1. Biology 1 Chapter 8
From DNA to Proteins

2. 8.1 Identifying DNA as the Genetic Material
Griffith’s Experiment
Two types of bacteria injected into mice (S and R)
Only the S type killed the mice.
The R type had no effect.
When the S type was killed with heat before injection, the mice were unaffected.
Only live S bacteria would cause the mice to die.

3. When he injected the mice with a combination of heat killed S bacteria and live R bacteria, the mice died.
When the blood of the mice was tested, he found live S bacteria.
He concluded that some of the material from the S bacteria must have been transferred to the R bacteria causing it to become harmful.
He called this material the transforming material.

5. Avery’s Experiment
Combined living R bacteria with an extract made from S bacteria.
Directly observed the transformation of R bacteria into S bacteria.
He developed a process to purify the extract.
Performed a series of tests to find out if the transforming principle was DNA or protein.

6. Test results:
Chemical tests showed no proteins but DNA was present
The elements found match those found in DNA not proteins.
Enzymes were added that can break down proteins, RNA, and DNA. The only molecule that broke down was DNA.
Avery concluded that DNA is the transforming material or genetic material.

7. Hershey and Chase Experiment
Studied bacteriophages which are viruses that infect bacteria.
By discovering which part of the phage entered the bacteria (the DNA or protein coat), they could determine which was the genetic material.
They grew phages in cultures that contained radioactive isotopes of sulfur (proteins) and phosphorus (DNA).

8. First Experiment
Bacteria infected with phages that had radioactive sulfur
The bacteria were separated from the phages
The bacteria had no radioactivity
Second Experiment
Bacteria infected with phages that had radioactive phosphorus
Radioactivity was present in the bacteria

9. The results of Hershey and Chase experiment showed that the genetic material in organisms is DNA and not proteins.

11. 8.2 Structure of DNA
DNA is a very long polymer which is a chain of repeating units.
The small units that make up DNA are called nucleotides.
Each nucleotide has 3 parts:
A phosphate group
Deoxyribose (a ring shaped sugar)
A nitrogen containing base

12. One molecule of DNA contains billions of nucleotides.
There are only 4 types of nucleotides in DNA.
Each nucleotide has a different nitrogen base.
The 4 nitrogen bases
Cytosine (C) – pyrimidine (single ring)
Thymine (T) – pyrimidine (single ring)
Adenine (A) – purine (double ring)
Guanine (G) – purine (double ring)

14. For a long time, scientists believed that DNA was made up of equal amounts of the four nucleotides.
This would make the DNA in all organisms exactly the same.
This was the reason that it was hard to convince scientists that DNA was the genetic material.

15. Erwin Chargaff experiment
The same four bases are found in the DNA of all organisms.
The proportion of the four bases is different in each type of organism.
In DNA, the amount of adenine is equal to the amount of thymine.
The amount of cytosine is equal to the amount of guanine.
Chargaff’s rule: A=T and C=G

16. James Watson and Francis Crick developed the first accurate model of DNA.
Linus Pauling was a biochemist that discovered that the structure of some proteins was a helix or spiral.
Watson and Crick hypothesized that DNA might also be a helix.

17. At the same time that Watson and Crick were doing their work, other scientists were studying DNA.
Rosalind Franklin and Maurice Wilkins were studying DNA using a technique called x-ray crystallography.
When DNA is bombarded with x-rays, the atoms in the DNA diffract the x-rays in a pattern that can be captured on film.

18. Franklin’s photographs showed an X surrounded by a circle.
This data gave Watson and Crick the clues they needed to determine the shape of DNA.
DNA is a helix consisting of 2 strands.

19. Watson and Crick made models to figure out the structure of DNA.
Their model had the sugar phosphate backbone on the outside and the bases on the inside.
Watson and Crick found that if they paired a double ringed nucleotide with a single ringed nucleotide, the bases fit together like a puzzle.

20. The Watson and Crick model was a double helix.
A double helix has 2 strands of DNA wound around each other like a twisted ladder.
The strands fit together and are opposite of each other.
The pairing of bases in their model explained Chargaff’s findings.

22. The nucleotides in a strand of DNA are joined together by covalent bonds.
The bonds connect the sugars of one nucleotide with the phosphate of the next nucleotide.
The alternating sugars and phosphates form the sides of the double helix.
The double helix is held together by hydrogen bonds between the bases in the middle.
Individually hydrogen bonds are weak but together they hold the DNA together.

23. The bases in DNA always pair up the same way.
Base pairing rules:
A always pairs with T
C always pairs with G
The bases always pair this way because of their sizes and hydrogen bonds
There are 2 hydrogen bonds between A and T
There are 3 hydrogen bonds between C and G

25. 8.3 DNA Replication
A single DNA strand can serve as a template for a new strand.
The process by which DNA is copied is called replication.
Replication assures that every cell has a complete set of identical genetic information.
DNA is divided into the 46 chromosomes found in each of your cells.
DNA is replicated during the S phase of the cell cycle

26. Enzymes and other proteins actually do the work of DNA replication.
The enzyme helicase unzips the DNA double helix to separate the strands of DNA.
Enzymes called DNA polymerases bond new nucleotides to the separated DNA strands.

27. DNA replication
Step 1
Enzymes unzip the double helix
Hydrogen bonds between base pairs are broken
Unzipping occurs in 2 directions

28. Step 2
DNA polymerases bond free nucleotides with the exposed strands of DNA.
DNA replication does not occur in the same way on both strands.
On one strand, replication is smooth and continuous. This is called the leading strand
On the other strand, replication is discontinuous and piece-by-piece. This is called the lagging strand.

29. Step 3
The result is 2 identical strands of DNA
Each new DNA molecule has one original strand and one new strand.
This type of replication is called semiconservative.

31. DNA replication is very fast in humans.
50 nucleotides added every second to a new strand of DNA
There are hundreds of origins of replication along each chromosome.
Because of this, DNA replication on a chromosome only takes a few hours.
DNA polymerase also acts as a proofreader which can remove the incorrect nucleotide and replace it with the correct one. This method is very accurate.

32. 8.4 Transcription The central dogma of molecular biology:
Information flows in one direction:
DNA RNA proteins
Central dogma 3 processes:
Replication: copies DNA
Transcription: converts message from DNA to RNA
Translation: interprets RNA message into a string of amino acids

33. In prokaryotes, all of the processes occur in the cytoplasm.
In eukaryotes, replication and transcription occur in the nucleus and translation occurs in the cytoplasm.

34. RNA stands for ribonucleic acid.
RNA has the same three structural parts as DNA.
RNA is a temporary copy of DNA that is used and then destroyed.

35. RNA differs from DNA in 3 ways:
The sugar in RNA is ribose (one extra oxygen)
RNA has the base uracil in place of thymine
It binds to adenine just like thymine does
RNA is a single strand which allows it to form certain shapes and catalyze reactions.

36. DNA – RNA Comparison

37. Transcription is the process of copying a sequence of DNA to produce a complementary strand of RNA.
During transcription, a gene (not the entire chromosome) is transferred into an RNA message.
Transcription is catalyzed by an enzyme called RNA polymerase which bonds nucleotides together to form an RNA molecule.

38. Steps of transcription
RNA polymerase recognizes the start site of a gene
A transcription complex consisting of the polymerase and other proteins begins to unwind a segment of DNA
Step 2
RNA polymerase strings together a strand of RNA nucleotides
The RNA strand hangs freely and the DNA zips back together.
Step 3
The RNA strand detaches once the entire gene has been transcribed.

40. Transcription produces 3 types of RNA.
Most of these play a role in translation.
Messenger (mRNA): message to form a protein
Ribosomal (rRNA): forms ribosomes
Transfer (tRNA): brings amino acids to a ribosome to make proteins.

41. Transcription and replication are very similar:
Occur in the nucleus
Catalyzed by enzymes
Unwinding of DNA double helix
Base pairing
Highly regulated

42. Differences between transcription and replication:
ensures that each new cell will have a complete set of genetic material.
The double stranded structure of DNA helps protect the DNA
only happens once during the cell cycle.

43. Transcription
Can adapt to changing demands
Makes a single strand of only a segment of DNA
Occurs only when needed.
Can occur multiple times at the site of a gene

44. 8.5 Translation
Translation is the process the converts an mRNA message into a polypeptide or protein.
RNA uses four nucleotides (A,U,C,G)
These four nucleotides combine in different combinations to code for 20 different amino acids.
Amino acids link together to form proteins.

45. A codon is a 3-nucleotide sequence that codes for an amino acid.
Amino acids are coded for by more than one codon.
In most cases, codons that represent the same amino acid share the same first two nucleotides.
Three stop codons signal the end of an amino acid chain.
There is also one start codon that starts translation.

47. For translation to occur correctly, codons must be read in the right order.
Codons are read as a series of three nucleotides. There are no spaces between codons.
The order of codons is called a reading frame.
Changing the reading frame completely changes the resulting protein.
Almost all organisms follow this genetic code.

48. Ribosomes are the site of protein synthesis.
Ribosomes and tRNA molecules are used to translate a codon into an amino acid.
Ribosomes are the site of protein synthesis.
Ribosomes catalyze or speed up the reaction that forms the bonds between amino acids.
Ribosomes have a large and small subunit that fit together and pull the mRNA strand through.
The small subunit holds onto the mRNA
The large subunit holds onto the protein

49. tRNA is used to carry free floating amino acids from the cytoplasm to the ribosome.
The tRNA folds into an “L” shape.
One end is attached to an amino acid
The other end is called anticodon and recognizes a specific codon
An anticodon is a set of 3 nucleotides that is complementary to an mRNA codon.

50. Translation happens in the cytoplasm of the cell and takes a lot of energy.
Before translation can begin, a small ribosomal subunit must bind to an mRNA strand in the cytoplasm.
A tRNA with methionine (start) binds to the AUG start codon.
A large ribosomal subunit joins the small subunit.

51. The ribosome pulls the mRNA strand through one codon at a time.
The exposed codon attracts a tRNA molecule that has an attached amino acid.
As the strand moves, each codon and its tRNA molecule shift into the next site.
The shift leaves the first site empty which exposes the next mRNA codon.
A peptide bond forms between amino acids. The tRNA leaves the ribosome and attaches to another amino acid.

53. 8.6 Gene Expression and Regulation
Gene expression in prokaryotic cells such as bacteria is regulated at the start of transcription.
The regulation of gene expression allows an organism to respond to stimuli and conserve energy and materials.
A gene includes a protein coding sequence and other nucleotides that play a part in controlling expression.

54. The start of transcription is controlled by sequences of nucleotides called promoters and operators.
A promoter is a segment of DNA that allows a gene to be transcribed.
Promoters help RNA polymerase find where a gene starts.
An operator is a DNA segment that turns a gene on or off by either increasing the rate of transcription or blocking transcription.

55. Prokaryotes have a lot less DNA than eukaryotes.
The genes of prokaryotes such as bacteria are organized into operons.
An operon is a region of DNA that includes:
A promoter
An operator
One or more genes that code for the proteins that do a specific task.

56. The lac operon was one of the first examples of gene regulation discovered.
The lac operon has 3 genes that code for enzymes that play a role in breaking down the sugar lactose.
The genes are transcribed as a single mRNA strand
The genes are all under the control of one promoter and one operator.

57. The lac operon is turned on and off like a switch.
When lactose is absent, the lac operon is switched off to prevent transcription and save resources.
When lactose is present, the lac operon is switched on and transcription.

58. Bacteria have proteins called repressors that can bind to the operator.
When lactose is absent, the repressor binds to the operator which blocks RNA polymerase and transcription does not occur.
When lactose is present, it binds to the repressor.
This causes the repressor to change shape and fall off of the lac operon.
RNA polymerase transcribes the genes and enzymes are formed that break down lactose.

59. Lactose Absent
Lactose Present

60. Eukaryotes have many different types of cells.
Every cell has the same set of DNA
Cells are different from each other because different sets of genes are expressed.
Eukaryotic cells control gene expression at many different points.
The most highly regulated step is at the start of transcription.

61. In eukaryotic cells RNA processing includes removing extra nucleotide segments from the mRNA transcript.
The start of transcription is controlled by regulatory DNA and proteins called transcription factors.
Regulatory DNA sequences are recognized by transcription factors and help RNA polymerase know where a gene starts.

62. DNA can change shape to bring sequences closer together.
Most eukaryotic cells have a promoter called a TATA box.
Eukaryotic cells also have more specific promoters.
DNA sequences called enhancers and silencers that can speed up or slow down the rate of transcription.
Some genes control the expression of other genes which can play a role in development.

64. mRNA that is produced by transcription is similar to a rough cut of film that needs editing.
A specialized nucleotide is added to the beginning of each mRNA molecule that forms a cap.
This cap helps the mRNA strand bind to the ribosome and prevents it from being broken down too fast.
The end of the mRNA gets a string of nucleotides called a tail that helps the mRNA leave the nucleus.

65. Exons are nucleotide segments that code for part of a protein.
Introns are segments that occur between exons.
Introns are removed from mRNA before it leaves the nucleus.
The exons are joined together.
Introns can regulate gene expression or protect the DNA.
Introns increase genetic diversity.

67. 8.7 Mutations A mutation is a change in an organism’s DNA.
Mutations that affect a single gene happen during replication.
Mutations that affect a group of genes happen during meiosis.
A point mutation occurs when one nucleotide is substituted for another.
A frameshift mutation involves a nucleotide being added or deleted.

69. Chromosome mutations occur when chromosomes do not line up with each other during meiosis.
When crossing over happens, segments can be different sizes because of a different number of genes. This is called gene duplication.
Translocation occurs when a piece of one chromosome moves to a nonhomologous chromosome.

71. Chromosome mutations affect a lot of genes.
A mutation can break up a gene and make it no longer work.
It could make a new hybrid gene with different functions.
Translocated genes can come under the control of a new set of promoters which can affect the activity of the gene.

72. Gene mutations affect coding regions of DNA.
These types of mutations will affect the proteins made which could affect the activity of enzymes.
Mutations can disrupt an mRNA site which could prevent an intron from being removed.
Mutations can keep proteins from being produced.

73. Many gene mutations do not effect an organisms phenotype.
Some substitutions have no effect if the same amino acid is produced.
If the same amino acid is produced then the same protein will be produced.
A mutation that does not affect a protein is called silent.
Proteins may remain the same size or be far away from an active site.

74. Mutations that occur in germ cells can be passed on to offspring.
These mutations are the source of genetic variation.
Mutations to germ cells affect the phenotype of offspring.
Often this effect is harmful.
Rarely, a mutation results in a more beneficial phenotype.

75. While DNA polymerase does have a built in proofreading function, a small number of replication errors are not fixed.
Over time these errors build up and affect how the cell works.
Mutagens are agents in the environment that can change DNA.
Mutagens speed up the rate of replication errors can even break DNA strands.

76. Some mutagens occur naturally such as UV radiation.
Some mutagens are industrial chemicals.
The human body has DNA repair enzymes that help find and fix mutations.
Enzymes can remove damaged DNA and replace it.
If mistakes interfere with regulatory sites and control mechanisms they may result in cancer.