Chapter 12 - DNA Technology and Genomics

Q: Why does the rapid reproduction of bacteria make them suitable choices for cloning foreign genes?
A: They are suitable because they are located within plasmid DNA which can be replicated each time the cell divides which results in man copies of the same gene.
Q: What are "sticky ends"?
A: These are single-stranded regions with unpaired bases that can hydrogen-bond to the complementary sticky ends of fragments made by restriction enzymes.
Q: What is DNA profiling?
A: This the analysis of DNA fragments to determine whether they come from a particular individual or not.

Five main facts:
1) Enzymes are used to essentially "cut and paste" DNA.
2) Cloned genes are able to be stored in a genomic library.
3) Nucleic acid probes help identify clones carrying certain genes.
4) The PCR method is used to amplify DNA sequences.
5) DNA profiling has aided in many investigations by use of forensics.

This depicts the PCR method. This method is used when the source of DNA is scanty or impure. IT allows for a specific gene segment to be targeted and amplified. 

This chapter focuses on DNA technology. There are several ways in which this is applied. One is through the research on cloning. Other ways include genetically modified organisms, for example the corn many of us eat. It had been modified genetically to be more resistant to certain diseases and to produce more corn itself. DNA profiling has aided in many forensic cases.

Key Terms:

1) Plasmids: small, circular DNA molecules that replicate separately from the much larger bacterial chromosome

2) Gene cloning: production of multiple identical copes of a gene-carrying piece of DNA

3) Genetic engineering: branch of biotechnology that involves the direct manipulation of genes for practical purposes

4) Vector: gene carrier

5) Clone: group of identical cells descended from a single ancestral cell

6) Genomic library: entire collection of all the cloned DNA fragments from a genome

7) Nucleic acid probe: complementary molecule

8) Vaccine: harmless variant or derivative of a pathogen that is used to stimulate the immune system to mount a defense against that pathogen

9) Gene therapy: alteration of an afflicted individual's genes

10) Primers: short, chemically synthesized single-stranded DNA molecules with sequences that are complementary to one strand at one end of the target sequence

http://www.youtube.com/watch?v=eEcy9k_KsDI

Chapter 11 - How Genes are Controlled

Q: How is it that densely packed DNA prevents gene expression?
A: RNA polymerase and other proteins necessary for transcription do not have viable access to DNA that is tightly packed.
Q: How is alternative RNA splicing used to enable a single gene that will encode more than one kind of polypeptide?
A: A polypeptide is encoded by a mRNA molecule that contains different combinations of exons.
Q: What can be learned from a DNA microarray?
A: In a DNA microarray it can be inferred what genes are active in a particular sample of cells.

Five main facts:
1) Proteins that interact with DNA turn prokaryotic genes on or off in response to outside changes such as environment.
2) Differentiation can result from the expression of many combinations of genes.
3) DNA packing in eukaryotic cells help regulate how genes will be expressed.
4) Eukaryotic RNA can be spliced in several different ways.
5) In the later stages of translation, gene expression may be subject to regulation.

This diagram shows the packing of DNA into a chromosome. It shows how spacers are used to keep genes from interfering with one another. 

In chapter 11 the main focus is how genes are expressed. There is a control in both prokaryotic and eukaryotic cells. This allows for certain genes to be expressed that will benefit an organism. Also the cloning fo plants and animals is talked about and can be regulated by scientists through differentiated cells and nuclear transcription. 

Key Terms:

1) Differentiation: when cells become specialized in structure and function

2) Histones: association of the DNA with small proteins

3) Barr body: the inactive X in each cell of a female condenses into this compact object

4) Transcription factors: assistance given from proteins in order for eukaryotic RNA to function

5) Enhancers: binding of activator proteins to DNA sequences 

6) Silencers: proteins that may bind to DNA sequences and inhibit the start of transcription

7) RNA interface: procedure in which researchers can take advantage of miRNA mechanisms to artificially control gene expression

8) Hometic gene: master control gene that regulates batteries of other genes that actually determine the anatomy of parts of the body

9) DNA microarray: glass slide with thousands of different kinds of single-stranded DNA fragments fixed to it in a tightly spaced array or grid

10) Adult stem cells: cells that are able to give rise to many but not all cell types in an organism 

http://www.youtube.com/watch?v=mUcE1Y_bOQE

Chapter 10 - Molecular Biology of the Gene

Q: What does a DNA polymerase do in the process of DNA replication?
A: DNA polymerase is used to line up new nucleotides on the already existing strand in terms of the base-pairing rules.
Q: What do transcription and translation do?
A: Transcription is where information is transfered from DNA to RNA and translation is where RNA is used to aid in the process of making a new protein.
Q: What is a promotoer?
A: A promoter is a certain nucleotide sequence of bases that starts off a strand of DNA.

Five main facts:
1) Transcription produces genetic messages in the form of RNA.
2) Ribosomes are what aid in the building up of polypeptides.
3) There are certain codons that initiate as well as marks the start of an mRNA message.
4) Mutations change genes.
5) A virus may use a host cell so that it may implement its own DNA into that of the host's cell DNA.

This is a model of mRNA. As you can see there is only one side of the helix. Also note that instead of T, in place there is instead U. This is an easy way to tell whether or not it is a normal DNA strand or and that of RNA.

This chapter focuses on how DNA, RNA is used in the cell. DNA holds genetic coding that allows for genes to be passed on through the process of DNA replication. RNA comes into play during the actual DNA replication process. DNA controls both phenotype as well as genotype. All living organisms are able to replicate their genes and even viruses are able to put their DNA into a host cell so that more of that virus may be made. 

Key Terms:

1) Molecular biology: study of DNA and how it serves as the chemical basis of heredity

2) Bacteriophages: a type of bacterial virus

3) Polynucleotides: a type of polymer that is in DNA

4) Double helix: two strands that make up the structure of DNA

5) DNA polymerase: enzymes that link DNA nucleotides to a growing daughter strand

6) DNA ligase: enzyme that links two polynucleotides together to form a single strand of DNA

7) Transcription: transfer of genetic information from DNA to RNA

8) Translation: transfer of information from RNA into a protein

9) Triplet code: flow of information from genes to proteins

10) Codons: genetic instructions for amino acid sequence of a polypeptide chain 

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

Chapter 9 - Patterns of Inheritance

Q: What is cross-fertilization?
A: This is a process of taking two plants with different traits and crossing the pollen of the two plants with one another.
Q: What is Mendel's law of segregation?
A: When sperm and egg unite at fertilization, each contributes its allele, restoring the paired condition in the offspring.
Q: What do homologous chromosomes do?
A: Homologous chromosomes bear the alleles for each characteristic of the new organism.

Five Main Facts:
1)Genetics use the testcross to determine unknown genotypes.
2) The law of independent assortment is revealed by tracking two characters at once.
3) Mendel's law reflect the rules of probability.
4) Genetic traits in humans can be tracked through family pedigrees.
5) Many genes have more than two alleles in the population.

This is a Mendel chart. This shows the possible phenotypes of the offspring due to the genotype of the parent plants.

Chapter nine focused on genetics. This includes genotype and phenotypes. Mendel studied genetics thoroughly and formulated many useful concepts of genetics. Human genetics follow Mendel's laws. 

Key Terms:

1) Rule of addition: probability that an event can occur in two or more alternative ways is the sum of the separate probabilities of the different ways

2) Pedigree: family tree

3) Carriers: possession of the recessive allele for the disorder but are phenotypically normal

4) Inbreeding: mating of close relatives

5) Amniocentesis: procedure performed between weeks 14 and 20 of pregnancy for fetal testing

6) Complete dominance: dominant allele had the same phenotypic effect whether present in one or two copies

7) Pleiotrophy: influence of multiple characters

8) Polygenic inheritance: additive effects of two or more genes on a single phenotypic character

9) Sex-linked gene: a gene located on either sex chromosome 

10) Hemophilia: a sex-linked gene recessive trait that results in excessive bleeding

http://www.youtube.com/watch?v=X9Qrm6o4tNQ

Chapter 8 - The Cellular Basis of Reproduction and Inheritance

Q: Where do cells come from?
A: Cells are made from preexisting cells through the process of cell division.
Q: How do prokaryotic cells reproduce?
A: Prokaryotic cells reproduce by a type of cell division called binary fission.
Q: What are the three cellular cycles called?
A: G1, S, and G2 and mitosis are the four stages of a cell.

Five Main Facts:
1) All cells come from preexisting cells.
2) Interphase is where the majority of a cells life is spent.
3) Sister chromatids contain identical copies of DNA.
4) Mitosis consists of prophase, prometaphase, metaphase, anaphase and telophase.
5) Anchorage, cell density and chemical growth factors affect the division of a cell.

This diagram shows metaphase. As you can see, the chromosomes are lining up on the metaphase plate so they will be able to be separated by the spindle fibers from the centrosome. 

Cell division is the basis for the reproduction of cells. Chromosomes are duplicated in order to make identical daughter cells. Cells are split into daughter cells through the process called mitosis. Meiosis is the production of sex cells. Four haploid cells are made from this process.

Key Terms:

1) Chromatin: combination of DNA and protein molecules

2) Centromere: two chromatids are joined together tightly at a narrow "waist"

3) Cell cycle: ordered sequence of events that extends from the time a cell is first formed from a dividing parent cell

4) Centrosomes: clouds of cytoplasmic material that in animal cell contain centrioles

5) Cleavage furrow: shallow groove in the cell surface

6) Cell plate: vesicles fuse to form a membranous plate

7) Growth factor: protein secreted by certain body cells that stimulate other cells to divide

8) Anchorage dependence: most animal cells must be in contact with a solid surface

9) Tumor: abnormally growing mass of body cells
10) Diploid cell: any cell with two homologous sets of chromosomes
http://www.youtube.com/watch?v=3kpR5RSJ7SA

Chapter 7 - Photosynthesis: Using Light to Make Food

Q: What is photosynthesis?
A: Photosynthesis is a process that converts light energy into glucose for energy the cell can use.
Q: What are the reactants of photosynthesis?
A: There are two reactants of photosynthesis, carbon dioxide, water, and light energy.
Q: What are the two stages of photosynthesis and how are they connected?
A: Light reactions and the Calvin Cycle are the two stages of photosynthesis and they are linked by ATP and NADPH.

Five Main Facts:
1) 6CO2 + 6H2O+ Light energy ---> C6H12O6+ 6O2
2) Photosystems are certain wavelengths of visible light, absorbed by pigments such as chlorophyll and carotenoids.
3) There are two stages of photosynthesis, light reactions and the Calvin Cycle.
4) ATP and NADPH power sugar synthesis in the Calvin Cycle.
5) Chemiosmosis powers ATP synthesis in the light reactions.

This is a diagram of an electron transport chain with provides energy for synthesis of ATP by chemiosmosis.

Photosynthesis uses light energy to create ATP. There are two stages of photosynthesis, light reactions and the Calvin Cycle. Photosystems make it able for light to be absorbed by pigments. This starts the chemical reaction. The Calvin Cycle converts CO2 into sugars. 

Key Terms:

1) Photosynthesis: chemical reaction in which light is converted into ATP

2) Autotrophs: plants are considered this because they are able to make their own food and sustain themselves

3) Producers: plants that make their own organic molecules and are the ultimate source of organic molecules for almost all other organisms

4) Chlorophyll: light absorbing pigment in the chloroplasts that plays a central role in converting solar energy to chemical energy

5) Mesophyll: green tissue in the interior of the leaf

6) Stomata: tiny pores in the leaf
7) Stroma: thick fluid that fills chloroplasts
8) Thylakoids: system of interconnected membranous sacs
9) Grana: concentrated stacks of thylakoids
10) Carbon fixation: incorporation  of carbon from CO2 into organic compounds

http://www.youtube.com/watch?v=hj_WKgnL6MI

Chapter 6 - How Cells Harvest Energy

Q: What is used in cells in order to harvest energy?
A: A cell uses sugar and air in order to convert it into a viable energy source for the cell.
Q: How are photosynthesis and cellular respiration different?
A: Photosynthesis uses light energy to convert into chemical energy whereas cellular respiration uses air and other reactants in order to create chemical energy.
Q: How many stages are there in cellular respiration?
A: There are three main stages in cellular respiration, glycolysis, citric acid cycle and oxidative phosphorylation.

Five Main Facts:
1) Glycolysis begins respiration by breaking glucose into two molecules of a three-carbon compound called pyruvate.
2) Cells create ATP in order to have energy for the cell to use.
3) When we breathe we are supplying all of our cells with oxygen in order to use for cellular respiration.
4) A concentration gradient is needed for cellular respiration to take place.
5) Fermentation allows for cells to produce ATP without oxygen.

This diagram shows the reactants, products and cycles that a cell goes through during cellular respiration.

Chapter six goes through how cells are able to produce energy to use for cellular function. Photosynthesis and cellular respiration are two ways energy is used. ATP is what these processes create. ATP is the main source of energy for a cell. In order for this process to take place, there must be a concentration gradient of hydrogen otherwise ATP synthase will not be able to take place. 

Key Terms:

1) Cellular respiration: the aerobic harvesting of energy from sugar by muscle cells

2) Redox reaction: movement of electrons from one molecule to another is an oxidation-reduction reaction

3) Oxidation: loss of electrons from one substance

4) Reduction: addition of electrons to another substance
5) Electron transport chain: NADH delivering electrons to the rest of the staircase.
6) Glycolysis: occurs in the cytoplasmic fluid of the cell
7) Citric acid cycle: takes place within the mitochondria
8) Oxidative phosphorylation: involves the electron transport chain and a process known as chemiosmosis
9) ATP synthase: protein complexes built into the inner membrane that synthesize ATP
10) Intermediates: final product of glycolysis also known as a pyruvate

http://www.youtube.com/watch?v=xbJ0nbzt5Kw