Goldfish Respiration Rate Lab

Goldfish Respiration Rate Lab

(Milan, Stefan, Rohan, Andreas)

Introduction:

In this lab, my group and I conducted some experiments with fish and their water environment, observing how this affected their respiration rate. The main change was in temperature (making the water cooler and warmer), but we also added Coke to see how this changed the respiration rate. The 5 temperature zones that were tested were coldest (5 - 100C), cold (10 - 140C), room temperature (15 - 200C), hot (21 - 250C), and hottest (26 - 300C). For each temperature zone, we observed how many breaths the fish made in 5 minutes, and recorded the data. The one Coke test we performed was adding 6ml of Diet Coke to a container of water at room temperature. The results from this experiment are separated from the results of changing the temperature, due to their difference.

Hypothesis:

As the temperature of the goldfish environment increases, so will the respiration rate of the goldfish.

Table of Results

BP5M = breaths per 5 minutes

Temp in C	Our Group BP5M	Group 2 BP5M	Group 3 BP5M	Group 4 BP5M	Average BP5M
26 - 300C	915	1280	780	780	939
21 - 250C	789	1260	700	700	862
15 - 200C	617	640	600	560	604
10 - 140C	460	340	250	480	383
5 - 100C	210	180	200	380	243

Graph of Data

Injustice Ted Talk E.C

Above is a link to a TED talk done by Bryan Stevenson, founder of the Equal Justice Initiative, who discussed racism and injustice (such as the death sentence) in the judicial system. To be honest, this is not a topic which I have put much thought into. I didn't realize the magnitude of unfair treatment in our system until recent Justice Summit conversations. As brought up by Mr. Stevenson, when 1/3 adult African-americans are either in prison or on parol, something is wrong. This brought up a few ideas. Is this statistic due to the fact of poverty or racism? Well, the TED talker united both ideas together to form his opinions about the matter. He used the example of replacing his 13 year-old African-american client with a 75 year-old wealthy caucasian in a court case. In fact, he mentioned translating this into a motion which he submitted to the court. Of course the court thought this was insane, but is it really? In the judicial system of today, it seems as if appearance and social stature play a major role. Why not keep the defendant anonymous and continue with the rest of the process? This would hopefully prevent the issue of racism and social stature in courts. Another issue discussed was the death penalty, a topic which I neither talk nor have much knowledge about. However, I understand arguments from both side. One side says an eye for an eye, a tooth for a tooth, a life for a life, while the other side believes in compassion and restorative justice. I find it hard to believe that a serial killer or mass murderer can change via restorative justice and live a normal life. Achieving restorative justice would be optimal, but it just seems close to impossible right now. The world is a messed up place. Restorative justice won't be effective on everyone, especially those who don't budge from their principles. However, killing someone doesn't do anything to help what that person did in the past. It promotes revenge and questions who has the authority to kill. Finally, he mentions how we are disconnected and oblivious to these concerning issues. I definitely agree and I also advocate that the injustices of the judicial system be exposed and changed. There are so many issues, but not enough is being done to protect more lives. Over all, I thought Mr. Stevenson's presentation was very well said and contained interesting facts that I didn't previously know about, further proving the point that racism still exists in this country. It is unbelievable that there are still racists and homophobes in the 21st century! It is infuriating how ignorant and single-minded so many American are. Bryan Stevenson is truly a man for others doing his best to fix injustices. 

Heart Beat Lab

Lab Investigation 7B (Stefan, Milan, Nathan)

Introduction:

In this experiment, my group and I measured blood pressure, beats per minutes (BPM), and recovery time for different levels of exercise. According to the instructions, we had to come up with exercises for three different intensity levels: mild, moderate, and strenuous. Although this is rather subjective, we finally reached a conclusion on what exercises should be performed to reach these levels. The decision is below.

Mild: 10 squats

Moderate: 20 perfect push-ups

Strenuous: Sprint to Lokey main door from Mr. Wong’s classroom

With these different tests, we observed how blood pressure, BPM, and recovery time changed for Stefan and I. For example, after performing 10 squats, I measured Stefan’s blood pressure and BPM. After, these results were compared to experimentation done at resting heart beat.

Results:

TABLE OF RESULTS BELOW

	Resting	10 Squats	20 Pushups	Sprinting
Milan	Pressure = (103/85) BPM = 70 Recovery = N/A	Pressure = (109/84) BPM = 85 Recovery = 45 seconds	Pressure = (108/80) BPM = 118 Recovery = 1:30 minutes	Pressure = (120/82) BPM = 145 Recovery = 4:53 minutes
Stefan	Pressure = (118/73) BPM = 76 Recovery = N/A	Pressure = (114/75) BPM = 81 Recovery = 40 seconds	Pressure = (120/81) BPM = 113 Recovery = 1:25 minutes	Pressure = (126/78) BPM = 139 Recovery = 5:15 minutes

GRAPH OF RESULTS BELOW (INSTRUCTIONS ONLY ASKED FOR BPM)

X axis = Intensity of Exercise (0 = resting, 1 = mild, 2 = moderate, 3 = strenuous)

Y axis = Beats per minutes (BPM)

Conclusions:

Based on the graph and resting time, the difference between data obtained from Stefan vs. Milan is barely noticeable. The resting BPM is somewhat different, but after, the graphs are very close to one another. This was probably just a lucky coincidence, due to the fact that Stefan and I are the same age and almost the same weight. However, the blood pressure yields different results. For me, the systolic number increases, while the diastolic number decreases. For Stefan, the systolic number begins to decreases but then increases, while the diastolic number increases but then goes down. These are some interesting observations that could show a possible relationship between systolic and diastolic numbers.

Extraction of Strawberry DNA

Introduction

  Today, my lab group and I performed DNA extraction on a strawberry. There were multiple steps to the extraction, but the steps were rather simple. This blog will include the steps of the extraction, why they were performed, and pictures of the lab.

Steps and Pictures

1. Make DNA extraction buffer
• 5 mL dish water detergent or shampoo
• Importance: Dish water detergent and shampoo both contain ingredients that break down the membranes within a cell, releasing DNA. The main ingredient in detergent and shampoo is sodiumdodecyl sulfate (SDS). SDS pokes holes in the cell membranes, weakening them, and then they are further broken down by a blender or crushed with hands. 
• 0.75 g of salt
• Importance: Once the DNA molecules are released they move around. By using salt in the extraction buffer, DNA molecules stick together. Salt also plays a role in DNA extraction by removing histone proteins that hold DNA molecules together.
• 45 ml of water
• Importance: Water is used in the extraction buffer to allow different substances to move around. Water is useful in a large variety of situations.
• Importance of DNA extraction buffer
• The DNA extraction buffer, along with hand grinding, breaks open the cells in a strawberry and releases DNA. Without this important buffer, the DNA would stay in the cells and wouldn't be visible.
• Picture (ingredients of DNA extraction buffer)
• 
• Salt on the left, detergent in the middle, water on the right 
2. Clean the strawberry, combine it with the extraction buffer, and crush the combination with your fingers. 
• Cleaning the strawberry + removing sepals
• Importance: Cleaning the strawberry is importance in order to make sure no unwanted materials are involved in the experiment. This can distort the data and result in the absence of DNA. You want to remove the sepals because they can get in the way and affect the data the same way that a dirty strawberry can.
• Combining the strawberry with extraction buffer
• Importance: You want to combine the strawberry and extraction buffer in a plastic bag so that the extraction buffer can perform its function. If you didn't mix the two, the DNA would remain in the strawberry cells.  
• Crushing the contents of the plastic bag
• Importance: The detergent or shampoo in the DNA extraction buffer poked holes in the cell and nuclear membrane. This weakened the membranes, but it wasn't enough to release DNA. By crushing the strawberry with your hands and exposing it to the DNA extraction buffer, more DNA can be obtained. Make sure not to crush too hard because DNA will degrade. 
• Picture of strawberry before combination with extraction buffer (ezwebrus.com)

• Picture of strawberry after combination with DNA extraction buffer



3. Use a filter, gauze, and test tube to filter the mixture
• Importance of filtering
• Filtering is an important process in DNA extraction. The gauze collects all strawberry cell debris and only allows the liquid solution to pass into the test tube. Because strawberry DNA dissolves into the DNA extraction buffer, the DNA can pass through the gauze into the test tube. Without filtering, the test tube would contain all parts of a cell, not just the DNA
• Picture of filtration process (i.ytimg.com)

• Picture of mixture after filtration

4. Add alcohol and use a wooden skewer to twirl the solution
• Importance of adding alcohol and mixing
• Because DNA is insoluble in alcohol, it precipitates. Alcohol allows the DNA to separate from the other ingredients used in the DNA extraction buffer. This splits the test tube into two layers; the top layer contains alcohol and DNA, and the bottom layer contains the junk ingredients from the extraction buffer. It is important to twirl the solution so the DNA comes together and is more visible. 
• Picture of test tube after adding alcohol

• Picture of DNA present in top layer of test tube after swirling





• Picture of DNA is a separate test tube



• Group Picture!!

Conclusion

  I found this experiment to be easier than I first thought and very fun. I never knew that DNA could be extracted in such a simple process that only requires household materials. Overall, my group and I received great DNA presence and we all had a great time. Extracting and observing the code of life is definitely an experiment worth conducting.

   

Biology Semester 1 Final Notes

Biology Semester 1 Final Notes

(sorry it is disorganized)

Prologue Book Notes

P.1

• Illness used to be attributed to bad blood
• Biology = study of life
• Biology will be the most influential science of the 21st century
• DNA = deoxyribonucleic acid

P.2

• AIDS = acquired immune deficiency syndrome
• AZT was first attempt to cure AIDS
• 14 million have died from AIDS
• HIV = human immunodeficiency virus, discovered in 1983
• Genetic material copied inside infected cells and then becomes part of the cell
• Infected cells become factories
• Genetic material mutates rapidly; vaccine would be hard to create

P.3

• GH = growth hormone
• Produced in pituitary gland
• Protein that controls growth
• GH used to be taken from pituitary glands of the dead
• Now genetic engineering lets scientists create GH by bacteria
• Bioethics = study of science and ethics

P.4

• Solve a problem = combine what you already know with new observations
• Problem solving based on interpretation of data
• Scientific Method
• Ask a Question
• Do Background Research
• Construct a Hypothesis
• Test Your Hypothesis by Doing an Experiment
• Analyze Your Data and Draw a Conclusion
• Communicate Your Results
• Evolution is one of the major unifying themes of biology

P.5

• Theory explains current observations and predicts new observations
• Jean Lamarck
• French biologist
• 1744-1829
• Proposed that organisms change through time
• If an animal uses some part of its body infrequently, that part will slowly weaken, become smaller, and disappear.
• If an animal uses some part frequently, that part will become stronger.
• Proven wrong by 100 years of experimentation
• Hypotheses - explanation that are testable through experimentation or observation
• Prediction from hypotheses can be written in if…then
• Charles Darwin
• 1809-1882
• Influence by Charles Lyell and Scott James Hutton
• uniformitarianism = natural forces existing in the past were the same as those that exist today

P.6

• Publish "On The Origin of Species"
• natural selection = survival and reproduction of organisms that are best suited to their environment.
• adaptations = characteristics that help an organism survive and reproduce
• variations = small differences that occur between populations
• some variations helpful, others not
• descent with modification = related organisms share a common ancestor
• chimps and gorillas

P.7

• Science has several characteristics

1. assumption that the natural world can be explained in understandable terms
2. based on results of observation and experiments
3. results must be verifiable by other scientists
4. findings of science must be refutable

• Galileo forced to sign and publish a statement saying that his work was incorrect (Earth wasn't center of universe), and sentenced to permanent house arrest

P.8

• Five biological issue questions

1. What is the question?
2. What are the data and how were they obtained?
3. What do the data mean?
4. Who is reporting the data?
5. Is that person qualified?
6. How complete is present state of knowledge?

Chapter 1 Book Notes

Quiz

• Formula for water?
• H20
• Smallest particle of element that still has properties
• Atom
• Formula for oxygen
• O2
• 6 most abundant atoms in human body
• Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, Sulfur
• Most abundant in human
• Oxygen

Notes

• Ancient Greece - 18th century people that all things made of earth, fire, air, and wind
• Lavoisier challenged that by stating fire is not a substance but a combustion.
• Used physical laws and measurement to understand how chemicals react
• Founded modern chemistry
• All organisms are composed of chemicals and understanding of life requires understanding of chemistry.
• Biochemistry - the chemistry of living organism
• Water exists in three states
• Gas
• Solid
• Liquid
• Living things are mostly water
• Molecules of water are the small units which water can be divided into with same characteristics of water
• Water is hydrogen and oxygen
• Hydrogen and oxygen are elements
• Dalton found atoms
• Atoms are smallest unit of an element that still has chemical properties of that element
• Created atomic theory
• Molecules made of atoms
• Molecule made of more than one type of atom = compound
• Elements can chemically combine to form millions of compounds
• Organism made mostly out of
• Carbon (C)
• Hydrogen (H)
• Oxygen (O)
• Nitrogen (N)
• Phosphorus (P)
• Sulfur (S)
• Parts of atom
• Subatomic particles
• Proton
• Positive charge
• Neutron
• Neutral charge
• Electron
• Negative charge
• Protons and neutrons in center, or nucleus
• Electron in negatively charged cloud outside nucleus
• Different electron shells in cloud
• Shells near nucleus are held tighter than shells farther
• Hydrogen is simplest atom
• 1 proton, 1 electron, and 0 neutrons
• Very reactive
• Every atom has equal protons and electrons
• Charge is balanced
• Atoms of same element can have different number of neutrons
• Called isotopes
• Some isotopes are radioactive, called radioisotopes 
• Molecular model constructed from inferences
• Quiz
  • Chemical reaction for H20 breakdown?
  • 2H20 ---> 2H2 + O2
  • Law of conservation of matter?
  • Amount of matter before and after a chemical reaction must be the same
  • Energy to start chemical reaction?
  • Activation energy
  • Two types of bonds?
  • Ionic
  • Covalent
  
  
  
  
  
  
  Notes
• Chemical bonds are the attractions, sharing, or transfer of outer shell electrons from one atom to another
• Chemical reaction involves the making and breaking of chemical bonds
• Substances interact and form new bonds and new substances
• Only outer shell electrons are involved when atoms react during a chemical change
• Outer electrons are reliable indicator of reactivity of an atom
• Cells are the basic units of life
• Chemical reactions are important to a cell
• The only way to form new molecules that the cell requires for such things as growth and maintenance
• Making and breaking of bonds involves changes in energy
• Breakdown of water
• 2H20 ----> 2H2 + O2
• Equation written to balance
• Law of conservation of matter = matter is neither created nor destroyed in chemical reactions
• Activation energy = energy needed to get a chemical reaction started
• Ion is an atom or molecule that has acquired a positive or negative charge as a result of gaining or losing electrons
• Ionic bond = attraction between oppositely charged ions (sodium chloride bond)
• Covalent bond = two atoms share one or more pairs of electrons (H2)
• Gives each hydrogen atom two electrons and fills the outer shell of oxygen with eight electrons
• Atoms do not share electrons equally
• Larger oxygen atom attracts the electrons more 
• If electrons of a bond are not shared equally, bond is called polar covalent
• If electrons in a molecule are shared equally, the covalent bond are non polar
• Hydrogen bond - bond between slightly positive hydrogen atom and a nearby slightly negative atom of another molecule
• When a nonionic compound is converted to ions, the process is called ionization
• pH scale = level of H+ and OH- ions in solution.
• Goes from 0 to 14
• Neutral solution = same number of H+ and OH- with pH of 7
• Pure water has a pH of 7
• Solution with more H+ is acidic
• pH less than 7
• Solution with more OH- is basic
• pH greater than 7
• pH scale is logarithmic
• Change of one pH unit is tenfold
• All cells rely on chemical reactions for growth and survival

• Most important chemical compound are organic compounds
• Carbon atoms combined with hydrogen and oxygen
• Carbon dioxide, carbon monoxide, carbonic acid are carbon compounds
• Carbon atoms can combine in macromolecules
• carbohydrates, lipids, proteins, and nucleic acids
• All cells contain carbs
• Simplest carbs are monosaccharides. 
• Most organisms use glucose as energy source.
• sugar phosphates
• Two simple sugar molecules can form disaccharide. 
• Several glucose can form polysaccharides
• Starch is energy storage
• Lipids are fats an macromolecules
• Two functions
• Long term energy storage
• Carbon and building of structural parts of cell membranes
• Lipids dont dissolve in water
• Contain carbon, hydrogen, and oxygen
• Unsaturated fats tend to be oily
• Saturated fats tend to be solids
• Fats are more efficient energy storage
• Two other types of lipid are phospholipids and cholesterol
• Phospholipids form with glycerol combines with two fatty acids
• Cholesterol is part of membrane structure of animal cells important in nutrition
• Every cell contains from several hundred to several thousand different macromolecules know as proteins
• Proteins are structural and messengers and receivers of messages.
• Play important role against disease
• Cells made of amino acids
• Amino acids are small molecules that contain carbon, hydrogen, oxygen, and nitrogen
• Amino acids have a central carbon atom, attatched to a hydrogen atom, amino group, an acid group, and a variable group.
• Covalent bonds between amino acids are peptide bonds
• When peptide bonds connect, long chains called polypeptide are made
• Longer polypeptide can form protein
• Protein made from 50 to 3000 amino acid
• Primary structure
• Sequence of amino acids in a polypeptide chain
• Secondary structure
• Chain folds or twists to form secondary structures
• Stabilized by hydrogen bonds
• Tertiary structure
• Complex global or spherical foldings
• Quaternary structure
• Two or more tertiary combine
• Hydrophobicity = tendency for non polar amino acids to avoid water.
• Nucleic Acids are macromolecules that control basic life processes
• Source of genetic information
• Connected nucleotides = nucleic acids
• Nucleotide made of three parts
• 5 carbon sugar (pentose): ribose or deoxyribose
• base of nitrogen: adenine, thymine, guanine, cytosine
• phosphate group
• Ribose in nucleotide = RNA
• In RNA, uracil replaces thymine
• single stranded
• Deoxyribose in nucleotide = DNA
• double stranded helix
• In 1953, James Watson and Francis Crick proposed a DNA model
• Still accept today with some modification
• Model found on the principle of specific nucleotides 
• Hydrogen bonds only formed between A and T or C and G
• Rosalind Franklin suggested that DNA molecules have double helix
• DNA double helix composed of two long chains of nucleotides.
• Connected by phosphate groups
• Sugar-phosphate backbones run in opposite directions
• Connected via hydrogen bonds
• Two strands intertwine
• RNA is single-stranded
• Functions of DNA
• DNA forms genes
• genetic information
• DNA stores information in a code consisting of units three nucleotides long called triplet codons
• Certain codons translated to certain amino acids

Chapter 1 Lecture Notes

• Matter is anything that has mass and occupies space
• Chemistry is study of matter
• Everything started at big bang theory - 14 billion years ago
• Expansion of universe
• Expansion of energy and matter
• Still expanding
• Matter
• Atoms make up matter
• 92 different pieces of matter (natural) (atoms)
• Periodic table of elements
• Made of 4 major (CHON) Oxygen, Carbon, Hydrogen, Nitrogen
• Atom
• Represented by a chemical symbol (H)
• Represented by atomic number (1)
• Number of protons
• That how atoms are distinguished
• First letter capitalized, second lower case
• Made of subatomic particles
• Protons (+)
• Neutrons
• Electrons (-)
• Protons and neutrons form nucleus
• Electrons in cloud flying around
• Atoms are electrically balanced
• Same number of protons and electrons 
• Number of protons = number of electrons
• Flea in a baseball stadium: size of nucleus
• Electrons fight in energy levels
• First energy level = 2 electrons
• Second energy level = 8 electrons
• Number of neutrons in same atom can be different
• Called isotopes
• Hydrogen isotopes
• 1 P, 0 N, 1 E = 1 Prodium
• 1 P, 1 N, 1 E = 2 Deuterium 
• 1 P, 2 N, 1 E = 3 Tritium
• Isotopes have mass number (proton + neutron)
• Mass = average weight of all isotopes of that atom

• Electrons located in energy levels
• If energy put into electron, it changes energy levels
• Way to identify an atom by exciting it and looking at electrons
• Eventually all electrons come to lower energy level
• Electrons are in steps
• Orbitals
• Sub-orbitals
• Energy levels
• Represented by electron shells
• Hydrogen has one electron
• In the first energy level
• Open football stadium, people will go into best seats
• Its a rush for electrons to go into various electron levels
• Chemistry is an electron game
• Niels Hendrik David Bohr (1885-1962)
• Came up with energy levels
• Went into quantum chemistry
• Bohr diagram
• Circle as nucleus with electrons around in circle
• Sub level called S orbital = 2 electrons
• Each level has an S orbital
• S orbitals are spherical
• 2 electrons
• Second has P and S orbital
• P orbitals are dumbbell like
• 8 electrons
• Third has P, S, and D orbital
• D orbitals are like double dumbbells
• 10 electrons
• Fourth has P, S, D, and F orbital
• 14 Electrons
• Screwed up shape
• Valence shell electrons are most important
• S = 2, P = 6, D = 10, F = 14
• Aufbau Principle
• Go to S first
• Pauli Exculsion Principle
• Two electrons
• Opposite spin
• Hund's Rule
• Electrons like symmetry 
• Parallel spins
• Hydrogen has one electron
• Electron goes to one S
• Best house
• Electron configuration 1s1
• Helium atomic number of 2
• 1s2
• Electrons occupy lowest energy orbital first
• Orbital at most two electrons opposite spin
• Lithium atomic number of 3
• 1s2 2s1
• Nitrogen
• 1s2 2s2 2p3
• Electron Configuration Fill-up Order
• 1s
• 2s, 2p
• 3s 3p 3d
• 4s 4p 4d 4f
• 5s 5p 5d 5f
• 6s 6p 6d 6f
• 7s 7p 7d 7f
• Cross out from top right diagonal to fin
• DIfferent atomic models
• Dalton's atom
• Thompson's atom
• Rutheford's model
• If orbits different and electrons different
• Determined chemical properties
• Bohr's Model
• Electrons found in orbits 
• Different energy levels
• Failed why different atoms had different spectrums
• Each electrons orbit has a fixed energy
• Electron cloud model
• Electrons not in a path or orbital
• Electrons in a cloud
• Everywhere at the same time
• Area of probability
• Atomic Orbitals
• Region of space where high probably of find an electrons
• Where electron is likely to be found

• Weight of O = 8
• 8 Protons
• 8 Electrons
• Probably 8 Neutrons
• Atomic weight = 15.9994
• It is 16 because some average of isotopes
• Electrons don't affect weight
• Electron figutarion
• 1s2, 2s2, 2p4, 
• 2s2 and 2p4 are valence electrons
• The only ones that count
• Wants two more electrons (p=6)
• If shells filled
• Oxygen would be O--
• Negative oxygen ion
• When two oxygens connect
• Creates covalent bond
• Electrons shared
• Single bond = electrons sharing
• Any time 10 ^ -7 moles per liter 
• which is why water has pH of 7
• Moles = 6.02 x 10 ^ 23
• Hydrogen = 1, add grams, so 1 grams
• There would be 6.02 x 10 ^ 23 atoms of hydrogen in that 
• M =  molarity
• Molarity = moles/L
• Sugar in water, certain concentration of sugar
• If you put more sugar in, concentration increased
• [sugar] = concentration of sugar
• moles per Liter - molarity (measure of concentration)
• H20 into H+  +   OH-
• If you could freeze water at any time there would be 10^ -7 ions of H+
• pH = 7, molarity of 10 ^ -7
• pH = 6, molarity of 10 ^ -6
• Lower pH, more hydrogen ions

Macromolecules

• Big, because of macro
• Organic because it has carbon
• Also hydrogen
• oxygen
• nitrogen
• phosphorus
• sulfur
• THEY ARE BIG

Organic Compounds

• 4 MaTypesin
• Carbohydrates
• Sugars and Starchs
• Functions
• Fuel source but also store energy
• Used for immediate energy
• Examples
• Starch
• Glycogen
• Building Blocks
• Simple sugars
• monomers = monosaccharides
• single sugars
• monosaccharides are not that big
• Trioses: 3 carbon sugar (C3 H6 O3)
• If C double bond O at end = aldose (alyrehide sugar (Glyceraldehyde))
• If C double bond O at middle = kentose (ketone sugar (Dihydroxyacetone))
• C double bond O called carbon yl group.
• Structural isomers
• same atoms
• different structure
• Monosaccharide
• 1 : 2 : 1 
• Carbon : Hydrogen : Oxygen
• Pentoses: 5 carbon sugar (C5 H10 05) (important for DNA and RNA)
• Ribose = carbon yl at end
• Ribulose = carbon yl in middle
• Hexoses: 6 carbon sugar (C6 H12 O6) (important for energy and structure)
• Glucose and Galactose = carbon yl at end
• Middle of Glucose = H - C - OH
• Middle of Galactose = HO - C - H
• Fructose = carbon yl in middle
• Glucose + Glucose (Dehydration Synthesis) = Maltose
• Fructose + Fructose (Dehydration Synthesis) = Sucrose
• Polysaccharides
• glycogen in live for energy storage
• Glucose
• Alpha
• Hydroxide on bottom
• Beta
• Hydroxide on top
• Alpha glucose = starch
• Beta glucose = cellulose
• Termites can eat wood because of enzyme
• Learn cow digestion process
• Other Carbohydrates
• Chiting = modified polysaccharide
• Lipids
• Fats, oils, waxes
• Hydrophobic (afraid of water, don't dissolve in water)
• Made of C, H, and O mainly
• Long term energy storage and insulation
• Help form cell membrane
• No polymers
• 3 Groups
• Triglycerides (butter, fat)
• Made of one glycerol and 3 fatty acids
• LEARN GLYCEROL STRUCTURE
• Dehydration synthesis happens twice to create triglycerides
• Fat molecule = triacylglycerol
• Ester linkage
• Saturated fats
• Single bonds
• Solids
• Unsaturated fats
• Double bond
• Oil
• CIS arrangement
• TRANS arrangement
• Phospholipids (cell membranes)
• Hydrophilic head
• Choline on top, Phosphate in middle, glycerol on bottom
• Hydrophobic tails
• Fatty acids
• Steroids (ring like structures)
• Cholesterol doesn't dissolve in water
• In cell membrane of animal cells
• Tend to form solid
• More animals we eat, more cholesterol we get
• uses stuff from cholesterol to make testosterone and other molecules to help
• if too much testosterone, can convert back to cholesterol
• LEARN CHOLESTEROL FORM
• How they are Built
• Lipids has no monomers
• Linking
• Fatty acid is a long hydrogen and carbon chain
• Hydroxil end
• Links to glycerol in dehydration synthesis
• No polarity in fat molecule
• very hydrophobic
• butter
• doesn't dissolve in water
• blood is mostly water
• fat is solid so creates plaque
• Triglyceride = fat
• How to Test
• If dissolves in water, not fat
• Proteins
• Structure
• Messengers and receivers of messages
• Enzymes
• Protein building
• Protein is like strand of pearls
• Each pearl is a monomer
• Each pearl is an amino acid
• Protein is a chain of amino acids
• Almost infinite number of proteins
• Amino acid (LEARN TWENTY TYPES OF AMINO ACIDS NAMES)
• Twenty types of amino acids
• OH in carboxyl group connects with upper right hydrogen in amine group
• The bond between carbon and nitrogen
• referred to as peptide bond
• Two amino acids = dipeptide
• Three + amino acids = polypeptide
• Dehydration Synthesis
• Amino acid 1 + amino acid 2 = peptide bond + H20
• Primary Structure
• Sequence of amino acids
• Sequence is crazy important
• Secondary Structure
• Polar attraction between nitrogen carbon backbone
• No r groups involved
• Alpha helix
• Beta sheet
• Tertiary Structure
• Attractions between radicals
• Quaternary structure
• Made of more than one polypeptide chain
• Types of Protein
• Hormonal proteins
• Structural proteins
• Defensive proteins
• Transport proteins
• Receptor proteins
• Enzymatic proteins
• PROTEINS ARE EVERYTHING!
• Denaturation
• Changing structure of a protein
• Denatured proteins don't work well
• Used in poison
• Nucleic acids
• DNA, RNA
• DNA codes for sequence of amino acid
• Heredity
• Code for making of protein
• All contain carbon atom
• Sequence of nucleotides in DNA dictates sequence of amino acids in proteins
• Always made up of the same types of atoms
• Carbon
• Hydrogen
• Nitrogen
• Oxygen
• Phosphorus
• Sulfur
• Building Macromolecules
• Except for lipids, macromolecules exist in two forms
• Monomer = simplest (individual units)
• Polymer = many units (repeating monomers)
• Glucose + Gluose + Glucose = Polyglucose
• Glucose = monomer
• Polyglucose = polymer
• Protein
• Amino acids = monomer
• Put together by dehydration synthesis
• Dehydration Synthesis
• Production of water
• Putting things together is anabolic (energy is necessary)
• Also is usually endergonic
• Link between monomer and polymer creates H20
• Oxygen bonds to carbon, so written as HO
• Hydroxyl = OH
• Alcohol Group
• C2 H5 OH = ethanol
• Hydrolysis
• Everybody puts things together and takes them apart (catabolic)
• Catabolic reactions are usually exergonic = energy released
• Exothermic = exergonic
• Eat food, you digest it, and then put the pieces together to make good Mr.Wong stuff.
• bad stuff rid of
• Reverse of dehydration synthesis
• Water is need to break things apart
• Reduces complexity
• Release energy
• Enzymes still required
• Takes apart polymers
• REASON WHY WATER IS KEY
• Difference between molecule and compound (LOOK UP MORE)
• molecule referes to covalent bond
• in order for compound to molecule must be covalent bond
• some type of sharing
• water is polar covalent bond
• oxygen hogs the electrons
• slight negative at oxygen
• slight positive at hydrogen
• A molecule is formed when two or more atoms join together chemically. A compound is a molecule that contains at least two different elements. All compounds are molecules but not all molecules are compounds.

Chapter 2 Book Notes

• Characteristics of Organisms
• Ability to absorb and convert energy is a basic characteristic of life.
• Study of energy flow and energy transformations among living systems is called bioenergetics
• Movement and growth are two characteristic you might include in a definition of life
• Living things move by obtaining energy and transforming it into motion
• Characteristics of Organisms
• Take in and convert materials and energy from the environment; releases waste
• Have a high degree of chemical organization compared to nonliving objects
• Have complex structural organization that is responsible for their appearance and activities
• Contain coded instructions for maintaining their organization and activities
• Sense and react to changes in their environment
• Grow and develop during some part of their lives
• Reproduce others like themselves
• Communicated with similar organism
• Move under their own power
• Summer of 1976, Viking 1 and 2 arrived at Mars
• Energy and Nutrients
• Living things need energy
• Energy is the capacity to do work or to cause change
• Organisms store energy in the organic molecules
• Energy known as chemical energy
• Portion of chemical energy that is available to do work is called free energy
• Chemical work includes construction and breaking gown large complex molecules
• Nutrients are raw materials needed to make complex molecules and to increase cellular organization
• Mechanical work includes movement
• Heterotrophs obtain energy from other organisms
• Autotrophs obtain energy from nonliving sources such as the Sun, minerals, and air.
• Photosynthesis: synthesize organic compounds from carbon dioxide and water
• Photoautotrophs capture energy from sunlight
• Some autotrophs use chemosynthesis to capture energy
• Known as chemoautotroph
• Heterotrophs consume autotrophs and other heterotrophs
• Autotrophs directly or indirectly supply energy and organic nutrients to heterotrophs
• Chemical reaction that releases free energy of organic compounds are known as cell respiration
• Energy and Ecosystems
• Autotrophs are the producers in a community
• Heterotrophs are consumers
• Things that break down are decomposers
• Producers, consumers, and decomposers form food web
• Organisms in a food web depend on abiotic, or nonliving factors.
• Organisms make up biotic, or living factors
• Biotic and abiotic components of a place make up an ecosystem
• Within each ecosystem are habitats
• All ecosystems combine to make Earth's biosphere

(2.4 - 2.5 QUIZ)

1. What are 5 abilities of living things
1. Ability to convert and absorb energy
2. Ability to organize more than other abiotic things
3. Ability to sense changes in the environment
4. Ability to grow and develop
5. Ability to reproduce

Energy Conversion (2.4)

• Energy conversion are described by principles called laws of thermodynamics
• First law is law of conservation of energy
• States energy can not be created nor destroyed, but it can change form
• Total energy of the universe is constant
• Energy can exist in many forms
• Energy in a log
• Chemical energy stored in its molecules
• When a log burns, most of its energy changes to heat energy
• Heat energy spreads to surroundings
• Organisms cannot create their own energy
• Must be obtained from outside source
• Autotroph source = Sun or inorganic chemicals
• Heterotrophs source = chemical energy in food
• If wolf eats rabbit, food digested to glucose, fatty acids, and amino acids
• Conversion of chemical energy releases free energy that is used to do work in living cells of animal
• Major distinction between living and non-living things

Energy and Entropy (2.5)

• Not all energy derived from food is useful
• Energy spreads out to surroundings
• Free energy in a system is slightly less after each energy conversion than before
• Second law of thermodynamics is entropy
• Entropy = systems change in a way that increases disorder
• World becomes disordered as free energy is released
• Free energy decreases and entropy increase as log burns
• Organization
• Key to organization in living systems is energy
• Producers do not use all the energy from photosynthesis
• Some of the energy goes to surroundings
• For consumers, converted chemical energy becomes heat energy and goes into surroundings
• There is a one-way flow of energy through food webs
• Total energy of universe remains the same, but is randomly dispersed as heat energy, which increases entropy

Enzymes and Energy (2.6)

• Cells must have a way to break and form chemical bonds
• Enzymes
• Protein
• All living cells contain them
• They lower the activation energy to make a reaction proceed
• Enzymes speed up chemical reactions
• Lower activation energies are called catalysts
• Specific reaction depends on a small area of enzymes's tertiary structure called the active site
• Active site has a shape that matches shape of starting molecules in a chemical reaction
• Close fitting known as substrate
• Molecules fit into enzymes, go through a chemical reaction, then leave the enzyme
• Many enzyme reactions are reversible
• Enzyme activity varies with the pH of the solution

Chemical Reactions in Organisms (2.7)

• Metabolism
• Two types
• Synthesis (building up)
• Larger, more complex molecules made from smaller ones
• Examples are starch from glucose and DNA from nucleotides
• Biosynthesis enables organisms to grow and maintain their structure
• Decomposition (breaking-down)
• Larger molecules break down into smaller molecules
• Example is breakdown of glycogen to glucose
• Releases free energy
• That energy used for biosynthesis

Energy Transfer and ATP (2.8)

• Oxidation
• Removal of electrons from a molecule
• Bonds broken and rearranged
• Some energy released 
• Ends up as ATP
• ATP
• adenosine triphosphate
• called "energy currency" of cells
• Made of adenine and ribose joined to three phosphates
• During chemical reaction, bond between second and third phosphate groups breaks
• Cells use energy in ATP to supply activation energy
• Energy carrier
• When one phosphate lost
• Known as ADP
• adenosine diphosphate
• Cells Need Energy
• Remove wastes
• Take in nutrients
• Maintain internal ion concentrations
• Move from place to place
• ATP used as energy carrier in all known living cells

2.9 Digestion Inside and Outside Cells

• Food is essential for growth and maintenance
• Each type of organism has a digestive system adapted to type of food consumed
• Heterotrophs must break down large food particles into macromolecules
• Then macromolecules must be broken into monomers
• Process known as digestion
• Digestion has two parts
• Physical
• Break down of larger pieces of food into smaller ones
• Performed by the mouth and oral cavity
• Chewing
• Grinding
• Larger surface area of food allows enzymes greater access to food particles
• Chemical
• Breaking down of complex food molecules into simpler ones
• Most animals rely on extracellular digestion, digestion that takes place outside cells
• Digestive track is where digestion occurs
• Plant digestion is intracellular digestion, occurs inside the cell
• Amino acids, sugars, minerals, water and oxygen can diffuse into cells
• Track
• Food enters the mouth at one end, and material that cannot be digested passes out of the anus at the other end
• Digestive tub divided into different regions with specialized functions

2.10 An Overview of Human Digestion

• Process
• Human digestion begins in the mouth, also known as the oral cavity. Ingestion, or chewing the food and placing it into the digestive tract, starts in the oral cavity. After the tongue mixes the food with saliva, it passes over the epiglottis. The epiglottis prevents any food or liquids from entering your airway. After, the food enters the esophagus, a tube which connects the mouth to the stomach. The food goes through the esophagus and reaches the stomach. Once the food reaches the stomach, the stomach turns the food into liquid, and a valve releases some of this liquid into the small intestine. The pancreas and liver transfer digestive juice to the small intestine. Undigested materials then go to the large intestine and feces are created. These feces are taken out of the body by the anus.
• Terms
• Saliva is a watery secretion that contains digestive enzymes
• Epiglottis is a trap-door like tissue which prevents food and liquids from enter the trachea (airway)
• Esophagus is a muscular tube connecting oral cavity to stomach
• Peristalsis moves food to the stomach in esophagus
• Stomach breaks up and mixes food
• Gastric juices break up the food
• Composed of enzymes, mucus, and acid
• Small intestine = a tube 6m long
• Large intestine = tube where undigested material goes
• Feces = waste product
• Anus = end of body where waste removed
• There are 9 meter of digestive track
• After average meal, stomach takes 4 hours to digest
• Food molecules absorbed through intestinal walls into the bloodstream.

2.11 Carbohydrates, Proteins, Fats, and Absorption

• Carbohydrate digestion
• begins in the mouth with an enzyme called salivary amylase
• Amylase digest starch to polysaccahrides and maltose
• Starch + Water -----> (Salivary Amylase) -----> maltose
• saliva has ph of 6.0 - 7.4
• stomach has contents of ph 1.0 - 3.5
• no carbohydrate digestion takes place in stomach, too acidic
• Carbohydrate digestion takes place in small intestine
• Pancreas delivers juices that convert acidic food to basic
• Maltose broken down into glucose
• Simplified process
• Similar to the regular digestion process, carbohydrate digestion starts in the mouth. In the mouth, an enzyme known as salivary amylase digests starch into polysaccharides and maltose. Unlike the regular digestion process, carbohydrate digestion happens in the small intestine rather than the stomach. In the small intestine, maltose is turned into glucose and absorbed by the body.
• Protein digestion
• occurs in stomach and small intestine
• enzymes needed to break down protein require strongly acidic environment 
• acid is provided by hydrochloric acid (HCl) from stomach glands
• acid can destroy living tissue
• doesn't destroy stomach lining because coated by mucus
• when food enter stomach, cells release a hormone called gastrin
• Gastrin triggers glands to release hydrochloric acid 
• Pepsin and Pepsinogen
• Pepsin is the active protein digesting enzyme
• Pepsinogen is the inactive version of it
• Hydrochloric acid converts pepsinogen to pepsin
• Pepsin breaks protein into polypeptides
• Further digestion occurs in the small intestine
• Trypsin breaks peptide bonds, creating amino acids
• Fat digestion
• digested in small intestine
• fats don't mix with water
• Fats prepared for digestion by bile
• Bile stored in gallbladder secreted by liver
• Physically breaks down fat droplets, increasing surface area
• Fat digesting enzyme is called lipase
• splits fats into fatty acids and glycerol
• Small molecules such as amino acids, sugars, fatty acids, and glycerol pass through cells in lining of small intestine
• Surface area of intestinal lining is increased by fingerlike projections called villi
• Each villi contains capillaries
• Capillaries are tiny, thin-walled blood vessels.

Chapter 2 Lecture Notes

• METABOLISM
• Similar to an Intel Dual (2) Core Processor
• Sending an impulse
• Processor = number of switches
• Like a train
• Metabolism = all chemical reactions that occur in cells and energy related (control) (making and breaking a bond)
• Exothermic (Exergonic mostly)
• Heat released
• Burning = bonds getting destroyed
• Getting oxidized
• To take electrons away
• Energy
• The ability to do work
• Something that can cause change
• Changes the atom around
• Break chemical bonds
• Kid on a slide
• Walk up to get to top of slide (kinetic energy)
• At the top (potential energy)
• Slides down (potential energy to kinetic energy)
• When energy is converted, heat is released
• Something 70 degrees has slower moving molecules that something 100 degrees
• Thermodynamics = energy change
• Gibbs Free ENergy
• (DELTA)G = (DELTA)H - T(DELTA)S
• G = change in free energy
• negative delta G = energy released (exergonic) (exothermic) (spontaneous reaction)
• entropy change (something ordered to disordered)
• positive delta G = energy absorbed (endergonic) (endothermic) 
• H = enthalpy
• T - absolute temperature
• S = change in entropy (heat)
• All energy came from the Big Bang
• Metabolic Reactions
• Catabolic
• Breaking things apart
• Always exergonic
• Usually exothermic
• Anabolic
• Putting things together
• Always endergonic
• Usually endothermic
• Woman on top of slide
• More free energy
• Less stable
• Greater work capacity
• Lesser entropy
• Positive delta G
• Woman on bottom of slide
• Less free energy
• Mores stable
• Less work capacity
• Higher entropy
• Negative delta G
• Law of Thermodynamics in Organisms
• When animal eats another
• Changes one form of energy to another
• Converted into heat
• motion
• H20
• CO2
• With every energy change there in an increase in entropy
• Types of Chemical Reactions
• Exergonic (negative delta G)
• Less energy from reactant to product
• Endergonic reaction (positive delta G)
• More energy from reactant to product.
• Enzymes lower the activation energy
• Up to 10 or 100s of thousands of times faster
• Hydrogen Peroxide (2H2O2)
• Breaks down into water + O2
• Reaction types
• Equilibrium reaction
• Most are equilibrium reaction
• A ---> C
• Anabolic and Catabolic 
• A + B ---> C
• A + B ----> C + D
• Chemical Reactions
• Covalent bonds resist change
• Must gain activation energy first
• From thermal energy of molecules
• Essential for life
• Allows cells to choose when reactions occur
• Amount of potential energy based on collision speed
• Molecules separate and make new bonds
• Catalyists used to decrease activation energy
• Most common is enzyme
• Incredibly speeds up the reaction
• Subrates converted into products in enzyme
• Enzyme has a pocket called active site
• Where the reactants go in
• Coenzymes and cofactors
• Change shape of enzymes and make them work
• Also provides site for the substrates 
• Puts stress on the bonds
• Metabolic pathway
• Series of enzymes involved
• Gives you a level of control
• Controlling enzymes
• Substrate analog
• Substrate analog, blocks real substrate
• Substrate analog looks like the substate
• Binds to active site
• Regulatory Protein
• Changes shape of the active site
• Either to make it work
• Or make it not work
• Easily reversed
• Larger than allosteric effector
• Organic
• Allosteric Effector
• Binds to a site on enzyme that doesn't resemble active site
• Changes shape of active site
• Easily reversed 
• 90% of medicines involve those controls
• Feedback Inhibition
• When enough products are created
• One of the products becomes an allosteric effector
• Stops the reaction
• Similar to a thermostat

DIGESTION

Bulk feed

• Snake gets all food in one attack

Vitamins

• Organic stuff that we can't make (Mr. Wong definition)
• Help enzyme work 
• MORE POSTED ONLINE

Minerals

• Cofactors of enzymes
• Mostly are not organic 

Eight essential amino acids acquired outside

• Tryptophan
• Methionine
• Valine
• Threonine
• Phenylalanine
• Leucine
• Isoleucine
• Lysine

Food Webs

• Plants are primary producers, they synthesize
• Then first level consumers (herbivores)
• Second level consumers (omnivore/carnivore)
• Third level consumers (omnivore/carnivore)
• Fourth level consumers (omnivore/carnivore)
• Only 10% of energy gets passed to next level.

Digestive System of Animal

• Simplest (Incomplete)
• Mouth
• Opening (gastrovacular cavity)
• Breaks apart; good stuff absorbed
• Bad stuff pushed back out the mouth
• Complexer
• There is a tube
• Tube = alimentary canal
• Two openings
• Complete digestive system
• Food coming in
• Broken apart
• What you don't use goes out the anus

Human Digestive System

• Two openings
• Food stays in mouth for 5-10 scones
• Teeth = grinds up food
• To make surface area larger
• So it can be exposed to more enzymes
• Glands = group of cells connected that makes stuff
• Salivary glands = salivary amylase
• Digests carbohydrates
• Saliva = salivary amylase + water + mucus
• Mucus needed for its slippyness
• Dogs don't have salivary amylase
• Esophagus = tube leading to stomach
• Peristalsis moves food down esophagus
• 1/3 of human esophagus = skeletal muscle
• Skeletal muscle can be controlled
• 3/3 of dog esophagus = skeletal muscle
• Bolus = ball of food
• Stomach
• Football size
• 2-6 hours in stomach
• Goes into cardiac orifice
• Not much digestion occurs in stomach
• Only protein
• Stomach secretes hydrochloric acid
• Acid good for pepsinogen to pepsin conversion
• Alcohol gets absorbed in stomach
• Solid to chyme in stomach
• Has holes called gastric pits
• Pyloric sphincter squirts chyme into small intestine
• Small Intestine
• 5-6 hours
• Starts with duodenum
• Total = 6 meter long
• First 12 in is where most digestion occurs
• Rest small intestine is where good stuff gets absorbed
• Pancreatic juice changes acid into basic or neutral
• Ileum is last part of small intestine
• Then feeds into large insetting
• CECEM AND APPENDIX ARE DUMB, WHY?
• Large Intestine
• No digestion
• Water absorption
• Ascending, transverse, descending = 3 parts of large intestine
• 12-24 hour process
• Known as fecal matter
• Pancreas
• Insulin (keeps blood sugar down)
• Keeps blood sugar down
• Insulin opens doors to cells that can take glucose in
• Diabetes 1: Not enough insulin (doors close)
• Glucagon (raises blood sugar)
• Opposite of insulin
• Flows in sugar from the liver
• What part of body produces major enzymes (ON PPT)

MORE NOTES ON CHAPTER 2

Heterotrophs eats stuff

Autotrophs convert here one nervy

Phototrophs converts energy from Sun

Chemoautotrophs convert energy by taking electrons away from a chemical reaction

Abiotic = not living

Biotic = living

Biosphere = all of the ecosystems

Ecosystem = abiotic and biotic factors that effect organisms

• Rainforest
• Swamp
• Pond
• Puddle

Decomposer = an organism that gets nutrients from dead organisms

Trophic levels = food levels (10% energy passed to next level)

• First = producer
• Second = consumers
• Third and Fourth

Laws of Thermodynamics

Activation Energy

Substrates

Products

Enzymes

Chemical Reactions

Formation of ATP

• ATP is energy currency
• Is a nucleotide
• Adenosine, ribose, and phosphate groups
• High energy bonds between phosphate groups
• ATP - ADP = exergonic reaction
• Food converted into ATP
• ATP = energy money of organisms
• Found in muscle cells, brain cells, kidney cells
• ADP + Phosphate = ATP (endergonic)
• ATP broken down = ADP (exergonic)

Oxidation and Reduction

• Oxidation = taking away of electron (exergonic)
• Reduction = gain an electron (endergonic)

CHAPTER 3 BOOK NOTES

Living Systems as Compartments

     3.1 Exchanged Materials

• Simplest living organism is a single-celed bacterium
• Cytoplasm is the cell interior
• Surrounded by a wall made of carbohydrates and proteins
• And a membrane made of phospholipids
• Phospholipid membrane
• Cell is a protected compartment
• What Cells Need
• Water
• Chemical reactions use molecules that are soluble in water
• Oxygen needed to release energy for cellular reactions
• Correct Balance of Ions
• Sodium
• Magnesium
• Calcium
• Hydrogen
• Chlorine
• Potassium
• Carbon dioxide (autotrophs only)
• Build food molecules
• Nutrients
• Sugars
• Amino Acids
• To supply energy and help build
• Hormones
• Transmit messages
• What Cells Remove
• Ammonium ions
• Toxic waste
• Other toxic materials

     3.2 Membrane as Barrier

• Membranes composed of two thin layers of phospholipids and proteins
• Lipids and proteins are fluid
• Not all molecules are equally soluble in a membrane
• Non polar phospholipid tails repel charge particles but allow fat-soluble molecules to pass
• Polarity, size, and electric charge of a molecule determines whether it can pass through a membrane
• Charge molecules can pass through with transport proteins
• Membrane is selectively permeable
• Membranes regulate the exchange of materials in a specific way
• Glycoproteins are proteins that are embedded in membranes that have sugars attached to them
• Glycolipids are similar but are lipids. 
• Glycoproteins and glycolipids act as antennae that receive chemical messages.

How Cells Exchange Materials

     3.3 Diffusion and Osmosis

• Diffusion = Movement of molecules
• Diffusion = Movement of molecules from an area of higher concentration to an area of lower concentration 
• They will move unless held back
• Random process
• Increases entropy
• Final state of diffusion = equilibrium
• Concentration gradient = difference in concentration of molecules across a distance
• Graph of distance (x), and concentration (y), would have a negative slope
• Rate of diffusion = depends on concentration gradient and surface area
• Steeper concentration gradients sends the molecules down faster
• Greater surface area = greater rate of diffusion
• Osmosis = Movement of water down its concentration gradient
• Responsible for movement of water across membranes
• If animal cell placed in pure water
• Water moves into cell (higher to lower concentration)
• Cell can burst
• If animal cell placed in non-water solution (glucose)
• Water escapes cell (high to lower concentration)
• Cell shrinks
• Outward pressure of a cell against its cell wall = turgor

 3.4 Passive and Active Transport

• Passive Transport = Diffusion without any input of energy
• Oxygen or CO2 into in out of cell
• Facilitated diffusion = moves without energy but uses transport proteins
• Transport proteins
• Form an open channel
• Or attach to and carry specific molecules
• Active Transport = Diffusion with input of energy and help of transport proteins
• Sources of energy
• Hydrolysis of ATP
• ATP ---> ADP = releases a phosphate
• Examples
• Na +, K +, CA +2, H +
• Coupling the movement of one substance against its gradient to the movement of another down its gradient
• Endocytosis = Absorption of very large molecules
• Membrane folds around substance that needs to be transport, making a pocket to carry it within the cell
• Exocytosis = Removal of very large molecules
• Opposite process of endocytosis

Exchange in Multicellular Organisms

     3.5 Gas Exchange in Water

• Cellular respiration = Oxygen is essential, CO2 is waster product
• Balance of oxygen and CO2 is key
• Gas exchange happens by diffusion across a membrane
• Gases (O2 and CO2) must be dissolved in water for diffusion to happen
• Gas Exchange in Water Dwellers
• Water contains dissolved oxygen in small amounts
• Need efficient gas-exchange system
• Efficiency
• Large surface area relative to volume
• Gills
• Large surface area made of many filaments (efficient)
• Each filament has a network of capillaries
• As water passes over, oxygen and CO2 are exchanged
• Diffusion can easily supply the small volume within filaments
• CO2 diffuses from the gills into the water

3.6 Adaptation to Life on Land

• Concentration of oxygen is higher in air than in water
• Organisms on land are constantly battling the tendency to dry out
• Every breath = water lost
• CO2 and O2 must be dissolved in water first
• Solution = exchange surfaces in an interior space
• Protects the surface from excess evaporation
• Human lungs is an example
• Simple Gas Exchange Process
• Small tube
• Smaller tuber (larger surface area : volume)
• Improves rate of gas exchange
• Smallest tubes
• Contact with muscles and other body tissues
• Lungs minimize the effects of drying out by eliminating the one-way flow of oxygen
• Chest expands ---> inhaled air moves into the lungs through highly branched tubular passage
• Exhaled air moves back out through the same passage
• Complex Gas Exchange Process

1. Breathe in through your nose
2. Filtered by hairs lining nasal cavities
• Moistened and warmed
3. Pharynx
4. Larynx
5. Trachea
6. Bronchus
7. Reaches cavities in lungs called alveoli 
• Each lung has millions of alveoli
• Alveoli thing walls supplied with capillaries
• O2 and CO2 diffuse across alveolar walls and walls of capillaries

• Ways of Conserving Water
• Creating barriers that limit permeability of outside of organism
• Glands in human skin secrete oils and waxes as a protective barrier
• In plants, cells secrete cuticle
• Cuticle = water-repellents covering
• Also blocks gas exchange
• In insects, spiracles minimize
• Spiracles = openings into the trachea
• Close when levels of CO2 fall below a certain point
• In plants, stomate gates open
• Stomate = openings in the leaf tissue
• Each stomate surrounded by guard cells that function like a gate
• When guard cells swollen with water, stomate openes.
• Allows CO2 to diffuse in and water vapor and oxygen to exit 
• Known as transpiration
• Closing the stomate can save water

3.7 Waste Removal

• Water Dweller Waste Removal
• Must constantly rid themselves of excess water
• Contractile vacuoles used to squeeze excess water from cell
• Other than water, other waster products must be removed
• Essential for homeostasis
• Homeostasis = balanced and controlled conditions in the internal environment of an organism
• Simple organisms excrete wastes directly though external surface
• Special organs have evolved for excretion
• For fish, excretion of CO2 takes place in gills
• Most troublesome by-product = nitrogen-containing waste from the metabolism of proteins and nucleic acids
• Amino groups removed form amino acids = ammonia (NH3)
• Very toxic to body tissues
• Some organisms convert nitrogenous waste to urea
• Less toxic than ammonia
• Urea can be safely excreted when dilute in water
• Uric-acid = insoluble and nontoxic form of nitrogenous waster requires almost no loss of water

3.8 Human Urinary System

• Urinary system = Kidneys, blood vessels the serve them, and plumbing that carries fluid formed in kidneys out the body
• Excretory tubules of humans = nephrons
• Long, coiled tube with one cuplike end that fits over a mass of capillaries
• Cup = glomerular capsule (Bowman's capsule)
• Ball of capillaries within cup = glomerulus
• Functions of Nephrons
• Filtration
• Occurs in the glomerulus
• Fluid portion of blood forced into glomerular capsule
• Filtrate = blood plasma, nitrogenous wastes, urea, salts, ions, glucose, and amino acids
• Reabsorption
• Occurs in tubule of the nephron
• Cells of tubule walls reabsorb substances need by body
• Includes salt, water, glucose, amino acids, some urea
• Secretion
• Molecules from blood are secreted into nephron tubules
• Other end opens into a duct that collects urine
• Collected into compact organs = kidneys
• Two kidneys are responsible for processing waste products of metabolism
• Blood cycles though kidneys and nitrogenous wastes are removed
• Waste fluid = urine
• Leaves kidneys through ureter
• Drains into holding tank = urinary bladder
• Drained when urine passes through tube called urethra during urination
• Excretion of sodium and potassium regulated by aldosterone
• Hormone secreted by the adrenal gland
• When potassium levels in blood are too high, aldosterone is release into the blood
• Feedback regulation = Process in which substances inhibit their own formation.
• Antidiuretic Hormone (ADH) = causes cell membranes to become more permeable to water

CHAPTER 3 LECTURE NOTES

MEMBRANES

Two Groups of Membranes

• Phospholipids
• Modified triglycerides
• Makes the molecule have polar and non-polar region
• Polar head
• Non polar tails
• Fatty acids
• Bilayer (two layers)
• Proteins
• 40%-50% proteins
• Proteins move
• Things don't pass through proteins
• Only protein channels
• Glycoproteins
• Give shape to the cell
• Other cells able to recgonize
• Receptors
• Protein + Carbohydrate
• Glycolipids
• Receptors
• Globular proteins
• Functions of Proteins in Cell Membrane
• Transport
• Enzymatic activity
• Signal transduction
• Intercellular joining
• Cells that are connected
• Cell-cell recognition
• Attachment to the cytoskeleton and extracellular matrix

Movement

• Diffusion
• Movement of molecules form areas of high concentration to low concentration
• Can occur through a membrane
• High to low concentration --> then reach a state of equilibrium
• More disorder because things are in two regions rather than one with material, and one without
• Area with less water = hypertonic
• Area with more water = hypotonic
• Same amount of water = isotonic
• Hypotonic solution
• Cell would pop
• For plants, cell doesn't explode because of cell wall
• Isotonic solution = same amount of water
• Equilibrium
• Hypertonic solution
• Shrivel up

     WASTE

Nitrogenous waste

• Proteins
• Goes to amino acids
• Goes to --NH2 (amino groups)
• Nucleic acids
• Goes to nitrogenous baes
• Goes to --NH2 (amino groups)
• Types of Waste
• Aquatic animals
• Ammonia
• Mammals
• Urea
• Water soluble
• Less dangerous
• Bird, insects, reptile, snails
• Uric acid
• Solid
• Need to get rid of waste but conserve water
• Where is water
• Bloodstream (7%) Plasma
• Between cells (30%) interstitial fluid
• Inside cell (60-70%) intracellular fluid
• Nephron (Tubes of the Kidney)
• 1 million nephrons per kidney 
• Blood supply forced into tube
• Tube has a selectively permeable membrane
• Some stuff goes back into blood
• Some leaves the body
• Stages
• Filtration
• Capillary = molmarius
• Reabsorption
• Things the body needs come back into blood stream
• Secretion
• Things put back into urine
• Excretion
• End up taking just waste product
• In the form of urine
• Kidney

• Blood pumps around your body and eventually reaches the kidney
• Renal artery = blood artery going into kidney
• Uses a lot of energy
• Process
• Afferent arteriole reaches Bowman's capsule
• Goes through glomerulus
• Efferent arteriole leaves glomerulus
• Proximal (near) tubule is closest to glomerulus
• Goes through Loop of Henle
• Then goes through distal (far) tubule
• Then goes into collecting duct
• 5-6 nephrons connect to collecting duct
• Feeds into excretion tube
• BE ABLE TO DRAW KIDNEY AND NEPHRON!!
• KNOW TERMS!!!!
• In And Out
• Urea
• Water
• Sodium
• Red = active transport
• Purple = passive transport
• Osmolarity looks at particles
• Water = 1
• NaCl = 2
• Two parts
• Regulated by process
• Brain measure blood concentration
• If osmolarity of blood is high, not enough water
• Hypothalamus in brain releases ADH (antidierutic hormone)
• Increases permeability of collecting duct
• More water reabsorbed 
• If blood pressure is too low (not a lot of water)
• Juxta-glomerulus apparatus (JGA) releases renin
• Renin turns angio-tensiongen to angioensin 2
• Goes to adrenal gland
• Creates aldosterone
• Increased sodium ion and water reabsorption in distal tubules

CHAPTER 4 BOOK NOTES

Book Notes on Chapter 4

4.1 What are Autotrophs?

• Photosynthesis
• Performed by plants, some bacteria, and algae
• Uses sunlight to turn CO2 into sugars
• Enzymes convert sugars into amino acids and other substances
• Chemoautotrophs
• Obtain energy by oxidizing inorganic substances
• Iron
• Sulfur
• Other minerals
• Use energy to form sugar from CO2

4.2 Overview of Photosynthesis

• Use sunlight as a source of energy
• Light
• Length of light determines color and energy 
• Shorter wave = greater energy
• Pigments in plant absorb visible light
• Thylakoids
• Contain these pigments
• Form closed sacs
• Thylakoids float inside the cell in simple cells
• Each thylakoid part of chloroplast in plants and algae
• Outer chloroplast membrane separates thylakoid from cytoplasm
• Stroma
• Outside of thylakoids
• Enzymes in stroma form sugar from carbon dioxide and water 
• Contains chloroplast's DNA and RNA and enzymes needed to make proteins for chloroplast
• Chlorophyll
• Green pigment
• Two forms
• Chlorophyll a
• Chlorophyll b
• Don't absorb green light
• Gives plants their green colored leaves
• Different pigments which absorb different colors of lights
• Photosynthesis Process (Occur in Two Group of Reactions)

1. absorption of light energy
2. conversion of light energy into chemical energy
3. storage of chemical energy in form of sugars

• Light Reactions
• Thylakoids absorb light and convert it into chemical energy, stored in molecules
• Calvin Cycle
• Molecules made in light reactions is used to make 3 carbon sugars from CO2
• 3 CO2 + 3 H2O = C3H6O3 + 3O2

4.3 The Light Reactions

• What Happens
• chlorophyll and other pigments in the thylakoid absorb light
  energy, water molecules are split into hydrogen and oxygen, and light
  energy is converted to chemical energy.
• Light Absorbing Pigments
• From two types of clusters
• Photosystems 1 and 2
• Process
• The reaction center molecules accumulate lots of energy from photons from the sun
• Some electrons jump to other molecules called electron carriers
• Electron carries form an electron transport systems between two photosystems
• Some electrons jump to other molecules called electron carriers
  
• Electrons from photosystem II move through the system to replace electrons lost from photosystem I.
• Enzyme near PS 2 breaks 2 H2O ---> 4 protons + 4 electrons + O2
• The electrons attract protons into the thylakoid sac
• The difference in concentration and charge between the inside and outside of the thylakoid creates a difference in potential energy across the membrane
• That energy can be used to do stuff
• As the protons diffuse out, their energy is transferred to the enzyme ATP synthetase. 
• ATP synthetase uses that energy to form ATP from ADP and a phosphate
• At PS1, electrons receive an energy boost from reaction center
• This energy boost allows them to reduce NADP+ (Nicotinamide adenine dinucleotide phosphate)
• Electrons + Protons from Water + NADP+ = NADPH
• NADPH is reduced form of NADP+
• NADPH and ATP then sent to Calvin cycle
• ATP, NADPH, and Oxygen Gas are products of light reactions

4.4 Calvin Cycle

• Process

1. Molecule of CO2 combines with 5 carbon-sugar phosphate (RuBP)
1. known as carbon fixation (carbon is fixed to organic molecule)
2. Rubsico fixes the carbon
2. Produces unstable 6 carbon molecule
3. Splits into two molecules of three carbon acid, phosphoglyceric acid (PGA)
4. One molecule of ATP and NADPH reduce PGA into PGAL (phosphoglyceraldehyde)
5. Series of enzymatic reaction combines and rearranges molecules of PGAL, producing 5 carbon-sugar phosphate.
6. ATP molecule from light reactions adds second phosphate group to 5 carbon-sugar phosphate
7. This produces a molecule of RuBP
8. Cycle goes three turns

• Six molecules of PGAL produced, 5 of which used to regenerate RuBP
• Sixth is given to organism for growth
• Types of Plants
• C3 plants called C3 plants because product is a 3-carbon acid PGA
• Why Calvin Cycle Doesn't Work at Night
• Sun provides energy for ATP and NADPH to be formed
• Light activates rubisco and other enzymes
• Sufficient CO2 isn't available when stomates closed at night

4.5 Rate of Photosynthesis

• Rate = Activity per unit of time
• Photosynthesis can be measured by how much CO2 consumed
• What Affects the Rate of Photosynthesis?
• Light intensity
• As light intensity increases, so does the rate of photosynthesis.
• Reaches a point where there is too much light, and rate of photosynthesis levels off
• Energy accumulated faster than energy can be transported
• Photoinhibition
• Some of extra energy can be passed to oxygen molecules
• Oxygen can react with water to form hydroxyl ions (OH-) or hydrogen peroxide (H2O2)
• These substances can damage chloroplast by reacting with pigments and proteins
• Temperature
• As temp increases, rate of photosynthesis increases then decreases
• Decreases at about 30 degrees celsius for C3 plants
• Concentrations of CO2
• The more CO2, faster rate of photosynthesis but will eventually decrease
• Similar to graph of light intensity
• Once maximum CO2 level reached, more CO2 will have no effect
• Limiting Factors = Factors in shortest supply have most effect on rate of photosynthesis 
• Plants grown in a greenhouse will not grow at maximum rate, even if in full sunlight, if greenhouse is cold

4.6 Photorespiration and Special Adaptations 

• Oxygen can decrease rate of photosynthesis in C3 plants
• Rubisco gets confused with bonding with CO2 or O2
• Similarities of CO2 and O2
• Both held together by double bonds
• Photorespiration
• When rubisco binds with CO2, 2 molecules of PGA form
• When rubisco binds with O2, 1 molecule of PGA forms and one molecule of 2-carbon acid glycolate.
• Glycolate transported out of chloroplast and partly broken down into CO2
• When rubisco binds with O2, known as photorespiration.
• Benefits of Photorespiration
• Enables organisms to recover some carbon in glycolate
• Helps to reduce photoinhibition
• Factors That Control Photorespiration vs. Photosynthesis
• Photorespiration = high levels of oxygen
• Photosynthesis = high levels of CO2
• In dry weather, plants close stomates
• CO2 levels drop
• Higher chance of photorespiration
• Adaptations
• C4 plants
• Examples
• Sugarcane
• Corn
• Crabgrass
• Process
• Mesophyll cells fix carbon dioxide to a 3 carbon acid
• Unlike rubisco, the enzyme which does this doesn't get confused between oxygen and carbon dioxide
• Resulting 4 carbon acid rearranged and transported to bundle sheath cells
• bundle sheath = layer of tightly packed cells surrounding each vein in leaves
• At bundle sheath cells, CO2 released and goes into Calvin cycle
• Advantages/Disadvantages
• C4 plants can function efficiently at high temperatures
• Keeps stomates partly closed to reduce water loss 
• C4 plants grow more rapidly than C3 plants
• CAM plants (crassulacean acid metabolism)
• Examples
• Cactus
• Jade
• Snake plants
• Process
• Stomates open at night instead of during the day
• During day, stomates close to conserve water
• Advantages/Disadvantages
• Grow very slowly
• Not efficient 

4.7 Photosynthesis and the Atmosphere

• Photosynthesis supplies O2 to Earth's atmosphere and food to organisms
• Most organisms use oxygen and release CO2
• Photoautotrophs use that CO2 again in photosynthesis to complete the cycle
• Facts
• Plants use 140 billion metric tons of CO2 each year for photosynthesis
• Plants use 110 billion metric tons of water each year for photosynthesis
• Produces more than 90 billion metric tons each of organic matter and oxygen gas
• CO2 levels are increasing
• Due mostly to burning of fossil fuels
• Extra CO2 could be used for photosynthesis
• Preserving balance of O2 and CO2 is key for life on Earth

4.8 Varieties of Chemoautotrophs

• Chemoautotrophs = bacteria that obtain energy by performing chemical reactions, and fix their own carbon
• Energy comes from oxidation from a substance
• Iron
• Sulfure
• Other inorganic minerals
• Doesn't provide as much energy as photosynthesis or heterotrophy
• Chemoautotrophs don't compete well with other organisms
• Survive where other organisms can't survive and light and organic compounds are in short supply
• Chemoautotrophs fix CO2 with the Calvin cycle
• They can switch electron donors
• Use whatever energy source is available

4.9 Chemoautotrophs and the Environment

• Bacterium called Deinococcus survives on rocks near South Pole
• Chemoautotrophs are mostly located in deep ocean
• They might take up the majority of life
• Oxidized end products of chemoautotrophs form important deposits of oxidized mineral ores.
• Chemoautotrophs oxidize ammonium ions (NH4+) to nitrite ions (NO2-) to nitrate ions (NO3-)
• Plants absorb these nitrate ions

CHAPTER 4 LECTURE NOTES

PHOTOSYNTHESIS

PREZI: http://prezi.com/-ivjb3dml_g_/copy-of-ap-bio-metabolism-3-photoautotrophic-nutrition/

Big Question

• How do living systems process energy?
• 99% of energy from Sun unused

Recap

• Light has ability to make food
• Plant's like blue/purple light, plants reflect green light
• Reason why plants are green

Energy Transfer Organelles

• Chloroplast
• Takes light
• Takes CO2 and H2O
• Magic happens in chloroplast
• Creates O2 and Food (Organic Molecules) (Glucose)
• Mitochondria
• Animals and plants have mitochondria
• Glucose comes in
• Energy produced as ATP
• Waste product is CO2 and H2O

Important Reactions (BE ABLE TO WRITE DOWN REACTIONS!!!)

• Photosynthesis
• 6CO2 + 6H2O ---> C6H12O6 + 602
• Cellular Respiration
• C6H12O6 + 602 ---> 6CO2 + 6H2O

Plants and Such

• Photosynthesis
• Bacteria
• Cyanobacteria
• Unicellular algae
• Seaweed

Plant Anatomy

• Magic box = leaf
• Purpose of leaf is to take into sunlight
• Solar receptor
• Leaf has
• Epidermal are top and bottom layers
• Green cells are mesophyll (middle) cells
• Spongy and solid
• Bottom of leaf has stomata
• Release O2, take in CO2
• Magic box is actually chloroplast
• Chloroplast = where photosynthesis occurs
• Double membrane
• Outer and inner membrane
• Internal membrane
• Thylakoid membranes
• Chlorophyll within them
• Stroma : Chloroplast as Cytoplasm : Cell

Light = Energy

• Light is a form of electromagnetic radiation
• Measured in terms of wave length
• Short wavelength = more energy
• Visible light = 380 - 750

Chlorophyll

• Magnesium is in the middle

Chemiosmosis 

• Two boxes within chloroplast
• Part of them need light (dependent)
• Light causes electrons to shoot up to higher energy level
• Part of them don't need light (independent)
• Used to be called light and dark reactions
• Photosystem 2
• Shoots electron to electron receiver
• Now oxidized
• Reaction center
• Many proteins
• P680 Chlorphyll inside
• Photons activates chlorophyll
• Goes to p680
• Loses an electron
• Oxygen comes form splitting of water
• Photosystem 1
• Similar to photosynthesis 2
• NADPH is like a taxi molecule

Light Reactions

• Electrons travel down electron transport gradient
• Proteins lured in
• Creates electron gradient
• Products
• NADPH
• ATP

Calvin Cycle (UNDERSTAND CYCLE)

• Occurs in stroma
• Wasteful cycle
• Oxygen is bad for the Calvin cycle

C4 Plants

• Absorbs CO2 in mesophyll cells
• Combines into a 4 carbon compound
• Less photorespiration 

CAM Plants

• Stomates open at night
• In the day, CO2 used

CHAPTER 5 BOOK NOTES

5.1 Metabolism and Cell Respiration

• Metabolism
• Two parts
• Synthesis
• Consume energy
• Decomposition
• Release energy
• ATP made during decomposition and used during synthesis so two processes linked
• Cell respiration
• Decomposition pathway that provides energy cells need to function
• Series of reactions that releases energy as sugars broken down to CO2 and H2O
• Each step catalyzed by enzyme
• Aerobic respiration
• Occuring in the presence of oxygen
• Oxygen is oxidizing agent that receives electrons from decomposed substrates
• Anaerobic
• Occurring without oxygen
• Substrate may only be partly decomposed
• Raw Materials
• Carbs
• Fats
• Proteins
• Important Substrates
• Glucose (C6H12O6)
• Glucose-phosphate (C6H11O6 --- H3PO3)
• Formula for Cellular Respiration
• C6 H12 O6  + 6 O2 ----> 6 CO2  + 6 H2 O + energy
• Slow Releases of Energy
• Energy from glucose is released slowly
• Otherwise it would be too explosive and too much energy release at one time

5.2 The Stages of Aerobic Respiration

• Three Stages
• Glycolysis
• Enzymes partially oxidize glucose and it is split into two 3-carbon molecules
• Energy released forms a small amount of ATP
• CO2 release from each two 3-carbon molecules
• Krebs Cycle
• Resulting 2-carbon molecules oxidized completely to CO2 in the Krebs Cycle
• More ATP molecules form
• As glucose oxidized, it loses electrons and protons
• These pass to NAD+
• Reduced to NADH
• Two hydrogen atoms from glucose reduce FAD
• FAD + 2H ---> FADH2
• Electron Transport System
• NADH is oxidized
• Donates protons and electrons to electron transport system
• NADH and FADH2 reduces oxygen to form water
• Stages 2 and 3 cannot happen without oxygen

5.3 Glycolysis

• Glucose is the usual raw material for glycolysis
• Important things that happen
• Glucose molecule breaks into two pieces
• Some ATP forms
• Some NAD+ reduced to form NADH
• Process
• Begins when an enzyme converts glucose to glucose-6-phosphate
• ATP provides phosphate and energy for reaction
• Another enzyme rearranges glucose-6-phosphate
• Second ATP molecule donates another phosphate group
• Resulting molecule splits into two 3-carbon sugar-phosphates
• Other enzymes catalyze rearrangement and oxidation of these molecules
• Forms 3-carbon compound pyruvic acid
• Oxidation of the sugar-phosphate results in the reduction of NAD+
• Products
• Four molecules of ATP
• Net gain 
• Two molecules of NADH
• Two molecules of pyruvate
• In Plants
• Starch and sucrose break to glucose or glucose 1-phosphate
• Then goes into glycolysis
• Three carbon sugar-phosphates formed in photosynthesis can enter later on in glycolysis
• Sugars and Organic acids formed during glycolysis can leave pathway and serve as carbon skeletons for biosynthesis
• Biological Roles
• Synthesis of ATP, NADH, and Pyruvate
• Formation of carbon skeletons
• Aerobic vs. Anaerobic
• Anaerobic (Lactic-acid Fermentation)
• Bacteria reverse oxidation that produced pyruvate
• Convert NADH and pyruvate into NAD+ and lactate, another 3-carbon acid
• NAD+ goes back to glycolysis, and glycolysis continues to provide small amount of ATP
• Aerobic
• Pyruvate enters the Krebs cycle
• Types of Fermentation
• Yeast and some bacteria ferment pyruvate to ethanol and vinegar

5.4 Mitochondria and Respiration

• Mitochondria
• Mitochondria are organelles where Krebs cycle and electron transport system occur
• Called powerhouses
• Site where most ATP is synthesized
• Some cells have 10-20 mitochondria
• Muscles cells have several thousand
• Size
• 2-3 micrometers long
• 1 micrometer thick
• Composition
• Outer and Inner membrane
• Consist of proteins and double layer of lipid molecules
• Inner membrane is more protein than lipid
• Inner membrane has many folds, or cristae
• On and In cristae are enzymes of electron transport system, enzymes for ATP formation, and some of the enzymes for Krebs cycle
• Matrix = fluid-filled interior space of mitochondria
• Glycolysis and Fermentation occur in cytoplasm

5.5 The Krebs Cycle

• Completes decomposition and oxidation of glucose to CO2
• Process
• Pyruvate transported to mitochondria
• Enzymes release CO2 from each 3-carbon pyruvate molecule
• This leaves a molecule of acetate, a 2-carbon organic acid
• Same step also reduces NAD+ to NADH
• Carrier molecule, coenzyme A (CoA), bins to acetate
• Result is known as acetyl CoA
• CoA delivers acetate to the Krebs cycle
• Acetate enters Krebs cycle, where enzyme combines acetate group of acetyl CoA with a 4-carbon acid (oxaloacetate)
• Forms 6-carbon acid (citrate)
• CoA release and recycle to deliver more acetate
• Other enzymes catalyze rearrangement and oxidation of citrate
• Two of the carbon atoms in citrate are oxidized to carbon dioxide
• Hydrogen atoms that these carbon atoms lose reduce two molecules of NAD+ to NADH
• Reactions produce a 4-carbon organic acid which is rearranged and further oxidized
• Result is a new molecule of oxaloacetate and the cycle begins again
• Each molecule of glucose = two molecules of pyruvate
• Products
• 6 CO2
• 6 NADH
• 2 FADH2
• 2 ATP

5.6 The Electron Transport System

• Oxidation of glucose in glycolysis and Krebs cycle reduces NAD+ to NADH and FAD to FADH2
• They carry hydrogen atoms to the electron transport system
• Electron Transport System consists of a series of easily reduced and oxidized enzymes + proteins called cytochromes
• Process
• Hydrogen atoms separated into electrons and protons
• Cytochromes transfer electron step by step through system
• Terminal cytochrome combines electrons and protons with oxygen, forming water
• Uses oxygen
• At each transfer, electrons release free energy
• Some of the energy used to have enzymes tensor protons from matrix to inter membrane space
• Protons become highly concentrated
• Protons diffuse back into matrix
• Pass through ATP-synthetase
• ATP is synthesized from ADP and a phosphate
• One molecule of NADH = 3 ATP
• One molecule of FADH2 = 2 ATP
• Bacteria
• Do not have mitochondria
• Contain electron transport system
• Sulfate and Nitrate are other oxidizers
• Instead of reducing oxygen to water, bacteria produce reduced sulfur or nitrogen compounds (hydrogen sulfide) and (ammonia)
• Process called anaerobic respiration
• Types of Aerobes/Anaerobes
• Facultative aerobes
• Can survive for long periods with or without oxygen
• Switch between fermentation and respiration
• Obligate Anaerobes
• Poisoned by oxygen
• Generate ATP from fermentation or anaerobic respiration 
• Obligate Aerobes
• Cannot survive without oxygen
• Summary of Process
• Electrons and protons from NADH and FADH2 reduce oxygen, forming water
• Energy released during this is used to synthesize ATP
• As electrons pass along transport system, they release free energy
• Proteins use this energy to pump protons out though inner membrane
• Difference in proton concentration supplies energy for ATP synthesize

5.7 Oxygen, Respiration, and Photosynthesis

• Some animals have lungs and circulatory systems that deliver oxygen to electron transport system
• Products of photosynthesis = raw materials for cell respiration
• Cell respiration provides raw materials for photosynthesis
• Two processes complement each other

CHAPTER 5 LECTURE NOTES

CELLULAR RESPIRATION

Cellular Respiration

• Get energy out of food (Glucose)
• Energy = ATP
• Units of energy = units of ATP
• NADH and FADH2 are mad bumblebees that can be used to make ATP
• Three big parts
• Glycolysis
• Occurs in cytoplasm
• Sugar splitting
• Electrons carried via NADH
• Glucose ----> 2 Pyruvic acids
• MEMORIZE THIS DIAGRAM
• 2 ATP needed to start reaction
• 4 ATP come out of reaction (Net 2)
• Net
• 2 Pyruvate + 2H20
• 2 ATP
• 2 NADH + 2H+
• Real Process
• ATP adds a phosphate to glucose by Hexokinase 
• Creates glucose 6 phosphate
• Phosphoglucoisomerase changes shape to Fructose 6 phosphate
• Phosphofructokinase adds a phosphate from ATP
• Becomes fructose 6 bi-phosphate
• Splits into Dihydroxyacetone phosphate and Glyceraldehyde 3 phosphate
• Look at diagram for rest
• When there is enough ATP, ATP connects with phosphofructokinase to turn off glycolysis
• AMP stimulates positive feedback in glycolysis
• Negative feedback loop in cellular respiration
• Products
• 2 ATP
• 2 NADH
• 2 Pyruvate molecules
• Krebs Cycle
• Occurs inside mitochondria
• More ATP
• Gives NADH and FADH2
• NAD+ = 2 electrons one protons
• Process
• Pyruvate goes into mitochondrial matrix
• CO2 comes out
• Electrons used to reduce NAD+ to NADH + H+
• Attaches to Coenzyme A
• Becomes Acetyl CoA
• KNOW NAMES OF SUBSTANCES AND HOW MANY CARBONS OF EACH AND WHEN CO2 COMES OUT WHERE NADH and FADH2 AND ATP COMES OUT (SUBSTRATE LEVEL PHOSPHORYLATION OCCURS BETWEEN SUCCINYL COA AND SUCCINATE 
• Products
• 6 NADH
• 2 FADH2
• 2 ATP
• Electron Transport Train
• Occurs in mitochondria inner membrane
• Almost identical with the one in photosynthesis
• Most ATP produced
• 3 protons = 1 ATP
• 1 NADH = 3ATP
• 1 FADH2 = 2 ATP
• 1 glucose = 38 ATP/36 ATP 
• Cellular Respiration Diagram
• Substrate-level phosphorylation
• ATP synthesized by enzymes

CHAPTER 6 BOOK NOTES

6.1 Cell Study and Technology

• All organisms are composed of cells, the basic units of life
• Cell theory

1. Cells, or products made by cells, are the units of structure and function in organisms
2. All cells from preexisting cells

• History
• Robert Hooke used microscope in 17th century to examine corks
• Looked like small little compartments
• Named them cells
• Robert Brown saw the nucleus in 1831
• M. J Schledien found plant cells contain nuclei and cell fluid
• Theodor Schwann used microscope to examine animals in 1839
• First saw cells as tiny blobs of jelly
• Modern day light microscopes can't see deep into cell
• Electron microscopes can reveal tiny cell parts
• Drawbacks
• Steps needed to prepare cell for examination kills cell
• Preparation can also alter cell structure
• Scanning tunnel microscopes
• Can be more powerful than electron microscopes
• Do not require such harsh preparation
• Sizes
• Cells difference in size from 10 - 20 micrometers in diameter
• Smaller cells can be only 1 micrometer long

6.2 Two Basic Types of Cells

• Two groups
• Prokaryotes
• Simplest cells
• Bacteria
• Everywhere
• Nearly always unicellular
• Smallest = 0.3 micrometers in diameter
• Average = 1 - 5 micrometers in diameter
• Eukaryotes
• Larger (10 - 50 micrometers)
• More complex
• Can form multicellular organisms
• Have many parts each with a specific function
• Have nucleus, prokaryotes don't
• Contains DNA
• Synthesis of proteins

6.3 Prokaryotic Cell Structure

• Nearly all have a rigid cell wall
• Prokaryotes usually have one chromosome made of a continuous circular molecule of DNA
• Nucleoid = Where chromosome is attached to plasma membrane
• Plasmids = Smaller circular DNA molecules
• Shapes of bacteria
• rod
• sphere
• corkscrew
• Flagella = long whip-like extensions made of proteins
• Rotate like propellers
• Enables cell to swim
• Swimming bacteria can sense their environment
• Go to food, away from harmful substances
• Bacteria can be useful for a source of antibodies

6.4 Eukaryotic Cell Structure

• Divided into small functional parts called organelles
• Reactions can occur at the same time because of organelles
• Compartmentation makes eukaryotic cells more efficient by separating process and having division of labor
• Plasma membrane
• 2 lipid layers
• Encloses eukaryotic and prokaryotic cells
• Controls passage in and out of cell
• For plants and some others, there is a cell wall that surrounds cell membrane
• Composed of stiff fibers of cellulose 
• Enabled for cell support
• Allows for development of turgor pressure
• Animals lack a cell wall
• Nucleus
• Genetic control center
• Contains chromosomes
• Nuclear Envelope
• Formed of 2 membranes
• Has pores
• Contains one or more nuclei
• Nucleoli
• Drops of concentrated RNA
• Where RNA is synthesized
• Cytoplasm
• Within cell membrane and outside nucleus
• Fluid + organelles
• Cytosol
• Fluid of the cytoplasm
• Surronds organelle
• Cytoskeleton
• Protein scaffolding
• Composition
• Hollow micro tubes
• Solid but flexible strands called microfilaments
• Connecting intermediate filaments
• Can hold organelles in place and move them around
• Provides shape, internal organization, and movement
• Ribosomes
• Small bodies composed of RNA and protein
• Catalyze synthesis of a cell's proteins
• Some ribosomes attached to endoplasmic reticulum (ER)
• Forms tubes and channels throughout cytoplasm
• Central role in biosynthesis
• Rough ER
• Has ribosomes
• Smooth ER
• Lacks ribosomes
• Proteins synthesized by ribosomes on ER go directly to ER
• Golgi apparatus
• Many substances pass through ER then to golgi
• Consists of membranous sacs that look like pancakes
• Modifies, sorts, and packages macromolecules for secretion or delivery
• Vesicles
• Spherical
• Pinch off Golgi membranes
• Proteins modified in Golgi
• Connected internal membrane system
• ER, Golgi, and vesicles form it
• Proteins made in it become part of membrane of cell or end up in organelles
• Lysosomes
• Special vesicles
• Contain enzymes that break cell's old macromolecules for recycling
• Can also fuse with vesicles
• Lysozyme protects eyes from bacterial infection
• Intracellular digestion
• Vacuoles
• Enlarge as cells mature
• Contain water, organic acids, digestive enzymes, salts and pigments
• Up to 90% of a cell's volume is the vacuole 
• Centrioles
• Tubular structures
• Participate in cell reproduction
• Consist of a pair of cylindrical bundles of microtubules
• Mitochondria
• Site of 2 phases of cellular respiration
• Chloroplasts
• Site of photosynthesis
• Eukaryotic flagella
• Covered by plasma membrane
• Consist of long bundles of microtubules
• Provide energy by breaking down ATP
• Cilia
• Short flagella
• Covered with hundreds in rows
• Move cell by whipping in oar like motion

6.5 Cooperation Among Cells

• A cluster of cells inside necessarily a multicellular organism
• Each cell has an individual life and can break away
• Colonies
• Where some unicellular organisms live
• Members of colonies are related
• Each individual is still separate organism
• Biofilms
• Bacteria that attach to solid objects
• Can contain several unrelated bacteria
• They can work together to change conditions in biofilm
• Volvox
• Colonial algae
• Individual cells take specific roles
• Each cell has 
• nucleus
• two flagella
• contractile vacuoles
• light-sensing structure
• cup-shaped chloroplast
• Some cells larger than others
• Has front and back end
• Larger cells usually in back
• Moves in a coordinated way
• Considered barely a multi-cellular organism

6.6 Division of Labor

• Most multicellular organisms are larger than Volvox
• Organism must have large surface area : volume ratio to exchange materials
• Larger organisms have blood vessels, lungs, and leaves to increase surface area
• Each cell has a special job
• Epidermis
• Organism's outer layer
• Skin for humans
• Human blood cells are like flattened spheres
• Tissue
• Group of cells with same specialization
• Organs
• Tissues can be organized into organs
• Eyes, heart, etc…
• System of Organs
• Organs can be incorporated into system of organs
• Circulatory system, etc…
• Junctions and Extracellular Matrix
• Cells in direct contact are often connected at plasma membrane
• Connected at junctions
• Hold cells together
• Communication
• Channels

6.7 Systems

• Circulatory system is needed to transport materials
• More than one system involved in most organisms
• Reasons why systems are necessary

1. A division of labor occurs among cells
2. Many individual cells cannot work together without regulation and coordination
3. Most cells are not in direct contact with outside environment

• Different systems unite all parts of an organism

CHAPTER 6 LECTURE NOTES

CELL STRUCTURE

Parts

• Cell membrane is important
• Defines the cell
• Sets boundary for the cell
• Phospholipid bilayer
• Proteins
• Fluid model
• Pores
• Made of protein complexes
• Endoplasmic Reticulum
• Continuous with outer membrane
• Phospholipid 
• Rough and Smooth
• Chromatin
• Stuff that makes up chromosomes
• DNA and protein
• Ribosomes
• Where proteins are partially produced 
• On the endoplasmic reticulum
• Nuclear Pores
• Lets stuff out
• Golgi complex
• Proteins created more
• Membrane factory