Chapter 18: Regulation of Gene Expression

Q: How are repressible and inducible operons different?

A: A repressible operon is usually on but can be inhibited when a specific small molecule binds allosterically to a regulatory protein. In contrast, an inducible operon is usually off but can be stimulated when a specific small molecule interacts with a regulatory protein.

Q: What are the three interrelated processes of transformation?

A: Cell division, cell differentiation, and morphogenesis.

Q: What is a maternal effect gene?

A: A gene that when mutant in the mother results in a mutant phenotype in the offspring, regardless of the offspring's own genotype.

1. Bacteria often respond to environmental change by regulating transcription.

2. Eukaryotic gene expression can be regulated at any stage.

3. Noncoding RNAs play multiple roles in controlling gene expression.

4. A program of differential gene expression leads to the different cell types in a multicellular organism.

5. Cancer results from genetic changes that affect cell cycle control.

Figure 18.3

(b) Tryptophan present, repressor active, operon off. As trytophan accumulates, it inhibits its own production by activating the repressor protein, which blinds to the operator, blocking transcription.

Accumulation of trytophan, the end product of the pathway, represses transcription of the trp operon, thus blocking synthesis of all the enzymes in hte pathway.

The controls that act on gene expression are much more complex in eukaryotes than in prokaryotes. In bacteria, genes are clustered into operons: gene clusters that encode the proteins necessary to perform coordinated function.

During normal growth on a glucose-based medium, the lac repressor is bound to the operator region of the lac operon, preventing transcription. However, in the presence of an inducer of the lac operon, the repressor protein binds the inducer and is rendered incapable of interacting with the operator region of the operon.

The trp operon encodes the genes for the synthesis of tryptophan. Since the activity of the trp repressor is enhanced in the presence of tryptophan, the rate of expression of the trp operon is graded in response to the level of tryptophan in the cell.

http://www.youtube.com/watch?v=oBwtxdI1zvk

Chapter 17: From Gene to Protein

Q: What are the three steps of transcription?

A: Initiation, Elongation, and Termination.

Q: What are introns and exons?

A: Introns are the noncoding segments of nucleic acid that lie between coding regions, also called intervening sequences. Exons are the other regions because they are eventually expressed, usually by being translated into amino acid sequences.

Q: How many arrangements of triplets of nucleotide bases would be sufficient to specify all the amino acids?

A: (4^3) 64

1. Genes specify protein via transcription and translation

2. Transcription is the DNA-directed synthesis of RNA: a closer look

3. Eukaryotic cells modify RNA after transcription.

4. Point mutations can affect protein structure and function.

5. While gene expression differs among the domains of life, the concept of a gene is universal.

Figure 17. 13

Translation: the basic concept

As a molecule of mRNA is moved through a ribosome, codons are translated into amino acids, one by one. The interpreters are tRNA molecules, each type with a specific anticodon at one end and a corresponding amino acid at the other end. A tRNA adds its amino acid cargo to a growing polypeptide chain when the anticodon hydrogen-bonds to a complementary codon on the mRNA. The figures that follow show some of the details of translation in a bacterial cell.

The DNA inherited by an organism leads to specific traits by dictating the synthesis of certain proteins. Proteins are the links between genotype and phenotype.

The DNA to RNA flow of genetic information is termed transcription. The term transcription reflects that the information in DNA is copied into a similar code in RNA. Then, the RNA to protein flow of genetic information is termed translation. The term translation reflects that the information in mRNAs is translated into a new language.Transcription occurs within the nucleus, where the DNA resides . Translation occurs within the cytosol, where the functional ribosomes reside. The three nucleotides that specify an amino acid during translation are called codons.

http://www.youtube.com/watch?v=B6O6uRb1D38&feature=related

Chapter 16: The Molecular Basis of Inheritance

Q: Why are the nitrogenous of the double helix paired in unusual, specific combinations, not like-with-like paring?

A: It is because adenine and guanine are purines, nitrogenous bases with two organic rings, and cytosine and thymine belong to the family of nitrogenous known as pyrimidines, which have a single ring.

Q: So how does the Watson-Crink model explain the basis for Chargaff's rule?

A: The Watson-Crink model surely explains it because the model describes how the two pairs of the nitrogenous bases are meant to be because of their formations; therefore it automatically proves Chargaff's rule because they have to be paired up having the same amount with the partner.

Q: What are telomeres?

A: Special nucleotide sequences at the ends of eukaryotic chromosomal DNA molecules that do not contain genes; instead, the DNA typically consists of multiple repetitions of one short nucleotide sequence. They postpone the erosion of genes near the ends.

1. DNA is the genetic material

2. Many proteins work together in DNA replication and repair.

3. A chromosome consists of a DNA molecule packed together with proteins.

4. The four nitrogenous bases that DNA consist are Adenine (A), Cytosine (C), Guanine (G), and Thymine (T).

5. DNA polymerases can add nucleotides only to the free 3'end of a primer or growing DNA strand, never to the 5'end.

Figure: 16.8

The Pairs of nitrogenous bases in a DNA double helix are held together by hydrogen bonds, shown here as pink dotted lines.

By the 1940’s scientists knew that chromosomes carry the hereditary meterial. DNA apeared to be a much simpler molecule about whch little was known, Therefore, in 1940 almost all scientists thought that proteins must be responsible for inheritance.

By 1944 scientists however knew that DNA was the hereditary material as a result of an experiment by Frederick Griffiths in the 1920’s. Watson and Crick discovered the double helix by building models to conform to X-ray data.

The replication of a DNA molecule begins at special sites, origins of replication. In bacteria, this is a specific sequence of nucleotides that is recognized by the replication enzymes. As each nucleotide is added to the growing end of a DNA strand, the last two phosphate groups are hydrolyzed to form pyrophosphate.

Each DNA strand has a 3’ end with a free hydroxyl group attached to deoxyribose and a 5’ end with a free phosphate group attached to deoxyribose.

Chapter 15: The Chromosomal Basis of Inheritance

Q: How does a sex-linked gene affect a human?

A: It is a gene located on either sex chromosome and in humans, it specifically refers to a gene on the X chromosome. Because males have only one locus, the terms homozygous and heterozygous lack meaning for describing their sex-linked genes in this case.

Q: What causes Down syndrome?

A: An extra chromosome 21.

Q: What is the production of offspring with new combinations of traits inherited from two parents called?

A: Genetic recombination.

1. Mendelian inheritance has its physical basis in the behavior of chromosomes

2. Sex-linked genes exhibit unique patterns of inheritance.

3. Linked genes tend to be inherited together because they are located near each other on the same chromosome.

4. Alterations of chromosome number or structure cause some genetic disorders.

5. Loci found on the same chromosome can be genetically recombined only via molecular recombination

Figure 15.15 (d)

A translocation moves a segment from one chromosome to a nonhomologous chromosome. In a reciprocal translocation, the most common type, nonhomologous chromosomes exchange fragments. In a nonreciprocal translocation, which is less common, a chromosome transfers a fragment without receiving a fragment in return.

Mendel proposed the idea that the factors responsible for traits of each pair are independent of every other pair in the process of their distribution into the gametes (law of independent assortment). It is now known that during meiosis, the chromosomes of various homologous pairs assort at random so that the chromosomes of each pair segregate independently of the chromosomes of every other pair.

Because females have twice as many copies of X-linked genes as males, one copy of each must be turned off. This occurs by inactivating one X chromosome in every cell of a female.

http://www.youtube.com/watch?v=n330FzHpI90

Chapter 13: Meiosis and Sexual Life Cycles

Q: Is each human sperm and egg haploid?

A: Yes, (n=23) it is haploid as a result of meiosis. Fertilization restores the diploid condition by combining two haploid sets of chromosomes, and the human life cycle is repeated, generation after generation.

Q: So in how many daughter cells does meiosis result?

A: During another round of cell division, the sister chromatids finally separate; four haploid daughter cells result, containing unreplicated chromosomes.

Q: How do sister chromatids stay together through meiosis I but separate from each other in meiosis II and mitosis?

A: Sister chromatids are attached along their lengths by protein complexes called cohesins. In mitosis, this attachment lasts until the end of metaphase, and in meiosis, the cohesions are cleaved at anaphase I and anaphase II, in two steps.

1. Offspring acquires genes from parents by inheriting chromosomes.

2. Fertilization and meiosis alternate in sexual life cycles.

3. Meiosis reduces the number of chromosome sets from diploid to haploid.

4. Genetic variation produced in sexual life cycles contributes to evolution.

5. Either haploid or diploid cells can divide by mitosis, depending on the type of life cycle. Only diploid cells, however, can undergo meiosis because haploid cells have a single set of chromosomes that cannot be further reduced.

This diagram shows Metaphase II of meiosis. In this phase, the chromosomes are positioned on the metaphase plate as in mitosis,and as we can see, because of crossing over in meiosis I, the two sister chromatids of each chromosome are not genetically identical. Also, the kinetochores of sister chromatins are attached to microtubules extending from opposite poles.

Meiosis is a basic and important process in sexually reproducing eukaryotic organisms, because it produces the haploid gametes that join to produce a new individual, and provides a mechanism for genetic variability, which is important for survival of the species.

Overall, meiosis involves one replication of the genetic material in the chromosomes, followed by two divisions of that genetic material. Therefore, the genetic material is reduced by half. The result of meiosis in a diploid cell is four haploid cells.

Chiasma: the x-shaped, microscopically visible region where homologous nonsister chromatids have exchanged genetic material through crossing over during meiosis, the two homologs remaining associated due to sister chromatic cohesion.

Homologous chromosomes: a pair of chromosomes of the same length, centromere position, and staining pattern that possess genes for the same characters at corresponding loci. One homologous chromosome is inherited from the organism's father, the other from the mother. Also called homologs, or a homologous pair.

Locus: a specific place along the length of a chromosome where a given gene is located.

Spore: in the life of a plant or alga undergoing alternation of generations, a haploid cell produced in the sporophyte by meiosis. A spore can divide by mitosis to develop into a multicellular haploid individual, the gametophyte, without fusing with another cell.

Synapsis: the pairing and physical connection of replicated homologous chromosomes during prophase I of meiosis.

Diploid cell: a cell containing two sets of chromosomes, one set inherited from each parent.

Haploid cell: a cell containing only one set of chromosomes.

Karyotype: a display of the chromosome pairs of a cell arranged by size and shape.

Sex chromosome: a chromosome responsible for determining the sex of an dindividual.

Crossing over: the reciprocal exchange of genetic material between nonsister chromatids during prophase I of meiosis.

http://www.youtube.com/watch?v=iCL6d0OwKt8

Chapter 12: The Cell Cycle

Q: What are the five stages that mitosis is conventionally broken down into?

A: Prophase, Prometaphase, metaphase, anaphase, and telophase.

Q: What is G1 phase?

A: This part of cell cycle is where the cell spends most of its functional life. This is the time when the cells are performing their assigned tasks, metablizing, synthesizing etc. At some point in the cycle something triggers the cell to being a cell division event.

Q: How are cancer cells different from normal cells?

A: If and when normal cells stop dividing, cancer cells do so at random points in the cycle, rather than at the normal checkpoints. Moreover, cancer cells can go on dividing indefinitely in culture if they are given a continual of nutrients; in essence, they are "immortal."

1. Cell division results in genetically identical daughter cells.

2. The mitotic phase alternates with interphase in the cell cycle.

3. The eukaryotic cell cycle is regulated by a molecular control system.

4. In each generation of humans, meiosis reduces the chromosome number from 46 to 23. Fertilization fuses two gametes together and returns the chromosome number to 46, and mitosis conserves that number in every somatic cell nucleus of the new individual.

5. It is hypothesized that mitosis had its origins in simpler prokaryotic mechanisms of cell reproduction.

Figure 12.5 The Cell Cycle

In a dividing cell, the mitotic (M) phase alternates with interphase, a growth period. The first part of interphase (G1) is followed by the S phase, when the chromosomes replicate; G2 is the last part of interphase. In the M phase, mitosis divides the nucleus and distributes its chromosomes to the daughter nuclei, and cytokinesis divides the cytoplasm, producing two daughter cells. The relative durations of G1, S, and G2 may vary.

The eukaryotic cell cycle is divided into four phases: M(mitosis), G1(the period between mitosis and the initiation of nuclear DNA replication), S(the period of nuclear DNA replication), G2(the period between the completion of nuclear DNA replication andmitosis).

Chromosome: a cellular structure carrying genetic material, found in the nucleus of eukaryotic cells. Each chromosome consists of one very long DNA molecule and associated proteins. (A bacterial chromosome usually consists of a single circular DNA molecule and associated proteins. It is found in the nucleoid region, which is not membrane bounded.)

Somatic Cells:

Gamete: a haploid reproductive cell, such as an egg or sperm. Gametes unite during sexual reproduction to reproduce a diploid zygote.

Chromatin: the complex of DNA and proteins that makes up a eukaryotic chromosome. When the cell is not dividing chromatin exists in its dispersed form, as a mass of very long, thin fibers that are not visible with a light microscope.

Cytokinesis: the division of the cytoplasm to form two separate daughter cells immediately after mitosis, meiosis I, or meiosis II.

Cleavage: the process of cytokinesis in animal cells, characterized by pinching of the plasma membrane.

Binary fission: a method of asexual reproduction by "division in half." In prokaryotes, binary fission does not involve mitosis; but in single-celled eukaryotes that undergo binary fission, mitosis is part of the process.

Mitotic spindle: an assemblage of microtubles and associated proteins that is involved in the movements of chromosomes during mitosis.

Checkpoint: a control point in the cell where stop and go-ahead signals can regulate the cycle.

Kinetochore: a structure of proteins attached to the centromere that links each sister chromatid to the mitotic spindle.

http://www.youtube.com/watch?v=lf9rcqifx34

Chapter 11: Cell Communication

Q: What are the three stages of signaling?

A: Signal reception, signal transduction, and cellular response.

Q: What are the three major types of plasma-membrane receptors?

A: They are G protein-coupled receptors, receptor tyrosine kinases, and ion channel receptors.

Q: Are all signal receptors membrane proteins?

A: No, some are proteins located in the cytoplasm or nucleus of target cells. To reach such a receptor, a chemical messenger must be able to pass through the target cell's plasma membrane. A number of important signaling molecules can do just that, either because they are small enough to pass between the membrane phospholipids or because they are themselves lipids and therefore soluble in the membrane.

1. External signals are converted to responses within the cell.

2. Reception: A signaling molecule binds to a receptor protein, causing it to change shape.

3. Transduction: Cascades of molecular interactions relay signals from receptors to target molecules in the cell.

4. Response: Cell signaling leads to regulation of transcription or cytoplasmic activities.

5. Apoptosis (programmed cell death) integrates multiple cell-signaling pathways.

Figure 11.2 Communication between mating yeast

Cells of the yeast Saccharomyces cerevisiae use chemical signaling to identify cells of opposite mating type and to initiate the mating process. First cells of mating type A release a-factor, which binds to receptors on nearby cells of mating type B. Meanwhile, B cells release b-factor, which binds to specific receptors on A cells. Both these "factors" are small proteins of about 20 amino acid in length. Binding of these factors to the receptors induces changes in the cells that lead to their fusion, or mating. The resulting A/B cell combines in its nucleus all the genes from both A and B cells, (diploid).

As humans communicate with each other, and so do other animals, it is definitely undoubtful that cell as well need to communicate among themselves. As mentioned above, there are several different ways of how the cells communicate.

All communication involving cells can be explained in terms of a force of attraction (called affinity) between molecules. Components that allow detection are called receptors and they often have a cavity shape which allows other molecules to lock into them. The receptor ahs an affinity for a particular message or signal.

Generally, we can think of chemical signals as being stimulatory-or inhibitory- for controlling levels of activity. However, the situation is seldom the simple as there are hundreds of different types of signals and they all work in concerted coordination to carefully regulate what happens in a cell according to a wide range of influencing factors. Cell processes are not so much on or off, but, held in a dynamic state of tension. Many different protein messages or components may determine the state of a cell (for example, the cell responsible for secreting a pituitary hormone - prolactin - has been shown to respond to at least twenty different signals).

Signal transduction pathway: a series of steps linking a mechanical or chemical stimulus to a specific cellular response.

Amplification: the strengthening of stimulus energy during transduction.

Apoptosis: a program of controlled cell suicide, which is brought about by signals that trigger the activation of a cascade of suicide proteins in the cell destined to die.

Gap junction: a type of intercellular junction in animals that allows the passage of materials between cells.

Growth factor: a protein that must be present in the extracellular environment (culture medium or animal body) for the growth and normal development of certain types of cells.

Ligand: a molecule that binds specifically to another molecule, usually a larger one.

Yeast: Single-celled fungus that reproduces asexually by binary fission or by the pinching of small buds off a parent cell; some species exhibit cell fusion between different mating types.

Protein kinase: an enzyme that transfers phosphate groups from ATP to a protein, thus phosphorylating the protein.

Local regulator: a secreted molecule that influences cells near where it is secreted.

Glycogen: an extensively branched glucose storage polysaccharide found in the liver and muscle of animals; the animal equivalent of starch.

http://www.youtube.com/watch?v=tMMrTRnFdI4&feature=related