Regulation of Gene Expression

1) What makes an operon?

- an operator (controls the access of RNA polymerase to the genes)

- the promoter (where RNA polymerase attaches here)

- genes of the operon (the entire strech of DNA required for all the enzymes produced by the operon)

2) The zygote undergoes transformation through three interrelated processes. What are these?

1. cell division
2. cell differentiation
3. morphogenesis

3) What controls differentiation and morphogenesis?

1. cytoplasmic determinants
2. cell-cell signals

Facts:

- Cells control metabolism by regulating enzyme activity or the expression of genes coding for enzymes.

- An operon site on the DNA switches the operon on or off; resulting in coordinate regulation of genes.

- Cells differ in structure and function not because they contain different portions of a common genome, but because they express different portions of a common genome.

- Differentiation is heralded by the appearance of tissue-specific proteins, which enable differentiated cells to carry out their specialized roles.

[Drosophila - gradients of morphogens encoded by maternal effect genes determine the body axes]

- A hyperactive version of a protein in an stimulatory pathway, such as Ras (a G protein), functions as an oncogene protein.

Summary:

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 lacrepressor is bounded 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.

Extra:

lac operon video

From Gene to Protein

1) What is gene expression?

It is the process by which DNA directs the synthesis of proteins.

2) What are the three steps of transcription?

Initiation, Elongation, and Termination.

initiation stage of translation

3) Define mutations and point mutations!

Mutations are alterations in the genetic material of the cell.

Point mutations are are alterations of just one base pair of a gene. They come in two basic types: 1. base-pair substitutions; 2. insertions and deletions

Facts:

- DNA controls metabolism by directing cells to make specific enzymes and other proteins

- Genes specify proteins via transcription and translation

- Eukaryotic cells modify RNA after transcription

- Genetic information is encoded as a sequence of nonoverlaping base triplets (codons)

- Ribosomes coordinate the three stages of translation

Summary:

The information content of DNA is in the form of specific sequences of nucleotides along the DNA strands. The DNA inherited by an organism leads to specific traits by dictating the synthesis of proteins. Gene expression, the process by which DNA directs protein synthesis, includes two stages called transcription and translation. Proteins are the links between genotype and phenotype. For example, Mendel’s dwarf pea plants lack a functioning copy of the gene that specifies the synthesis of a key protein, gibberellin. Gibberellins stimulate the normal elongation of stems.

Extra:

translation rap video

The Molecular Basis of Inheritance

1) How was it proved that DNA (not protein) is the genetic material?

In 1952, Alfred Hershey and Martha Chase answered this question utilizing bacteriophages (viruses that infect bacteria). They used a radioactive isotope of phosphorous to tag the DNA in one culture of bacteriophages and radioactive sulfur to tag the protein in a second culture. The results showed that only DNA entered the bacteria infected by the virus. --> DNA must be the genetic material!

2) What is the basic structure of DNA?

1. double helix
2. nitrogenous bases - A, C, T, G
3. the strands are termed antiparallel

3) List some of the bacterial DNA replication proteins and their functions.

- helicase - unwinds parental double helix at replication forks

- topoisomerase - relieves "overwinding" strain ahead of replication forks by breaking, swiveling, and rejoining DNA strands

- primase - synthesizes an RNA primer at 5' end of the leading strand of each Okazaki fragment of lagging strand

- DNA ligase - joins 3' end of DNA that replaces primer to rest of leading strand and joins Okazaki fragments of lagging strand

Facts:

- DNA must be the genetic material

- DNA is a double helix, built up from 4 nitrogenous bases (A,T,C & G) with antiparallel strands

- A & T always pair as well as do C & G

- DNa polymerase can add nucleotides only to the 3' end of a molecule

- As DNa becomes more highly packaged, it becomes less accessible to transcription enzymes

Summary:

In 1950s, Harshey and Chase proved that DNA is the actual genetic material. The next big discussions in this area were based on the DNA structure. It is now known that DNA is a double helix, built up from 4 nitrogenous bases (A,T,C & G) with antiparallel strands.

Replication is the making of DNA from an existing DNA. The replication occurs in six major points:

1) it begins at origins of replication

2) replication bubble formation

3) DNA polymerases catalyze the elongation of the new DNA

4) DNA polymerase adds nucleotides to the growing chain (5' to 3')

5) continuous replication from 5' to 3' strands

6) Okazaki fragments (lagging strand) sealed together by DNA ligase

Extra:

DNA replication non-melodical song! :D

The Chromosomal Basis of Inheritance

1) What is the chromosomal basis of sex in humans?

x chromosome - medium sized chro

mosome with a large number of traits

y chromosome - much smaller chromosome with a few traits

2) What are sex-linked genes and what is their function?

A gene located on either sex chromosome, although in humans the term has historically referred specifically to a gene on the X

chromosome. Sex-linked genes in humans follow the same pattern of inheritance that Morgan observed for the eye-color locus he studied in Drosophila (fruit fly). Fathers pass sex-linked alleles to all of their daughters but to none of their sons. In contrast, mothers can pass sex-linked alleles to both sons and daughters.

3) What might the consequences of the abnor

mal chromosome number be?

- nondisjunction - when the members of a pair of homologous chromosomes do not separate properly during meiosis I, or sister chromatids don't separate properly during meiosis II

- aneuploidy - result of nondisjunction - abnormal chromosome number in the zygote

- polyploidy - condition of having more than two complete sets of chromosomes, forming a 3n or 4n individual

Human disorders caused by chromosome alterations include the following: Down syndrome, Klinefelter syndrome, Turner syndrome...

- Down syndrome

Facts:

- Mendelian genes have specific loci (positions) along chromosomes, and it is the chromosomes that undergo segregation and independent assortment. [chromosome theory of inheritance]

- Chromosomes are the location of Mendel's heritable factors

- A sex-linked gene is located on either sex chromosome

- Duchenne muscular distrophy (sex-linked disorder -> weakening of the muscles) affects about one out of every 3500 males born in the United States

- If either of the aberrant gametes unites with a normal one at fertilization, the zygote will also have an abnormal number of a chromosome (condition called aneuploidy)

Summary:

Mendelian inheritance has its physical basis in the behavior of chromosomes during sexual life cycles . In the early 1900s, geneticists showed that chromosomal movements in meiosis account for Mendel’s laws.

Morgan’s discovery that the X chromosome in Drosophila carries a gene for eye color supported the chromosome theory of inheritance.

Linked genes tend to be inherited together because they are located on the same chromosome. Each chromosome has hundreds or thousands of genes. Linked genes do not assort independently.

Independent assortment of chromosomes and crossing over produce genetic recombinants. Recombinant offspring, which exhibit new combinations of traits inherited from two parents, result from events of meiosis and random fertilization. These events include crossing over and independent assortment of chromosomes during the first meiotic division. A recombination frequency under 50% indicates that the genes are linked but that crossing over has occurred. During prophase I, paired homologous chromosomes break at corresponding points and switch fragments, creating new combinations of alleles that are then passed on to the gametes.

Geneticists can use recombination data to map a chromosome’s genetic loci. One way to map genes is to deduce their order and a rough indication of the relative distances between them from crossover data. The further apart genes are on a chromosome, the more likely they are to be separated during crossing over. Cytological mapping is a technique that pinpoints the physical locus of a gene by associating a mutant phenotype with a chromosomal defect seen in the microscope.

The chromosomal basis of sex varies with the organism. Sex is an inherited phenotypic character usually determined by the presence or absence of special chromosomes; the exact mechanism varies among different species. Humans and other mammals have an X-Y system, as do fruit flies. An XY male gives either an X chromosome or a Y chromosome to the sperm, which combines with an ovum containing an X chromosome from an XX female. The offspring’s sex is determined at conception by whether the sperm carries X or Y.

Sex-linked genes have unique patterns of inheritance. The sex chromosomes carry certain genes for traits that are unrelated to maleness or femaleness. Hemophilia is a sex-linked recessive disorder whose gene is on the X chromosome. In mammalian females, one of the two X chromosomes in each cell is randomly inactivated during early embryonic development.

Alterations of chromosome number or structure cause some genetic disorders. Errors during meiosis can change the number of chromosomes per cell or the structure of individual chromosomes. Such alterations can affect phenotype. Aneuploidy, an abnormal chromosome number, can arise when a normal gamete unites with one containing two copies or no copies of a particular chromosome as a result of nondisjunction during meiosis. Polyploidy, in which there are more than two complete sets of chromosomes, can result from complete nondisjunction during gamete formation. A variety of rearrangements can result from chromosome breakage. A lost fragment leaves one chromosome with a deletion and may produce a duplication, translocation, or inversion by reattaching to another chromosome. Such alterations cause a variety of human disorders, such as Down syndrome (usually due to trisomy of chromosome 21).

The phenotypic effects of some mammalian genes depend on whether they were inherited from the mother or the father (imprinting). Individuals imprint certain parts of chromosomes in their gamete-producing cells with either a male or a female "stamp," probably in the form of methylation. This affects the way some genes are expressed in offspring. Genomic imprinting helps explain the inheritance pattern of some hereditary disorders, including fragile X syndrome.

Extranuclear genes exhibit a non-Mendelian pattern of inheritance. Mitochondria and chloroplasts contain some of their own genes. Because the zygote’s cytoplasm comes from the ovum, certain features of the offspring’s phenotype depend solely on these maternal cytoplasmic genes. Some diseases affecting the nervous and muscular systems are caused by defects in mitochondrial DNA that prevent cells from making enough ATP.

Extra:

DNA structure video

Meiosis and Sexual Life Cycles additional

meiosis I and II

Extra: meiosis vs mitosis video

Meiosis and Sexual Life Cycles

What is meiosis?

--> cell division that produces reproductive cells in sexually reproducing organisms (the nucleus divides into four hapoloid cells/nuclei)

What are the stages of meiosis?

meiosis I: prophase I, metaphase I, anaphase I, telophase I and cytokinesis (division of the cytoplasm)

meiosis II: prophase II, metaphase II, anaphase II, telophase II and cytokinesis

What are the differences between mitosis and meiosis?

Basically, meiosis reduces the number of chromosome sets from two (diploid) to one (haploid), whereas mitosis conserves the number of chromosome sets. Therefore, meiosis produces cells that differ genetically from their parent cell and from each other, whereas mitosis produces daughter cells that are genetically identical to their parent cell and to each other.

Facts:

- We inherit one set of chromosomes from our mother and one from our father

- In sexual reproduction, a single parent produces genetically identical offspring by mitosis

- Normal human somatic cells have 46 diploid chromosomes.

- The two cell divisions of meiosis produce 4 haploid daughter cells.

- Mutations are the original source for genetic variation.

JK Key terms:

Heredity (inheritance) = transmission of traits from one generation to next

Genetics = the scientific study of heredity

Clone = a group of genetically identical individuals

Gametes = reproductive cells

Somatic cells = any cell other than those involved in gamete formation

Karyotype = display of paired chromosomes (map of chromosomes)

Sex chromosomes = x and y, determine the sex

Autosomes = other chromosomes

Diploid cell= any cell with two chromosome sets (2n)

Haploid cell= any cell with a single chromosome set (n)

Summary:

A cell undergoing meiosis will divide two times; the first division is meiosis 1 and the second is meiosis 2. The phases have the same names as those of mitosis. A number indicates the division number (1st or 2nd):

meiosis 1: prophase 1, metaphase 1, anaphase 1, and telophase 1

meiosis 2: prophase 2, metaphase 2, anaphase 2, and telophase 2

In the first meiotic division, the number of cells is doubled but the number of chromosomes is not. This results in 1/2 as many chromosomes per cell.

The second meiotic division is like mitosis; the number of chromosomes does not get reduced.

The Cell Cycle

What are the results of cell division? + example

--> genetically identical daughter cells

--> example: hydra(budding)

What are the phases of the cell cycle?

--> Mitotic (M) phase usually includes mitosis and cytokinesis

--> interphase (G1 - first gap, S - synthesis, G2 - second gap)

Mitosis is usually broken down to 5 stages:

prophase, prometaphase, metaphase, anaphase, telophase

What is a checkpoint of the cell cycle?

It is a control point where stop and go-ahead signals can regulate the cycle.

Facts:

- Cells duplicate their genetic material before they divide.

- DNA is partitioned among chromosomes.

- Eukaryotic cell division consists of mitosis and cytokinesis.

- Animal cells carry out cytokinesis by cleavage, and plant cells from a cell plate.

- Cancer cells elude normal regulation and divide out of control, forming tumors.

Key terms:

genome = genetic information

chromosome = package of DNA

somatic cells = all body cells except the reproductive cells

gametes = reproductive cells

chromatin = a complex of DNA

sister chromatids = two chromatids containing the same DNA molecule

centromere = a region where 2 sister chromatids are attached

meiosis = cell division

cytokinesis = division of the cytoplasm

MPF = maturation-promoting factor, a protein complex required for a cell to progress from late interphase to mitosis (cyclin and a protein kinase when active)

growth factor = a protein released by certain cells that stimulates other cells to divide

mitosis phases

Summary:

We have already discussed how the two main events of cellular reproduction are the copying of cellular components and the cleavage of the cell. These two events, copying and cleaving, represent the two larger phases of the cell cycle, interphase and Mitosis. Mitosis is the part of the cell cycle when the cell prepares for and completes cell division. During interphase, appropriate cellular components are copied. Interphase is also a time of checkpoints to make sure that the cell is ready to proceed into mitosis. Both of these two phases have further sub-divisions. Since the cell cycle is a "cycle" it has no distinct beginning or ending. Cells are continually entering and exiting the various phases of the cycle.

Extra: mitosis song, found by my teacher