made of??? DNA and Protein.

II. What is DNA Structure: What do we already know about DNA’s structure? (think back to biochem!)

II. What is DNA Structure: The backbone of DNA is made of covalent bonds between the phosphate and sugar

II. What is DNA Structure: DNA you have a choice of 4 bases: Purines

II. What is DNA Structure: DNA you have a choice of 4 bases: Pyrimidines

II. What is DNA Structure: - Two strands of DNA are connected through weaker Hydrogen bonds that form between bases - Only certain bases can form these hydrogen bonds with each other - They are called complementary

II. What is DNA G and C form 3 hydrogen bonds

II. What is DNA A and T form 2 hydrogen bonds

II. What is DNA Why can’t the others pair up?

II. What is DNA Structure: Therefore all A’s are bound to T’s all G’s are bound to C’s Chargaff’s Rule: in a given piece of DNA – A’s = T’s; G’s = C’s

II. What is DNA Structure: Heating DNA causes it to denature Which is harder to denature? - GCCGGCGCG or - AATATTATAA

III. Replication –Semi-conservative:

III. Replication Happens in the nucleus (of course!) Ingredients: –Energy – Form??? –Free Nucleotides: single, not attached –Specific Enzymes

There are three basic steps. Watch the animation and tell me what is happening. –Helicase –DNA Polymerase –Ligase –Involves many other enzymes, as well as primers. III. Replication lication.html

III. Replication Telomere problem: Ends of chromosomes difficult to copy - lose a little DNA each time The good news: telomeres do not code for anything The bad news: telomeres are only so long.

III. Replication Solution: - in a few cells – telomerase - in other cells – Hayflick limit (max. number of cell divisions before self destructing)

Replication uses existing DNA as a template to make more DNA Why? When? DNA is ALSO used as a template to make an RNA “copy” of a gene Why? When? So first a little about RNA….

Structure of RNA Think back: what are the structural differences between RNA and DNA? –SS –Uracil –Ribose sugar –Location

Types of RNA mRNA – –Has the encoded info to assemble proteins rRNA – –Make up part of the ribosome tRNA – - brings Amino Acids to ribosome

Transcription: transfer of information from DNA to RNA – only genes that encoded proteins necessary to that cell get transcribed

IV. Transcription: Similar to replication in mechanism - Watch the animation and tell me what is different!

Transcription: transfer of information from DNA to RNA in nucleus –Using sequence of DNA to make a complementary strand of RNA –The WHOLE strand of DNA doesn’t get turned into RNA at once –Instead, as needed, small sections of DNA are transcribed into RNA Sections are called??? GENES

IV. Transcription: Step 1: DNA strands are separated and then “copied” - New RNA will have a Complementary sequence except A’s in DNA bind to U’s in RNA - RNA Polymerase is the enzyme that links the RNA nucleotides

IV. Transcription: 5’ 3’ 5’ 3’ 5’ 3’ 5’ 3’ 5’ RNA Pol. 5’ RNA Pol. 3’ 5’ RNA Pol. 5’ 3’ RNA Pol. At the end, DNA goes back to its double stranded helix; Pre-mRNA “transcript” needs to be edited

IV. Transcription: In eukaryotes, mRNA transcript has to be modified before leaving the nucleus to be translated. In prokaryotes, the mRNA is ready to go as it is transcribed!

IV. Transcription: Step 2: Splicing: Editing or Processing of pre-mRNA into mRNA - remove “introns”: unused sections - glue together “exons”: important sections

5’ IV. Transcription: 3’ Exons linked together Exon Intron Introns discarded Exon

IV. Transcription: Step 3: GC Cap added to one end; Poly A tail added to other end of exons to make mature mRNA Specialized Guanine Several Adenines in a row

IV. Transcription: Step 4: Mature mRNA leaves the nucleus and moves to the ribosomes where the message will be read and translated into a protein sequence. 5’ 3’ Specialized Guanine Several Adenines in a row

IV. Transcription: If a gene is transcribed into mRNA it is being “expressed” Having the gene in your DNA is not enough It MUST be turned into RNA to do anything

IV. Transcription: Remember transcription is the KEY to getting a protein!! - some genes within a cell are NEVER transcribed due to a permanently “OFF” On/Off switch that precedes the start codon.

V. Genetic Code:

How many 3 base combinations are there of ATGC? How many amino acids are there? What does this mean?

V. Genetic Code: You are responsible for knowing 4: AUG UAA, UAG, UGA You MUST be able to use a codon table

VI. Translation: Decoding the information in the mRNA to build a protein. We need: 1.The mRNA 2.The ribosome 3.tRNA’s

V. Translation: Ribosomes: - two subunits made of rRNA and protein - sandwich mRNA between them

V. Translation: Ribosomes: - Have three spots that tRNA’s can fit in A site – acceptor site P site – peptidyl site (carries the growing chain of aa E site – has the exiting tRNA (with no aa attached)

V. Translation: tRNA - Twisted up piece of RNA - amino acid gets attached to one end - opposite end is the anticodon

V. Translation: So how does it work? Watch the animation and explain it to me! animat/molgenetics/translation.swf

Central Dogma

What’s strange about the term Central Dogma??? What does dogma mean? Hmmmmmm good essay question