1. Chapter 7: Molecular Biology
AP Biology Exam Review

2. Frederick Griffith (1928)
Conclusion: living R bacteria transformed into deadly S bacteria by unknown, heritable substance
Oswald Avery, et al. (1944)
Discovered that the transforming agent was DNA

3. Hershey and Chase (1952)
Bacteriophages: virus that infects bacteria; composed of DNA and protein
Protein = radiolabel S
DNA = radiolabel P
Conclusion: DNA entered infected bacteria  DNA must be the genetic material!

4. Edwin Chargaff (1947) Chargaff’s Rules:
DNA composition varies between species
Ratios:
%A = %T and %G = %C

5. Structure of DNA Scientists: Watson & Crick Rosalind Franklin
DNA = double helix
“Backbone” = sugar + phosphate
“Rungs” = nitrogenous bases

6. Structure of DNA Nitrogenous Bases Pairing: Adenine (A) Guanine (G)
Thymine (T)
Cytosine (C)
Pairing:
purine + pyrimidine
A = T
G Ξ C
purine
pyrimidine

7. Structure of DNA
Hydrogen bonds between base pairs of the two strands hold the molecule together like a zipper.

8. Structure of DNA
Antiparallel: one strand (5’ 3’), other strand runs in opposite, upside-down direction (3’  5’)

11. DNA Comparison Prokaryotic DNA Eukaryotic DNA Double-stranded Circular
One chromosome
In cytoplasm
No histones
Supercoiled DNA
Double-stranded
Linear
Usually 1+ chromosomes
In nucleus
DNA wrapped around histones (proteins)
Forms chromatin

12. Replication is semiconservative

14. Major Steps of Replication:
Helicase: unwinds DNA at origins of replication
Initiation proteins separate 2 strands  forms replication bubble
Primase: puts down RNA primer to start replication
DNA polymerase III: adds complimentary bases to leading strand (new DNA is made 5’  3’)
Lagging strand grows in 3’5’ direction by the addition of Okazaki fragments
DNA polymerase I: replaces RNA primers with DNA
DNA ligase: seals fragments together

15. 1. Helicase unwinds DNA at origins of replication and creates replication forks

16. 3. Primase adds RNA primer

17. 4. DNA polymerase III adds nucleotides in 5’3’ direction on leading strand

18. Replication on leading strand

19. Leading strand vs. Lagging strand

20. Okazaki Fragments: Short segments of DNA that grow 5’3’ that are added onto the Lagging Strand
DNA Ligase: seals together fragments

23. Proofreading and Repair
DNA polymerases proofread as bases added
Mismatch repair: special enzymes fix incorrect pairings
Nucleotide excision repair:
Nucleases cut damaged DNA
DNA poly and ligase fill in gaps

24. Nucleotide Excision Repair
Errors:
Pairing errors: 1 in 100,000 nucleotides
Complete DNA: 1 in 10 billion nucleotides

25. Problem at the 5’ End DNA poly only adds nucleotides to 3’ end
No way to complete 5’ ends of daughter strands
Over many replications, DNA strands will grow shorter and shorter

26. Eukaryotic germ cells, cancer cells
Telomeres: repeated units of short nucleotide sequences (TTAGGG) at ends of DNA
Telomeres “cap” ends of DNA to postpone erosion of genes at ends (TTAGGG)
Telomerase: enzyme that adds to telomeres
Eukaryotic germ cells, cancer cells
Telomeres stained orange at the ends of mouse chromosomes

27. Flow of genetic information
Central Dogma: DNA  RNA  protein
Transcription: DNA  RNA
Translation: RNA  protein
Ribosome = site of translation
Gene Expression: process by which DNA directs the synthesis of proteins (or RNAs)

28. Flow of Genetic Information in Prokaryotes vs. Eukaryotes

29. one gene = one polypeptide
DNA
RNA
Nucleic acid composed of nucleotides
Single-stranded
Ribose=sugar
Uracil
Helper in steps from DNA to protein
Nucleic acid composed of nucleotides
Double-stranded
Deoxyribose=sugar
Thymine
Template for individual

30. RNA plays many roles in the cell
pre-mRNA=precursor to mRNA, newly transcribed and not edited
mRNA= the edited version; carries the code from DNA that specifies amino acids
tRNA= carries a specific amino acid to ribosome based on its anticodon to mRNA codon
rRNA= makes up 60% of the ribosome; site of protein synthesis
snRNA=small nuclear RNA; part of a spliceosome. Has structural and catalytic roles
srpRNA=a signal recognition particle that binds to signal peptides
RNAi= interference RNA; a regulatory molecule

31. The Genetic Code
For each gene, one DNA strand is the template strand
mRNA (5’  3’) complementary to template
mRNA triplets (codons) code for amino acids in polypeptide chain

32. The Genetic Code
64 different codon combinations
Redundancy: 1+ codons code for each of 20 AAs
Reading frame: groups of 3 must be read in correct groupings
This code is universal: all life forms use the same code.

33. Transcription
Transcription unit: stretch of DNA that codes for a polypeptide or RNA (eg. tRNA, rRNA)
RNA polymerase:
Separates DNA strands and transcribes mRNA
mRNA elongates in 5’  3’ direction
Uracil (U) replaces thymine (T) when pairing to adenine (A)
Attaches to promoter (start of gene) and stops at terminator (end of gene)

34. 1. Initiation
Bacteria: RNA polymerase binds directly to promoter in DNA

35. 1. Initiation Eukaryotes:
TATA box = DNA sequence (TATAAAA) upstream from promoter
Transcription factors must recognize TATA box before RNA polymerase can bind to DNA promoter

36. 2. Elongation
RNA polymerase adds RNA nucleotides to the 3’ end of the growing chain (A-U, G-C)

37. 2. Elongation
As RNA polymerase moves, it untwists DNA, then rewinds it after mRNA is made

38. 3. Termination
RNA polymerase transcribes a terminator sequence in DNA, then mRNA and polymerase detach.
It is now called pre-mRNA for eukaryotes.
Prokaryotes = mRNA ready for use

39. Additions to pre-mRNA:
5’ cap (modified guanine) and 3’ poly-A tail ( A’s) are added
Help export from nucleus, protect from enzyme degradation, attach to ribosomes

40. RNA Splicing
Pre-mRNA has introns (noncoding sequences) and exons (codes for amino acids)
Splicing = introns cut out, exons joined together

41. Ribozyme = RNA acts as enzyme
RNA Splicing
small nuclear ribonucleoproteins = snRNPs
snRNP = snRNA + protein
Pronounced “snurps”
Recognize splice sites
snRNPs join with other proteins to form a spliceosome
Spliceosomes catalyze the process of removing introns and joining exons
Ribozyme = RNA acts as enzyme

42. Why have introns? Some regulate gene activity
Alternative RNA Splicing: produce different combinations of exons
One gene can make more than one polypeptide!
20,000 genes  100,000 polypeptides

43. Components of Translation
mRNA = message
tRNA = interpreter
Ribosome = site of translation

44. tRNA Transcribed in nucleus Specific to each amino acid
Transfer AA to ribosomes
Anticodon: pairs with complementary mRNA codon
Base-pairing rules between 3rd base of codon & anticodon are not as strict. This is called wobble.

45. tRNA
Aminoacyl-tRNA-synthetase: enzyme that binds tRNA to specific amino acid

46. Ribosomes
Ribosome = rRNA + proteins
made in nucleolus
2 subunits

47. Ribosomes A site: holds AA to be added
Active sites:
A site: holds AA to be added
P site: holds growing polypeptide chain
E site: exit site for tRNA

48. Translation: 1. Initiation
Small subunit binds to start codon (AUG) on mRNA
tRNA carrying Met attaches to P site
Large subunit attaches

49. 2. Elongation

50. 3.Termination Stop codon reached and translation stops
Release factor binds to stop codon; polypeptide is released
Ribosomal subunits dissociate

51. Polyribosomes
A single mRNA can be translated by several ribosomes at the same time

52. Protein Folding
During synthesis, polypeptide chain coils and folds spontaneously
Chaperonin: protein that helps polypeptide fold correctly

53. Cellular “Zip Codes”
Signal peptide: 20 AA at leading end of polypeptide determines destination
Signal-recognition particle (SRP): brings ribosome to ER

54. The Central Dogma
Mutations happen here
Effects play out here

55. Mutations = changes in the genetic material of a cell
Large scale mutations: chromosomal; always cause disorders or death
nondisjunction, translocation, inversions, duplications, large deletions
Point mutations: alter 1 base pair of a gene
Base-pair substitutions – replace 1 with another
Missense: different amino acid
Nonsense: stop codon, not amino acid
Frameshift – mRNA read incorrectly; nonfunctional proteins
Caused by insertions or deletions

57. Pulmonary hypertension
Sickle Cell Disease
Symptoms
Anemia
Pain
Frequent infections
Delayed growth
Stroke
Pulmonary hypertension
Organ damage
Blindness
Jaundice
gallstones
Caused by a genetic defect
Carried by 5% of humans
Carried by up to 25% in some regions of Africa
Life expectancy
42 in males 48 in females

58. Sickle-Cell Disease = Point Mutation

59. Mutation occurs in the beta chain – have them look at their amino acid structures and think about why the change may be important

61. Prokaryote vs. Eukaryote

62. Prokaryotes vs. Eukaryotes
Transcription and translation both in cytoplasm
DNA/RNA in cytoplasm
RNA poly binds directly to promoter
Transcription makes mRNA (not processed)
No introns
Transcription in nucleus; translation in cytoplasm
DNA in nucleus, RNA travels in/out nucleus
RNA poly binds to TATA box & transcription factors
Transcription makes pre-mRNA  RNA processing  final mRNA
Exons, introns (cut out)

63. A Summary of Protein Synthesis
Most current definition for a gene: A region of DNA whose final product is either a polypeptide or an RNA molecule