1. DNA – Molecular Genetics

2. DNA STRUCTURE – Review……
DNA is made of monomers called nucleotides.
Nucleotides consists of
5 carbon sugar
Phosphate group
Nitrogenous base (A,T,C,G)
Backbone- made of covalent bonds between bonds between the phosphate and sugar
“Rungs of Ladder” – made of pairs of nitrogenous bases.
A-T
C-G

3. Nitrogenous Bases
In DNA, there are 4 types of bases

4. STRUCTURE Sides of Ladder – Sugar/Phosphate backbone-
Sides of Ladder – Sugar/Phosphate backbone
Rungs of Ladder – Base Pairs
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

5. How many hydrogen bonds between
C-G?
A-T?
Would A-G be possible????

6. CHARGAFF’S RULE Amount of Adenine = The amount of Thymine
Amount of Guanine = The amount of Cytosine
If a sample of DNA contained 16% adenine……….?
PURINES = PYRIDAMINES

7. What does DNA need to be able to do?
Be copied– every time a cell divides
DNA Replication
Be “read” – every time we need to make a protein.
Transcription

8. DNA REPLICATION Overview Semi-conservative Molecule opens up
Each side is a template to build a complementary side
End up with two DNA molecules, each one half old and half new.

9. Step 1  Unzipping the DNA
Enzyme called helicase which breaks the hydrogen bonds between the base pairs.
OPENS THE MOLECULE UP!
Step 2  Complementary Base Pairing
Each of the DNA strands can now act as templates to construct complimentary sides.
Enzyme DNA polymerase attaches complementary nucleotides to each of the open strands

10. Semi-Conservative Replication
Each of the resulting DNA molecules are identical to each other and each contains one original strand and one new one.

11. Not that simple though……
Antiparallel strands….
The two sides of the DNA molecule run in opposite directions. The 5 and 3 refer to the orientation of the ribose molecule

12. Because they are anti-parallel….
The copying can only happen in one direction along the
35 side of the template.
Leading strand
Built continuously as fork opens
Lagging Strand
Built in fragments,
Needs patching together by ligase

15. Animations
Overview
hill.com/olcweb/cgi/pluginpop.cgi?it=swf::535::535::/sites/dl/free/ /120076/micro04.swf::DNA%20Replication%20Fork
Detailed

16. Replication Bubbles DNA is LOOOOOOOOONNNNNNGGGGGG!
In order to speed-up copying, replicate in several places at once.

17. RNA vs. DNA 3 Main Differences Why use these replacements?????
Single Stranded
Sugar in RNA is ribose
In RNA, thymine is replaced by uracil
Why use these replacements?????
CHEAPER!!!!

19. 3 types of RNA
Messenger (mRNA)  carries the RNA copy of the DNA gene out of the nucleus to the ribosomes.
Ribosomal (rRNA)  make-up portion of the ribosome.
Transfer (tRNA)  bring individual amino acids to the ribosome for assembly into polypeptides.

20. 2 key steps to making proteins
Transcription
Copy DNA code on mRNA
Translation
Reading the mRNA molecule code and turning it into a polypeptide chain (linking together amino acids)

21. Transcription Goal: Copy DNA code (gene) onto an mRNA molecule. Steps:
Helicase opens DNA molecule at specific section (gene)
Enzyme RNA polymerase binds to a promoter site (specific base sequence) just before the gene sequence
RNA polymerase moves along gene sequence and creates a complementary RNA strand

22. Transcription
Animation:

23. Transcription
When RNA polymerase reaches terminator sequence (specific base sequence), new RNA molecule released from DNA molecule
mRNA molecule travels to the cytoplasm where the message will be translated into polypeptides
YOU TRY IT!

24. Difference in cell types?
In eukaryotes, mRNA transcript has to be modified before leaving the nucleus to be translated.
RNA EDITING!
SIGNIFIGANCE – One gene can code for many different proteins!!!!
Introns – What gets cut out (stay in the nucleus)
Exons – What gets left it (Exits the nucleus)
In prokaryotes, the mRNA is ready to go  No Editing Needed!

25. RNA EDITING
Exons vs. Introns

26. Translation
Goal: mRNA  Polypeptide (will be a protein once the 3D folding occurs)
Review
Proteins made by linking together amino acids
20 different amino acids
Sequence of amino acids going to determine protein properties (shape).
So how can a code of 4 letters (bases) code for 20 different amino acids?

27. The Genetic Code
In the genetic code, three bases will code for one amino acid
Why 3?  4^3 = 64 different combinations with nucleotide triplets, compared with 4^ 2 = 16 different combinations with pairs.
Would 2 bases be enough???
The three bases that code for a specific amino acid are called codons
ONE CODON = ONE AMINO ACID!!!!

28. Translation Codons- You are responsible for knowing 4: AUG
UAA, UAG, UGA

29. Translation - Interpreting the Code
Sequence of mRNA GGUACGUCCCCA
Read as GGU-ACG-UCC-CCA

31. Translation (the details)
The players
mRNA – code for making polypeptide
rRNA – ribosome - assembles polypeptide
tRNA – transfers amino acids to ribosome for assembly
All RNA made by the NUCLEOLUS

32. tRNA and rRNA structure/function
tRNA is a folded RNA strand
- amino acid on one end
- anti-codon on the other end
rRNA makes up part of the ribosomes
- ribosomes made of rRNA and protein
- Consists of two subunits

33. Translation in action…..
Best to watch a video first
Simple
anslation.swf
Complex

34. Overall Process Initiation
Start codon read, first tRNA binds to mRNA bringing methionine
Ribosome assembles
Elongation
See animations for detail
Chain builds
Termination
Stop codon reached
Whole assembly falls apart
Polypeptide formed

35. Mutations Mistakes happen!
Sometimes during DNA replication, bases can get inserted, removed or switched!!
Changes in the DNA base sequence are called MUTATIONS!!!
Can be single nucleotides – Point
Can be whole chunks of DNA- Chromosomal

36. Point Mutations One base in the sequence is affected
Substitution – one base switched out for another
Insertion – base put into code
Deletion – base removed from code

37. Point - Substitution
If this happens on a gene portion of the DNA molecule, it can result in a change in one of the amino acids in a polypeptide sequence.

38. Point - Insertion/Deletion
When a base is inserted or deleted, much bigger changes
Changes like this are called frame shift mutations
shift the reading frame of the genetic code. (how we read it)
These mutation affect all amino acids that follow the mutation point

39. Example of frameshift

40. Point - Substitutions Missense mutations
new nucleotide alters the codon so as to produce an altered amino acid in the protein product.
Can cause big changes in polypeptide if new amino acid in chain is chemically different than the one it replaced.
Can be neutral if new amino acid is chemically similar to one it replaced.

41. Point - Substitutions (cont.)
Nonsense mutations
With a nonsense mutation, the new nucleotide changes a codon that specified an amino acid to one of the STOP codons (TAA, TAG, or TGA).
Significance?
The earlier in the gene that this occurs, the more truncated (shortened) the protein product and the more likely that it will be unable to function.

42. Point - Silent mutations
Most amino acids are encoded by several different codons.
For example, if the third base in the TCT codon for serine is changed to any one of the other three bases, serine will still be encoded. Such mutations are said to be silent because they cause no change in their product

43. Chromosomal Mutations
Involve large-scale changes to structure or number of a chromosome!
Have much greater consequences than point mutations
WHY???
MANY GENES AFFECTED!!!!

45. Mutations-
So all mutations are bad right?????