1. CHAPTER 11 Molecular Biology of the Gene

2. Viruses provided some of the earliest evidence that genes are made of DNA
Molecular biology studies how DNA serves as the molecular basis of heredity

3. Experiments showed that DNA is the genetic material
THE STRUCTURE OF THE GENETIC MATERIAL
Experiments showed that DNA is the genetic material
The Hershey-Chase experiment showed that certain viruses reprogram host cells to produce more viruses by injecting their DNA
Head
DNA
Tail
Tail fiber
= Protein coat

4. The Hershey-Chase Experiment1
Mix radioactively labeled phages with bacteria. The phages infect the bacterial cells. 2
Agitate in a blender to separate phages outside the bacteria from the cells and their contents. 3
Centrifuge the mixture so bacteria form a pellet at the bottom of the test tube. 4
Measure the radioactivity in the pellet and liquid.
Radioactive protein
Empty protein shell
Radioactivity in liquid
Phage
Bacterium
Phage DNA
DNA
Batch 1 Radioactive protein
Centrifuge
Pellet
Radioactive DNA
Batch 2 Radioactive DNA
Centrifuge
Radioactivity in pellet
Pellet

5. Phage reproductive cycle – how a virus works
Phage attaches to bacterial cell.
Phage injects DNA.
Phage DNA directs host cell to make more phage DNA and protein parts. New phages assemble.
Cell lyses and releases new phages.

6. DNA and RNA are polymers of nucleotides
DNA is a nucleic acid, a polymer made of long chains of nucleotides
A nucleotide = a phosphate + a 5-carbon sugar + a nitrogenous base
Phosphate group
Nitrogenous base
Nitrogenous base (A, G, C, or T)
Sugar
Phosphate group
Nucleotide
Thymine (T)
Sugar (deoxyribose)
DNA nucleotide
Polynucleotide
Sugar-phosphate backbone

7. DNA has four kinds of bases, A, T, C, and G
Thymine (T)
Cytosine (C)
Adenine (A)
Guanine (G)
Pyrimidines
Purines
C5H6N2O2
C5H5N5O
C4H5N3O
C8H17N

8. Nitrogenous base (A, G, C, or U)
RNA is also a nucleic acid
RNA has a slightly different sugar – ribose
RNA has U instead of T
Nitrogenous base (A, G, C, or U)
Phosphate group
Uracil (U)
Sugar (ribose)

9. DNA is a double-stranded helix
James Watson and Francis Crick worked out the three-dimensional structure of DNA, based on work by Rosalind Franklin

10. Abstract from "The Double Helix" by James D. Watson:
... I quickly cleared away the paper from my desk top so I would have a large, flat surface on which to form pairs of bases held together by hydrogen bonds. Though I went back to my like-with-like prejudices, I saw all to good that they led nowhere Suddenly I became aware that an adenine-thymine pair held together by two hydrogen bonds was identical in shape to a guanine-cytosine base pair held together by at least two hydrogen bonds. All the hydrogen bonds seems to form naturally; no fudging was required to make the 2 type of base pairs identical in shape...

11. The structure of DNA consists of two polynucleotide strands wrapped around each other in a double helix
1 chocolate coat,
Blind (PRA)
Twist

12. A pairs with T G pairs with C
Hydrogen bonds between bases hold the strands together
Each base pairs with a complementary partner
A pairs with T
G pairs with C

13. Partial chemical structure
Three representations of DNA
Hydrogen bond
Ribbon model
Partial chemical structure
Computer model

14. DNA replication depends on specific base pairing
In DNA replication, the strands separate
Enzymes use each strand as a template to assemble the new strands A A
Nucleotides
Parental molecule of DNA
Both parental strands serve as templates
Two identical daughter molecules of DNA

16. Untwisting and replication of DNA

17. DNA replication: A closer look
DNA replication begins at several sites
Parental strand
Origin of replication
Daughter strand
Bubble
Two daughter DNA molecules

18. Each strand of the double helix is oriented in the opposite direction
5 end
3 end P P P P P P P P
3 end
5 end
Figure 10.5B

19. Overall direction of replication
How DNA daughter strands are synthesized 3
DNA polymerase molecule
5 end 5
Daughter strand synthesized continuously
Parental DNA 5 3
Daughter strand synthesized in pieces
The daughter strands are identical to the parent molecule 3 P 5 5 P 3
DNA ligase
Overall direction of replication
Figure 10.5C

20. Genes  Proteins

21. THE FLOW OF GENETIC INFORMATION FROM DNA TO RNA TO PROTEIN
The DNA genotype is expressed as proteins, which provide the molecular basis for phenotypic traits
The information constituting an organism’s genotype is carried in its sequence of bases

22. A specific gene specifies a polypeptide
The DNA is transcribed into RNA, which is translated into the polypeptide
DNA
TRANSCRIPTION
mRNA
TRANSLATION
Protein
Figure 10.6A

23. Gene 1 Gene 3 Gene 2 Codon Amino acid
DNA molecule
Gene 2
DNA strand
TRANSCRIPTION
RNA
Codon
TRANSLATION
Polypeptide
Amino acid
Figure 10.7

24. The “words” of the DNA “language” are triplets of bases called codons
Genetic information written in codons is translated into amino acid sequences
The “words” of the DNA “language” are triplets of bases called codons
The codons in a gene specify the amino acid sequence of a polypeptide

25. The genetic code is the Rosetta stone of life
Virtually all organisms share the same genetic code
Read this chart from the mRNA strand to find out the sequence of amino acids
Figure 10.8A

26. About the DNA code….
There are a number of important features of the genetic code outlined below:
The code is a triplet code, i.e. three nucleotides specifies an amino acid in a protein
The code is read continuously from the first methionine start codon to the stop codon at the end.
The RNA is read in successive groups of three nucleotides, without punctuation. The RNA could be read in any of three "frames" but only one is correct (see the 'bla bla bla' overhead).
The code is almost universal, i.e. the same codon encodes the same amino acid in different organisms. There are only a couple of exceptions to this.
The code is degenerate: more than one codon exists for all of the amino acids apart from methionine and tryptophan.
The code has start and stop signals. AUG indicates the start of translation at the start of the RNA molecule (AUG encodes methionine) and sets the correct reading frame at the start of the protein. A number of codons (UAA, UAG, UGA) indicate the end of translation.

27. How to read the code….
Translation must start at a defined position in the RNA and the code must be read in codons of 3 bases.
BLABLATHEBOYATETHEBUGBLA
This looks like a load of jibberish in this format. However, if we apply a couple of simple rules it is possible to make sense of this. Here are the 2 rules that we need here:
We only start reading this sentence at the first THE word, equivalent to the first AUG in a mRNA.
We read the sentence only in groups of 3 letters with no punctuation between words. When we apply these rules, this is what we get:
BLABLA THE BOY ATE THE BUG BLA

28. An exercise in translating the genetic code
Transcribed strand
DNA
Transcription
RNA
Start codon
Stop codon
Translation
Polypeptide
Figure 10.8B

29. Give it a try! DNA Code: ---ATC ATG TTT CCT GAT ACT
m-RNA Code: ____ ____ ____ ____
t-RNA Code: -____ ____ ____ ____
Amino Acids: ____ ____ ____ ____

31. Transcription produces genetic messages in the form of RNA
RNA nucleotide
RNA polymerase
Direction of transcription
Template strand of DNA
Newly made RNA
Figure 10.9A

32. In transcription, the DNA helix unzips
RNA polymerase
In transcription, the DNA helix unzips
DNA of gene
Promoter
DNA
Terminator
DNA
Initiation
RNA nucleotides line up along one strand of the DNA following the base-pairing rules
The single-stranded messenger RNA peels away and the DNA strands rejoin
Elongation
Area shown in Figure 10.9A
Termination
Growing RNA
Completed RNA
RNA polymerase
Figure 10.9B

33. Eukaryotic RNA is processed before leaving the nucleus
Noncoding segments called introns are spliced out
A cap and a tail are added to the ends
Exon
Intron
Exon
Intron
Exon
DNA
Transcription Addition of cap and tail
Cap
RNA transcript with cap and tail
Introns removed
Tail
Exons spliced together
mRNA
Coding sequence
NUCLEUS
CYTOPLASM
Figure 10.10

34. 5’ cap and poly-A tail

35. Transfer RNA molecules serve as interpreters during translation
In the cytoplasm, the mRNA attaches to a ribosome and translates its message into a polypeptide
The process is aided by transfer RNAs (tRNA)
Amino acid attachment site
Hydrogen bond
RNA polynucleotide chain
Anticodon
Figure 10.11A

36. Each tRNA molecule has a triplet anticodon on one end and an amino acid attachment site on the other
Figure 10.11B, C

37. Ribosomes build polypeptides
Next amino acid to be added to polypeptide
Growing polypeptide
tRNA
molecules
P site
A site
Growing polypeptide
Large subunit
E site
tRNA
tRNA P A E
mRNA
mRNA binding site
Codons
mRNA
Small subunit
Figure 10.12A-C

38. An initiation codon marks the start of an mRNA message
Start of genetic message
End
Figure 10.13A

39. mRNA, a specific tRNA, and the ribosome subunits assemble during initiation
Large ribosomal subunit
Initiator tRNA
P site
A site
Start codon
Small ribosomal subunit
mRNA 1 2
Figure 10.13B

40. The mRNA moves a codon at a time relative to the ribosome
Elongation adds amino acids to the polypeptide chain until a stop codon terminates translation
The mRNA moves a codon at a time relative to the ribosome
A tRNA pairs with each codon, adding an amino acid to the growing polypeptide

41. More detailed: http://207.207.4.198/pub/flash/26/transmenu_s.swf
Amino acid
ANIMATION:
More detailed:
Polypeptide
A site
P site
Anticodon
mRNA 1
Codon recognition
mRNA movement
Stop codon
New peptide bond 2
Peptide bond formation 3
Translocation
Figure 10.14

42. Review: The flow of genetic information in the cell is DNARNAprotein
The sequence of codons in DNA spells out the primary structure of a polypeptide
Polypeptides form proteins that cells and organisms use

43. Summary of transcription and translation
DNA
Stage mRNA is transcribed from a DNA template. 1
mRNA
RNA polymerase
Amino acid
TRANSLATION
Stage Each amino acid attaches to its proper tRNA with the help of a specific enzyme and ATP. 2
Enzyme
tRNA
Initiator
tRNA
Anticodon
Stage Initiation of polypeptide synthesis 3
Large ribosomal subunit
The mRNA, the first tRNA, and the ribosomal subunits come together.
Start Codon
Small ribosomal subunit
mRNA
Figure 10.15

44. New peptide bond forming
Growing
polypeptide
Stage Elongation 4
A succession of tRNAs add their amino acids to the polypeptide chain as the mRNA is moved through the ribosome, one codon at a time.
Codons
mRNA
Polypeptide
Stage Termination 5
The ribosome recognizes a stop codon. The poly-peptide is terminated and released.
Stop
Codon
Figure (continued)

45. Mutations can change the meaning of genes
Mutations are changes in the DNA base sequence
These are caused by errors in DNA replication or by mutagens
The change of a single DNA nucleotide causes sickle-cell disease

46. Point mutations – error of just one base
NORMAL GENE
mRNA
Protein
Met
Lys
Phe
Gly
Ala
BASE SUBSTITUTION
Met
Lys
Phe
Ser
Ala
BASE DELETION
Missing
Met
Lys
Leu
Ala
His
Figure 10.16B

47. Sickle-cell hemoglobin
Normal hemoglobin DNA
Mutant hemoglobin DNA
mRNA
mRNA
Normal hemoglobin
Sickle-cell hemoglobin
Glu
Val
Figure 10.16A

48. Single Gene Mutations
Many more human diseases result from single gene mutations than from chromosome abnormalities.
sickle-cell anemia
cystic fibrosis
Huntington disease
phenylketonuria (PKU)
alkaptonuria.
These disorders, referred to as inborn errors of metabolism, cause the absence of, or incorrect form of, the protein for which that gene codes.
Usually autosomal recessive traits. In heterozygotes, the cell's normal gene compensates by making more protein.

49. Types of Mutations
Missense mutation : change in one base pair,  substitution of one amino acid for another in the protein made.
Nonsense mutation: also a change in one base pair, however, the altered DNA prematurely signals cell to stop building a protein.  shortened protein that may function improperly or not at all.
Insertion: changes the number of bases in a gene by adding a piece of DNA.  protein made by the gene may not function properly.
Deletion: changes the number of bases by removing a piece of DNA. Small deletions may remove one or a few base pairs within a gene, while larger deletions can remove an entire gene or several neighboring genes.  may alter the function of the resulting protein(s).
Duplication: a piece of DNA is abnormally copied one or more times. -> may alter the function of the resulting protein.
Frameshift mutation: addition or loss of DNA bases changes a gene’s reading frame (3-letter codons).  changes the code for amino acids. Resulting protein is usually nonfunctional. Insertions, deletions, and duplications can all be frameshift mutations.
Repeat expansion: Short DNA sequences are repeated several times in a row normally in DNA. An expansion increases the number of repeats.  can cause the resulting protein to function improperly.