1. CHAPTER 10
PROTEIN SYNTHESIS

2. DNA

3. The primary function of DNA in organisms is:
to store and transmit the genetic information that tells cells which proteins to make and when to make them

4. REVIEW STRUCTURE OF DNA
A DNA molecule consists of 2 long chains of nucleotides
Each nucleotide has:
- a sugar molecule called DEOXYRIBOSE
- a phosphate group
- a nitrogen-containing base
The sugar and phosphate groups are identical in all DNA molecules, but nitrogen bases differ

5. Nitrogen bases can be:
Adenine
Guanine
Cytosine
Thymine
- these are abbreviated A,G,C,T

6. - Adenine and guanine have 2 rings of carbon and nitrogen atoms, and are called PURINES
- Cytosine and thymine have only 1 ring of carbon and are called PYRIMIDINES

7. In 1953, James Watson and Francis Crick came up with a model for DNA called the DOUBLE HELIX
- 2 nucleotide chains wrap around each other to form a double spiral
- individual nucleotides are connected by covalent bonds between the sugar and phosphate

8. - alternating sugar and phosphate molecules form a backbone that the nitrogen-containing bases attach to
- the nitrogen-containing bases face toward the center of the helix
- bases on one DNA chain face the bases on the other DNA chain and form HYDROGEN BONDS with each other

9. RECALL:
- hydrogen bonds are different from covalent and ionic bonds
- hydrogen bonds are weak bonds that form between molecules
- in DNA, hydrogen bonds form between hydrogen, and either oxygen or nitrogen
- the most common form of DNA found in living organisms has a right-hand twist and 10 base pairs per turn

10. BASE PAIRING
Nitrogen bases only pair up with COMPLEMENTARY BASE PAIRS:
- cytosine pairs with guanine, and adenine pairs with thymine
- these make up 2 rules called the BASE-PAIRING RULES and describe the pairing behavior of the bases

11. - complementary base pairs are connected by hydrogen bonds
- the nucleotide sequence in one chain of the DNA molecule is the exact complement of the nucleotide sequence in the other chain
- it is important for DNA to make exact copies of itself because cells must pass exact copies of their DNA to their offspring cells

12. DNA REPLICATION REPLICATION- the process of copying DNA in a cell
- the 2 nucleotide chains of a DNA molecule separate, and each chain serves as a “master” to make a new nucleotide chain
STEPS IN DNA REPLICATION
1. Separation of the 2 nucleotide chains
- the point where the 2 chains separate is called the REPLICATION FORK

13. - the chains are separated by enzymes called HELICASES
- the helicase enzymes move along the DNA molecule breaking hydrogen bonds between nitrogen bases
2. New chains of DNA are assembled
- enzymes called DNA POLYMERASES bind to the separated chains of DNA

14. - as DNA polymerases move along the separated chains, new chains of DNA are assembled using the surrounding medium
- these chains are complementary to the existing DNA chains

15. The complementary nature of the chains of DNA is the key to accurate DNA replication
- if the sequence in the original DNA molecule is A-T-C-G-A-C-C-G-T-T, what would the new chain look like?
T-A-G-C-T-G-G-C-A-A
- replication does not begin at one end of the DNA molecule and go to the other end

16. - DNA polymerases begin replication simultaneously at many points along the separated nucleotides
- this allows for faster replication
- at the completion of replication, 2 new exact copies of DNA are produced

17. HOW ACCURATE IS REPLICATION?
DNA replication occurs with only about 1 error in every 10,000 paired nucleotides
- a MUTATION is a change in the nucleotide sequence  may lead to serious effects in new cells
Cells have a backup system:
- enzymes proofread and repair errors in DNA
- if noncomplementary bases are paired, this can be recognized and repaired

18. Some errors do still occur
- DNA can also be damaged by chemicals and ultraviolet radiation

19. RNA

20. The primary function of RNA in organisms is to move genetic information from the DNA in the nucleus to the site of protein synthesis in the cytosol

21. STRUCTURE OF RNA RECALL:
- RNA is also made up of repeating nucleotides
- the sugar molecule in RNA is RIBOSE
- in RNA, the nitrogen base URACIL replaces thymine  pairs with adenine

22. TYPES OF RNA There are 3 types of RNA:
1. MESSENGER RNA (mRNA)- consists of RNA nucleotides in a single uncoiled chain
- carries genetic information from the DNA in the nucleus to the cytosol of a eukaryotic cell
2. TRANSFER RNA (tRNA)- consists of a single chain of RNA nucleotides folded into a “T” shape
- binds to specific amino acids

23. 3. RIBOSOMAL RNA (rRNA)- most abundant form
- consists of RNA nucleotides in a globular, 3-dimensional form
- along with proteins, makes up the ribosomes where proteins are made

24. TRANSCRIPTION
TRANSCRIPTION- process by which genetic information is copied from DNA to RNA
STEPS OF TRANSCRIPTION
1. RNA polymerase (primary transcription enzyme) makes RNA copies of certain sequences of DNA
- RNA polymerase begins transcription by binding to specific regions of DNA called PROMOTERS

25. - these promoters mark the beginning of the DNA chain that will be transcribed
- when RNA polymerase binds to a promoter, the DNA molecule in that region separates
- only one of the separated chains (called the template) is used for transcription

26. 2. RNA polymerase attaches to the first DNA nucleotide of the template
- it begins adding complementary RNA nucleotides to a newly forming RNA molecule
- complementary base-pairing determine the sequence of RNA nucleotides
3. Transcription continues until RNA polymerase reaches a region of DNA called the TERMINATION SIGNAL

27. - this sequence of nucleotides marks the end of transcription
- RNA polymerase releases both the DNA molecule and the new RNA molecule
- all 3 types of RNA are transcribed this way and are involved in protein synthesis
- after transcription, mRNA will move through the nuclear pores and into the cytosol

28. PROTEIN SYNTHESIS

29. PROTEIN SYNTHESIS- the production of proteins
- the amount and kind of proteins that are produced in a cell determine the structure and function of the cell
- proteins carry out the genetic instructions of DNA

30. PROTEIN STRUCTURE RECALL: Proteins are made up of polypeptides
- each polypeptide consists of a chain of amino acids linked together by peptide bonds
- there are 20 different amino acids that make up polypeptides
- the sequence of amino acids determines how polypeptides fold into a 3-D protein

31. GENETIC CODE- relationship between a nucleotide sequence and an amino acid sequence
- the genetic information necessary for making proteins is encoded in a series of three mRNA nucleotides
- each combination of 3 nucleotides is called a CODON
- each codon codes for a specific amino acid

32. A few codons do not code for any amino acids
- START CODON (AUG)- signal for translation of an mRNA to start
- STOP CODONS (UAA, UAG, UGA)- signal for translation of a mRNA to stop

33. TRANSLATION
TRANSLATION- process of assembling polypeptides from information encoded in mRNA
- this process begins when mRNA leaves the nucleus through pores in the nuclear envelope
- the mRNA then goes to a ribosome in the cytosol  site of protein synthesis

34. tRNA
- tRNA molecules transport amino acids floating in the cytosol to the ribosome
- opposite the site of amino acid attachment, the tRNA has a sequence of 3 amino acids called an ANTICODON
- this is complementary to an mRNA codon- the mRNA sequence determines the sequence of amino acids

35. RIBOSOMES
- ribosomes are made of rRNA and proteins
- they can be free in the cytosol or attached to the ER
- ribosomes that are free in the cytosol are those that will make proteins that are used in the cell

36. - ribosomes have special binding sites:
* one holds an mRNA
* the other 2 hold tRNAs

37. STEPS OF PROTEIN ASSEMBLY
1. The ribosome attaches to the start codon (AUG) on a mRNA  the start codon codes for the amino acid methionine, so this is the first amino acid in the polypeptide
2. The ribosome continues to move along the mRNA and pair the mRNA codon with a tRNA anticodon

38. - this causes a specific amino acid to attach to the previous amino acid with a covalent bond called a peptide bond
3. Eventually the ribosome reaches a stop codon on the mRNA and translation stops
- the mRNA is released from the ribosome, and the polypeptide is complete

39. There may be several ribosomes translating the same mRNA molecule
The polypeptide chain will fold and become a functional protein

40. CHAPTER 11
GENE EXPRESSION

41. CONTROL OF GENE EXPRESSION
Cells use information in genes to make hundreds of proteins, each with a unique function
- not all proteins are needed by the cell at the same time
- cells can regulate which genes are expressed, so then they can control when each protein is made

42. GENE EXPRESSION- activation of a gene that results in the formation of a protein
- a gene is said to be “expressed” or turned “on” when transcription occurs
- the complete genomic material contained in an individual is called the GENOME
- by regulating gene expression, cells are able to control which portion of the genome will be expressed and when

43. GENE EXPRESSION IN PROKARYOTES
Gene expression occurs in 2 steps  TRANSCRIPTION AND TRANSLATION
FRANCOIS JACOB and JACQUES MONOD
- French scientists that discovered how genes control the metabolism of the sugar lactose in E. coli, a bacterium that lives in the human intestines

44. When you drink cow’s milk, the presence of lactose stimulates E
When you drink cow’s milk, the presence of lactose stimulates E. coli (in your intestines) to produce 3 enzymes
- these enzymes control metabolism of lactose, and they are located next to each other on a chromosome

45. The production of these enzymes is controlled by:
1. Structural genes- genes that code for particular polypeptides (proteins and enzymes)
2. Promoter- a DNA segment that recognizes RNA polymerase and starts transcription

46. 3. Operator- a DNA segment that serves as a binding site for an inhibitory protein that blocks transcription and prevents protein synthesis from occurring
- all 3 of these together make up an OPERON
- Jacob and Monod named the operon that they studied the lac operon, because its genes coded for the enzymes that regulate lactose metabolism

47. Jacob and Monod found that the genes for these enzymes were expressed ONLY when lactose was present
- how could the bacteria “shut off” these genes when there was no lactose?
- they found that gene expression shows 2 forms: REPRESSION, AND ACTIVATION

48. REPRESSION When there is no lactose:
- a protein called a repressor attaches to the operator
- this protein inhibits a specific gene from being expressed
- the protein “blocks” RNA polymerase from binding to the structural genes, and transcription cannot occur
- this is called REPRESSION

49. - transcription is controlled by a REGULATOR GENE that codes for the production of the repressor protein

50. ACTIVATION When lactose is present:
- lactose binds to the repressor protein on the operator, and removes it
- this allows RNA polymerase to transcribe the structural genes of the lac operon
- all 3 genes are “turned on”
- because it activates, or induces, transcription, lactose acts as an INDUCER- a molecule that begins gene expression

51. GENE EXPRESSION IN EUKARYOTES
Eukaryotes are much different from bacteria
- their genomes are much larger
- they have many different cell types, all of which produce many different proteins
- operons have not been found in eukaryotes

52. Much control of gene expression in eukaryotes occurs at the level of the chromosome
- after mitosis or meiosis, certain regions of DNA relax, making transcription possible
- some regions remain coiled though, so their genes cannot be transcribed

53. As in prokaryotes (bacteria), the promoter is the binding site of RNA polymerase
- in eukaryotes, there are 2 kinds of segments beyond the promoter: INTRONS and EXONS
INTRONS- sections of a structural gene that do not code for amino acids; are not translated into proteins
EXONS- sections that are translated into proteins

54. Eukaryotes can control gene expression by modifying RNA after transcription
- when transcription occurs, both introns and exons are transcribed
- this forms a large molecule called pre-mRNA
- a molecule of mRNA is formed after the introns are removed, and the remaining exons are spliced together

55. - this mRNA is what leaves the nucleus and enters the cytoplasm to begin the making of a protein on the ribosomes

56. CANCER
TUMOR- an abnormal growth of cells that results from uncontrolled, abnormal cell division
- cells of a BENIGN tumor remain within a mass, and usually are not life-threatening
- in a MALIGNANT tumor, uncontrolled dividing cells invade and destroy healthy tissues elsewhere in the body

57. - malignant tumors are commonly called CANCER
- METASTASIS is the spread of cancer cells beyond their original site
KINDS OF CANCER
- malignant tumors are categorized by the types of tissues they affect:
CARCINOMAS- grow in skin and the tissues that line organs of the body
Ex: lung and breast cancer

58. SARCOMAS- grow in bone and muscle tissue
LYMPHOMAS- grow in tissues that form blood cells
Ex: leukemia is caused by the uncontrolled production of white blood cells

59. WHAT CAUSES CANCER?
In normal cells, cell division is controlled by certain genes
- these genes code for GROWTH FACTORS, regulatory proteins that ensure that cell division occurs normally
- mutations that alter the expression of these genes can lead to cancer

60. These mutations can occur spontaneously, but often occur because of exposure to carcinogens
CARCINOGEN- any substance that increases the risk of cancer
Tobacco
Asbestos
X-rays
UV light (from sun)

61. Whether a person will develop cancer or not depends on many factors:
- possibly caused by genetics
- number of exposures to carcinogens
Usually more than one mutation is needed to produce a cancer cell
- cancer risk increases with age
- the longer a person lives, the more mutations they will accumulate