1. Biology 1 Notes Chapter 12 - DNA and RNA Prentice Hall pages 286-317
A. Griffith and Transformation
1. Griffith’s Experiments
2. Transformation
B. Avery and DNA
C. The Hershey-Chase Experiment
1. Bacteriophages
2. Radioactive Markers
D. The Components and Structure of DNA
1. Chargaff’s Rules
2. X-Ray Evidence
3. The Double Helix
12–2 Chromosomes and DNA Replication
A. DNA and Chromosomes
1. DNA Length
2. Chromosome Structure
B. DNA Replication
1. Duplicating DNA
2. How Replication Occurs
12–3 RNA and Protein Synthesis
A. The Structure of RNA
B. Types of RNA
C. Transcription
D. RNA Editing
E. The Genetic Code
F. Translation
G. The Roles of RNA and DNA
H. Genes and Proteins
12–4 Mutations
A. Kinds of Mutations
1. Gene Mutations
2. Chromosomal Mutations
B. Significance of Mutations

2. What is DNA?
Although the environment influences how an organism develops, the genetic information that is held in the molecules of DNA ultimately determines an organism’s traits.
DNA achieves its control by determining the structure of proteins.
All actions, such as eating, running, and even thinking, depend on proteins called enzymes.
Enzymes are critical for an organism’s function because they control the chemical reactions needed for life.
Within the structure of DNA is the information for life—the complete instructions for manufacturing all the proteins for an organism.
Many scientists have contributed to our current knowledge of DNA.
Miescher studied material in nucleus and found it to be half protein and half DNA in 1868.
In the 1900’s, Walter Sutton and Thomas Hunt Morgan showed that genes are the units of heredity and are located on chromosomes

3. Griffith’s Experiment
In 1928, Frederick Griffith conducted an experiment in which he was studying how pneumonia causing bacteria made people sick.
Griffith injected mice with four different samples of bacteria from the smooth and rough colonies.
When injected separately, neither heat-killed, disease-causing bacteria nor live, harmless bacteria killed the mice.
The two types injected together, however, caused fatal pneumonia.
Some factor from the dead bacteria had “transformed” the harmless bacteria into disease-causing ones.
From this experiment, biologists inferred that genetic information could be transferred from one bacterium to another.

4. Griffith’s Experiment (Figure 12-2)
Disease-causing bacteria (smooth colonies)
Harmless bacteria (rough colonies)
Heat-killed, disease-causing bacteria (smooth colonies)
Control (no growth)
Dies of pneumonia
Lives
Live, disease-causing bacteria (smooth colonies)

5. DNA or Proteins?
But…. Griffith was unsure whether it was DNA or protein that was being transformed.
Almost 20 years later, (1944), Avery, MacLeod, and McCarty recreated Griffith’s experiment in order to determine if the transforming material was DNA or proteins.
They discovered that the nucleic acid DNA stores and transmits the genetic information from one generation to the next.
Avery, Macleod and McCarty published strong evidence that DNA was the transforming material, but not enough to convince everyone.
Many scientists need several different experiments to convince them of a discovery of this importance.

6. DNA is the genetic material
In 1952, Alfred Hershey and Martha Chase performed an experiment using radioactively labeled viruses (bacteriophages) that infect bacteria.
These viruses (phages) were made of only protein and DNA.
The bacteriophages, or viruses, attach to the outside of bacterium, inject its genetic material into bacterium, take over its processes, and kill it while releasing new phages

7. The Hershey- Chase Experiment
To determine if the genetic material was DNA or protein, radioactive substances were used as markers.
Hershey and Chase labeled the virus protein with a radioactive isotope of sulfur (pink neon label) and the virus DNA with a different isotope -phosphorus (blue neon label).
By following the infection of bacterial cells by the labeled viruses, they demonstrated whether it was DNA or protein that entered the cells and caused the bacteria to produce new viruses.

8. The Hershey- Chase Experiment
The bacteriophages injected only DNA into the bacteria, not proteins.
From these results, Hershey and Chase concluded that the genetic material of the bacteriophage was DNA.

9. Genes… Scientists now knew that genes are made of DNA. They also knew:
genes had to carry information from one generation to the next
genes had to put that information to work by determining the heritable characteristics of organisms
genes had to be easily copied, because all of a cell’s genetic information is replicated every time a cell divides
Scientists now wanted to know more about the molecule DNA.

10. The Components and Structure of DNA
DNA is a polymer (long chain) made of repeating subunits called nucleotides.
Nitrogenous base
Phosphate group
Sugar (deoxyribose)
Nucleotides have three parts: a simple sugar, a phosphate group, and a nitrogenous base.
The simple sugar in DNA, called deoxyribose, gives DNA its name— deoxyribonucleic acid.
The phosphate group is composed of one atom of phosphorus surrounded by four oxygen atoms.

11. The Components and Structure of DNA
A nitrogenous base (nitrogen-containing) is a carbon ring structure that contains one or more atoms of nitrogen.
In DNA, there are four possible nitrogenous bases: adenine (A), guanine (G), cytosine (C), and thymine (T).
Thus, in DNA there are four possible nucleotides, each containing one of these four bases.
Adenine (A)
Guanine (G)
Thymine (T)
Cytosine (C)

12. DNA Nucleotides
Adenine and Guanine are in a group known as the purines (they are larger).
Cytosine and Thymine are in a group called the pyrimidines (they are smaller).
Nucleotides join together to form long chains, with the phosphate group of one nucleotide bonding to the deoxyribose sugar of an adjacent nucleotide.
The phosphate groups and deoxyribose molecules form the backbone of the chain, and the nitrogenous bases stick out like the teeth of a zipper.
The nucleotides can be joined together in any order, meaning that any sequence of bases is possible.

13. Chargaff’s Rule
In the 1950’s Erwin Chargaff analyzed the amounts of four compounds in DNA (A, T, C, G).
Chargaff’s Rule: [A] = [T] and [G] = [C]
He found that the amount of adenine is always equal to the amount of thymine, and the amount of guanine is always equal to the amount of cytosine.

14. X-ray Evidence
X-ray studies done in the 1950’s by Rosalind Franklin and Maurice Wilkins revealed the basic spiral (coiled double helix) structure of DNA.
X-ray diffraction (crystallography) - x-rays pass through a crystal of a substance onto photographic film; molecules of substance scatter the x-rays in characteristic patterns
shows that the strands in DNA are twisted around each other like the coils of a spring, a shape known as a helix
angle of the X suggests that there are two strands in the structure
nitrogenous bases are near the center of the molecule

15. The Double Helix
In 1953, Watson and Crick proposed that DNA is made of two chains of nucleotides (wound around each other) held together by nitrogenous bases (they used the Franklin’s x-ray pattern).
Because DNA is composed of two strands twisted together, its shape is called double helix.
They discovered that hydrogen bonds could form between certain nitrogenous bases and hold the two strands together.
Because of the size of each of the bases, only adenine and thymine and guanine and cytosine could form bonds between them.
This also, supported and explained Chargaff’s rule.

17. DNA Structure

18. DNA Building Block
phosphate
sugar
base

19. Deoxyribose Sugar

22. The importance of nucleotide sequences
The sequence of nucleotides (A,T,C,G) forms the unique genetic information of an organism. The closer the relationship is between two organisms, the more similar their DNA nucleotide sequences will be.
Scientists use nucleotide sequences to determine evolutionary relationships among organisms, to determine whether two people are related, and to identify bodies of crime victims.

23. Prokaryotic Chromosome Structure
Most prokaryotes, such as this E. coli bacterium, have only a single circular chromosome.
This chromosome holds most of the organism’s DNA.

24. Prokaryote vs. Eukaryote DNA
Eukaryotes have as much as 1000 times the amount of DNA as prokaryotes.
Unlike prokaryotes that lack a nucleus, eukaryotic DNA is found in the nucleus.
Eukaryotic DNA is organized into chromosomes.
The number of chromosomes in each cell can vary by organism.
Humans have 46 chromosomes -Giant Sequoia trees have 22
Fruit flies have 8 chromosomes
1 base pair
DNA Length
E. coli (bacteria in human colon) contains 4,639,221 base pairs
Length = 1.6 mm; A typical bacterium is less than 1.6 μm in diameter
DNA must be folded into a space only one one-thousandth of its length

25. Chromosome Structure of Eukaryotes
4. Nucleosome
1. Chromosome
6. DNA double helix
3. Coils
2. Supercoils
5. Histones
A chromosome is made up of a tangled mass of chromatin fiber.
Each chromatin fiber is a tightly wound supercoil.
Each supercoil is made up of coils.
A coil, in turn, is a chain, of beadlike structures called nucleosomes.
Each nucleosome consists of DNA wound around proteins called histones
The strand of DNA is a double helix made up of nucleotides.

26. DNA Replication (Background)
During most of the cell cycle, DNA is unwound, so that the chromosomes are not visible.
During mitosis, the tightly packed chromosomes form in order to move more efficiently.
Before cell division, DNA must make a copy of itself during S phase of interphase.
This process is called DNA Replication.
This process ensures that each resulting cell will have a complete set of DNA molecules.
It is important that the new copies are exactly like the original molecules.

27. DNA Replication
During DNA replication, the DNA molecule separates into two strands.
In most prokaryotes, replication begins at a single point in the chromosome and proceeds, often in two directions, until the entire chromosome is replicated.
In the larger eukaryotic chromosomes, DNA replication occurs at hundreds of places at the same time.
Replication proceeds in both directions until each chromosome is completely copied.
The sites where separation and replication occur are called replication forks.

28. Steps of DNA Replication
1. DNA Replication begins when the two strands separate as the hydrogen bonds that hold the base pairs together breaks.
2. This allows to the two strands to unzip and unwind.

29. Steps of DNA Replication
Because each original strand can be used to make a new strand, the strands are said to be complementary.
3. Each strand of the double helix of DNA serves as a template, or model, for the new strand.
4. The enzyme DNA polymerase helps free-floating nucleotides match up with their complementary bases on each of the exposed, original strand.
Adenine pairs always with thymine and cytosine always pairs with guanine, following the rules of base pairing.
Free Nucleotides
Original DNA
New DNA Strand
New DNA Strand
Free Nucleotides
Original DNA

30. Steps of DNA Replication
The addition of nucleotides occurs in both directions of the DNA molecules simultaneously.
Original strand
DNA polymerase
New strand
Growth
DNA polymerase
Growth
Replication fork
Replication fork
Nitrogenous bases
New strand
Original strand

31. Steps of DNA Replication
5. Two new complementary strands are produced.
Each molecules contains one original strand and one new strand.
This is why DNA Replication is called semi-conservative
Original Strand:
ATCGGCTAA
Complementary Strand:
Original DNA Molecule
Replication
TAGCCGATT
Two New DNA Molecules

32. Steps of DNA Replication
1. Enzymes break hydrogen bonds that hold bases
together
2. DNA unwinds and unzips
3. Each single strand of DNA serves as a template
for a new complementary strand to be made.
4. Free-floating DNA nucleotides pair up with
complementary DNA nucleotides on parent
strand by enzyme DNA polymermase
5. Two new identical double helixes are formed

33. 12-3: RNA RNA is very similar to DNA; but there are some differences:
Structure
Double Stranded
Single Stranded
Bases- Purines
Adenine (A)
Guanine (G)
Bases - Pyrimidines
Cytosine (C)
Cytosone (C)
Thymine (T)
Uracil (U)
Sugar
Deoxyribose
Ribose
RNA
Uracil
Hydrogen bonds
Adenine
Ribose
The main job of RNA is to make proteins (protein synthesis)

34. Types of RNA
There are three main types of RNA: messenger RNA, ribosomal RNA, and transfer RNA.
1) messenger RNA (mRNA)- molecules of RNA that carries instructions from the gene (DNA) in the nucleus to the ribosome
2) ribosomal RNA (rRNA)- molecule of RNA that combines with proteins to form the ribosome; the ribosome is where proteins are made
3) transfer RNA (tRNA)- RNA molecule transfers each amino acid to the ribosome as it is specified by coded messages in mRNA during the construction of a protein

35. Protein Synthesis Overview
There are two main steps to protein synthesis:
1) Transcription (nucleus)
DNA RNA
2) Translation (cytoplasm)
RNA  protein

36. Transcription
1) Transcription begins when the enzyme RNA polymerase binds to DNA at a promoter region.
Promoters are signals in DNA that indicate to the enzyme where to bind to make RNA.
2) The enzyme separates the DNA strands by breaking the hydrogen bonds, and then uses one strand of DNA as a template from which nucleotides are assembled into a strand of RNA.
3) RNA polymerase pairs up free-floating RNA nucleotides with DNA template and joins the nucleotides together to form the backbone of the new mRNA strand.
The strand continues to lengthen.
4) When mRNA hits a termination sequence, it separates from the DNA.
5) Then the mRNA leaves the nucleus and enters the cytoplasm

37. Transcription Nucleus Adenine (DNA and RNA) Cystosine (DNA and RNA)
RNA polymerase
Adenine (DNA and RNA)
Cystosine (DNA and RNA)
Guanine(DNA and RNA)
Thymine (DNA only)
Uracil (RNA only)
Nucleus

38. Transcription vs. Replication
The main difference between transcription and DNA replication is that transcription results in the formation of one single-stranded RNA molecule rather than a double-stranded DNA molecule.
Practice
DNA template
DNA Complement (replication)
mRNA (transcription)
ATTCGGAGC
TAAGCCTCG
UAAGCCUCG

39. The Genetic Code
Proteins (polypeptides) are long chains of amino acids that are joined together.
There are 20 different amino acids.
The properties (structure and function) of proteins are determined by the order in which different amino acids are joined together to produce polypeptides.
The four bases (letters) of mRNA A, U, G, and C are read three letters at a time (and translated) to determine the order in which amino acids are added to a protein.
A codon consists of three consecutive nucleotides that specify a single amino acid that is to be added to the polypeptide (protein).

40. The Codon Table
Sixty-four combinations are possible when a sequence of three bases are used; thus, 64 different mRNA codons are in the genetic code.
Some codons do not code for amino acids; they provide instructions for making the protein.
More than one codon can code for the same amino acid.
However, for any one codon, there can be only one amino acid.
All organisms use the same genetic code (A,T,C,G).
This provides evidence that all life on Earth evolved from a common origin.

41. Cracking the Code
The genetic code shows the amino acid to which each of the 64 possible codons corresponds.
To decode a codon, start at the middle of the circle and move outward.
Ex: CGA
Argenine
Ex: GAU
Aspartic Acid

42. Translation Translation takes place on ribosomes, in the cytoplasm.
The cell uses information from messenger RNA to produce proteins, by decoding the mRNA message into a polypeptide chain (protein).
Translation takes place on ribosomes, in the cytoplasm.

43. Messenger RNA
The mRNA that was transcribed from DNA during transcription, leaves the cell’s nucleus and enters the cytoplasm.
During translation, or protein synthesis, the cell uses information from mRNA to produce proteins.
The cell uses all 3 main forms of RNA during this process

44. Transfer RNA
2) The mRNA enters the cytoplasm and attaches to a ribosome at the AUG, which is the start codon. This begins translation.
3) The transfer RNA (tRNA) bonds with the correct amino acid and becomes “charged.” (in the cytoplasm)
4) The tRNA carries the amino acid to the ribosome.
Each transfer RNA has an anticodon whose bases are complementary to a codon on the mRNA strand. (The tRNA brings the correct amino acid to the ribosome.)
Ex: The ribosome positions the start codon to attract its anticodon, which is part of the tRNA that binds methionine.
The ribosome also binds the next codon and its anticodon.

45. The Polypeptide “Assembly Line”
5) The ribosome moves along the mRNA and adds more amino acids to the growing peptide or protein
The tRNA floats away, allowing the ribosome to bind to another tRNA.
The ribosome moves along the mRNA, binding new tRNA molecules and amino acids.

46. Completing the Polypeptide
6) The process continues until the ribosome reaches one of the three stop codons on the mRNA, and then the ribosome falls off the mRNA.
7) The result is a polypeptide chain or protein that is ready for use in the cell.

48. Practice DNA template DNA Complement (replication)
mRNA (transcription)
tRNA
Amino Acid Sequence
(translation)
TAC GGT CCA AAC ACT
ATG CCA GGT TTG TGA
AUG/CCA/GGU/UUG/UGA
UAC/GGU/CCA/AAC/ACU
Met-Pro-Gly-Leu-Stop

49. 12-4: Mutations
Organisms have evolved many ways to protect their DNA from changes.
In spite of these mechanisms, however, changes in the DNA occasionally do occur
Any change in DNA sequence is called a mutation.
Mutations can be caused by errors in replication, transcription, cell division, or by external agents.

50. Mutations in reproductive cells
Mutations can affect the reproductive cells of an organism by changing the sequence of nucleotides within a gene in a sperm or an egg cell.
If this cell takes part in fertilization, the altered gene would become part of the genetic makeup of the offspring.
The mutation may produce a new trait or it may result in a protein that does not work correctly.
Sometimes, the mutation results in a protein that is nonfunctional, and the embryo may not survive.
In some rare cases a gene mutation may have positive effects.

51. Mutations in body cells
What happens if powerful radiation, such as gamma radiation, hits the DNA of a nonreproductive cell, a cell of the body such as in skin, muscle, or bone?
If the cell’s DNA is changed, this mutation would not be passed on to offspring.
However, the mutation may cause problems for the individual.
Damage to a gene may impair the function of the cell.
When that cell divides, the new cells also will have the same mutation
Some mutations of DNA in body cells affect genes that control cell division.
This can result in the cells growing and dividing rapidly, producing cancer.

52. The effects of point mutations
A point mutation is a change in a single base pair in DNA.
A change in a single nitrogenous base can change the entire structure of a protein because a change in a single amino acid can affect the shape of the protein.
mRNA
Normal
Protein
Stop
Replace G with A
Point mutation
mRNA
Protein
Stop

53. Gene Mutations
Substitution
Insertion
Deletion

54. Frameshift mutations
What would happen if a single base were lost from a DNA strand?
This new sequence with the deleted base would be transcribed into mRNA. But then, the mRNA would be out of position by one base.
As a result, every codon after the deleted base would be different.
mRNA
Protein
Frameshift mutation
Deletion of U
mRNA
Normal
Protein

55. Frameshift mutations
This mutation would cause nearly every amino acid in the protein after the deletion to be changed.
A mutation in which a single base is added or deleted from DNA is called a frameshift mutation because it shifts the reading of codons by one base.
mRNA
Protein
Frameshift mutation
Deletion of U
mRNA
Normal
Protein

56. Chromosomal Alterations
Changes may occur in chromosomes as well as in genes.
Alterations to chromosomes may occur in a variety of ways.
Structural changes in chromosomes are called chromosomal mutations.
Chromosomal mutations occur in all living organisms, but they are especially common in plants.
Few chromosomal mutations are passed on to the next generation because the zygote usually dies
In cases where the zygote lives and develops, the mature organism is often sterile and thus incapable of producing offspring. (This prevents the organism from passing on this mutation to its offspring).

57. Chromosomal Alterations
When a part of a chromosome is left out, a deletion occurs.
Deletion
When part of a chromatid breaks off and reattaches to its sister chromatid, an insertion occurs.
The result is a duplication of genes on the same chromosome.
Duplication

58. Chromosomal Alterations
When part of a chromosome breaks off and reattaches backwards, an inversion occurs
Inversion
When part of one chromosome breaks off and is added to a different chromosome, a translocation occurs.
Translocation

59. Causes of Mutations
Some mutations seem to just happen, perhaps as a mistake in base pairing during DNA replication.
These mutations are said to be spontaneous.
However, many mutations are caused by factors in the environment.
Any agent that can cause a change in DNA is called a mutagen
Mutagens include radiation, chemicals, and even high temperatures
Forms of radiation, such as X rays, cosmic rays, ultraviolet light, and nuclear radiation, are dangerous mutagens because the energy they contain can damage or break apart DNA.

60. Causes of Mutations
The breaking and reforming of a double-stranded DNA molecule can result in deletions
Chemical mutagens include dioxins, asbestos, benzene, and formaldehyde, substances that are commonly found in buildings and in the environment.
Chemical mutagens usually cause substitution mutations

61. Repairing DNA
Repair mechanisms that fix mutations in cells have evolved.
Enzymes proofread the DNA and replace incorrect nucleotides with correct nucleotides.
These repair mechanisms work extremely well, but they are not perfect.
The greater the exposure to a mutagen such as UV light, the more likely is the chance that a mistake will not be corrected.