1. Section 12-1:
DNA
Chapter 12 – DNA and RNA

2. Mendel helped to figure out what genes were, but how exactly where these genes passed on?
In 1928, Frederick Griffith (British) was doing experiments with bacteria and mice to figure out how bacteria make us sick

3. He found 2 different strains of pneumonia bacteria; Smooth (S) and Rough (R)
The smooth bacteria caused death but the rough bacteria seemed harmless
When Griffith heat killed the smooth bacteria, the bacteria no longer killed

4. Then Griffith mixed heat killed smooth bacteria with living rough bacteria (neither should have caused disease) and it caused death
Griffith called this a transformation  the rough strain was permanently changed by the smooth strain
Griffith hypothesized that some factor was transferred from one strain to another and that the factor might be a gene

5. In 1944, Oswald Avery (Canadian) repeated Griffiths experiment and found similar results
In 1952, Alfred Hershey and Martha Chase were performing experiments to verify Avery’s discovery
They were studying viruses, specifically bacteriophages = viruses that infect bacteria
Bacteriophages are made of DNA or RNA inside a protein coat

6. Hershey and Chase decided if they could tell if the DNA or the protein was being injected into the bacteria, they could determine what genes were made of
They used 2 radioactive markers, phosphorus-32 and sulfur-35

7. Proteins contain almost no phosphorus  so if they found the phosphorus marker, it was DNA carrying the genes
DNA contains no sulfur  so if they found the sulfur marker, it was proteins carrying the genes
They found all of the radioactivity in the bacteria was from phosphorus, making the genetic material DNA

8. Scientists wanted to know more about the structure of DNA
DNA is a long molecule made up of nucleotides
A nucleotide if made of 3 components;
a 5-carbon sugar called deoxyribose,
a phosphate group,
and a nitrogen-containing base

9. There are 4 kinds of nitrogen-containing bases in DNA; adenine, guanine, cytosine, and thymine
Two belong to a group known as purines (two rings in their structure)  adenine and guanine
Two belong to a group known as pyrimidines (one ring in their structure)  cytosine and thymine

10. The sugar and phosphate form the backbone of the DNA and the nitrogen-containing bases stick out sideways – the bases can be in any order
This set up of DNA seemed almost too simple, so of course scientists did more experiments to find out more about it

11. Erwin Chargraff observed that in different types of organisms that the percentages of guanine [G] and cytosine [C] were almost equal and the percentages of adenine [A] and thymine [T] were almost equal
Chargraff’s rules says [A] = [T] and [C] = [G]

12. In the early 1950’s, Rosalind Franklin (British) studied DNA using a X-ray diffraction
The photos from the X-rays showed an X-shaped pattern  showing that the strands of DNA are twisted around each other like a helix
The angle of the X showed that there were 2 strands in the structure

13. Around the same time, James Watson and Francis Crick were working to build a model of the structure of DNA
Watson and Crick’s model of DNA was a double helix where the 2 strands wound around each other
A double helix looks like a twisted staircase

14. They found hydrogen bonds could form between certain base pairs – they called this base-pairing and it helped explain Chargraff’s rules
Adenine always pairs with thymine and guanine always pairs with cytosine
The double helix helped explain some of DNA’s properties, but they weren’t sure what held the strands together

15. Section 12-2: Chromosomes and DNA Replication

16. So where is the DNA located within a cell?
Prokaryotes do not have a nucleus, so their DNA is found in their cytoplasm
Most prokaryotes have a single circular DNA molecule – this is called the cell’s chromosome

17. In eukaryotes, there is much more DNA than in prokaryotes
The DNA is found in the nucleus in the form of multiple chromosomes
The number of chromosomes varies from species to species

18. DNA molecules can be surprisingly long and must be folded into a tiny space
The nucleus of a human cell contains more than 1 meter of DNA, so how does it all fit?
In eukaryotes, DNA and proteins are packed tightly to form chromatin
In the chromatin, DNA is wound around proteins called histones  they almost look like beads on a string

19. These pack together to form a thick fiber that gets shortened into loops & coils
Normally, these fibers are dispersed through the nucleus, but during mitosis, they condense into visible chromosomes

20. The double helix structure helped to explain how DNA can be replicated
One strand of DNA has the information needed to complete the other half through base pairing
This means that the strands are complementary to one another and that when split up, each half can be used to create the other half and thereby create two new identical DNA molecules

21. In eukaryotes, DNA replication occurs at hundreds of places
In prokaryotes, DNA replication usually starts at one point and proceeds in two directions until the whole chromosome of replicated

22. At each point, replication happens in 2 directions until the whole chromosome is copied
Replication forks = the sites where separation and replication occur
Each strand serves as a template as to how to add on base pairs
Ex. A sequence of TACGTT will produce a complimentary strand of ATGCAA

23. Several enzymes are involved in the process of DNA replication
DNA helicase is used to “unzip” the 2 strands of DNA
DNA polymerase joins individual base pairs to the DNA molecule  it can also “proofread” new DNA strand to make sure they are a perfect copy of the original

24. RNA and Protein Synthesis
Section 12-3:
RNA and Protein Synthesis

25. Genes are just instructions coded on DNA – we just need a way to put those instructions to work  that’s where RNA comes in

26. RNA has a similar structure to DNA but there are 3 major differences
1. The sugar is ribose instead of deoxyribose
2. RNA is a single strand instead of a double strand
3. RNA contains uracil in place of thymine
RNA is basically a disposable copy of DNA, it can help make hundreds or thousands of copies without hurting the master copy

27. Most RNA is involved in protein synthesis – assembling amino acids into proteins
There are 3 main types of RNA involved in protein synthesis; mRNA, rRNA, tRNA

28. 1. Messenger RNA (mRNA) – It carries copies of instructions for proteins from the DNA to the rest of the cell – it basically acts as a messenger

29. 2. Ribosomal RNA (rRNA) – it makes up parts of ribosomes - they serve as sites where the proteins are made
3. Transfer RNA (tRNA) – it transfers amino acids to the ribosome guided by the instructions of the mRNA

30. Transcription = the process of copying part of a nucleotide sequence from DNA to RNA
Transcription requires an enzyme known as RNA polymerase (similar to DNA polymerase)

31. During transcription, RNA polymerase binds to DNA and separates the DNA strands  it then uses one strand of DNA as a template to form a strand of RNA
RNA polymerase can’t start copying at just any point – it has to bind at a specific spot

32. Promoter = a region where the enzyme can bind that has a specific sequence of nucleotides
The promoter basically tells the enzyme where to start copying
There is a similar signal to stop copying

33. Once copied, the RNA does get edited before leaving the nucleus with instructions for proteins
In DNA there are areas that are called introns – they are not involved in coding proteins
There are also areas called exons – they are involved in coding proteins (they are “expressed”)
Introns are cut out of the RNA  the exons are spliced together and this forms the mRNA that leaves the nucleus

34. Now that we have mRNA instructions, how do those eventually make proteins
The instructions carried by the mRNA is the genetic code – the code consists of the 4 nitrogen-containing bases  there are basically 4 letters in the code
These 4 letters in the code can create 20 different amino acids  this is possible because the code is read 3 letters at a time

35. Each “word” of the code is 3 bases long  each of these “words” is known as a codon
Ex. The code UCGCACGGU would be broken into groups of 3 bases  UCG-CAC-GGU
Because there are 4 bases, there are 64 possible 3-base codons

36. Some amino acids are coded for by several codons
There is one codon that acts as a start for protein synthesis and there are three codons that act as a stop for synthesis

37. These instructions are carried by the mRNA to the ribosomes where they are used to create proteins in a process known as translation
During translation, the cell uses information from mRNA to produce proteins

38. Translation occurs in a series of steps
1. mRNA in the cytoplasm attaches to a ribosome
2. As each codon of the mRNA moves through the ribosome an amino acid is brought to the ribosome by tRNA
Each tRNA molecule only carries one type of amino acid
Each tRNA molecule also has 3 unpaired bases (anticodon) so that it knows where to match up on the mRNA  codons and anticodons are complementary

39. 3. Peptide bonds form between the adjacent amino acids – at the same time the bond between the amino acid and the tRNA is broken so the tRNA is free to pick up another amino acid
4. The amino acid chain grows until the ribosome reaches a stop codon – the ribosome then releases both the mRNA and the newly formed polypeptide

40. Over all, DNA gets replicated to form new DNA  it then gets transcribed into RNA  the RNA then gets translated into proteins

41. Section 12-4:
Mutations

42. Mutations are changes in the genetic material
There are 2 main classifications of mutations; gene mutations and chromosome mutations

43. Gene mutations are mutations in just a single gene
Point mutations involve changes in just one or a few nucleotides
Substitutions happen when one nucleotide is swapped for another  this usually only effects one amino acid

44. Frameshift mutations shift the reading frame of the nucleotides  this affects any amino acids after the mutation
Insertions happen when one nucleotide is inserted in the wrong place
Deletions happen when a nucleotide is deleted

45. Chromosomal mutations involve changes in a number of structures of the chromosome
Deletions – involve the loss of all or part of the chromosome
Duplications – extra parts of the chromosome are made

46. Inversions – parts of the chromosome are reversed
Translocations – part of the chromosome breaks off and attaches to another

47. Some mutations are “neutral” – they don’t cause any change in protein function
Some mutations causes dramatic changes that disrupt normal activity
There are many genetic disorders that are caused by mutations
Harmful mutations are also associated with cancer
Some mutations are beneficial