Monday, April 02, 2007

IB Testing

Study for the big test with Assessment Statements.

Tuesday, October 17, 2006

Attention Future Classes

I hear that this website is not sanctioned in IB Biology anymore. Good that's how it should be. If you're lucky enough to have found this resource, keep it on the downlow. Also, the notes from first and second tri are all here, you have to use the ARCHIVES on the side to find them. The longer ago the ARCHIVE is dated, the longer ago the notes are from. Hence notes from september/october will be the earliest ones in the ARCHIVES. Use the ARCHIVES. Anyone interested in completing this project? email me at kagcole@gmail.com

Sunday, June 18, 2006

BIO Final yay!

Always remember- WERE YOU THERE?

1.1.5 Outline the advantages of using a electron microscope
-3d images
-1,000,000x zoom
-.2 nm resolution

-inanimate subjects

1.1.7. Compare relative sizes of :
Molecules (1 nm)
Membranes (10 nm)
(viruses 100 nm)

(bacteria 1 micrometer)
(organelles 10 micrometer)

cells (100 micrometers)

1.1.9 Explain the importance of the surface area to volume ratio
Surface area is important for the cell to maintain water and nutrients. Because these things pass through the membrane, which is the surface area, it needs to have a large surface area to volume ratio. However, when the cell increases in size, the volume increases much faster then the surface area. For example, a cube that is 1x1x1 has a surface area to volume ratio of 6:1. But make the cube 2x2x2 the ratio is 24:8 or 3:1. If you change to 3x3x3, its 54:27, or 2:1. As you can see, the volume increases at a larger rate then surface area. That means to stay happy, the cell must keep that ratio in favor of surface area and split after increasing t a size that makes it hard to keep nutrients coming in and out.

1.3.1 Draw a diagram to show the structure of a eukaryotic cell with ribosomes, rough endoplasmic reticulum, lysosome, golgi apparatus, mitochondria and nucleus


1.3.2 State one function of each of the following organelles:
Ribosomes: Site where the Amino Acids are assembled into polypeptides
Rough Endoplasmic Reticulum: Processing, Transport, and temporary storage of protiens
Lysosome: Destorys old or damaged organelles and foreign particles
Golgo Apparatus: Protiens and Lipids undergo final modification then are sorted out and packaged for specific desitinations
Mitochondria: Uses carbon compounds (glucose) and oxygen to generate energy (ATP) that can be used by the cell as an energy source
Nucleus: Carries out the functions of control and cell reproduction

1.3.4 State three differences between plant and animal cells
Plant cells have rigid cell walls
Plant cells contain vacuoles full of water
Plant cells have chloroplasts.

1.4.1 Draw the fluid mosaic model of cell membranes

1.4.4 Define diffusion and osmosis
osmosis- the passive movement of water mole
cules across a partially permeable membrane from high concentration to low concentration.
Diffusion: the tendency of molecules to move from high concentrations to low concentration

1.4.6 Explain the role of protein pumps and ATP in active transport across membranes
Protein pumps act to actively transport sodium, potassium and other materials across the cell membrane to bring in nutrients or dispose of waste
ATP: stores energy in its bonds to fuel cell work, especially transportation in the cell membrane

1.5.3 Describe the events that occur in the four phases of mitosis
prophase: Chromatin condenses into sister chromosomes held by a centromere. Tubules and stuff all made.

metaphase: sister chromosomes line up in the center on metaphase plate attached to centrosome poles
anaphase: the chromosomes are split and pulled apart
telophase: chromatin reforms, nuclear envelope is reformed, clean up occurs.

2.1.2. State that a variety of other elements are needed by living organisms including nitrogen, calcium, phosphorus, iron and sodium
Other elements are needed by living organisms

2.1.3 What do above elements do?
Nitrogen: part of DNA
Calcium: plants use it for transmitting food
Phosphorus: ATP
Iron: Hemoglobin
Sodium: Na-K pump

2.3.3 Explain the effects of temperature, pH and substrate concentration of enzyme activity.
Temperature, pH and substrate concentration a
ll effect enzyme activity by maximizing conditions for reactions or denaturating enzymes (heat and pH only)

2.3.4 Define denaturation:
A structural change in a protein that results in a loss of its biological properties. Heat and pH.

2.4.1 Outline DNA nucleotide structure in terms of sugar, base and phosphate
A DNA nucleotide is a phosphate-sugar-base

2.6.1 Compare the structure of RNA and DNA (sugars, bases, and number of strands)
Compare the structure of RNA and DNA (sugars, bases, and number of strands) RNA: Ribose, Base = Uracil, and single strand DNA: Deoxyribose, base = Thymine, two strand

2.6.2 Outline DNA transcription in terms of the formation of an RNA strand complementary to the DNA strand by RNA polymerase.
Helicase unwinds DNA, RNA polymerases I, II and III come in and do there work. The exons and introns are cut by spliceosome

2.8.3 State that chlorophyll is the main photosynthetic pigment
Chlorophyll in the main photosynthetic pigment.

2.8.8 Outline the effects of temperature, light intensity and carbon dioxide concentration on the rate of photosynthesis
they do shit

3.1.4 Define gene, allele and genome.
Gene- a heritable factor that controls a specific characteristic
Allele- one specific form of a gene, differing from other alleles.
Genome- the whole of the genetic information of an organism

3.1.6 Explain the consequences of a base substitution mutation in relation to the process of transcription and translation, using the example of sickle cell anemia
GAG has mutated to GTG causing glutamic acid to be replaced by valine and hence sickle cell anemia. Good in areas of high malaria to be heterozygous, but fatal in homozygous.

3.2.6 State Mendel's Law of segregation
Alleles distribute independently of one anothe
r

3.3.5 Describe ABO blood groups as an example of co dominance and multiple alleles.
O is recessive A and B are codominant.

3.3.8 Define sex linkage
A trait linked to gender through chromosomes

3.4.2 State that gel electrophoresis involves the separation of fragmental pieces of DNA according to their charge and size
Gel electrophoresis separates fragmented DN
A by charge and size

3.4.5 Define genetic screening
Genetic screening involves testing an individuals genome for genetic predispositions to certain conditions

3.4.6 Discuss three advantages and/or disadvantages of genetic screening
Can help prepare for genetic disorders
Can correct genetic problems in fetus


Can result in genetic discrimination
GATTACA

4.1.1 Define:
ecology: the study of the relationship between organisms and their environment
ecosystem: a community and its abiotic environment
population: a group of the same species in th
e same area
community: a group of populations in a given area
species: a group of organisms which can interbreed and produce fertile offspring
habitat: normal living environment for a species.

4.1.3 Define
Autotroph: producer
Heterotroph: consumer

Detritivore: decomposes organic matter
Saprotroph: decomposes inorganic matter.

4.1.5 Describe what is meant by a web web
A food web shows all the interactions of species in a community

4.2.3 explain sinusoidal growth
a population once established will grow exp
onentially until the environment cannot sustain growth any further and then the population plateaus as K capacity is reached.

4.2.4 Define carrying capacity
Carrying capacity is the maximum amount of individuals a habitat can sustain.

4.2.7 Describe catch-recatch counting technique
Catch, mark, release, catch, count, mark, rele
ase.
4.3.1 Define evolution
Scientists trying to kill god with lies.
A series of slow changes changing one species to another.
4.3.8 Two examples of evolution in response
to environmental change
Antibiotic resistance. Moth in England.
4.4.5 List hiercy
Kingdom, Phylum, Class, Order, Family, Genus, Species


6.1.3 Describe the structure of DNA including parallel and anti-parallel strands.
DNA has two strands which go in the 3-5 direction. A and T are paired as are G and C, they are purines and pymridines. AG are purines, T
C are pymridines.

6.3.6
State
that reverse transcriptase catalyses the production of DNA from RNA
Reverse transcriptase catalyses the production of DNA from RNA. (AIDS as an example)
6.4.2 Outline the structure of ribosomes, includin
g protein and RNA composition, large and small subunits, two tRNA binding sites and mRNA binding sites.
6.4.5 Explain the process of translation including ribosomes, polusomes, start codons, and stop codons
A small riboseribosomal subunit brings a start codon to the mRNA which indicates the mRNA to build protein. Then it is joined by a large ribosomal subunit and a tRNA. Then Methionine is added to the start codon and the process go
es down stream with AA being introduced at the A side, put togther on the P site, and leaving on the E site. Later the tRNA reaches a stop codon and a protein Explain the process of translation including ribosomes, polysomes, start codons and stop codons.

6.5.1 Explain the four levels of protein structure, indicationg each level's significance:
Primary Structure: amino acid sequence
Secondary Sequence: highly patterned sub-structures
Tertiary structure: the overall shape of a single protein molecule
Quaternary structure: the shape or structure of the whole chain of protein molecules

6.6.2 D
escribe the induced fit model
This is a modification to the lock and key model. It states that the active site of an enzyme is not precise, but roughly the right shape. The enzyme moves so the substrate fits into it, which causes but it stresses the substrate and the enzyme moves to fit the enzyme. It is like how a glove changes its shape when you pull it over your hand. (the glove is the enzyme). This tendency causes the enzyme to stress the bonds of the substrate. It can also change the pH or covalently bond with the substrate, which causes the activation energy to lower. The stress on the enzyme can help break bonds in the substrate.

6.6.4
Explain the differences between competitive and non competitive inhibitions with reference to one example of each
Competitive inhibitors compete directly with substrates at the active sites. They block the entrances to the active sites. The neurotoxin Diisopropylfluorophosphate binds to the active site of cholinesterase, which produces a neurotransmitter responsible for movement.
Noncompetitive inhibitors change the shape of the active site by binding to the enzyme somewhere else. This contorts the entire shape of the enzyme rendering it unable to work. Cyanide binds to oxidase, changing its shape so it can’t perform respiration

7.1.6 Explain the relationship between a mitochondria’s shape and its function
The mitochondria’s cristae are folded to allow maximum surface area to create a proton gradient. The spaces between the cristae holds protons.

7.2.6 Explain the relationship between the structure of a chloroplast and its function.
Thylakoid have large surface area to increase light absorption. The small spaces inside the thylakoid holds protons.

7.2.9 Explain the concept of limiting factors with reference to light intensity, temperature and concentration of carbon dioxide.

8.3.1 State the difference between autosomes and sex-chromosomes.
Autsomes are identical pairs of chromosomes in a species despite gender.
Chromosomes that determine sexual characteristics are sex-chromosomes.

8.4.1 Define polygenetic inheritance
Multiple genes code for one trait

13.2.2 Describe the process of mineral uptake into roots by active transports

13.2.3 Explain the process of root uptake by root epidermis cells and its movement by the symplastic and apolplastic routes across the root to the xylem.

13.2.7 State that guard cells close and open stomata
Guard cells close and open stomata

13.3.1 Draw the structure of a dicot


13.3.3 Distinguish between pollination, fertilization and seed dispersal.

d.1.2 Outline the experiments of Miller and Urey in the origin of organic compounds
The replicated primordial soup conditions and organic compounds were formed, including amino acids.

d.2.3 Explain the Darwin-Wallace theory of evolution by natural selection
The fittest survive to pass on their traits.

d.3.1 Describe the eveidence for evolution as shown by the geographical distribution of living organisms, including the distribution of placental, marsupial and monotreme animals.

d.3.10 Explain the evidence of evolution provided by homologous anatomical structures, including vertebrate embryos and the pentadactyl limbs.
Homologous structures, for example seal flippers and human hands. Vertebrate embryos essentially show reverse evolution.

d.3.11 Outline two modern examples of observed evolution. One example must be the changes to the size and shape of the beaks of Galapagos finches.
Galapagos finches
British Moths.

d.4.4 Outline the trends illustrated by the fossils of Australopithecus including A. afarensis, A. africanus and A. robusto and homo including H. habulis, H erectus, H neadanderthalensis and H sapiens.

d.5.4 adaptations may occur as the result of an allele frequency increasing in a populations gene pool over a number of generations.

d.5.6 State that a species is a potentially interbreeding population having a common gene pool.

d.5.9 Discuss ideas on the pace of evolution including gradualism and punctuated equilibrium.
Gradualism is the slow change from one form to another. Punctuated equilibrium, however, implies long periods with no change and short periods of rapid evolution. (natural diasters change conditions)

d.6.2 Explain how the Hardy-Weinberg equation (p2+ 2pq + q2 is derived)
P represents the probability of a dominate (hetro or homo) individual and q represents the probability of a recessive individual (homo), so 1 individual is represented by P+Q, or the sum of the probability that is dominate and and the probability it is recessive. This is of course equal to 1. When one theoretical individual reproduces with another individual, their probabilities are multiplied together. (P+Q) * (P+Q) yielding P^2 + 2pq + q^2

d.6.5 State the Hardy-Weinberg principle and the conditions under which it applies
Random mating, large population. No mutation, nor mortality nor migration. Under these conditions population remains at equilibrium originally established

Monday, February 13, 2006

Retroviruses and mutations

Chapter 15 Retroviruses and Chapter 14 Gene Regulation
I Retroviruses and Reverse Transcriptase
-A. Overview
--1. Viruses that use the enzyme reverse transcriptase to make sequences of single and double stranded DNA sequences from RNA.
--2. Example (need to know): AIDS (Acquired Immune Deficiency Syndrome):
---a. The genome of HIV is made of RNA, not DNA
---b. Reverse transcriptase has a high error rate (up to about 1 in 2,000 bases when transcribing RNA into DNA, which allows retroviruses to mutate rapidly)
---c. When HIV enters lymphocyte cells, it makes DNA from RNA using reverse transcriptase
---d. this DNA becomes inserted into the lymphocyte’s chromosome
---e. now when the lymphocyte replicates, the viral DNA is replicated as well.
---f. when the DNA is transcribed it produces viral mRNA, some of which will eventually be translated into viral proteins
---g. drugs can fool reverse transcriptase into incorporating it into the growing DNA strand instead of the HIV which then halts further DNA synthesis
---h. the reverse transcriptase of the virus HIV prefers AZT 3phosphate to the normal nucleotide, deoxribose nucleoside triphosphate that has no 3 hydroxyl to which to add the next nucleotide therefre chain elongation comes to a halt and the virus cannot replicate
-B. Use of Reverse Transcriptase in Molecular Biology
--1. Reverse transcriptase can be used to make DNA from mature mRNA
---a. example: the mature mRNA that codes for human insulin can be made into DNA using reverse transcriptase.
---b. This is then spliced into host DNA such as E. Coli (most E. Coli is good) which reproduce, making more of the DNA that codes for insulin, making E. Coli into our slaves!
II. Gene Regulation
-A. Overview
--1. In all species, most of the genes, most of the time are shut down and only a very small portion are transcribing/translation in order to make proteins
--2. There must be a coordination between when a gene is transcribed and cellular metabolism
--3. Two basic “ports” of a gene
---a. Coding region- codes for mRNA and protein
---b. Regulator region- controls transcription of the coding region
-B. Gene Regulation in prokaryotes
--1. Operon: several protein coding regions on a gene under the control of a regulatory region consists of a prometer and an operator.
--2. Example: The Lac Operon Complex in E. Coli
---a. E. Coli can use lactose when glucose is not available
---b. The enzymes necessary to do this are normally no produced by E. Coli.
---c. However, they can be produced when lactose is present
----i. therefore lactoscis is an inducer molecule
-C. Gene regulation in Eukaryotes
--1. Much less is known than in prokaryotes
--2. Control systems utilizing regulatory proteins to bind to DNA much like operon represors, also exists in eukaryotes
--3. Some genes are activated by:
---a. heat
---b steroid binding
---c. uncoiling of nucleosomes
III. Chapter 17 DNA changes
-A. DNA is stable
--1. bases are protected
--2. Tigh wrapping around histone (eukaryotes) and coiling don’t allow for direct access to DNA
--3. Complimentary base pairings to fix any accidental changes
-B. Frequency of Mutations
--1. In humans and other mammals, uncorrected Errors in mutations occur at the rate of about 1 in 50 million nucleotides added to the chains. With 6 billion base pairs in a human cell, that means each new cell contains about 120 new mutations.
--2. However, not that big of deal because of synomous codons and repetitive DDNA that doesn’t code for proteins.
--3. For eukaryotes, this often happens during S phase of interphase where all DNA is replicated into 2 copies called chromatids.
-C. DNA Damage:
--1. Mutagens are agents that cause mutations- a failure to repair DNA
--2. Radiation forms of energy (gamma rays, x-rays, UV) that penetration the cells and damage DNA
--3. Chemicals damage DNA through chemical reactions
-D. 3 levels of mutational change
--1. Point or Single Base Mutations
---a. Involves changes in one or only a few nucleotides in DNA
---b. 3 types:
----i. Base substitution: Substitution of a single base pair. 3 outcomes:
-----Silent mutation has no effect on structure of resulting protein because of degenerative
-----Neutral Mutations- changes in amino acide in protein but has no effect
----- Drastic mutation- has serious effects on structure or proteins. Example: Sickle Cell disease and Tay Sacs disease.
----ii. Chain Termination mutations- either new mutated codon produced is stop codon or stop codon is made into a not stop codon
---iii. Frameshift mutation- results from the deletion and additions of bases into a nucleotide sequence. These cause shifts in the reading of codons during transcription and results in an abnormal polypeptide
--2. Chromosomal Mutation
---a. involves major changes in chromosomal structure rather then simple DNA sequence changes
---b. There is a complete breaking, misalignment and rejoing of the double helix in one or more chromosomes.
---c. Three types:
----i. delections- entire sections left out
----ii. Inversion- a middle fragment of DNA may flip over and rejoins
----iii. Translocation- 2 nonhomologous chromosomes break, swap segments and fuse together
--3. Transpositions:
---a. certain segments of DNA frequently “jumps” (sometimes called jumping genes) to new locations in the same DNA molecule or a different one these are called transposable elements
---b. Not caused by mutagens but are considered mutagens themselves because they cause the mutations
---c. First found in corn and then in E. Coli
---d. discovered by Barbara Clinton (nobel Prize)

Tuesday, November 29, 2005

Chapter 7 notes: Photosynthesis

I. Photosynthesis Overview:
-A. Highly endergonic process where the energy of sunlight is used to bond molecules together to produce glucose and other substances.
-B. Makes use of visible light (400-760 nm)
--1. ROYGBIV (red, orange, yellow, green, blue, indigo and violet)
--2. Plants make more use of red, orange, blue, indigo and violet than green and yellow.
-C. 6CO2 + 12H2O => C6H12O6 + 6H2O + 6O2
--1. Change in energy = 686 kcal/moles
-D. Two parts of photosynthesis
--1. Light-dependent reactions
---a. Needs a continual supply of sunlight
---b. Occurs in the thylakoid membrane and lumen of the thylakoids
---c. H2O is broken down by sunlight (photolysis) which makes O2
---d. Sunlight energy is used to make intermediate compounds (ATP and NADPH) that are used in the light independent reactions later on
--2. Light independent reactions (Calvin Cycle)
---a. Can carry out for some time in darkness, but it also occurs in light
---b. Occurs in the stroma of chloroplasts
---c. glucose, amino acids and other organic compounds are made.
II. Chloroplasts
-A. Have a double membrane with outer and inner membrane
--1. Stroma is the watery area within inner membrane, which contains starch grains, enzymes, ribosomes, DNA and lipids.
---a. Calvin cycle takes place here.
-B. Have a third membrane system that are foldings which create thylakoids.
--1. Contain many proteins
--2. Occur in stacks called grana.
--3. Lumen is channel like, continuous interior for accumulation of H+.
--4. Light dependent reaction takes place here.
III. Photosystems I and II
-A. Contained in the thylakoid
-B. Contain:
--1. Hundreds of pigment molecules that absorb and concentrate light energy such as:
---a. Chlorophyll a
---b. Chlorophyll b
---c. Carotenoids
-C. An absorption spectrum shows wavelength of light that is absorbed by pigments.
-D. The action spectrum makes connection between light absorption and photosynthetic process
--1. It shows what percent of wavelength of light is used most efficiently in photosynthesis.
-E. Reaction Center
--1. Contains one molecule of chlorophyll a and a protein
---a. Those that absorb light most strong at 700 nm are Photosystem I or P700
---b. Those that absorb light most strong at 680 nm are Photosystem II or P680
--2. Light energy from light harvesting complex is concentrated and transformed into chemical energy
---a. This excites an electron that is immediately captured by an electron acceptor and put to work in the ETS
---b. Water in the lumen of the thylakoid keeps the supply of electrons coming and procedure Oxygen as a waste product
-F. Electron Transport System
--1. Contain numerous electron carries arranged in thylakoid
--2. Two roles
---a. Use energy of electrons to concentrate H in the lumen where their free energy can be used to generate ATP
---b. Electrons (along w/ protons) are used to reduce NACP+ to NADPH+H+
IV. Light Dependent Reactions of photosynthesis
-A. Three main processes
--1. Non cyclic photophosphorylation
---a. Photosystems I and II act together to make the chemiosmotic gradient in order to reduce NADP+ to NADPH+H+ and establish H+ gradient so ATP can be made
---b. The energy from a photon is used to excite an electron in Photosystems II which is passed into the ETS (and therefore draws H+ to the lumen of thylakoid and onto photosystem I in order to replace another electron that has been excited by a photon that is finally accepted by NADP+ in order to make NADPH+
---c. his original electron excited in photosystem II is replaced by photolysis of water (water split by light) and Oxygen and Hydrogen are formed as byproduct
--2. Cyclic photophosphorylation
---a. Photosystem I acts alone to make a chemiosmotic (H+) gradient so ATP can be made
---b. No reduction of NADP+ occurs
---c. This occurs because there is plenty of light and too much NADPH is being made which creates a shortage of NADP that is the final electron acceptor in noncyclic phosphorylation
---d. Therefore electron passes along carriers (drawing H+) and back to photosystem I instead of being accepted by NADP+
--3. Chemiosmotic Phosphorylation
---a. H+ is built up. Goes through ATPase. Makes ATP. Thanks Jansen for giving us all of the notes.

Chapter 6 Notes: Energy and Chemical Activity in the Cell

I. Pages 126- 132
-A. Energy: the ability to do work.
-B. 1st Law of Thermodynamics: Energy can neither be created nor destroyed, but it can be converted from one form to another.
-C. 2nd Law of Thermodynamics: Energy transitions lead to an increase in disorder (Entrophy)
-D. Figures 6.4; 6.6; 6.7
-E. Free Energy: The available energy after bonds are broken in a chemical reaction
-F. Activation Energy: The energy required to get a reaction started
-G. Transition State: Point at which atoms of molecules in a reaction start coming apart
-H. Reversible Chemical Reaction: Where molecules can react both ways (break apart and come together), until the molecules reach a state of equilibrium
-I. Catalysts: A substance that speeds up a chemical reaction
-J. Exergonic vs Endogonic reactions: Exergonic puts out energy, endogonic takes it in
II. Enzymes
-A. Characteristics
--1. Globular proteins that act as biological catalysts
--2. Lower the activation energy
--3. Speed up reactions to rates useful to the cell.
--4. Has no effect on change in energy of a given reaction
--5. Each enzyme grabs specific molecule in the reactant called substrate
--6. Are unaltered by reactions and ready to go again
--7. Can be catabolic (breaks) or anabolic (builds)
-B. Enzyme specificity
--1.Enzymes contain an active site which is a specific location on the enzyme where reactions occur
--2. Generally, a given enzyme is able to catalyze only a single chemical reaction or at most, a few reactions involving substrates sharing general structure
--3. Enzymes and substrates meet by random motion of molecules and connections
--4. The connection is made by weak ionic bonds and H bonds between substrate and active site
--5. The enzyme undergoes a slight change in shape brining reactive amino acid R-groups in the enzyme closer to the substrates (induced fit), which lowers activation energy by:
---a. Physically stressing substrates which helps break bonds
---b. Changes pH with active site
---c. Can covalently bond with substrate
--6. The entire reaction occurs in thousandths-millionths of a second
-C. Enzyme Helpers
--1. Cofactors
---a. Non-proteins that assist enzymes to carry on activity
----i. Some are metal atoms, Zinc, Iron, or Copper that bind reactants to the enzyme
----ii. Some are organic, called coenzymes. Most vitamins are coenzymes
-D. Metabolic pathways
--1. Sequence of enzyme-catalyzed reactions
--2. Product of first reaction becomes reactant for the next enzyme, and so on down a chain
---a. For example the Calvin cycle of photosynthesis
---b. Once the final product is abundant, acts to stop first enzyme in the pathway, to stop production
-E. Mechanisms of Enzyme Control
--1. Some enzymes can remain inactive until chemicals prompt action
--2. Others are active but chemicals inactivate them
--3. Common ways of interference:
---a. Competitive- blocks substrates by fitting into active site.
----i. Example: penicillin binds to the prokaryotic enzyme that produces peptoglycen, the building blocks of a bacteria’s cell wall. The bacteria then produces a malformed wall which ruptures.
---b. Non-competitive- changes shape by binding to the enzyme
----i. This alters enzyme’s shape enough so substrate doesn’t fit well, slowing rate of reaction, or;
----ii. Changes enzyme’s shape so substrate doesn’t fit at all, stopping rate of reaction.
-F. Allosteric enzyme system
--1. Enzyme has two binding sites:
---a. The usual site where substrate binds
---b. An allosteric site where a chemical can inhibit or activate the enzyme binding with the substrate
----i. Depends on cell’s requirements
-----example: in bacteria, there is a metabolic pathway where threonine is converted to isoleucine by enzymes when isoleucine is abundant, it binds to allosteric site at the beginning of the pathway and slows down production of isoleucine. As isoleucine is used and concentration decreases, production speeds up.
----ii. This is called negative feedback.
-G. Rates of enzyme reaction are influenced by:
--1. Substrate concentration
---a. As substrate concentration increases, enzymes have easier time of finding reactants
---b. Enzyme saturation
----i. All active sites are engaged at once (Terminal Rate of Reaction)
-2. pH
---a. Each enzyme has an optimal operating pH
-3. Temperature
---b. Each 10 degrees C increased ROUGHLY doubles reaction rate
---c. Extreme heat denatures enzyme.
III. Adenosine Triphosphate (ATP)
-A. ATP Basics
--1. All living cells use ATP
--2. Energy can’t be taken directly from lipids, carbohydrates and proteins
--3. Energy must be transferred from the high-energy ATP bond
--4. ATP is an energy coupling agent and not a fuel
--5. It is produced by one set of reactions and immediately consumed by another reaction
--6. When energy is needed, it is released by the chemical bonds in ATP
-B. ATP is consumed (broad):
--1. In synthesis of polysaccharides, fats, proteins and assembly of DNA + RNA
--2. Movement:
---a. Cilia/Flagella
---b. Muscled contraction
---c. Intracellular transport
---d. Chromosome separation
---e. Cytoplasmic separation
--3. Active transport of molecules and ions through plasma membrane
---a. Na/K Pump
-C. ATP Structure
--1. 3 parts:
---a. adenine base
---b. ribose
---c. 3 phosphates
-D. Release of Energy
--1. When the third phosphate group of ATP is removed by hydrolysis, 7.3 kilocalories/mole of free energy is released.
ATP + H20 => ADP + PO4 + ENERGY
--2. The phosphate is easily removed due to close negative charges of the oxygen in each phosphate
--3. ATPase is an important enzyme in this process
-E. Work of ATP
--1. Released energy of ATP is coupled with endogonic reactions in which ATP is put to work
--2. These reactions begin with Phosphorylation
---a. Phosphate from ATP is added to different molecule (the phosphorylated molecule)
---b. This molecule gains free energy from phosphate and enters into a chain of chemical reactions
-F. Cycling of ATP
--1. The terminal phosphate is efficiently restored from ADP to ATP
--2. Most common means of ATP regeneration are:
---a. Substrate level phosphorylation in the cytoplasm (enzymes)
---b. Mitochondria by oxidative phosphorylation
---c. Chloroplasts by photphosphorylation
---d. Bacterial cell membranes/wall
-G. Process of making ATP
--1. Redox Reaction (Oxidation and Reduction)
---a. Much of life depends on the shifting and passing of electrons
---b. Electron shifting takes place in paired reactions called redox reactions involving both oxidation and reduction.
---c. Oxidation- process where electrons are removed from a substance
----i. reducing agent is the atom giving electron away
----ii. Protons (H) are drawn towards e(lectrons)
----iii. OIL (Oxidation is losing electron)
---d. Reduction- process where electrons are added to a substance
----i. Oxidation agent is the atom that accepts e
----ii. Proton drawn toward e
----iii. RIG (Reduction is gaining e)
---c. Therefore, when a molecule is oxidized, the electrons almost instantly join with another molecule, which becomes reduced
-H. Electron Transport System (ETS)
--1. Electrons get passed around by:
---a. Coenzymes
---b. Stationary carriers
--2. Coenzymes:
---a. Referred to as electron carriers
----i. Gains electrons (reduced) with protons close behind and gains free energy
----ii. Passes them on to another molecule in a lower free energy state
---b. small and mobile
-NAD + 2H => NADH + H
-NADP + 2H => NADPH + H
-FAD + H => FADH2
--3. Stationary Electron Carriers
---a. Large, stationary carriers of electrons found embedded in membranes
---b. Most are proteins found in inner membranes of chloroplasts (thylakoids) and mitochondria (inner membrane) and fall into a family of proteins called cytochromes
-I. Chemiosmotic Phosphorylation (Chemiosmosis)
--1. Oxidative phosphorylation and photophosphorylation
--2. Use an osmotic concentration gradient of H ions to produce ATP
--3. Energy from electrons being passed along ETS in membranes draws protons to one side of a membrane and in a small space
--4. H accumulates and creates electrochemical gradient
---a. H volts difference
---b. chemical difference
---c. pH more H = more acidic
---d. Simple concentration gradient
--5. H then flows down through channels via protein ATPase
--6. This flow of H powers ATPase to phosphorylate ADP into ATP

Chapter 6 Resources and Objectives

Need to learn about enzymes? For some basic information go here.
For the animations shown in class that explain everything, go to here.
ATP Synthesis as shown in class here.

Insights:
When you understand the basic principles of enzymes, the rest is just logic. Try to keep a few specific examples in mind, they are all over the internet or you can just use the ones here.
The thing to remeber about ATP is that it isn't the ATP that is energy, it is the bonds between the phosphates. The A and the P's last forever, and are continously put together and broken apart for energy. The interaction of electrons and protons (which are just hydrogens) is important to understand.
OBJECTIVES ARE ALWAYS ON THE TEST IN THE EXACT FORM YOU SEE HERE

Objectives:
2.3.1 Define enzyme and active site:
An enzyme is a protein that catalyzes (accelerates) a chemical reaction
An active site is where the binding of substrates and reactions occur.

2.3.2 Explain enzyme substrate specificity
The active sites of enzymes are shaped to fit specific substrates i.e. Catalase is shaped to fit hydrogen peroxide) This is called the lock and key model.

2.3.3 Explain the effects of temperature, pH and substrate concentration on enzyme activity.
Enzymes typically have a higher rate of reaction at higher temperatures, and lower at lower temperature. However, once it becomes to heated, the enzyme is denatured and ceases to work.
Different enzymes perform better at different pH. They react slower when their optimal pH is altered. If put in a solution that is too basic or acidic, then they are denatured and cease to work.
When the substrate concentration is increased, the rate of reactions in enzyme increases until all active sites are engaged. Then the enzyme reacts at a maximum until substrate concentration is lowered.

2.3.4 Define denaturation
Denaturation is the structural change in proteins that results in a loss (usually permanent) of its biological properties. Only heat and pH are denaturating agents.

2.3.5 Explain the use of pectinase in fruit juice production and one other commercial application of enzymes in biotechnology
Pectinase breaks down the pectin in the cell walls of plants- which softens them and makes from easy extraction of fruit juice.
Glucose Isomerase breaks glucose into fructose which makes the high fructose corn syrups in many products. High fructose syrups are lower in caloric value and are better sweeteners.

6.6.1 State that metabolic pathways consist of chains and cycles of enzyme catalyzed enzymes
A metabolic pathway consists of chains and cycles of enzyme catalyzed enzymes.

6.6.2 Describe the induced fit model (VERY LIKELY TEST QUESTION)
This is a modification to the lock and key model. It states that the active site of an enzyme is not precise, but roughly the right shape. The enzyme moves so the substrate fits into it, which causes but it stresses the substrate and the enzyme moves to fit the enzyme. It is like how a glove changes its shape when you pull it over your hand. (the glove is the enzyme). This tendency causes the enzyme to stress the bonds of the substrate. It can also change the pH or covalently bond with the substrate, which causes the activation energy to lower. The stress on the enzyme can help break bonds in the substrate.

6.6.3 Explain that enzymes lower the activation energy of the chemical reactions that they catalyze
Enzymes lower the energy necessary to cause a chemical reactions. Normally chemical reactions occur through random encounters between molecules. Enzymes bring the reactants together at a faster rate, reducing the randomness of reactions.

6.6.4 Explain the differences between competitive and non competitive inhibitions with reference to one example of each
Competitive inhibitors compete directly with substrates at the active sites. They block the entrances to the active sites. The neurotoxin Diisopropylfluorophosphate binds to the active site of cholinesterase, which produces a neurotransmitter responsible for movement.
Noncompetitive inhibitors change the shape of the active site by binding to the enzyme somewhere else. This contorts the entire shape of the enzyme rendering it unable to work. Cyanide binds to oxidase, changing its shape so it can’t perform respiration.

6.6.5 Explain the role of allostery in the control of metabolic pathways by end-product inhibition
Allosteric enzymes have an allostearic site in addition to normal enzymic areas. Enzymes in metabolic pathways are generally allostearic, and the final product binds with the first enzyme in the allostearic site, to slow down or halt production. This is called negative feedback.

7.1.1 State that oxidation involves the loss of electrons from an element whereas reduction involves a gain in electrons and that oxidation frequently involves gaining oxygen or losing hydrogen, whereas reduction frequently involves loss of oxygen or gain in hydrogen
Oxidation involves the loss of electrons from an element. (OIL) Reducing agents (ones that lose electrons) frequently loses hydrogen or gains oxygen.
Reduction involves the gain of electrons to an element. (RIG) Oxidizing agents (ones that gain electrons) frequently loses oxygen or gains hydrogen.

7.1.5 Explain oxidative phosphorylation in terms of chemiosmosis
The synthesis of ATP is coupled to electron transport and the movement of protons (H+ ions) - the chemiosmotic theory. Briefly, the electron transport carriers are strategically arranged over the inner membrane of the mitochondrion. As they oxidize NADH + H and FADH2, energy from this process forces protons to move, against the concentration gradient, from the mitochondrial matrix to the space between the two membranes (using proton pumps). Eventually the H+ ions flow back into the matrix through protein channels in the ATPase molecules in the membrane. As the ions flow down the gradient, energy is released and ATP is made. Or watch this

Chapter 5 Notes: Plasma Membranes

I. Structure
-A. Basic Characteristics
--1. Thickness of 7-8 nm
--2. Made up of phospholipids
--3. Have different proteins and cholesterol dispersed between phospholipids
-B. Fluid Mosaic Model
--1. Membrane can move and yet is very stable
--2. Hydrophobic and Hydrophilic properties cause this
-C. Proteins are visible by freeze fracture technique where tissues are frozen and split along the phospholipid bilayer through hydrophobic tails and an electron microscope
II. Three Components
-A. Cholesterol
--1. Amphipatic
---a. Hydrophilic and Hydrophobic
--2. Prevents fatty acids from packaging tightly
--3. Decreases permeability to small water and soluble molecules
-B. Proteins
--1. Functions
---a. Hormone binding site
---b. Some are enzymes that carry out reactions in membrane
---c. Electron carriers
---d. Channels for passive and active transportation of materials in and out
--2. Categories of Proteins
---a. Integral proteins
----i. Amphipathic
----ii. Some go through only one layer (lipid anchored) others are transmembranal
---b. Peripheral protein
----i. lie on the surface of membrane
----ii. Usually attached to the protruding portions of integral proteins
-C. Glycocalyx
--1. Visible by TEM as a fuzzy outermost region of cell
--2. A sugar coating over membrane surface
---a. made up of short chains
---b. glycoproteins are attached to proteins
---c. glycolipids are attached to lipids
--3. Functions
---a. protects the cell
---b. Helps cell to:
----i. recognize
----ii. Identify others
----iii. Interact with chemicals, viruses and bacteria
III. Transportation:
-A. Overview
--1. The admission/rejection of substances depends on:
---a. size
---b. polarity
---c. electrical charges
--2. Lipid bilayer is permeable to:
---a. Water, small uncharged molecules like oxygen and carbon dioxide
--3. Lipid bilayers is not permeable to:
---a. ions, like K+, Na+, Ca+ and CI-, HCO3_
---b. Hydrophilic molecules like glucose
---c. Macromolecules like proteins and RNA
-B. Two categories of cellular transportation
--1. Passive transportation doesn’t require ATP, or energy and includes 3 types:
---a. Diffusion: moves from high concentration to low concentration
---b. osmosis- water moves across selectively permeable membrane from high concentration to low concentration
---c. Osmotic pressure is the tendency of water to cross a selectively permeable membrane, proportional to the difference of concentrations
---d. Pressure in cells can change depending on the environment outside of cells
----i. Isotonic environment is the same inside and outside the cell
----ii. Hypotonic environment is a higher concentration of water inside the cell
----iii. Hypertonic is a higher concentration of water outside
---e. Facilitated diffusion
----i. Transport proteins change their shape to allow specific diffusing molecules to enter from the outside.
----ii. “gated” can be opened or closed
--2. Active Transportation
---a. Requires ATP
---b. If proteins are transportation proteins, they have four characteristics:
----i. Transmembranal
----ii. Each one has sites whose shape matches the molecules it transports
----iii. Work faster when large number of molecules are present
----iv. Work through conformation changes in shape
---c. Five kinds of active transport
----i. Sodium/Potassium pump
----- Almost one third of all ATP generated by mitochondria in animal cells is used for this pump
----- Actively transports 3 Na+ ions out for each 2 K+ in cell
----- can help in two ways: establishing a net charge across the membrane, which prepares muscles for contraction and accumulation of Na+ outside draws water, enabling osmotic balance
----ii. Calcium Ion pump- important in animals for nerves and muscles
----iii. Proton pumps- helps with storage of energy in mitochondria and chloroplasts
----iv. Exoctosis- process through which materials are expelled
----- upon contact a vesicle fuses with the membrane dumps load and becomes part of the membrane
----v. Endocytosis- engulfs materials by becoming filled with materials than pinching off
----- phagocytosis: cell eating, like white blood cells eating pathogens. The plasma membrane surrounds an object, pinches off and forms a phagocyte that fuses with lisosome
----- Pinocytosis: cell drinking- eats liquids
----- Receptor remediated endocytosis: engulfs cell after protein recognition
IV. Cell Junctions
-A. Involved in:
--1. Cell to Cell transport
--2. Barriers between cells
--3. Structural support
-B. Four kinds
--1. Gap junctions (animals only)
---a. proteins that firmly hold adjacent cells together while forming pores (1-2 nm) between cells that allow passage of water, ions, sugars, hormones
--2. Plasmodesmata (plants)
---a. Fine strands of cytoplasm extend through pores in the cell wall connecting each other
---b. Not structural
--3. Desmosomes (animals)
---a. bind together
---b. filaments provide support
---c. common in cells that need to be tough
--4. Tight junctions (animals)
---a. proteins that prevent passage through intercellular space
---b. actin filaments provide support

Chapter 6 Enzyme Packet

I. Enzyme Packet
-A. Enzyme Types:
--1. Hydrolases break down proteins, carbohydrates, and fats such as during the process of digestion. They do this by adding a water molecule, thus the name hydrolases.
--2. Isomerases catalyze the rearrangement of chemical groups within the same molecule.
--3. Ligases catalyze the formation of a bond between two substrate molecules through the use of an energy source.
--4. Lyases catalyze the formation of double bonds between atoms by adding or subtracting chemical groups.
--5.Oxidoreductases make oxidation-reduction (the process by which an atom loses an electron to another atom) possible.
--6. Transferases transfer chemical groups from one molecule to another. Your body contains many enzymes from each group.
-B. Food Enzymes:
--1. Lipase breaks down fats that are found in most dairy products, nuts, oils, and meat.
--2. Lactase breaks down lactose (milk sugars).
--3. Protease breaks down proteins that are found in meats, nuts, eggs, and cheese.
--4. Amylase breaks down carbohydrates, starches, and sugars, prevalent in potatoes,fruits, vegetables, and many snack foods.
--5. Cellulase breaks down cellulose, the fibrous structure that makes up most plant cell walls -C. What our body produces:
--1. Our body produces virtually all of the above listed food enzymes, with the exception of cellulose. Most non-Caucasians do not have lactase (lactose intolerant)
-D. Saliva enzymes digest:
--1. 30% of proteins
--2. 60% of starches
--3. 10% of fats
--4. Only active in pH over 5
--5. Only work 30-60 minutes after ingestion
-E. Cooked and processed foods
--1. Most raw foods contain the necessary enzymes for successful digestion
--2. When cooked, enzymes denatured.
--3. 20 million Americans have digestive malfunctions
--4. Our diet does not supply enzymes needed
-F. Pancreatic, Plant and Microbial enzymes
--1. Pancreatic enzymes:
---a. derived from animal tissues
---b. activity limited to a narrow pH range
---c. very specific in action
---d. activated by body’s enzymes
---e. easily destroyed by acidity of the stomach
---f. delayed effect
---g. does not break down fibers/certain carbohydrates
---h. no sucrose, maltase, or lactase activity
--2. Plant enzymes:
---a. derived from certain plants such as pineapple or papaya
----b. effective within a broad pH range
---c. predominantly proteolytic activity
--3. Microbial (fungal) enzymes:
---a. derived from selected microorganisms by the process of fermentation
---b. broad pH range (approximately 3.0 - 9.0)
---c. activated in upper stomach
---d. begin working immediately
---e. broad action on a variety of foods
-G. Why take supplemental enzymes?
--1. Our diet does not allow us many enzymes
--2. Enzymes are good for digestion
--3. Ergo, take enzymes because they are good and you have too few.

Chapter 4 Notes:

II. Prokaryotes
-A. Characteristics
--1. Single Celled
--2. 1-10 micrometer
--3. 4 billion years old
--4. Most likely only form of life for 2 billion years
-B One way of categorizing prokaryotes: Energy Sources
--1. Heterotrophs- other feeding
---a. Requires complex food sources such as carbohydrates, lipids and proteins
--2. Autotrophs- self feeding
---b. produces own food from inorganic sources
-C. Types of Prokaryotes
--1. Parasites or Pathogens- feed on living hosts
--2. Decomposers use dead organisms and wastes as energy sources
--3. Photoautotrophs blue green bacteria use photosynthesis
--4. Fermentation absorb organic substances, convert them and release
--5. Nitrogen Fixation- bacteria convert unusable N2 into a N compound
-D. Structure and Function
--1. Cell Wall
---a. dense tough protective outer layer made from peptidalglycon
--2. Plasma membrane (Cell membrane)
---a. Inside and outside cell wall
---b. Controls entry and exit of substances
--3. Mesosome
---a. Inward extension of plasma membrane that may aid in division of cell
---b. Increases the cell’s surface area for metabolic reactions
--4. Cytoplasm
---a. Material inside cells other than DNA materials
---b. Holds/suspends organelles
--5. Ribosomes
---a. Very small organelles that assemble proteins
--6. Flagellum or pili
---a. Long tails that spin in order to move the bacteria or many small ones used for environmental interaction
--7. Naked DNA
---a. A closed circuit of double stranded DNA that stores genetic information in nucleoid
--8. Plasmids
---a. Small amount of DNA that are separate from chromosomes
---b. Plasmids enter the bacterial cells with ease
III. Eukaryotes
-A. Plants, Animals, Fungi and Protists
-B. Different than prokaryotes in that they have man organelles in the cytoplasm
--1. Physically separate chemical reactions in the space of cytoplasm
--2. Separate chemical reactions in time
-C. Surface structures
--1. Cell wall
---a, occur among protests, fungi and plants
---b. protect and support the cell
---c. in plants, cellulose polymers are organized into micro fibrils and the criss-cross patterns
--2. Plasma Membrane
---a. Keeps inside in and outside out
---b. Highly active in transportation
---c. double phospholipid with polar heads and nonpolartails
---d. Interspersed in membrane are enzymes, transport proteins, supporting protein, glycolipids and glycoproteins
-D. Internal support (cytoskeleton)
-1. Vast maze like structure of supporting protein fibers made up of three fibrous elements:
---a. Actin filaments
----i. Diameter of 6 nm
----ii. 2 slender chains of actin wound up
----iii. Important in muscle contraction, amoeboid movements and cell division
---b. Intermediate filaments
----i. Diameter of 10 nm
----ii. Many are made of protein keratin
----iii. Common in epithelial cells (inner and outer line of the body)
---c. Microtubules
----i. diameter of 25 nm
----ii. Are made up of spiraling, two part subunit of tubulin (a globular protein)
----iii. Make up spindle fibers that move chromosomes during cell divisions
----iv. Form many structures important in cell movement
-E. Movement
--1. Organelles can help move cells
--2. Centrioles and Basal Bodies
---a. Come in pairs arranged in right angles to each other
---b. comprised of bundles of microtubules as 9 sets of 3
---c. Mostly in animal cells, play role in cell division
---d. Basal body is like centriole except that is found at the base of a cilium
----i. Give rise to microtubules that form flagella/cilium
----ii. Control movement of cilia/flagellum
--3. Cilia (10-20 nm) and Flagella (100 micrometers)
---a. Fine hair like movable organelles that move cell or move stuff past cell
---b. Pair of single microtubules running through center (9+2 arrangement)
---c. Extension of membrane- entire assembly sheathed in plasma membrane
-F. Control and reproduction
--1. Nucleus carries out functions of control and reproduction
--2. Four compounds of nucleus:
---a. Nuclear envelope
----i. Membrane of phospholipids with 25 nm “nuclear pores” a network of proteins that control movement of materials in and out of nucleus
---b. Nucleolus
----i. Dark area when stained in nucleus made up of genes that synthesize RNA that combined with proteins to make ribosomes for the cytoplasm
---c. Chromosomes
----i. Each chromosome is really long DNA with an equal mass of protein
----ii. Collectively DNA of nucleus with proteins are called chromatin
---d. Nucleoplasm
----i. Goo inside nucleus (older terminology that disguises complexity)
-G. Synthesis, processing and storage
--1. Endoplasmic Reticulum (ER)
---a. Continuous membrane folded back and forth within cytoplasm
---b. Typically makes up more than half of the membrane
---c. Creates lumen, an open space created by folds
---d. Function is to transport chemicals between and within cells
---e. Provides large surface area for the organization of chemical reactions and synthesis
---f. Two Types
----i. Rough ER
----- Primary role is the processing, transport and temporary storage of proteins
----- Ribosomes adhere to its outer surface
----ii. Smooth ER
----- No ribosomes
----- Involved in synthesis and secreting and storage of carbohydrates, steroids, lipids and other non-proteins
--2. Ribosomes
---a. Contain sites where amino acids are assembled into polypeptides
---b. Two subunits
----i. RNA
----ii. Protein
--3. Golgi Complex/ Apparatus
---a. Where proteins and lipids undergo final modifications and then are sorted and packaged
---b. They do this by accepting vesicles from ER, modifying them and budding them off the opposite side
--4. Lisosomes “Suicide Particles”
---a. Fuse with other bodies to:
----i. Digest material for feeding
----ii. Destroy old or damaged organelles and foreign particles
---b. 40 enzymes have been detected in Lisosomes
--5. Vacuoles
---a. Refers to any membrane-bound body with little or no inner structure
---b. Often stores food, waste, water and more
---c. Very important to stay filled with water in plants to keep pressure up
-E. Energy Generating Organelles
--1. Chloroplasts
---a. Only in plants, algae and some protests
---b. Carry out photosynthesis
---c. Parts of inner membrane are organized as stacked disks called grana and the watery , clear region in between is called stroma
---d. Have their own DNA and ribosome
--2. Mitochondria
---a. Use carbon compounds (glucose) and oxygen to generate ATP that can be used by the cell as an energy source
---b. Have two membranes with inner membrane having numerous folds called cristae that is divided into inner/outer compartments
---c. Have their own DNA and ribosomes.

Saturday, November 05, 2005

Chapter 3 Notes The Molecules of Life

Chapter 3: The Molecules of Life
I. Carbohydrates (Carbon + Water = CH2O)
-A. Sugar and starches to most people
-B. General Functions:
--1. Transports energy when carried by blood
--2. Stores energy as starch
--3. Structural support for plants (cellulose)
-C. Monosaccarides
--1. Simplest Sugars
--2. Short chain of carbon atom or a ring of 5-6 Carbon atoms with an OH and H
--3. 3 common monosaccarides ( C6H2O6)
---a. Glucose, the immediate source of energy for cellular respiration.
----i. Most important monosacharride and most common
---b. Galactose, the sugar in milk and yogurt
---c. Fructose, the sugar found in fruits and honey
-D. Disaccharides
--1. Double sugar
--2. Two monosaccharides are covalently bonded together through a dehydration reaction
--3. Three common Disaccharides:
---a. Sucrose- Glucose + Fructose (table sugar)
---b. Lactose- Major sugar in milk Glucose + Galactose
---c. Maltose- Product of Starch digestion Glucose + Glucose
-E. Polysaccharides
--1. Longer chains of simple sugars (mostly glucose)
--2. Serve principally as food storage and structural molecules
--3. 3 types of Polysaccharides
---a. Starches
----i. Polymers of glucose
----ii. The storage polysaccharide for plants
----iii. Rice, wheat, potato, and corn are all major sources of starch in the human diet
----iv. Starches are insoluble in water and thus can serve as storage depots of glucose
---b. Glycogen
----i. A short term storage polysaccharide for animals
----ii. Highly branched glucose units put together that are broken down to meet energy demands of the body
---c. Cellulose
----i. Most abundant polysaccharide on earth
----ii. The major structural material of with plants are made (wood and plant fibers)
----iii. Insoluble and has great tensile strength because hydroxyls (-OH) are reversed on the carbon compared to other polysaccharides
----iv. The polymers can be drawn together into dense cable-like strands called micro fibrils that can then be organized into fibrils
----v. Most organisms cant break cellulose down into simple sugars because the don’t have then enzyme cellulose which is necessary to hydrolyze the glycoside linkages
----vi. As a result, plant cell walls are among the strongest of biological structures

II. Lipids
-A. Greasy, oily
-B. Non-polar so will not dissolve in water, therefore called hydrophobic (water fearing)
-C. General functions:
--1. Energy storage: fat in humans, oil in plants
---a. Fats provide out most concentrated form of energy with 9kcal/gram. Carbohydrates and proteins are 4 kcal/gram
--2. Heat insulation: layer of fat under skin reduces heat lost
--3. Buoyancy: lipids are less dense than water so helps animals float
--4. 4 types of Lipids
---a. Triglycerides => energy storage. The flabby stuff most of us have on certain parts of our bodies is cells filled with triglycerides
----i. How are they made?
----- Dehydration reaction (condensation) causes 3 fatty acids chains to covalently bond to a molecule of glycerol
----- Produces 3 molecules of water
----- This bond between a carboxyl group (on the fatty acid) and an hydroxyl group (on the glycerol) is called an ester linkage
----ii. The fatty acids found in triglycerides and other lipids are
----- Saturated fat: contains all the hydrogen’s possible in the chain of carbon. Have high melting point. Example: Lard
----- Unsaturated fat: have double bonds between one or more of the carbons in the chain that cause a kink in the carbon chain which prevents them from packing close together and therefore have low melting point. Example: Vegetable oil
---b. Phospholipids => major structural components of cell membranes
----i. Two fatty acids, a glycerol with a phosphate functional group, and a choline (molecule that varies)
----ii. The charged “heads” love water (hydrophilic)
----iii. The uncharged “tails” avoid water (hydrophobic)
----iv. These phospholipids bilayers have a tendency to automatically
----- Self-perpetuate
----- Form micells (spheres)
----- Repair holes
---c. Waxes => useful in organisms that need to retain water
----i. One fatty acid joined by an ester linkage to an alcohol
----ii. All are very hydrophobic which is good for retaining water
----iii. Plants-wax on leaf surface
----iv. Animals-insect body surfaces, ear wax
---d. Steroids-essential to life, been responsible from 17 Noble Prizes
----i. Structurally different from other lipids they contain four interlocking rings of carbon and hydrogen
----ii. A common steroid is cholesterol
----- Good for humans – helps in fat digestion and to make sex hormones
----- Bad for humans- contributes to arterial plaque in arteries that decreases blood flow

III. Amino Acids: the molecular building blocks of proteins.
-A. 150+ different (many are rare and found only in meteorites, some plants, and bacteria)
-B. Only 20 of these are used to synthesize almost all the proteins in almost all living cells
--1. 9 of 20 are called essential amino acids are there because they cannot be made in our body so we have to eat them.
-C. amino acids readily ionize – the carboxyl group (COOH) gives off an H+ and the amino group (NH3) takes in an H+
-D. Therefore amino acids has both a + and – charge
-E. The different R-groups and their position strongly affect the proteins shape which in turn, affects the proteins function.
-F. There are four significant properties of amino acids that are determined by characteristic of their R-groups
--1. Some are non polar and therefore hydrophobic and tend to cluster in water
--2. Some are polar and therefore hydrophilic and tend to form hydrogen bonds with water and each other
--3. Some Ionize get a charge in water and for ionic bonds with each other
--4. Some form a strong covalent bond between two sulfhydryl groups called a disulfide linkage R-SH + HS-R  R-S-S-R
-G. Dehydration Reaction (condensation) links two amino acids together
--1. Enzymes are necessary for this reaction
--2. Link is between carboxyl group on one a.a. and the amino group on the other
--3. Water is formed and remaining N and C link together called a peptide bond
--4. The beginning of polypeptide is called the N terminal (the free amino end) and the end is the C terminal (the free carboxyl end)
-H. End result – a protein!
-I. All the properties of a.a. and their R groups when hooked together is finally a protein
-J. This final 3-D shape is called its conformation

IV. Proteins
-A. Functions of proteins
--1. Membrane proteins
--2. Non-membrane proteins
---a. Enzymes: ex. catalase – changes hydrogen peroxide (toxic) to water and oxygen
---b. Structural: ex. collagen – principle component of tendons and ligaments and keratin in cells of hair, skin, claws, scales, feathers.
---c. Transport: ex. hemoglobin – bind O2 in the lungs transport to tissues
---d. Movement: ex. myosin – cause contraction in muscle fibers
---e. Hormones: ex. insulin – bind to cells and cause them to remove glucose from the blood.
---f. Defense: ex. Immunoglobulin – act as antibodies
-B. Two basic types of proteins according to their final shape
--1. Globular proteins – fold spontaneously into compact globs, mostly soluble in water
---a. enzymes, hormones, antibodies
--2. Fibrous proteins – long and narrow. Mostly insoluble in water
---a. muscle, ligaments, and tendons
-C. Four Levels of Structure:
--1. Primary Structure:
---a. determined by the number, kind, and order of amino acids. in the polypeptide
---b. held together by simple peptide bonds
---c. also shows location of any disulfide linkages
--2. Secondary Structure:
---a. Two types of spontaneous, regular, repeating structures as the polypeptide is made:
----i. alpha helix – a coil or zigzag shape that results from the hydrogen bonds along the strand
----ii. beta pleated sheets – back and forth folding of polypeptides because of hydrogen bonds between adjacent polypeptides or in the same strand
--3. Tertiary Structure
---a. Highly specific looping and folding of the polypeptide because of the following interactions between their R-groups
----i. ionic bonds
----ii. hydrophilic interactions
----iii. hydrophobic interactions
----iv. covalent disulfide linkages (cysteine only because has S in R-group)
---b. This tertiary level is the final level of organization for proteins containing only a single polypeptide chain
--4. Quaternary Structure:
---a. Linkage of two or more polypeptides to form a single protein in precise ratios and with a precise 3-D configuration.
---b. Some proteins have a prosthetic group (a non-peptide). These proteins are called conjugated proteins.
----i. hemoglobin.

Chapter 3 Insights and Objectives

Insights:
This chapter was all about the basic building blocks of biology- carbohydrates, lipids and proteins. Know it. All of it. Be able to draw it. There isn't much more to say then that.

Objectives:
2.2.1 Define Organic:
Molecules or compounds containing carbon that are found in living organisms are considered organic.
2.2.2 Draw the basic structure of a generalized amino acid
Amino Acid
2.2.3
Draw the ring structure of a glucose and ribose:
See convenient drawings here for ribose, and here for glucose
2.2.4 Draw the structure of a glycerol and a generalized fatty acid:
Glycerol; Generalized Fatty Acid (an unsaturated acid would have no double bond)
2.2.5 Outline the rold of condensation and hydrolysis in the relationships between monosaccharides,
disaccharides and polysaccharides; fatty acids, glycerol and glyercides; amino acids, dipeptides and
polypeptides.
For the monomers of carbohydrates (monosaccharides), lipids (fatty acids) and proteins (amino acids)
to become polymers, disaccharides, polysaccharides; glycerol, glyercides; dipeptides and polypeptides
respectivly, a condensation reaction must occur. The reverse is true for hydrolysis reactions.
2.2.7 List two examples for each of monosaccharides, disaccharides and polysaccharides.
Glucose and Fructose are monosaccharides, lactose and maltose are disaccharides, starch and cellulose
are polysaccharides.
2.2.8 State one function of a monosaccharide and one function of a polysaccharide
Glucose, a monosaccharide, is a major component of cellular respiration. Celluslose, a polysaccharide,
is found in plant cell walls.
2.2.9 State three functions of lipids
Lipids can insulate, provide buoyancy and store energy.
2.2.10 Discuss the use of carbohydrates and lipids in energy storage
Energy is stored in carbohydrates through polymers, such as starch in plants, and glycogen in animals
and is released when demanded by the body. Animals store energy in lipids as fat for long term storage

Non Chapter Emphasis Notes: Reactions that make and break molecules

I. Dehydration reaction (In IB terms, Condensation)
-A. Requires enzymes, the proteins that speed up chemical reactionsB. The OH of 2 monomers are brought together and one O stays while the remaining H2 and O form a water molecule. The O links the monomers into a polymer
-C. A-OH + B-OH=> H2O+ A-O-B (2 monosaccharides=> Disaccaride + water)
II. Hydrolysis
-A. The reverse of dehydration
-B. The decomposition of a substance by the insertion of water molecules between certain of its bonds
-C. Food is digested by hydrolysis
-D. A-O-B + H2O => A-OH + HO-B (Disaccharide+ water => 2 monosaccharide)

Chaper 2 Notes: The Chemistry of Life

I. Matter
-A. Has mass and volume
II. Elements
-A. Found on periodic table
-B. Cant be separated anymore
-C. 115+ known elements
-D. “ Maggyie’s SPONCH CaFe” elements
--1. Elements that occur in 99% of living matter
---a. Sulfur, Phosphorus, Oxygen, Nitrogen, Carbon, Hydrogen
---b. Most important of these is carbon, if it contains carbon it is considered organic
----i. Forms the backbone for the major molecules of life
----ii. Has 4 valence electrons
----iii. Can covalently bond to each other
----iv. Can form single, double, and triple bonds
----v. Can form chains
----vi. Can form rings
-E. Elements that are NEEDED by living organisms are
--1. Nitrogen
---a. Part of protein, DNA, RNA
---b. N2 is 78% of air, it is not usable by most organisms nitrogen, fixing bacteria can fix N2, NH4, or NO3 ions that would be usable for most organisms
--2. Calcium
---a. Needed to make the mineral that strengthens bones and teeth
---b. Plants need for transmitting food
--3. Phosphorus
---a. Normally as phosphate PO3-2
---b. In ATP which is a energy carrier that all organisms use
--4. Iron
---a. Need to make hemoglobin to carry oxygen in blood
---b. Plants need for enzymatic reactions
--5. Sodium
---a. Used to transport nerve impulses in a nerve cell
---b. Na/K pumps
-F. Type of Chemical Bonds
--1. Covalent bonds
---a. Atoms with a small difference in electron negativity share valence electrons
---b. Unshared electrons affect the shape of the molecule
---c. Electron negativity affects the polarity of the molecule
---d. Atoms with a strong electron negativity pull electrons toward it and away from the atom with the weaker electron negativity
--2. Ionic Bonds
---a. Between atoms with great difference in there elector negativity electrons are taken and giving
---b. Ions atoms with a charge + or – because they have lost or gained electrons and become stable
---c. Dissociation
----i. The ions in ionic bonds separate when placed in water because the polarity or water pull them apart
--3. Hydrogen Bonds
---a. Do not involve transferring 1 sharing electrons but are weak electrostatic forces between polar molecules
-G. Why a chemical reaction occurs
--1. Matter has a tendency to go from a high energy state to a low energy state
--2. Matter tends to go from an unstable status to a stable status
-H. Functional Groups
--1. Are specific combinations of atoms that appear frequently in many land or organisms molecules
--2. Their chemical behavior is pretty much the same regardless what kind of molecules they are attached to (this attached molecule is referred to as R)
-I. Water
--1. Most living organisms are 50%-90% water
--2. Water is polar (has neg. and pos. end)
--3. Properties or water and how they are significant to living organisms
--4. Solvents- Water polarity can pull apart other polar molecules
--5. Good to dissolve solutes for planets to transport sap and animals to transport blood
--6. Adhesion and Cohesion
---a. Water sticks to things and to itself
---b. Produces capillary action
---c. The rising of water in small tubes, very important in the transportation of water in plants
---d. Responsible for surface tension in water, the sticky part of water
--7. Thermal Properties
---a. High specific heat
----i. Takes lots of energy to heat water up and cool it down
-----This keeps aquatic habitat at a stable temperature
-----Good for cooling/sweating in animals and plants
---b. Transparent
----i. Aquatic plants need light
----ii. Light must pass through water in plants cells
----iii. Vision in animals

Chapter 2 Insights and Objectives

Insights:
This chapter teaches us the minor chemistry of Biology- the SPONCH elements are crucial to know. The properties of water are also important. Have a passing knowledge of the different types of bonds.
Objectives:
2.1.1 State that the most frequently occurring chemical elements in living things are carbon, hydrogen and oxygen.
The most frequently occurring chemical elements in living things are carbon, hydrogen and oxygen. (SPONCH)
2.1.2 State that a variety of other elements are needed by living organisms including nitrogen, calcium, phosphorus, iron and sodium.
A variety of other elements, including nitrogen, calcium, phosphorus, iron and sodium (Maggies SPONCH CaFe) are needed by living organisms. (don't forget magnesium!)
2.1.3 State one role for each of the elements mentioned in 2.1.2:
Nitrogen- Part of DNA
Calcium-Strengthens bones and teeth
Phosphorus- Used in ATP, the energy of cells
Iron- binds Oxygen in Hemoglobin!
Sodium- Transports nerve impulses to nerve cells
2.1.4 Outline the differences between an atom and an ion
An atom has the same amount of protons as electrons, so it is neutral in charge. An ion has either a positive or negative charge because there are unequal numbers of electrons and protons. A positive ion is called a cation, while a negative ion is called an anion. (from Nease IB Biology)
2.1.5 Outline the properties of water that are significant to living organisms, including transparency, cohesion, solvent properties and thermal properties. Refer to the polarity of water molecules and hydrogen bonding where relevant.
- Water is transparent, allowing light to permeate its surface, allowing aquatic plant life to conduct photosynthesis.
- Water is cohesive, as the hydrogen bonds hold water together due to their polar properties. This allows surface tension on water.
- Water is a good solvent. Its H bond pull most polar molecules apart. It dissolves many organic and inorganic material.
- Water molecules are unable to more due to H bonds. Since heat is the measurement of cell movement, water does not heat very quickly or well. This high specific heat (the heat at which it change states) has sustained stable habitats to many organisms, because large amounts of energy is required to heat up and water and change its state.
2.1.6 Explain the significance to organisms of water as a coolant, transport medium and habitat, in terms of its properties. (Verbatim from Nease)
Water's high specific heat allows it to absorb large amounts of energy and act as an insulator for all living things. For example, our bodies use water in the for of sweat to lower body temperature. The sweat absorbs a large amount of heat, and then evaporates carrying that heat away from the body.

Chapter 1 Notes: Science and Life

I. Experiments
-A. Successful Experiments:
--1. Controls are the hardest part
---a. You need more than one control
---b. Is there anything that could have influenced, or be the cause of results? (Variables)
---c. Conclusions are more than your results, you should:
----i. State your results
----ii. Explain your results
----iii. Compare and cite with similar findings in literature
----iv. Evaluate your experiment by identifying weakness and suggesting improvements
II. Properties/Characteristics of Life
-A. Organized structures composed of different chemicals in cells
-B. Metabolism, chemical and energy transformation
-C. Maintain internal conditions separated from an outside environment (homeostasis)
-D. Growth, conversion of materials from the environment into components of organisms
-E. Reaction to stimuli, physiologically and/or behaviorally
-F. Reproduction, making copies of individuals via the mechanism of replicating DNA
-G. Evolution: change in characteristics of individuals resulting from mutation, natural selection, and/or genetic drift

Chapter 1: Insights and Objectives

Insights:
This chapter is relatively straight forward. Know the characteristics of life, which can vary. Know that in certain cases microorganisms that are smaller than a cell can count as life. Understand that this is introducing you to cell theory, and in Biology, there are no laws like Gravity or Boyle. A theory is about as close as you can come.
Objectives:
1.1.1 Discuss the theory that living organisms are composed of cells.
Cell theory states that one of the criterion for assessing whether something is alive. Cell theory originated from a nerd who looked at cork in the microscope and said the small blocks that made up the shape looked like monk's cells. Since then, six central pillars to cell theory have emerged (from wikipedia.org):
-The cell is the fundamental unit of structure and function of all living things.
- All known living things are made up of one or more cells.
-All cells come from pre-existing cells through division.
-Cells contain hereditary information which is passed on to daughter cells during division.
-All cells are essentially the same in chemical composition.
-All energy flow of life occurs within cells.
1.1.3 State that all cells are formed from other cells.
All cells are formed from other cells through division.

Friday, November 04, 2005

Notes on Notation

Note to readers
This website is skeptical of indentation. The notes, which should be obvious by spacing, are all aligned on the left, which is terrible. For my purposes, the notes following this format
I. Roman numerals indicate categories under the chapter
-A. Capital letter indicates subcatergory within sub topic
--1. Number represents specfic points atributed to subcategory
---a. small number indicates examples, more data, or a hyposubcategory
----i. small roman numerals indicate that I am running out of tools to denote with
-----Five bullets indicate an example to a small roman numeral

iBiology: Overview

This site is intended for CHS IB Biology students in Mr. Jansen's class. It will have notes verbatim, an analysis of those notes, previews of quizzes and tests, post-views of quizzes and tests, IB objectives, and other useful items. Special thanks to Ben Hollingsworth for providing an electronic copy of his notes for chapters 1-4. Please comment on the post with questions, answers, tips and analysis. Email me if you have specific queries. The first real entry will be Chapter One notes.

Welcome to iBiology!

Welcome fellow IBer's. If you are here to study, you have come to the right place. This is an open forum of notes, IB objectives and fun! Please make use of this site. Over time, entries from the begining will find there way into the "archives." This will be a valuable tool for when it is time for finals and tests. Feel free to make appropiate comments. Email me with suggestions for improvment as well. Keep in mind these notes should be paired with the book and in class labs.