BioLOG: 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

assumption that the natural world can be explained in understandable terms
based on results of observation and experiments
results must be verifiable by other scientists
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

What is the question?
What are the data and how were they obtained?
What do the data mean?
Who is reporting the data?
Is that person qualified?
How complete is present state of knowledge?

Chapter 1 Book Notes

Quiz

Formula for water?

Smallest particle of element that still has properties

Atom

Formula for oxygen

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?
- Law of conservation of matter?
- Energy to start chemical reaction?
- Two types of bonds?
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

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)

What are 5 abilities of living things

Ability to convert and absorb energy
Ability to organize more than other abiotic things
Ability to sense changes in the environment
Ability to grow and develop
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

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

Breathe in through your nose
Filtered by hairs lining nasal cavities

Moistened and warmed

Pharynx
Larynx
Trachea
Bronchus
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)

absorption of light energy
conversion of light energy into chemical energy
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

Molecule of CO2 combines with 5 carbon-sugar phosphate (RuBP)

known as carbon fixation (carbon is fixed to organic molecule)
Rubsico fixes the carbon

Produces unstable 6 carbon molecule
Splits into two molecules of three carbon acid, phosphoglyceric acid (PGA)
One molecule of ATP and NADPH reduce PGA into PGAL (phosphoglyceraldehyde)
Series of enzymatic reaction combines and rearranges molecules of PGAL, producing 5 carbon-sugar phosphate.
ATP molecule from light reactions adds second phosphate group to 5 carbon-sugar phosphate
This produces a molecule of RuBP
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

Cells, or products made by cells, are the units of structure and function in organisms
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

A division of labor occurs among cells
Many individual cells cannot work together without regulation and coordination
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

BioLOG

Sunday, December 16, 2012

Biology Semester 1 Final Notes

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