Physical Properties

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Physical Properties

• Due to the polar nature of water
• Hydrogen bond- weak attraction between hydrogen
  on adjacent molecules such as water

H H O
H H O
Hydrogen bond
2
Water and its importance to Life

• Life evolved in water
• Waters unique properties have made life as we
  know it possible

3
Physical Properties

• Heat of vaporization- amount of energy that is
  released or gained when changing state from
  liquid to gas or back

4
Physical Properties

• High Specific Heat- the amount of heat absorbed
  or released when water changes temperature by one
  degree C. ( 1 cal. )

5
Ice Floats

• As a liquid waters hydrogen bonds continuously
  break and reform
• As a solid four molecules form hydrogen bonds
  creating crystals with open channels and thus
  fewer molecules per area.

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Physical Properties

• Water reaches maximum density at 4 degrees C.
• Water is a universal solvent due to its polar
  nature

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Evaluate the importance of the following and
explain the property of water responsible.

• Cytoplasm is 98 water
• Ice Floats
• Lake effect temperature moderation
• Evaporative Cooling
• Spring-Fall Overturn

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Most Abundant Chemicals in Life

• Carbon
• Oxygen
• Hydrogen
• Nitrogen
• Ca, P, K, S, Na, Cl, Mg gt 4

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9
Carbon is special

• Tetrahedral structure- four valence electrons
  shared
• Covalent bonds - stability

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Carbon is Special

• Variations are possible in carbon molecules that
  provide diversity
• Isomers are possible
• structural- differ in structure same
  chemical formula
• geometric-differ in spatial
  relationship
• enantiomers-mirror images of each
  other

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Condensation Synthesis
A
B
A
B
H2O

A and B could be monosaccharides or amino acids
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Hydrolysis

H2O
Addition of water breaks the bond
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Polymers
Polymers are repeating units of monomers. They
are very important to Biology. They are made or
synthesized by the removal of water called
CONDENSATION SYNTHESIS They are broken down by
the addition of water or HYDROLYSIS
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Classes of Biomolecules

• Carbohydrates- used for energy and structures(
  building living organisms)
• Lipids- used for energy storage, communication
  and structures
• Proteins- used for a variety of life functions
• Nucleic Acids-the instructions for building life

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Carbohydrates

• Three common forms
• Monosaccharides
• Disaccharides
• Polysaccharides

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Carbohydrates

• Monosaccharides- single sugars or simple
  sugars,ex. Glucose ( C6H12O6)
• Disaccharides- double sugar, ex. Sucrose
• Polysaccharides- polymers of glucose such as 1.
  Starch 2. Cellulose 3. Glycogen 4. Chitin
  

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Review

• What will happen here?
• AOH HB ?
• And here

CH2OH
CH2OH
O
O
OH
OH
H
OH
OH
H
OH
OH
OH
OH
H2O
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Dehydration Synthesisor a Condensation Reaction

• A B AB H2O

CH2OH
CH2OH
O
O
OH
O
OH
OH
OH
H2O
OH
OH
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Review

• What will happen here?
• AB H2O ?
• And here

CH2OH
CH2OH
H2O
O
O
OH
O
OH
OH
OH
OH
OH
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Hydrolysis or Reaction

• AB H2O AOH HB

Molecules have been HYDROLIZED!
CH2OH
CH2OH
O
O
OH
OH
OH
OH
OH
OH
OH
OH
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Glucose
CH2OH
Glucose has a chemical formula of C6H12O6
C
O
H
OH
OH
C
C
H
OH
H
H
C
C
OH
H
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FRUCTOSE
O
CH2OH
CH2OH
C
C
H
H
HO
H
C
C
OH
OH
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Disaccharides

• Sucrose and Lactose
• 2 monosaccharides bonded together

Alpha or Beta?
CH2OH
CH2OH
O
O
O
OH
OH
OH
OH
OH
OH
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Polysaccharides

• 3 or more Monosaccharides bonded together

CH2OH
CH2OH
CH2OH
O
O
OH
O
O
OH
OH
OH
O
OH
OH
OH
OH
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Polysaccharide

• Starch-storage in plants
• Cellulose-structural part of plant cell wall
• Glycogen- storage in animals, liver
• Chitin structural component for arthropods,
  exoskeleton. Also found in fungi.

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Polysaccharides Starch

• Plants use it as energy storage
• Difficult for humans to break down
• Ex. Avoid a high starch diet

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polysaccharides
Glucose monomers
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Polysaccharides Cellulose(B 1, 4 linkage)

• Long fibers
• Up to 15,000 Glucose units per strand
• Most abundant biological substance on earth
• Ex. Cotton, Trees, Paper
• Why is cellulose so strong?
• Why cant humans breakdown cellulose and cows
  can?

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Polysaccharides Glycogen

• Animals use it as energy storage
• Lots and lots of it in the liver
• Forms huge branched storage units which allow for
  easy break down for energy

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Other polysaccharides

• Chitin
• Found in the exoskeleton of insects, and
  arthropods
• Ex. Crabs, lobsters, grasshoppers
• Pectin
• Found in plant cell walls
• Provides rigidity
• Heteropolymers
• Glycoproteins and peptidoglycans

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Protein
Polymers of amino acids With 20 natural amino
acids there are a variety of proteins
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Amino AcidsThe building blocks of protein
H
O
H
N -C - C
H
OH
R
R- there are twenty different R groups possible
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Alanine NH2-CH-COOH
Glycine NH2-CH2-COOH
CH3
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Peptide bond- is a bond between amino acids a
molecule of water is removed
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Protein Structure
1. Primary- order of the amino acids 2.
Secondary- hydrogen bonds cause pleats and
helix 3. Tertiary- folds and loops create shape
by R Group bonds 4. Quaternary-interaction
of several proteins
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A protein with secondary structure
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A protein with Tertiary Structure
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Lipids

• Large molecules that do NOT have an affinity for
  water not soluble in.
• May have hydrophobic-water fearing and
  hydrophilic-water loving parts.

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Triglycerides
hydrophilic
hydrophobic
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Types of Lipids

• Made of hydrocarbons -
• Triglycerides- fats, waxes, and oils(saturated
  all single bonds C-C, unsaturated have double CC
  bonds
• Phospholipids- attached phosphate replaces one
  of the hydrocarbon tails
• Steroids- Ring Forms of Hydrocarbons cholesterol
  and some hormones

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Triglycerides

• Saturated fats- single bonds make this a solid at
  room temperature and more difficult to digest.

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Unsatured Fats

• Triglycerides that contain double bonds (
  dehydrogenated) are liquids at room temp and more
  digestable

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Nucleic Acids

• Made of monomers called nucleotides
• DNA- deoxyribonucleicacid
• RNA- ribonucleic acid
• These molecules carry all the hereditary
  information of living things

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DNA Basic Composition

• DNA is made up of nucleotides
• Nucleotides are made of
• ...Deoxyribose sugar
• Phosphate
• Base
• bases are guanine,cytosine, thymine and adenine

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RESPIRATION
SYNTHESIS
C A T A B O L I S M
A N A B O L I S M
ATP SYNTHESIS FROM ADP Pi
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Free Energy

• Ability to do work in the cell or ecosystem.

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Energy Transfer

• ATP formation
• G
• ENDERGONIC
• Stores energy in phosphate bond

• ATP breakdown
• - G
• EXERGONIC
• Releases energy between phosphates

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Enzyme Characteristics

• Lower the activation energy
• Speed up the rate of a reaction
• Act as catalysts
• Are proteins (occasionally RNA)

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Enzyme Characteristics

• Conformation or shape is most important feature (
  Lock and Key Hypothesis)
• Substrate Specific
• Do NOT become part of reaction

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Enzyme activity.
7
pH
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Enzyme activity.
7
pH
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Enzyme activity.
10
Temperature o C
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Enzyme activity.
30
10
Temperature o C
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Active site
Allosteric site
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substrate
Enzyme
products
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Cofactors

• Non protein helpers for enzyme activity
• May bind to active site tightly or loosely
• Many are inorganic such as zinc or iron
• If organic they are called Coenzymes

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Allosteric site

• Regulatory site other than the active site.

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Competitive Inhibitor
substrate
inhibitor
Enzyme-Substrate Complex
Enzyme
Noncompetitive Inhibitor
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Allosteric Regulation
Active site
activator
Inactive form
Active conformation
Allosteric site
inhibitor
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Feedback inhibition

• Product may cause negative feedback (act to
  inhibit, disrupt conformation)
• Reactants may cause positive feedback ( act to
  preserve enzyme conformation)

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Enzyme c
Initial substance
Enzyme b
Enzyme a
End product
- feedback
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Prokaryotic Cells

• Lack a nucleus
• Lack membrane bound organells
• Include bacteria and other Monerans

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Eukaryotic Cells

• Have a nucleus
• Have membrane bound organells
• Plants, Animals, Fungi, and Protists have these
  cell types

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Organells Membrane Bound ( endomembrane) Nucleus
Endoplasmic reticulum (rough) Endoplasmic
reticulum ( smooth ) Golgi apparatus Lysosome Vacu
oles Vesicles Peroxisome ( single membrane)
Mitochoindria Chloroplasts
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Non membrane bound organells Nucleolus Microtubule
s Microfilaments Centrioles Cilia Flagella
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Nucleus

• Chromatin- DNA organized with protein (histone)
• Controls Protein Synthesis
• Double Membrane with pores
• may be continious with ER
• Nucleolus- made of and synthesizes RNA

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Endoplasmic Reticulum

• Rough ER- contains ribosome for protein synthesis
• Smooth ER- lacks ribosomes, synthesis of lipids,
  metabolism of carbohydrates, detoxification of
  drugs and poisons
• Muscle ER- calcium ion transfer

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ER and protein synthesis and Transport Vesicles

• Export Proteins become enclsed in vesicle of
  the ER Pinch closed
• Especially secretory proteins ( glycoproteins )

E R..
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Golgi Apparatus

• Manufacture, storage shipping , and packaging
  secretion products
• Cis
• Trans
• Vesicles

trans
cis
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Phospholipids are amphipathic - have both
hydrophobic and hydrophilic portions
hydrophilic
hydrophobic
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Membrane Fluidity

• Unsaturated hydrocarbons in the phospholipids
  make it flow laterally
• Cholesterol maintains some rigidity at low
  temperatures and prevents too much fluidity at
  high

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Membrane proteins

• Integral-penetrate into or through the lipid
  bilayer
• used for transport

• Peripheral protein- attach to the surface of the
  lipid layer
• used for- receptors, recognition(carbohydrates
  attached)

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Permeablility

• What passes through easily
• Oxygen
• Carbon dioxide
• water

• What does not pass through easily
• ions
• proteins
• carbohydrates

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Transport

• Passive
• Requires no expenditure of ATP
• Moves from high to low
• Can be facilitative-aided by protein conformation
  change
• Gatted channels

• Active
• Requires ATP energy
• Generally moves from low to high
• Gatted channels
• Na-K pump
• Proton Pumps
• Phagocytosis or Pinocytosis

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Solutions

• Homogeneous-same throughout
• solvent- what you are dissolving into
• solute- what you dissolve

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solution

SOLUTE




SOLVENT
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Hypertonic
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.5M glucose Distilled water 1.5 M glucose
.5M glucose
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Water Balance

• Plasmolysis( plasmolyzed) plant cell shrinks or
  looses water
• Flacid -plant cell gains water and looses at same
  rate
• Turgid- Plant cell gains

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Plasmolysis

• Membrane shrinks due to water loss
• Restricted to cells with walls
• Occurs in a Hypertonic environment

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Facilitated Diffusion

• Proteins make movement of polar molecules, ions,
  or larger compounds possible by providing a
  passage.
• Often protein changes conformation
• NO ATP required
• Movement from high to low concentration

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Active Transport

• Sodium Potasium Pump
• Proton pumps

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Membrane Potential

• Voltage across a membrane
• -50 to-200 millivolts
• Electrochemical gradients- combination of ion
  potential and electric charge difference

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Gated Channels

• Chemical or electrical impulses cause them to
  change shape-OPEN

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Na-K Pump

• Membrane Potential-voltage difference across a
  membrane
• Chemical Gradient-difference in concentration of
  solute across a membrane
• Electro-chemical Gradient- combination of the
  above ex.
• Na,K, Cl-(8.13)

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Exocytosis and Endocytosis

• Phagocytosis- engulf pseudopodia
• Pinocytosis- gulps
• Receptor mediated pinocytosis

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Signal Transduction

• Binding of extracellular molecule to receptor
  protein see model on pg. 156 Campbell

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Cell types determine cycle

• Prokaryotes- binary fission circular
  chromosome attaches to inner membrane.
  Replication is followed by reattachment at two
  sites.

• Eukaryotes-have a larger genome and nuclear
  genetic material must be carried on several
  chromosomes by specialized structures.

No spindle fibers
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Can be Confusing?
Chomosomes Chromatids Sister chromatids Homologous
chromosomes Centromere Centrosome Centrioles Kine
tochore Nonkinetochore
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Chromosomes
DNA is continuous and wound around protein which
is coiled and super coiled into a dark staining
body. Chromosomes can be seen as having two arms
and often one is longer. When duplicated the
chromosome has identical sister chromatids held
together at the centromere.
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chromatid
centromere
Sister chromatid
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Chromosome Number is fixed in each species
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Cell Cycle
Events in the growth, development
and reproduction of the cell. Go cells have
stopped dividing or have lost the potential to
divide.
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G1- gap or growth after cell division. Cell
grows in size. this stage contains the
RESTRICTION point S- synthesis of new DNA from
existing template(replication) G2- gap 2 or
growth prior to cell division M- mitosis or
chromosome division C- cytokinesis or cell
division
Interphase G1, S, and G2
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Control of Cell Cycle
Restriction point- go/no go control during G1 G0
- a non-dividing stage for a cell Growth
Factors-compounds which regulate growth and
division. Ex.PDGF platelet derived growth
factor Density-dependent inhibition- crowding
inhibits cell division. Adhesiveness- cells ECM
causes them to stick together Metastasis-cells(ca
ncerous) migrate
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Cell Clock Regulators

• Proteins ( enzymes) regulate cell cycle
• Produced by internal cell clock genes
• Protooncogenes- cause cells to divide
• Tumor suppressor genes- prevent cell division

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Cancer and the Cell Cycle

• Normal Cells
• Adhesive
• Contact inhibition

• Cancer cells
• Lost adhesiveness
• Lost contact inhibition

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Principles of Heredity

• Alternative versions of genes (alleles) account
  for variations in a trait.
• For each character, an organism inherits two
  alleles, one from each parent.
• If alleles differ, then the dominant will be
  fully expressed over the recessive.
• The two alleles segregate (separate) during
  gamete formation.
• Alleles on different chromosomes segregate
  independently of one another

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Crossing over

• During prophase of meiosis homologous pairs may
  exchange genetic material.

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New Genetic Combinations

• Recombination during fertilization brings
  together two sets of genetic instructions
• Meiosis-crossing over brings about new
  combinations
• Random genetic mutation can result in random
  genetic change

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Electron Carriers

• NAD nicotinamide adenine dinucleotide
• NAD When oxidized
• NADH 2 H When reduced
• FAD or FADH2

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Types of Respiration

• Anaerobic-without oxygen 1. Alcoholic fermentaion
  2.Acetic Acid fermentaion 3. Lactic Acid
  fermentaion
• Aerobic-with oxygen
• ALL OF THESE BEGIN WITH THE ANAEROBIC PROCESS OF
  GLYCOLYSIS

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GLYCOLYSIS
Glucose is made ready to metabolize by addition
of phosphates and then it is broken down into
2- 3 carbon compounds (PYRUVATE)
This yields a net gain of 2 ATP
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ACETYL COA FRORMATION

• Pyruvate is converted into a 2 Carbon compound
  and added to an enzyme
• CO2 is released

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Krebs Cycle

• Breaks C-H-O bonds
• Energy is transferred via carriers to other steps
• CO2 released
• Some small amount of ATP is produced

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Electron Transport

• Hydrogen Pathway- pumps H ions
• Electron Transfer
• Chemiosmosis- H ions flow through ATP syntase
  proteins to make ATP from ADP P

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Substrate level phosphorylation

• ATP is formed as a direct transfer of electrons
  from the substrate to as ADP P? ATP

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Oxidative phosphorylation

• Electrons made available in metabolism are
  transferred to oxygen and ATP is produced in the
  process. Chemiosmosis

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Fermentation generates ATP by substrate level
phosphorylation. It is anaerobic Three
Types Alcoholic- Lactic Acid-
2NAD2Lactate
2 Ethanol 2CO2NAD
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Photosynthesis
CO2H2O light CnH2n0nO2
Light- measured as an absorption spectrum, the
wavelengths that are most important are
different for different types of autotrophs
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CO2
H2O
Light rxn.
Dark rxn.
light
Calvin Cycle
NADPH
PS1
Calvin Cycle
Thylakoid
ATP
PS2
Photolysis and Photophosphorylation
Stroma
O2
CnHnOn
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Visible Spectrum
Reflected
Absorbed
Absorbed 680-700
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Primary acceptor
NADP 2H
-e
pq
NADPH
Cytochrome complex
pc
Photosystem I P700
Chl a
700nm LIGHT
Photosystem II P680
680nm
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Photosystem I

• Also known as P700-receives electrons from those
  released in PSII to replace photoexcited
  electrons uses light at far end of the red
  wavelength
• PSI 700
• PSII 680 the II in PSII H2O

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Photosystem II

• P680
• due to an association with different proteins
• this system utilizes different wavelengths
• causes water to split capturing its electron
• it then transfers the electron to PSII
  chlorophyll molecules

145
Noncyclic Electron Flow
Water is split (photolysis) and electrons pass
continuously from water to NADP. Primary
electron acceptors pass photoexcited electron to
the electron transport chain(Pq), (Pc),
cytochromes.
.

Uses both PSI and PSII
Generates O2, NADPH, and ATP
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Cyclic Electron Flow
Excited Electrons pass through the electron
transport chain from P700 (PS I ) and return to
the starting point. Uses only PSI
Only ATP is generated
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3CO2
Carbon Fixation
Calvin Cycle
RuBP
rubisco
6ATP
6ADP
3ATP
6NADPH
3ADP
6NADP
Regeneration RuBP
G3P--Glucose
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Photorespiration
CO2 can act as a limiting factor. In cases where
there is not sufficient Carbon dioxide plants
will combine oxygen with RuBP to form
compounds that are broken down into CO2
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Adaptations for Photosynthesis

• C4 Plants
• CO2 is added to PEP phosphophenolpyruvate
• stored in BUNDLE SHEATH CELLS near veins of leaf
• example- Corn

• CAM plants
• in hot dry areas plants must close stomates
• CO2 taken in at night is stored as an acid

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Discovery of DNA

• Frederick Griffith
• Was studying Streptococcus Pneumonia
• Smooth vs. Rough Strains
• Smooth had a mucous coat and were pathogenic
  (caused pneumonia)
• Rough were non-pathogenic
• Conducted an experiment with mice
• Found out that the Rough bacteria became
  transgenic

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Discovery of DNA

• Avery, McCarty and MacLeod
• What was the genetic material in Griffiths
  experiment?
• Purified the heatkilled S-bacteria
• Into DNA, RNA, and Protein
• Mixed each with the R cells to see which one
  transformed

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Discovery of DNA

• Hershey-Chase Experiment
• Studied viruses that infect bacterial cells
• Bacteriophages
• Protein or DNA responsible for take-charge
  actions of the virus?
• Tagged the Protein with radioactive S
• Why?
• Tagged the DNA with radioactive P
• Why?

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The Structure of DNAa double helix?

• Chargaffs Nucleic Acid Ratios
• Measured the base compositions of several species
• Percentage of each base present
• Human DNA
• A 30 and T 29
• G 20 and C 19

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The Structure of DNAa double helix?

• Rosalind Franklin and Maurice Wilkins use X-Ray
  diffraction to view structure
• Watson and Crick propose a double helix using
  their X-Ray pictures

158
DNA Double Helix
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DNA Three Parts

• DNA is made up of nucleotides
• Nucleotides are made of
• Deoxyribose sugar
• Phosphate
• Base
• Guanine, Cytosine, Thymine and Adenine

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DNA The Deoxyribose Sugar
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DNA The Phosphate
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DNA The Nitrogenous Bases

• Purines
• Adenine and Guanine
• Double Ring Structure
• Pyrimidines
• Thymine and Cytosine
• Single Ring Structure

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Single Stranded DNA Nucleotides can only be
added to the 3 end of the nucleotide and
therefore addition of new nucleotides is always
5-----gt 3 DNA is anti-parallel!!
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DNA STRUCTURE
165
How does it know to pair up?

• ADENINE ALWAYS PAIRS WITH THYMINE
• Two hydrogen bonds
• GUANINE ALWAYS PAIRS WITH CYTOSINE
• Three hydrogen bonds

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Why do they pair up?

• Double helix had a uniform diameter
• Purine Purine
• too wide
• Pyrimidine Pyrimidine
• too narrow
• Purine Pyrimidine
• fits the x-ray data

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One last look
Why does it twist?
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DNA Replication
169

Meselson-Stahl demonstrate the Semiconservative
Replication of DNA using radioactive nitrogen

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Why must DNA Replicate?

• Species Survival
• DNA must replicate BEFORE cell division
• Synthesis during Interphase
• All genes must be present in the daughter cells

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Origins of Replication

• Sites along DNA that contain specific nucleotides
  are recognized by specific proteins that initiate
  process
• In eukaryotes there are hundreds of thousands of
  such points
• Form replication bubbles

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How does DNA Replicate?

• Hydrogen bonds break, forming bubbles
• Enzymes unwind and unzip
• Free nucleotides in the nucleus start process of
  complementary base pairing
• Nucleotides are fused together by DNA Polymerase
  only 5 to 3
• Results in two identical double helixes

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Replication Steps

• DNA helicase enzymes open double strand
• DNA uncoils and unzips exposing the DNA template
• Primase adds a RNA primer as binding proteins
  hold strands together
• DNA polymerase attaches to template at
  replication fork
• Nucleoside triphosphates add bases pairing A-T
  and G-C as new strand is added to a 3 end,
  primer removed

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replication3
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How does DNA Replicate?
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How does DNA Replicate?
178
Leading Strand is Continuous

• A single RNA primers initiates the addition of
  nucleotides to the 3 end of the leading strand

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Lagging Strand

• Must wait for replication fork to open and then
  add primer
• Form Okazaki fragments
• RNA is removed only after addition of about 100
  to 200 nucleotides
• Fragments are joined by a ligase enzyme ( DNA
  glue)

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DNA Replication
181
The result

• DNA Replication results in TWO double helixes.
  DNA unwinds and unzips, and new daughter strands
  form, each complementary to an old parental
  strand.

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RNA - Structure

• Ribonucleic Acid different from DNA
• Always Single Stranded
• Ribose Sugar Base Unit
• Phosphate group (same in DNA)
• Nitrogenous Bases
• Cytosine always pairs with Guanine
• BUT! Adenine always pairs with URACIL
• (different in DNA!!!!!)

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Four kinds of RNA

• Ribosomal RNA
• Messenger RNA
• Transfer RNA
• snRNA ribozyme in spliceosome

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rRNA

• Ribosomal RNA or rRNA
• represents about 70 of cellular RNA
• joins with Ribosomal proteins to make the
  cellular organelle RIBOSOMES
• FUNCTION As a manufactured ribosome, supplies a
  location for tRNA to join with mRNA to synthesize
  a protein

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mRNA

• 2. Messenger RNA or mRNA
• represents about 10 of cellular RNA
• contains the sequence of bases coding for a
  particular amino acid sequence in a polypeptide
  chain
• removal of non-coding, internal sequences
  (introns)
• modification of the 5' base (cap)
• addition of adenines to 3' end (poly A tail)
• FUNCTION reads the DNA code (base sequence) and
  becomes a copy that is read at the ribosome to
  make a protein

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hn RNA

• Pre-mRNA contains introns-non-coding regions as
  well as exons-coding regions

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Processing mRNA

• Deletion of introns
• Join exons
• Add cap ( GTP) and poly A tail

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RNA splicing

• Spliceosome-several snurps
• snRNPs small nuclear
• Ribonucleoproteins-splicing enzyme( cuts and
  glues)

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Transcription

• DNA unzips at the locus of the gene being coded
• mRNA makes a copy of the gene
• Then
• mRNA is enzymatically modified
• A cap and a tail are added
• it then leaves the nucleus and finds a ribosome
  (composed of rRNA and protein)

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tRNA

• Transfer RNA or tRNA
• represents about 20 of cellular RNA
• each tRNA molecule is specific for one amino acid
  
• there is an enzyme for each amino acid which
  recognizes the amino acid and its specific tRNA
  and joins the two together
• the specific joining of tRNA to amino acid is the
  only place where the genetic code" applies
• FUNCTION Pairs with Amino Acids and delivers
  them to ribosomes at the right time to synthesize
  a protein

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Protein Synthesis

• Why should cells do this?
• Cells would not be able to grow and change
  without proteins.
• Proteins are found everywhere
• As enzymes, cell membranes, muscles, heart,
  blood
• What happens when proteins are not made correctly
  or not made at all?
• Ex. Cystic Fibrosis
• What part of DNA holds the code for the protein?

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PROTEIN SYNTHESISEveryone is involved

• Transcription
• DNA, mRNA
• Translation
• mRNA, rRNA and tRNA

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Pre-Translation

• mRNA binds to the ribosome
• Meanwhile, tRNAs are attaching to their amino
  acids using tRNA Transferase
• Free tRNAs, with their amino acids attached,
  circulate in the cytoplasm and match up with the
  triplet codes in the mRNA

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Translation

• Initiation
• The first tRNA enters the ribosome at the A site
• The second tRNA enters the ribosome (at the P
  site) and the amino acids are bonded together
  PEPTIDE BOND
• Elongation
• Both tRNAs shift in one direction and make room
  for the next tRNA to enter the ribosome
• this pattern continues until the protein is
  complete
• Termination
• Stop codon is read UAA, UAG, UGA

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Quick Definitions

• A-site aminoacyl-tRNA binding site
• P-site peptidyl-tRNA binding site
• Triplet code DNA
• Codon RNA
• Anti-codon - tRNA
• Introns removed from initial mRNA
• Exons bonded together to make the finished mRNA
  product for translation
• Polyribosomes more than one ribosome reading
  the mRNA at one time

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Codons and anti-codons

• Triplet code on DNA TAC
• mRNA copies it CODON AUG
• tRNA carries the ANTICODON UAC
• The Genetic code reads the codon
• AUG, the amino acid Methionine
• 45 different anti-codons exist
• AUG is always the initiation codon
• GTP supplies energy needed to synthesize protein
• initiator tRNA always carries Methionine first!
• Initiation factors - proteins that bring all
  parts together (mRNA, small subunit, large
  subunit, and tRNAs)

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Genetic Code

• Interprets what the DNA triplet code reads
• Is written in both DNA base language A, G, C, T
  or RNA base language A, G, C, U
• Determines the order for Amino Acids
• Is universal within all species
• Reads the same as the anti-codon (on tRNA) except
  T is now U

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Genetic Code
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Gene Regulation

• Control of gene expression occurs at four levels
  in human cells
• Transcription and posttranscription control
  (nucleus)
• Translation and posttranslation control
  (cytoplasm)
• Various cells express different genes
• Genes can be turned on or off
• Genes respond to activity outside of the cell
• Control of transcription is most important
  regulatory mechanism (binding factors and
  enhancers) Presence of TF determines
  specialization
• Some binding factors are sensitive to hormones

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DNA Technology

• Biotechnology or genetic engineering the use of
  natural biological systems to produce a product
  desired by human beings
• Examples include
• Gene Cloning
• DNA Amplification
• Transgenic Organisms
• Gene Therapy
• Chromosome Mapping and Sequencing

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Gene Cloning
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Gene Cloning

• Recombinant DNA DNA from two different sources
  (human and E. coli)
• Plasmid circular DNA used to transport the gene
  into the organism
• Enzymes needed Restriction and Ligase
• Host cell usually bacteria, wall must become
  competent in order for the bacteria to uptake the
  plasmid
• Restriction enzyme cleaves DNA and allows for DNA
  fragment to insert at the sticky ends
• Vector method of transporting a gene (virus,
  plasmid)

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pVIB lux genes

• 2 genes to produce LUCIFERASE
• Aldehyde (energy source) synthesis
• several genes
• Regulatory genes to turn of and on

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DNA Amplification

• Polymerase Chain Reaction PCR
• Used to make multiple copies of the same gene
• Copies can be examined to see if they match any
  other sources
• Prevents constant extraction from the organism
  and better results

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Other Technologies

• Recombinant DNA - gene splicing
• Transgenic organism- an organism that contains
  another organisms DNA

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Transgenic Organisms

• Transgenic possessing gene(s) from another
  organism
• Gene Pharming Using transgenic farm animals to
  produce pharmaceuticals
• ex. CF, cancer, blood clots
• Genetically altering crops to be resistant to
  insects and produce larger
• http//biology.about.com/science/biology/gi/dynami
  c/offsite.htm?sitehttp//abcnews.go.com/sections/
  science/DailyNews/gmcorn5Fbutterflies000821.html
• Suicide Genes
• Insulin

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Gene Therapy

• Delivering the defective gene to the cells that
  need it to produce a protein
• Familial hypercholesteremia
• SCID severe combined immunodeficiency syndrome
  (missing maturation enzyme for T and B cells)

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Chromosome Mapping

• 100,000 human genes
• RFLPs Restriction Fragment Length Polymorphisms
  used to probe a region of DNA visible under a
  microscope
• Restriction enzymes sequence AA
• Specific base digestion
• CF LAB

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Human Genome Project

• HGP due for completion in 2002
• Already sequenced the Fruit Fly and E. Coli

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Gene Therapy

• Delivering the defective gene to the cells that
  need it to produce a protein
• Cystic Fibrosis
• Vector method of transporting a gene (virus,
  plasmid)
• Mechanical - usually a laboratory tool used
  (inoculating loop)
• Biological - part or whole of an organism
  (bacteria)

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Chromosome Mapping

• 30,000 human genes
• RFLPs Restriction Fragment Length Polymorphisms
  used to tag a region of DNA visible under a
  microscope
• Restriction enzymes sequence AA
• Specific base digestion

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Sanger Method of DNA Sequencing

• 1. Heat DNA Strands until they separate
• 2. Add nucleotides and DNA Polymerase
• 3. Add Dedeoxynucleotides (A, T, G, and C) at
  different time periods to stop replication
• 4. Place fragments in to Gel Electrophoresis
• 5. Allow to migrate and read the Base Sequence

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Human Genome Project

• HGP due for completion in 2002
• Already sequenced the Fruit Fly and E. Coli
• The ultimate goal of HGP is to associate human
  traits and inherited diseases with particular
  genes.
• It promises to revolutionize both therapeutic and
  preventive medicine techniques for many human
  diseases.

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Human Genome Project

• Genome - the complete collection of an organism's
  genetic material.
• The human genome is composed of an estimated
  30,000
• A single human chromosome may contain more than
  250 million DNA base pairs, and it is estimated
  that the entire human genome consists of about 3
  billion base pairs.

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DNA Fingerprinting

• Treat suspects blood with the same restriction
  enzyme
• Place sample in Gel Electrophoresis
• Allow samples to migrate
• Compare the suspects with the blood found at the
  crime scene
• Used in Criminal Trials OJ Simpson
• OJ DNA was an exact match yet he was found not
  guilty?