1. Chapter 12
DNA & RNA

2. Deoxyribonucleic acid
12 – 1 DNA
Deoxyribonucleic acid

3. In the middle of the 1900’s biologists were wondering how genes work
In the middle of the 1900’s biologists were wondering how genes work. What they are made of, and how they determine the characteristics of organism
If the structures that carry genetic information could be identified, it might be possible to understand how genes control the inherited characteristics of living things

4. How does DNA do the following things?
Carry info from one generation to the next
Put info to work by determining the inheritable characteristics
Copies itself, every time a cell divides

5. Nucleotides Units that make up DNA molecule Made of three parts
5 carbon sugar (deoxyribose)
Phosphate group
Nitrogen bases

6. 4 kinds of nitrogen bases
Adenine (A)
Guanine (G)
Cytosine (C)
Thymine (T)

7. Chargaff’s Rule
A=T and G=C

8. X-Ray Evidence Rosalind Franklin British Scientist
Used a technique called X-Ray diffraction
Provided important clues about the structure of DNA

9. X-Ray Evidence There were 2 strands
Strands were twisted around each other (helix)
The nitrogen bases are in the middle

10. Watson & Crick

11. The Double Helix Francis Crick & James Watson
Trying to understand the structure of DNA by building models
Unsuccessful until early 1953, Watson was shown a copy of Franklin’s X-ray pattern
“The instant I saw the picture my mouth fell open and my pulse began to race.”
James Watson
Within weeks Watson and Crick had figured out the structure of DNA
Published their results in a historic one page paper in April of 1953

13. Watson and Crick later discovered what held the two strands together
Hydrogen bonds could form between certain nitrogen bases and provide enough force to hold the two strands together
Hydrogen bonds could only form between certain base pairs adenine and thymine and guanine and cytosine
This principal is called Base pairing
This explains Chargaff’s Rule

17. Chromosomes and DNA Replication

18. To extract DNA for analysis, you need to know where to find it and how its organized
DNA is located in the nucleus
DNA is organized into chromosomes

19. Prokaryotic Cells
Prokaryotic cells have a single circular DNA molecule that contains nearly all of its genetic information
Located in the cytoplasm

20. Eukaryotic Cells Much more complex
1000 times the amount of DNA as prokaryotes
DNA is located in the nucleus in the form of chromosomes

21. Chromosome Structure
Q: If eukaryotic DNA can contain a meter or more of DNA, how does it get packed in so tight into chromosomes?
A: Eukaryotic chromosomes contain both DNA and protein that form a substance called chromatin

22. Histones Proteins that coil up DNA
DNA + histone molecules form a bead-like structure called a nucleosome
Nucleosomes pack together to form thick fibers that loop and coil together to form chromosomes

23. DNA coils around histones to form nucleosomes, which coil to form chromatin fibers. The chromatin fibers super coil to form chromosomes that are visible in the metaphase stage of mitosis.

25. DNA Replication
When Watson and Crick discovered the double helix structure of DNA they recognized immediately how DNA could copy itself
The strands are complementary
If you could separate the two strands, the rules of base pairing would allow you to reconstruct the base sequence of the other strand

26. Replication
When the DNA splits into 2 strands, then produces 2 new strands following the rules of base pairing

27. Semiconservative Replication
Parental strands of DNA separate, serve as templates, and produce DNA molecules that have one strand of parental DNA and one strand of new DNA.

28. How Replication Occurs
Unwinding
Synthesizing
Joining

29. Getting Started
Origins of replication- short stretched of DNA having a specific sequence of nucleotides.
The place where DNA replication begins.
Replication fork- Y-shaped region where the parental strands of DNA are being unwound.

30. 1. Unwinding Replication is carried out by enzymes
Before DNA replicates, the double helix must unwind and unzip.
DNA Helicase-enzyme that is responsible for unwinding and unzipping the double helix.

31. 1. Unwinding
When the double helix unwinds/unzips the H+ bonds between the bases are broken, leaving single strands of DNA.
Then, proteins called single-stranded binding proteins associate with the DNA to keep the strands separate during replication.
As the helix unwinds, another enzyme, RNA Primase, adds a short segment of RNA, called RNA primer on each DNA strand.

32. 1. Unwinding
The untwisting of the double helix causes tighter twisting and strain ahead of the replication fork.
Topoisomerase- helps relieve this strain by breaking, swiveling, and rejoining DNA strands.

33. 1. Unwinding
Helicase

34. 2. Synthesi zing
Within a bubble, the unwound sections of parental DNA strands are available to serve as templates for the synthesis of new complementary DNA strands.
As the helix unwinds, another enzyme, RNA Primase, adds a short segment of RNA, called RNA primer on each DNA strand.

35. 2. Base Pairing Also proof reads each new DNA strand DNA Polymerase:
Joins individual nucleotides to produce a DNA molecule, which is a polymer
The nucleotides are added to the 3’ end of the new strand.
Also proof reads each new DNA strand

36. 2. Base Pairing
DNA polymerase continues adding new DNA nucleotides to the chain by adding to the 3’ end of the DNA strand.
A binds with T / C binds with G
This allows for identical copies to be made
Leading Strand: elongated as the DNA unwinds
Continuously added to 3’ end
Lagging Strand: elongates away from fork
Done by adding small fragments. (Okazaki fragments)

37. 3. Joining
When the DNA polymerase comes to an RNA primer on the DNA, it removes the primer and fills in the place with DNA nucleotides.
When the RNA primer has been replaced, DNA ligase links the two sections.

40. Do Now Place the following steps of Replication in order.
DNA Unzips
DNA unwinds
Sugar and phosphate groups form the side of each new strand
The bases attach from a supply in the cytoplasm

41. Do Now Place the following steps of Replication in order.
DNA replication results in 2 DNA molecules
Each with two new strands
One with two new strands and the other with two original strands
Each with one new strand and one original strand
Each with two original strands 1.
DNA unwinds 2.
DNA Unzips 3.
The bases attach from a supply in the cytoplasm 4.
Sugar and phosphate groups form the side of each new strand

42. 12 – 3 RNA and Protein Synthesis

43. Genes
Coded DNA instructions that control the production of proteins

44. DNA never leaves the nucleus, therefore the code must be copied into
RNA, or ribonucleic acid
There are 3 main differences between RNA and DNA
It has the sugar ribose, instead of deoxyribose
RNA is single stranded
RNA contains uracil in place of thymine

45. RNA is like a disposable copy of a segment of DNA
RNA is like a working copy of a single gene

46. Types of RNA Messanger RNA (mRNA)
Serve as messangers from DNA to the rest of the cell
2. Ribosomal RNA (rRNA)
Type of RNA that makes up parts of ribosomes
3. Transfer RNA (tRNA)
Transfers each amino acid to the ribosome as it is specified by the mRNA

47. Types of RNA

48. Transcription
RNA molecules are produced by copying part of the DNA sequence into RNA
Transcription requires an enzyme known as RNA polymerase
During transcription, RNA polymerase binds to DNA and separates the DNA strands. RNA polymerase then uses one strand of DNA as a template from which nucleotides are assembled into a strand of RNA.

49. Q: How does RNA polymerase “know” where to start and stop making a RNA copy of DNA?
A: promoters
Signals in DNA that indicate to the enzyme where to bind to make RNA
Similar signals in DNA cause transcription to stop

52. RNA Editing Remember, a lot of DNA doesn’t code for proteins
Introns – not involved in coding for proteins
Exons – code for proteins

53. The introns get cut out of the RNA molecules before the final mRNA is made

54. The Genetic Code
Proteins are made by joining amino acids into long chains called polypeptides
Each polypeptide contains a combination of any or all of the 20 different amino acids
The properties of proteins are determined by the order in which different amino acids are joined together
The language of mRNA instructions is called the genetic code

55. The code is read three letters at a time
Each 3 letter “word” is called a codon
Each codon corresponds to an amino acid that can be added to the polypeptide

57. UCGCACGGU UCG-CAC-GGU
This sequence would be read three bases at a time as:
UCG-CAC-GGU
The codons represent the different amino acids:
Serine-Histidine-Glycine

58. Translation
The sequence of nucleotide bases in an mRNA molecule serves as instructions for the order in which amino acids are joined to make a protein
Proteins are put together on ribosomes

59. Translation
Decoding mRNA into a protein

60. Steps of Translation
mRNA is transcribed from DNA in the nucleus and released into the cytoplasm
mRNA attaches to a ribosome
3. as each codon of the mRNA molecule moves through the ribosome, the proper amino acid is transferred to the growing amino acid chain by tRNA
tRNA carries only one kind of amino acid and three unpaired bases called the anticodon

61. 4. The amino acid chain continues to grow until the ribosome reaches a stop codon on the mRNA molecule

63. The Roles of RNA and DNA
You can compare the different roles played by DNA and RNA molecules in directing protein synthesis to the two types of plans used by builders. A master plan has all the information needed to construct a building. But builders never bring the valuable master plan to the building site, where it might be damaged or lost. Instead, they prepare inexpensive, disposable copies of the master plan called blueprints. The master plan is safely stored in an office, and the blueprints are taken to the job site. Similarly, the cell uses the vital DNA “master plan” to prepare RNA “blueprints.” The DNA molecule remains in the safety of the nucleus, while RNA molecules go to the protein-building sites in the cytoplasm—the ribosomes

64. Genes and Proteins
Q: If most genes contain nothing more than instructions for assembling proteins, what do proteins have to do with traits?
A: Everything, proteins are microscopic tools designed to build or operate a component of a living cell

65. 12 – 4 Mutations

66. Mutations
Changes in the genetic material

67. Point mutations Changes in one or a few nucleotides
Ex.) substitutions, insertions, deletions

71. Frameshift mutations
Mutation that shifts the “reading” frame of the genetic message by inserting or deleting a nucleotide

72. Chromosomal Mutations

76. Significance of Mutations
Most mutations don’t do anything
Mutations that cause drastic changes in proteins produce defective proteins that disrupt normal biological activities
Mutations are also a source of genetic variability which can be beneficial

77. Polyploidy
When plants produce triploid (3N) or tetraploid (4N) organisms
These plants are often larger and stronger

79. Do Now Look at the bottom strand of DNA on the window blinds
Suppose the second T was changed to a C
How would this specifically alter the resulting amino acid chain?
What kind of mutation is this?

80. Do Now #2
What if we got rid of the first G in the bottom strand of DNA
How would this specifically alter the amino acid chain produced?
What kind of mutation is this?

81. Do Now #3
How are substitution/point mutations and frameshift mutations similar?
How are they different?