Chapter 21: Genomes and Their Evolution

Q: What is the percentage of rise of repetitive DNA's that are not related to transposable elements due to mistakes during DNA replication or recombination?

A: 15% of the human genome

Q: What is a homeobox?

A: A 180-nucleotide sequence that specifies a 60-amino-acid homeodomain in the encoded proteins.

Q: What are multigene families?

A: Collections of two or more identical or very similar genes.

1. New approches have accelerated the pace of genome sequencing

2. Scientists use bioinformatics to analyze genomes and their functions.

3. Genomes vary in size, number of genes, and gene density.

4. Multicellular eukaryotes have much noncoding DNA and many multigene families.

5. Duplication, rearrangement, and mutation of DNA contribute to genome evolution.

Figure 21.12

Gene duplication due to unequal crossing over.

One mechanism by which a gene can be duplicated is recombination during meiosis between copies of a transposable element flanking the gene. Such recombination between misaligned nonsister chromatids of homologous chromosomes produces one chromatid with two copies of the gene and one chromatid with no copy.

The sequencing of the human genome has been seen as the most ambitious mapping project. It officially began as the Human Genome Project in 1990, in major, going through three stages: genetic mapping, physical mapping, and DNA sequencing. Humans have 20,488 genes and we can make 75,000 polypeptides. Humans and other mammals have the lowest gene density and the number of genes is not correlated to genome size.

It seems that the rate of duplications and inversions have accelerated about 100 million years ago.

http://www.youtube.com/watch?v=gngsL9FRpqc

Chapter 20: Biotechnology

Q: What is a stem cell?

A: It is a relatively unspecialized cell that both reproduce itself indefinitely and, under appropriate conditions, differentiate into specialized cells of one or more types.

Q: What is a genome library?

A: The complete set of plasmid-containing cell clones, each carrying copies of a particular segment from the initial genome.

Q: Then, what are plasmids?

A: Small circular DNA molecules that replicate separately from the bacterial chromosome.

1. DNA cloning yields multiple copies of a gene or other DNA segment

2. DNA technology allows us to study the sequence, expression, and function of a gene.

3. Cloning organisms may lead to production of stem cells for research and other applications.

4. The practical applications of DNA technology affect our lives in many ways.

5. Many early animal embryos contain stem cells capable of giving rise to differentiated embryonic cells of any type.

Single nucleotide polymorphisms as genetic markers for disease-causing alleles. This diagram depicts homologous segments of DNA from a family in which some members have a genetic disease. In this family, unaffected family members have a T at a particular SNP locus. If a family member has a C at that locus, there is a high probability that the individual has also inherited the disease-causing allele.

It is the genetic manipulation of organisms and humans have been doing this for thousands of years. Basic tools of bioengineering include restriction enzymes, ligase, plasmids, DNA libraries and advanced tools include PCR, DNA sequencing, gel electrophoresis, southern blotting, etc.

Word processing metaphors are used, and they are cut, paste, copy, and find.

There have been many experiments cloning organisms, like plants and animals. Also, some of the applications can affect our lives, like forensic evidence and genetic profiles, environment, agriculture, or in medical world.

http://www.youtube.com/watch?v=rrT5BT_7HdI

Chapter 19: Viruses

Q: How small can a virus get?

A: The tiniest viruses are only 20 nm in diameter-smaller than a ribosome.

Q: How do viruses identify host cells?

A: They do so by a "lock-and-key" fit between viral surface proteins and specific receptor molecules on the outside of cells.

Q: What is a phage that reproduces only by a lytic cycle called?

A: a virulent phage

1. A virus consists of a nucleic acid surrounded by a protein coat.

2. Viruses reproduce only in host cells.

3. Viruses, viroids, and prions are formidable pathogens in animals and plats.

4. The RNA animal viruses with the most complicated reproductive cycles are the retroviruses.

5. Viruses that appear suddenly or are new to medical scientists are often referred to as imerging viruses.

Viral infection of plants:

More than 2,000 types of viral diseases of plants are known, and there are a lot of annual loss worldwide due to their destruction of agriculture, etc. Common signs of viral infection include bleached or brown spots on leaves and fruits, stunted growth, and damaged flowers or roots, all tending to diminish the yield and quality of crops.

Viruses are particles of nucleic acid, protein, and, in some cases, lipids. All viruses have one thing in common: They enter living cells and, once inside, use the machinery of the infected cell to produce more viruses. Viruses are parasites, not considered to be living things because they are not made up of cells. Once the virus is inside a host cell, two different processes may occur and they are lytic infection and lysogenic infection.

There are viruses that cause diseases and they are called as pathogens.

http://www.youtube.com/watch?v=Rpj0emEGShQ

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