1. Chapter 25: Molecular Basis of Inheritance

2. DNA Structure and Replication
In the mid-1900s, scientists knew that chromosomes, made up of DNA (deoxyribonucleic acid) and proteins, contained genetic information.
However, they did not know whether the DNA or the proteins was the actual genetic material.

3. Various reseachers showed that DNA was the genetic material when they performed an experiment with a T2 virus.
By using different radioactively labeled components, they demonstrated that only the virus DNA entered a bacterium to take over the cell and produce new viruses.

4. Viral DNA is labeled
In the first experiment, phage (viral) DNA was labeled with radioactive 32P. The phage was allowed to attach to and inject its genetic material into E. coli cells. Then the culture was agitated to remove the remaining phage material outside the bacterial cells. In this experiment, investigators found most of the 32P-labeled DNA in the cells and not in the liquid medium.

5. Viral capsid is labeled
In the second experiment, phage protein in capsids was labeled with 35S. The phages were allowed to inject their genetic material into E. coli bacterial cells. Scientists this time found the 35S-labeled protein in the liquid medium and not in the bacterial cells and concluded protein was not the genetic material.

6. Structure of DNA
The structure of DNA was determined by James Watson and Francis Crick in the early 1950s.
DNA is a polynucleotide; nucleotides are composed of a phosphate, a sugar, and a nitrogen-containing base.
DNA has the sugar deoxyribose and four different bases: adenine (A), thymine (T), guanine (G), and cytosine (C).
The two purine bases (adenine and guanine) have a double ring; the two pyrimidine bases (cytosine and thymine) have a single ring.

7. One pair of bases
Notice that the 3’ and 5’ refer to a numbering system for the carbon atoms that make up the sugar.

8. Watson and Crick showed that DNA is a double helix in which A is paired with T and G is paired with C.
This is called complementary base pairing because a purine is always paired with a pyrimidine.

9. When the DNA double helix unwinds, it resembles a ladder.
The sides of the ladder are the sugar-phosphate backbones, and the rungs of the ladder are the complementary paired bases.
The two DNA strands are anti-parallel – they run in opposite directions.

10. DNA double helix
On the left is the DNA double helix. When the helix is unwound, a ladder configuration shows that the uprights are composed of sugar and phosphate molecules and the rungs are complementary bases. Notice that the bases in DNA pair in such a way that the phosphate-sugar groups are oriented in different directions. This means that the strands of DNA end up running antiparallel to one another, with the 3’ end of one strand opposite the 5’ end of the other strand.

11. Replication of DNA
DNA replication occurs during chromosome duplication; an exact copy of the DNA is produced with the aid of DNA polymerase.
Hydrogen bonds between bases break and enzymes “unzip” the molecule.
Each old strand of nucleotides serves as a template for each new strand.
DNA polymerase is an enzyme.

12. New nucleotides move into complementary positions are joined by DNA polymerase.
The process is semiconservative because each new double helix is composed of an old strand of nucleotides from the parent molecule and one newly-formed strand.
Some cancer treatments are aimed at stopping DNA replication in rapidly-dividing cancer cells.

13. Overview of DNA replication
Replication is called semiconservative because each new double helix is composed of an old (parental) strand and a new (daughter) strand.

14. Ladder configuration and DNA replication
Use of the ladder configuration better illustrates how complementary nucleotides available in the cell pair with those of each old strand before they are joined together to form a daughter strand.

15. Gene Expression
A gene is a segment of DNA that specifies the amino acid sequence of a protein.
Gene expression occurs when gene activity leads to a protein product in the cell.
A gene does not directly control protein synthesis; instead, it passes its genetic information on to RNA, which is more directly involved in protein synthesis.

16. RNA
RNA (ribonucleic acid) is a single-stranded nucleic acid in which A pairs with U (uracil) while G pairs with C.
Three types of RNA are involved in gene expression: messenger RNA (mRNA) carries genetic information to the ribosomes, ribosomal RNA (rRNA) is found in the ribosomes, and transfer RNA (tRNA) transfers amino acids to the ribosomes, where the protein product is synthesized.

17. Structure of RNA
Like DNA, RNA is a polymer of nucleotides. In an RNA nucleotide, the sugar ribose is attached to a phosphate molecule and to a base, either G, U, A, or C. Notice that in RNA, the base uracil replaces thymine as one of the pyrimidine bases. RNA is single-stranded, whereas DNA is double-stranded.

18. Two processes are involved in the synthesis of proteins in the cell:
Transcription makes an RNA molecule complementary to a portion of DNA.
Translation occurs when the sequence of bases of mRNA directs the sequence of amino acids in a polypeptide.

19. The Genetic Code
DNA specifies the synthesis of proteins because it contains a triplet code: every three bases stand for one amino acid.
Each three-letter unit of an mRNA molecule is called a codon.
Most amino acids have more than one codon; there are 20 amino acids with a possible 64 different triplets.
The code is nearly universal among living organisms.
The fact that the genetic code is about universal in living things suggests that the code dates back to the first organisms on earth and that all living things are related.

20. Messenger RNA codons
Notice that in this chart, each of the codons (white rectangles) is composed of three letters representing the first base, second base, and third base. For example, find the rectangle where C for the first base and A for the second base intersect. You will see that U, C, A, or G can be the third base. CAU and CAC are codons for histidine; CAA and CAG are codons for glutamine.

21. Central Concept
The central concept of genetics involves the DNA-to-protein sequence involving transcription and translation.
DNA has a sequence of bases that is transcribed into a sequence of bases in mRNA.
Every three bases is a codon that stands for a particular amino acid.

22. Overview of gene expression
Transcription occurs when DNA acts as a template for mRNA synthesis. Translation occurs when the sequence of the mRNA codons determines the sequence of amino acids in a protein.

23. Transcription
During transcription in the nucleus, a segment of DNA unwinds and unzips, and the DNA serves as a template for mRNA formation.
RNA polymerase joins the RNA nucleotides so that the codons in mRNA are complementary to the triplet code in DNA.

24. Transcription and mRNA synthesis
During transcription, complementary RNA is made from a DNA template. A portion of DNA unwinds and unzips at the point of attachment of RNA polymerase. A strand of mRNA is produced when complementary bases join in the order dictated by the sequence of bases in DNA. Transcription occurs in the nucleus, and the mRNA passes out of the nucleus to enter the cytoplasm.

25. Processing of mRNA DNA contains exons and introns.
Before mRNA leaves the nucleus, it is processed and the introns are excised so that only the exons are expressed.
The splicing of mRNA is done by ribozymes, organic catalysts composed of RNA, not protein.
Primary mRNA is processed into mature mRNA.
Introns are intragene sequences that are not expressed; exons are the portions of a gene that are expressed. Only exons result in a protein product.
Alternative splicing, that occurs particularly during development, produces different mRNA molecules.

26. Function of introns
Introns allow alternative splicing and therefore the production of different versions of mature mRNA from the same gene.

27. Translation
Translation is the second step by which gene expression leads to protein synthesis.
During translation, the sequence of codons in mRNA specifies the order of amino acids in a protein.
Translation requires several enzymes and two other types of RNA: transfer RNA and ribosomal RNA.

28. Transfer RNA
During translation, transfer RNA (tRNA) molecules attach to their own particular amino acid and travel to a ribosome.
Through complementary base pairing between anticodons of tRNA and codons of mRNA, the sequence of tRNAs and their amino acids form the sequence of the polypeptide.

29. Transfer RNA: amino acid carrier
A tRNA is a polynucleotide that folds into a bootlike shape because of complementary base pairing. At one end of the molecule is its specific anticodon – in this case UCG; at the other end an amino acid attaches that corresponds to this anticodon – in this case serine.

30. Ribosomal RNA
Ribosomal RNA, also called structural RNA, is made in the nucleolus.
Proteins made in the cytoplasm move into the nucleus and join with ribosomal RNA to form the subunits of ribosomes.
A large subunit and small subunit of a ribosome leave the nucleus and join in the cytoplasm to form a ribosome just prior to protein synthesis.

31. A ribosome has a binding site for mRNA as well as binding sites for two tRNA molecules at a time.
As the ribosome moves down the mRNA molecule, new tRNAs arrive, and a polypeptide forms and grows longer.
Translation terminates once the polypeptide is fully formed; the ribosome separates into two subunits and falls off the mRNA.
Several ribosomes may attach and translate the same mRNA, therefore the name polyribosome.

32. Polyribosome structure and function
At the top is a side view of a ribosome that shows the positioning of mRNA and the growing protein. In the middle is the frontal view of a ribosome. Finally, several ribosomes, collectively called a polyribosome, move along an mRNA at one time. Therefore, several proteins can be made at the same time.

33. Translation Requires Three Steps
During translation, the codons of an mRNA base-pair with tRNA anticodons.
Protein translation requires these steps:
Chain initiation
Chain elongation
Chain termination.
Enzymes are required for each step, and the first two steps require energy.

34. Chain Initiation
During chain initiation, a small ribosomal subunit, the mRNA, an initiator tRNA, and a large ribosomal unit bind together.
First, a small ribosomal subunit attaches to the mRNA near the start codon.
The anticodon of tRNA, called the initiator RNA, pairs with this codon.
Then the large ribosomal subunit joins.

35. Initiation
During initiation, a small ribosomal subunit binds to mRNA; an initiator tRNA with the anticodon UAC pairs with the codon AUG.
The large ribosomal subunit completes the ribosome. Initiator tRNA occupies the first binding site. The second binding site is ready for the next tRNA.

36. Chain Elongation
During chain elongation, the initiator tRNA passes its amino acid to a tRNA-amino acid complex that has come to the second binding site.
The ribosome moves forward and the tRNA at the second binding site is now at the first site, a sequence called translocation.
The previous tRNA leaves the ribosome and picks up another amino acid before returning.

37. Elongation
First, a tRNA-amino acid approaches the second binding site of the ribosome.
Second, two tRNAs can be at the ribosome at one time; the anticodons are paired to the codons.
Third, as the initiator tRNA leaves the first binding site, its amino acid is passed to the resident tRNA-amino acid complex.
Finally, the ribosome has moved forward, making room for the next incoming tRNA-amino acid complex.

38. Chain Termination
Chain termination occurs when a stop-codon sequence is reached.
The polypeptide is enzymatically cleaved from the last tRNA by a release factor, and the ribosome falls away from the mRNA molecule.
A newly synthesized polypeptide may function along or become part of a protein.

39. Termination The ribosome comes to a stop codon on the mRNA.
Protein synthesis ceases as ribosomal subunits dissociate. The completed polypeptide, the last tRNA, and the mRNA molecule are released.

40. Review of Gene Expression
DNA in the nucleus contains a triplet code; each group of three bases stands for one amino acid.
During transcription, an mRNA copy of the DNA template is made.
The mRNA is processed before leaving the nucleus.
The mRNA joins with a ribosome, where tRNA carries the amino acids into position during translation.

41. Gene expression
Gene expression leads to the formation of a product, most often a protein. The two steps required for gene expression are translation, which occurs in the nucleus, and translation, which occurs in the cytoplasm at the ribosomes.
One DNA strand serves as a template.
mRNA is processed before leaving the nucleus.
mRNA moves into the cytoplasm and becomes associated with ribosomes.
tRNAs with anticodons carry amino acids to the mRNA.
Anticodon-codon complementary base pairing occurs.
The peptide will be transferred to the tRNA-amino acid at the second binding site, and the tRNA at the first binding site will depart; the ribosome then moves forward.

42. Control of Gene Expression
The lac operon model explains how one regulator gene controls the transcription of several structural genes — genes that code for proteins.
The promoter is a short sequence of DNA where RNA polymerase first attaches when a gene is to be transcribed.

43. The operator is a short sequence of DNA where the repressor protein binds to the operator and prevents RNA polymerase from attaching to another portion of DNA called the promoter.
Transcription does not occur until lactose binds to the repressor preventing the repressor from binding to the operator.

44. Now RNA polymerase binds to the operator and brings about transcription of the genes that code for enzymes necessary to lactose metabolism.
Structural genes code for enzymes of a metabolic pathway that are transcribed as a unit.
A regulator gene codes for a repressor that can bind to the operator and switch off the operon; therefore, a regulator gene regulates the activity of structural genes.

45. The lac operon
The regulator gene codes for a repressor protein that is normally active. When active, the repressor protein binds to the operator and prevents RNA polymerase from attaching to the promoter. Therefore, transcription of the three structural genes does not occur.

46. When lactose is present, it binds to the repressor protein, changing its shape so it can no longer bind to the operator. Now RNA polymerase binds to the promoter and the structural genes are expressed.
Thus, these structural proteins (enzymes) are only produced when they are needed to metabolize lactose.

47. Control of Gene Expression in Eukaryotes
In eukaryotes, cells differ in which genes are being expressed.
Levels of control in eukaryotes include:
transcriptional control,
posttranscriptional control,
translational control, and
posttranslational control.
The first two methods occur in the nucleus; the second two, in the cytoplasm.

48. Eukaryotic control of gene expression
Transcriptional and posttranscriptional control occur in the nucleus. Translational and posttranslational control occur in the cytoplasm.

49. Transcriptional Control in Eukaryotes
Rarely are there operons in eukaryotic cells.
Instead, transcriptional control in eukaryotes involves:
The organization of the chromatin, and
Regulator proteins called transcription factors.

50. Activated Chromatin
The existence of chromosome puffs in developing eggs of many vertebrates suggests that DNA must decondense in order for transcription to occur.
The chromosomes within many vertebrate egg cells are called lampbrush chromosomes because they have many decondensed loops; here mRNA is synthesized in great quantity.
This form of transcriptional control is useful when the gene product is tRNA or rRNA.
In larval fly tissues, chromosomes duplicate without the cells dividing mitotically.
This is useful for producing much tRNA or rRNA.

51. Lampbrush chromosomes
These chromosomes, which are present in maturing amphibian egg cells, give evidence that when mRNA is being synthesized, chromosomes most likely decondense. Each chromatid has many loops extended from the axis of the chromosome (white). Many mRNA transcripts are being made from these DNA loops (red).

52. Transcription Factors
Transcription factors regulate transcription of DNA in eukaryotes.
Signals received from inside and outside the cell turn on particular transcription factors.
Activation probably occurs when the transcription factors are phosphorylated by a kinase.
As cells mature, they become specialized. Specialization is determined by which genes are active, and therefore perhaps by which transcription factors are present in that cell.
Kinases are enzymes that add a phosphate group to molecules. Kinases, along with phosphatases, which remove a phosphate group, are known to be signaling proteins involved in growth regulatory pathways.

53. Gene Mutations Frameshift Mutations
A gene mutation is a change in the sequence of bases within a gene.
Frameshift Mutations
Frameshift mutations involve the addition or removal of a base during the formation of mRNA; these change the genetic message by shifting the “reading frame.”

54. Point Mutations
The change of just one nucleotide causing a codon change can cause the wrong amino acid to be inserted in a polypeptide; this is a point mutation.
In a silent mutation, the change in the codon results in the same amino acid.

55. If a codon is changed to a stop codon, the resulting protein may be too short to function; this is a nonsense mutation.
If a point mutation involves the substitution of a different amino acid, the result may be a protein that cannot reach its final shape; this is a missense mutation.
An example is Hbs which causes sickle-cell disease.

56. Sickle-cell disease in humans
Portion of the chain in normal hemoglobin HbA and in sickle-cell hemoglobin HbS. Although the chain is 146 amino acids long, the one change from glutamate to valine in the sixth position results in sickle-cell disease. Glutamate has a polar R group, while valine has a nonpolar R group, and this causes HbS to be less soluble and to precipitate out of solution, distorting the red blood cell into the sickle shape.

57. Cause and Repair of Mutations
Mutations can be spontaneous or caused by environmental influences called mutagens.
Mutagens include radiation (X-rays, UV radiation), and organic chemicals (in cigarette smoke and pesticides).
DNA polymerase proofreads the new strand against the old strand and detects mismatched pairs, reducing mistakes to one in a billion nucleotide pairs replicated.

58. Transposons: Jumping Genes
Transposons are specific DNA sequences that move from place to place within and between chromosomes.
These so-called jumping genes can cause a mutation to occur by altering gene expression.
It is likely all organisms, including humans, have transposons.

59. Cancer: A Failure of Genetic Control
Cancer is a genetic disorder resulting in a tumor, an abnormal mass of cells.
Carcinogenesis, the development of cancer, is a gradual process.
Cancer cells lack differentiation, form tumors, undergo angiogenesis and metastasize.
Cancer cells fail to undergo apoptosis, or programmed cell death.
Cancer may actually take years to develop.
Malignancy is present when metastasis establishes new tumors distant from the primary tumor. Cancer cells produce proteinase enzymes that degrade the basement membrane and allow cancer cells to invade underlying tissues.

60. Cancer cells
Cancer cells differ from normal cells in many ways. Cancer cells exhibit uncontrolled growth, have no contact inhibition, are disorganized and multilayered, nondifferentiated with abnormal nuclei, and do not undergo apoptosis.

61. Angiogenesis is the formation of new blood vessels to bring additional nutrients and oxygen to a tumor; cancer cells stimulate angiogenesis.
Metastasis is invasion of other tissues by establishment of tumors at new sites.
A patient’s prognosis is dependent on the degree to which the cancer has progressed; early diagnosis and treatment is critical to survival.
Prognosis is the probable outcome. Prognosis is dependent on (1) whether the tumor has invaded surrounding tissues, (2) if there is any lymph node involvement, and (3) whether there are metastatic tumors in distant parts of the body.

62. Origin of Cancer
Mutations in at least four classes of genes are associated with the development of cancer.
1) The nucleus has a DNA repair system but mutations in genes for repair enzymes can contribute to cancer.
2) Mutations in genes that code for proteins regulating structure of chromatin can promote cancer.

63. 3) Proto-oncogenes are normal genes that stimulate the cell cycle and tumor-suppressor genes inhibit the cell cycle; mutations can prevent normal regulation of the cell cycle.
4) Telomeres are DNA segments at the ends of chromosomes that normally get shorter and signal an end to cell division; cancer cells have an enzyme that keeps telomeres long.

64. Regulation of Cell Division
Proto-oncogenes are part of a stimulatory pathway that extends from membrane to nucleus.
Tumor-suppressor genes are part of an inhibitory pathway extending from the plasma membrane to the nucleus.
The balance between stimulatory signals and inhibitory signals determines whether proto-oncogenes or tumor-suppressor genes are active.

65. Plasma membrane receptors can receive growth stimulatory factors and growth inhibitory factors.
Cytoplasmic proteins can therefore be turned on or off and in turn either stimulate or inhibit certain genes in the nucleus.

66. Oncogenes
Proto-oncogenes can undergo mutations to become cancer-causing oncogenes.
An oncogene may code for a faulty receptor in the stimulatory pathway.
Or an oncogene may produce either an abnormal protein product or abnormally high levels of a normal protein product that stimulates the cell cycle to begin or to go to completion; both lead to uncontrolled growth.

67. About 100 oncogenes have been discovered that cause increased growth and lead to tumors.
Alteration of a single nucleotide pair can convert a normal rasK proto-oncogene to an oncogene implicated in lung, colon, and pancreatic cancer.
The rasN oncogene is associated with leukemia and lymphoma.

68. Tumor-Suppressor Genes
Tumor-suppressor genes ordinarily suppress the cell cycle; when they mutate they stop suppressing the cell cycle and it can occur nonstop.
RB tumor-suppressor gene malfunctions are implicated in cancers of the breast, prostate, bladder, and small-cell lung carcinoma.

69. Another major tumor-suppressor gene is p53, a gene that is more frequently mutated in human cancers than any other known gene.
The p53 protein acts as a transcription factor and as such is involved in turning on the expression of genes whose products are cell cycle inhibitors.
P53 can also stimulate apoptosis.

70. Causes of cancer
Two types of regulatory pathways extend from the plasma membrane to the nucleus. In the stimulatory pathway, plasma membrane receptors receive growth-stimulatory factors. Then proteins within the cytoplasm and proto-oncogenes within the nucleus stimulate the cell cycle. In the inhibitory pathway, plasma membrane receptors receive growth-inhibitory factors. Then proteins within the cytoplasm and tumor-suppressor genes within the nucleus inhibit the cell cycle from occurring. Whether cell division occurs or not depends on the balance of stimulatory and inhibitory signals received. Hereditary and environmental factors cause mutations of proto-oncogenes and tumor-suppressor genes. These mutations can cause uncontrolled growth and a tumor.
Agents that can bring about the activation of oncogenes and the inactivation of tumor-suppressor genes include heredity, organic chemicals, radiation, and viruses.

71. Chapter Summary
Since DNA is the genetic material, its structure and functions constitute the molecular basis of inheritance.
Because the DNA molecule is able to replicate, genetic information can be passed from one cell generation to the next.
DNA codes for the synthesis of proteins; this process also involves RNA.

72. In prokaryotes, regulator genes control the activity and expression of other genes.
In eukaryotes, the control of gene expression occurs at all stages, from transcription to the activity of proteins.
Gene mutations vary; some have little effect but some have a dramatic effect.
Loss of genetic control over genes involved in cell growth and/or cell division cause cancer.