The History of Life on Earth_Chapter 25

1. What about fossils?

The fossil record is the sequence in which fossils appear in the layers of sedimentary rock that constitutes the surface.

2. What is heterochrony?

Heterechrony is an evolutionary change in the rate or timing of developmental events. changing relative rates of growth even slightly can change the adult form of organisms substantially, thus contributing to the potential for evolutionary change.

3. What are hox genes?

Hox genes are one class of homeotic genes. changes in hox genes and in the genes that regulate them can have a profound effect on morphology.

5 facts on this chapter:

. conditions on early earth made the origin of life possible.

. the fossil record documents the history of life.

. ket events in life's history include the origins of single-celled and multicelled organisms and the colonization of land.

. the rise and fall of dominant groups reflect continental drift, mass extinctions, and adaptive radiations.

. major changes in body form can result from changes in the sequences and regulation of developmental genes.

A video about the history of life on earth:

http://www.youtube.com/watch?v=uVrzNR_UK_4

In this chapter, we learnt the age of Earth, characteristics of the arly planet, fossils, evidence of endosymbiosis, and the continental drift and tis effects.

The Origin of Species_Chapter 24

1. What are the prezygotic and postzygotic barriers?

Prezygotic Barriers: habitat isolation, temperol isolation, behavioral isolation, mechanical isolation, and gametic isolation. These barriers impede mating or hinder fertilization if mating does occur. Postzygotic Barriers: Reduced hybrid vialibility, reduced hybrid fertility and hybrid breakdown. These barriers prevent a hybrid zygote from developing into a viable, fertile adult.

2. Allopatric speciation, and sympatric speciation.

In allopatric speciation, gene flow is interrupted when a pop is divided into geographically isolated subpopulations. (an exemple of founder's effect) In sympatric speciation, speciation occurs in pop that live in the same geographic area when chromosomal changes and nonrandom mating reduces the gene flow. In plants, sympatric speciation can result from accidents during cell division that result in extra sets of chromosomes, a mutant condition known as polyploidy. In animals, it may result from gene-based shifts in habitat or mate preference.

video on speciation:

http://www.youtube.com/watch?v=YCoEiLOV8jc&feature=related

3. Gradualism and punctuated evolution.

gradualism proposes that species descended from a common ancestor and gradually diverge more and more in morphlogy as they acquire unique adaptations. punctuated equilibrium is a term used to describe periods of apparent stasis punctuated by SUDDEN CHANGE observed in the fossil record.

5 facts on this chapter:

. reproductive isolation is defined as the existence of biological barriers that impede members of two species from producing viable, fertile hybrids.

. reduced hybrid viability is when a zygote is formed, genetic incompatibility may cause development to cease.

. adaptive radiation occurs when many new specis arise froma single common ancestor. this occurs when a few organisms make their way to new and distant areas.

. polyploid speciation occurs in animals, but not common. in animals sympatric speciation can result from part of the pop switching to a new habitat, food source, or other sources.

. two species mate and produce viable fertile hybrids, but when the hybrids mate their offspring are weak and sterile.

This chapter was fun. I learned the prezygotic and postzygotic barrier that maintain reproductive isolation in natural populations. i learned about different types of speciations.

The Evolution of Populations_Chapter 23

1. Explain the Hardy Weinberg Equilibrium.

The Hardy-Weinberg theorem describes the gene pool of a nonevolving population.This theorem states that the frequencies of alleles and genotypes in a population’s gene pool will remain constant over generations unless acted upon by agents other than Mendelian segregation and recombination of alleles. The shuffling of alleles by meiosis and random fertilization has no effect on the overall gene pool of a population. A population must satisfy five conditions if it is to remain in Hardy-Weinberg equilibrium:Extremely large population size. In small populations, chance fluctuations in the gene pool can cause genotype frequencies to change over time. These random changes are called genetic drift.No gene flow. Gene flow, the transfer of alleles due to the migration of individuals or gametes between populations, can change the proportions of alleles.No mutations. Introduction, loss, or modification of genes will alter the gene pool.Random mating. If individuals pick mates with certain genotypes, or if inbreeding is common, the mixing of gametes will not be random.No natural selection. Differential survival or reproductive success among genotypes will alter their frequencies.

2. What are the three major factors that alter allele frequencies in a population?

Natural selection, genetic drift ( founder effect and bottleneck effect) and the gene flow.(immigration/emigration)

3. How is genetic variation preserved in a population?

The tendency for natural selection to reduce variation is countered by mechanisms that preserve or restore variation, including diploidy and balanced polymorphisms.Diploidy in eukaryotes prevents the elimination of recessive alleles via selection because recessive alleles do not affect the phenotype in heterozygotes.Even recessive alleles that are unfavorable can persist in a population through their propagation by heterozygous individuals.Heterozygote protection maintains a huge pool of alleles that may not be suitable under the present conditions but may become beneficial when the environment changes.

5 facts on this chapter:

. Chromosomal mutations delete, disrupt, duplicate, or rearrange many loci at once.

. Gene pool is all of the alleles at all loci in all the members of a population. in diploid species each individual has two alleles for a particular gene, the individual may be either homozygous or hetero.

. if all members of a pop are homozygous for the same allele, the allele is said to be fixed.

. relative fitness refers to the contribution an organism makes to the gene pool of the next generation relative to the contribution of other members.

. Mutations can alter gene frequency but are rare.

Natural selection cannot produce perfect organisms because selection can only edit existing variations. evolution is limited by historical constraints, adaptations are often compromises, and chance, natural selection, and the environmental interact. there are 3 different types of selections:directional, disruptive, and stabilizing selections.

A long video about mutations, genetic drift, and gene flow:

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

Descent with Modification_Chapter 22

1. What are natural and artificial selections?

Adaptations are essential to understand the evolution. Darwin's explanation of how adaptatins arise centered on natural selection, a process in which individuals with certain inherited traits leave more offspring than individuals with other traits. another words, nature determines who survives, who fits the best to that specific environment. Artifical selecion is the process by which species are modified by humans.like plants we have developed.

artificial selection image:

2. What are the evidences of evolution?

Darwin's theory provided many evidences. Similarity in characteristic traits from common ancestry is known as homology. For example, the forelimbs of human, cats, whales, and bats share the same skeletal elements, even though the appendages have very different functions.These forelimbs are homologous structures that represent variations on the ancestral tetrapod forelimb. Comparative anatomy confirms that evolution is a remodeling process, an alteration of existing structures. Anatomical resemblances among species are generally reflected in their genes (DNA) and gene products (proteins). The geographical distribution of species—biogeography—first suggested evolution to Darwin. Species tend to be more closely related to other species from the same area than to other species with the same way of life that live in different areas. The succession of fossil forms is consistent with what is known from other types of evidence about the major branches of descent in the tree of life.

3. What do we need to be succesul in evolution?

Survival, reproduction, whoever lives long and reproduce is the winner.

http://www.youtube.com/watch?v=FnzmxeZJeho&feature=fvw

5 facts on this chapter:

. Catastrophism is the principle that events in the past occures suddenly and by different machanisms than those occuring today.

. Uniformatirianism is the idea that the geologic processes that have shaped the planet have not changed over the course of earth's history.

. distantly related organisms can resemble one another for a different reason: convergent evolution, the independent evolution of similar features in different lineages.

. Vestigial structures are remnants of features that served important functions in the organism's ancestors.

. Fossils show that past organisms differed from living organisms, that many species have become extinct and that species have evolved over long period of time.

This chapter was fun. I liked to learn the ideas that are against the evolution, i learnt how the evolution works, its evidences, its role in the history of earth.

Genomes and Their Evolution_Chapter 21

1. What is genomics?

With the genomes of many species fully sequenced, scientists can study whole sets of genes and their interactions.
2. What is bioinformatics?

The applicaiton of computational methods to the storage and analysis of biological data.

3. How can we determine genome evolution?

By comparing genome sequences provides clues to evolution and development

5 facts on this chapter:

. new approaches have accelerated the pace of genome sequencing

. scientists use bioinformatics to analyze genomes and their function

. genome vary in size, number of genes, and gene density

. multicellular eukaryotes have much noncoding DNA and many multigene families

. duplication, rearrangmnent, and mutation of DNA contribute to genome evolution.

video on genome sequencing:

http://www.youtube.com/watch?v=-gVh3z6MwdU

DNA Technology and Genomics_Chapter 20

1. DNA Clonning.

2. What are the practical applications of DNA technology?

3. What is a gel electrophoresis?

1. Dna clonning manipulate and analyze dna and produce useful new products and organisms.

The cloning of genes occurs in five steps. identify and isolate the gene of interest and a cloning vector. cut both gene of interest and the vector with the same restriction enzyme. join the two pieces of dna. get the vector carrying the gene of interest into a host cell.

Video on Gene Clonning:

http://www.youtube.com/watch?v=Jy15BWVxTC0

2. Diagnosis of disease, gene therapy, the production of pharmaceuticals, forensic applications, environmental cleanup, agricultural applications.

Gene therapy image:

3. Gel electrophoresis is a one indirect method of rapidly analyzing and comparing genomes. it separtes macromolecules on the basis of their rate of movement through a gel in an electrical field.

5 facts about this chapter:

. The major goal of most animal cloning is reproduction, but not for humans. in humans, the major goal is to produce stem cells.

. When a dna molecule is cut by restriction enzymes, the result will always be a set of restriction fragments, which will have at least one single-stranded end, called sticky end.

. A genomic library is a set of thousands of recombinant plasmid clones, each of which has a piece of the original genome being studied.

. PCR is a method used to greatly amplify a particular piece of dna without the use of cells.

. a cDNA library is made up of complementary dna made from mRNA transcribed by reverse transcriptase. this technique rids th gene of introns but may not contain every gene in the organism.

This chapter is quiet complicated for me. I dont think I understood the whole concept.

Viruses_Chapter 19

1. Structure of a virus.

2. Lyctic and lysogenic cycles.

3. Viroids and Prions.

1.Viruses are not plants, animals, or bacteria, but they are the quintessential parasites of the living kingdoms. Without a host cell, viruses cannot carry out their life-sustaining functions or reproduce. They cannot synthesize proteins, because they lack ribosomes and must use the ribosomes of their host cells to translate viral messenger RNA into viral proteins. Viruses cannot generate or store energy in the form of adenosine triphosphate (ATP), but have to derive their energy, and all other metabolic functions, from the host cell. They also parasitize the cell for basic building materials, such as amino acids, nucleotides, and lipids. All viruses contain nucleic acid, either DNA or RNA (but not both), and a protein coat, which encases the nucleic acid. Some viruses are also enclosed by an envelope of fat and protein molecules. Capsid - The capsid is the protein shell that encloses the nucleic acid; with its enclosed nucleic acid, it is called the nucleocapsid. This shell is composed of protein organized in subunits known as capsomers. Envelope - Many types of virus have a glycoprotein envelope surrounding the nucleocapsid. The envelope is composed of two lipid layers interspersed with protein molecules (lipoprotein bilayer) and may contain material from the membrane of a host cell as well as that of viral origin. Nucleic Acid - Just as in cells, the nucleic acid of each virus encodes the genetic information for the synthesis of all proteins. While the double-stranded DNA is responsible for this in prokaryotic and eukaryotic cells, only a few groups of viruses use DNA. Most viruses maintain all their genetic information with the single-stranded RNA.

2. The lyctic cycle ends in the death of the host cell by rupturing it. In thic cycle, a bacteriophage injects its DNA into a host cell and takes over the host cell's machinery to synthesize new copies of the viral DNA as well as protein coats. In the lysogenic cycle the bacteriophage's DNA becomes incorporated into the host cell's DNA and is replicated along the host cell's genome. The viral DNA is called prohage.

3. Viroids, smaller and simpler than even viruses, consist of tiny molecules of naked circular RNA that infect plants. Their several hundred nucleotides do not encode for proteins but can be replicated by the host’s cellular enzymes.These small RNA molecules can disrupt plant metabolism and stunt plant growth, perhaps by causing errors in the regulatory systems that control plant growth. Prions are infectious proteins that spread disease.They appear to cause several degenerative brain diseases including scrapie in sheep, “mad cow disease,” and Creutzfeldt-Jakob disease in humans.Prions are likely transmitted in food.

video on the cycles: http://www.youtube.com/watch?v=wLoslN6d3Ec

5 facts on this chapter:

. Retroviruses are RNA viruses that use the enzyme reverse transciptase to transcribe dna from an rna template. the new dna then permanently integrates into a chromosome in the nucleus of an animal cell.

. Viruses have a limited host range. This means they can infect only a very limited variety of hosts.

. A phage that reproduces only by a lyctic cycle is a virulent phage.

. Phages capable of using both modes of reproducing within a bacterium are called temperate phages.

. Viruses enter plant cells through damaged cell walls or are inherited from a parent.

In this chapter, we learned the components of a virus and the differences between lyctic and lysogenic cycles.

Regulation of Gene Expression_Chapter 18

1. What does an operon consist of?

2. Cell division, differentiation, and morphogenesis?

3. What controls differentiation and morphogenesis?

1. An operon consist of 3 parts. operator, promoter, and the genes of the operon. Operator controls the access of rna polymerase to the genes, it is found within the promoter site or between the promoter and the protein coding genes of the operon. promoter is a place where rna polymerase attaches. the genes of the operon is the entire strecth of dna required for all the enzymes produced by the operon.

2. cell divison is the series of mitotic divisions that increases the number of cells. cell differentiation is the process by which cells become specialized in structure and function. morphogenesis is the organization of cells into tissues and organs.

3. cytoplasmic determinants are maternal substances in the egg that influence the course of early development. these are distributed unevenly in the early cells of the embryo and result in different effects. cell-cell signals result from molecules, such as growth factors, produced by one cell influencing neighboring cells, a process called induction which causes cells to differentiate.

video on cell division:

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

image of an operon:

5 main facts on this chapter:

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

. Normal cells are converted to cancer cells by the accumulation of nutations affecting proto-oncogenes and tumor suppressor genes.

. Some operons are also subject to positive control via stimulatory protein, such as catabolite activator protein CAP, shich promotes transcription when bound to a site within the promoter.

. The expression of eukaryotic genes can be turned off and on at any point along the pathway from gene to functional protein.

. Determination is the series of events that lead to observable differentiation the a cell.

In this chaper, we learned the functions og the three parts if an operon,the role of repressor genes in operons, the impact of DNA methylation and histone acetylation on gene expression, and the role of oncogenes, proto-oncogenes, and tumor suppressor genes in cancer.

From Gene to Protein_Chapter 17

1. What are the stages of transcription?

2. What is RNA splicing?

3. What are point mutations?

1. Initiation, elongation, and termination are the three stages of transcription.

2. Rna splicing takes places in eukaryotic cells. In rna splicing, large populations of the newly synthesized rna strand are removed. The sections of the mrna that are spliced out are introns, and the sections that remain and spliced together by a splicesome are called exons.

3. Point mutations are alterations of just one base pair of a gene. They come in two basic types. Base pair substituition, and insertation and deletion.

link on rna splicing :

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

point mutation:

5 main facts:

. The basic mechanics of transcription and translation are similar in eukaryotes and prokaryotes.

. The initial RNA transcript of any gene is called a primary transcript.

. Several codons may specify the same amino acid, but no codon specifies more than one amino acid.

. Some introns play a regulatory role in the cell. These introns contain sequences that control gene activity in some way.

. A point mutation that results in the replacement of a pair of complementary nucleotides with another nucleotide pair is called a base-pair substitution.

In this chapter we learnt that 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.

The Molecular Basis of inheritance_Chapter 16

The structure of DNA.

The structure of DNA is double helix, with about 10 nucleotide pairs per helical turn. Each spiral strand, composed of a sugar phosphate backbone and attached bases, is connected to a complementary strand by hydrogen bonding (non- covalent) between paired bases, adenine (A) with thymine (T) and guanine (G) with cytosine (C). Adenine and thymine are connected by two hydrogen bonds (non-covalent) while guanine and cytosine are connected by three. This structure was first described by James Watson and Francis Crick in 1953.

Replication of DNA, and the enzymes.

the video link below describes the replication of dna very well.

http://www.johnkyrk.com/DNAreplication.html

Nucleoid, chromatin, and telomerase.

Telomerase is an enzyme that catalyzes the lenghthening of telomeres in eukaryotic germ cells, so it restores their original lenght abd compensating for the shortening that occurs during the replication. Nucleoid is the dense region of DNA in a bacterium, but is is not bounded by membrane. Eukaryotic DNA is precisely combined with a large amount of protein. Together, this complex of dna and protein, called chromatin, fits into the nucleus through an elaborate, multilevel system of DNA packing.

5 facts on this chapter:

. Nucleic acid strands are always antiparallel, whether it is DNA/DNA or DNA/RNA or R NA/RNA interactions.

. DNA replication is semiconservative.

. The strand that alongs 5' to 3' is called leading strand, and the strand that goes along 3' to 5' is called lagging strand.

. The lagging strand is synthesized in separate pieces called Okazagi Fragments, which are then sealed together by DNA Ligase.

. As DNA becomes more highly packaged, it becomes less accessible to transcription enzymes. This reduces the gene expression.

The Chromosomal Basis of Inheritance_Chapter 15

1. What are the genetic symbols, and their meanings?

Mendel used upper and lower cases.T tall, t short. + means that its wild. (mutant phenotype)

dominant-recessive, dominant is upper case, recessive is lower case. F1 is the first generation, F2 is the second generation from F1 generation.

2. Mutations;

.deletion

.duplication

.inversion

.translocation

3. Human disorders, their results.. (caused by chromosome alterations)

down syndrome: an aneuploid condition that's the result of having an extra chromosome 21. Characteristic facial features, short stature, heart defects, mental retardation.

klinefelter syndrome: an aneuploid condition in which a male possesses he sex chromosomes XXY. males have male sex organs but are sterile.

turner syndrome: a monosomic condition in which the female has just one sex chromosome, an X. sterile female organ.

Video on Chromosome Mutations:

http://www.youtube.com/watch?v=OrXRSqa_3lU

A good website about human disorders due to chromosome alterations:

http://www.biology.iupui.edu/biocourses/n100/2k2humancsomaldisorders.html

Patterns of Inheritance with Sex-Linked Traits

5 main facts on this chapter:

. In humans, there are two types of sex chromosomes. X is for females, Y is for males. Males have one X and one Y.

. Sex linked genes are usually located in X chromosome. So if a boy is hemophilia, that means that his mom has a recessive/dominant hemophilia gene.

. While genes that are on the same chromosome tend to be inherited together, the process of crossing over enables "linked" genes to sort independently. Those that are linked but located farther apart on the chromosome will undergo crossing over more frequently than those located very close together on a chromosome simply because there are more sites between the two genes at which crossing over can take place.

. Turner syndrome is the only known viable monosomy in humans.

. Fertilization restores the diploid number in a sexually reproducing organism. The two major events in the life cycle of sexually reproducing organism are meiosis and fertilization.