Atoms of one element that vary only in the number of neutrons in the nucleus

Chemically, all isotopes of the same element are identical because they have the same number of electrons in the same configurations

Energy is released when a bond is formed, and energy must be supplied to break a bond.

Atoms bond to acquire a stable configuration (completed outer shell)

Result from the transfer of electrions.

An atom that gains electrons becomes an anion (a negative ion)

An atom that loses electrons becomes a cation (a positive ion)

Form when atoms share electrons, resulting structre is called a molecule.

Single covalent = 1 pair of shared electrons

Double = 2 pairs

Triple = 3 pairs

If electrons are shared equally between two identical atoms, the bond is nonpolar (found in diatomic molecules like H-H)

If electrons are shared unequally, the bond is polar (any two different atoms like C-H)

Non-polar = symmetrical

Polar = unbalanced

Weak attractions exist between nonpolar molecules, while strong attractions exist between polar molecules.

These attractions are responsible for the physical characteristics of the substance such as solubility.

Hydrophobic = "water hating/repelled by water"

Hydrophilic = "water loving/attracted to water"

Polar substances will dissolve in water, Nonpolar substances will not

"Like dissolves like"

Oxygen atom exerts a greater pull on the shared electrons than the hydrogen atoms, making one side of the molecule have a negative charge, and the other have a positive charge.

Molecule is asymmetrical and highly polar.

Molecules held together by hydrogen bonding (responsible for the special characteristics of water)

*High Specific Heat : (specific heat is amount of heat a substance must absorb to increase 1g of the substance by 1*C) Bodies of water resist changes in temp and provide stable environmental temp for the organisms that live in them. Large bodies of water moderate temp of nearby land.

*High heat of vaporization: evaporating water requires great amount of heat, why evaporation of sweat cools the body

*Universal Solvent: Highly polar, dissolves all polar and ionic substances

*Strong cohesion tension: molecules of water tend to attract one another

Results in several biological phenomena:

1. Water moves up tree from roots to leaves without expenditure of energy (transpirational pull). As one molecule of water is lost from leaf, another molecule is drawn in at the roots

2. Capillary action

3.Surface tension (allows insects to walk on water)

A measure of the acidity and alkalinity of a solution.

pH less than 7 = acid

pH greater than 7 = base

pH = 7 = neutral

Value of pH is the negative log of the hydrogen ion concentration in moles per liter

A substance with a pH of 3 has 1.0 x 10^-3 or 0.001 moles/liter of hydrogen ions in solution

A substance with a pH of 4 has 1.0 x 10^-4 or 0.0001 moles/liter of hydrogen ions in solution

Therefore, a solution with pH = 3 is 10 times more acidic than a solution with a pH of 4

Stomach acid = 2

Human blood = 7.4

Acid Rain = 1.5 - 5.4

Internal pH of most cells is close to 7 (Regulate their pH by use of buffers: substances that resist changes in pH)

Buffers work by absorbing excess hydrogen ions or donating hydrogen ions when there are too few.

Most important buffer in human blood: bicarbonate ion

Organic compounds that have the same molecular formula but different structures, therefore they have different properties.

*Structural isomers: differ in arrangement of atoms

*Geometric isomers: differ in spatial arrangement around double bonds

*Optical isomers: molecules that are mirror images of each other (L- left handed and D- right handed versions) Important in pharmaceuticals, two mirror images may not be equally effective.

Compounds that contain carbon.

Carbohydrates, lipids, proteins and nucleic acids

Consist of C, H, and O

Ratio of hydrogen to oxygen atoms is always 2:1

Empiral formula for all carbohydrates = C_nH₂O

1g of any carbohydrate releases 4 calories

Dietary sources: rice, pasta, bread, cookies and candy

 C₆H₁₂O₆

Glucose, galactose, fructose (isomers of each other)[image]

C₁₂H₂₂O₁₁

Two monosaccharides joined together, with one molecule of water released (dehydration synthesis, condensation)

monosaccharide + monosaccharide = disaccharide + water

glucose + glucose = maltose + water

glucose + galactose = lactose + water

glucose + fructose = sucrose + water

Hydrolysis: the breakdown of a compound by adding water (reverse of dehydration synthesis)

sucrose + water = glucose + fructose

Polymers of carbohydrates, found as monosaccharides joined together by dehydration synthesis.

*Cellulose: makes up plant cell walls

*Starch

*Chitin: makes up exoskeleton in arthropods

*Glycogen: "animal starch"

Include fats, oils, waxes and steroids

All hydrophobic

Most consist of 1 glycerol an 3 fatty acids

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an alcohol, only exists in one form

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A hydrocarbon chain with a carboxyl group at one end

*Saturated: contain only single bonds, come from animals, solid at room temp (butter)

*Unsaturated: have at least one double bond, extracted from plants, liquid at room temp

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Consist of four fused rings

(Cholesterol, testosterone, estradiol)

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*Energy storage: one gram of any lipid will release 9 calories per gram

*Structural: phospholipids are a major component of the cell membrane

*Endocrine: some steroids are hormones

Complex macromolecues

Carry out many functions including:

*growth and repair

*cell signaling

*defense against invaders

*cataylzing chemical reactions

Dietary sources include: fish, poultry, meat and certain plants

1g of protein releases 4 calories

Consist of elements S, P, C, O, H, and N

Polymers/polypeptides consisting of amino acids joined by peptide bonds

Consist of a carboxyl group, and amine group and a variable (R) all attached to central carbon atom

20 different amino acids

*Primary structure: the unique linear sequence of amino acids

*Secondary structure: how the polypeptide coils or folds into two disticnt shapes (alpha helix or beta pleated sheet)

*Tertiary Structure: the three dimensional shape of a protein, determines the protein's specificity

*Quaternary Structure: proteins that consist of more than one polypeptide chain

The form of a molecule determines the function of the molecule

Ribonucleic acid (RNA) or deoxyribonucleic acid (DNA)

Polymers that carry all hereditary information, consist of repeating nucleotides

Nucleotide consists of a phosphate, 5 carbon sugar (ribose or deoxyribose) and a nitrogen base (adenine, cytosine, guanine, thyamine or uracil)

Components of organic molecules that are most often involved in chemical reactions

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Living systems transform one form of energy to another in order to carry out essential life functions.

*First law of thermodynamics: energy cannot be created or destroyed, only transferred (law of conservation of energy)

*Second law of thermodynamics: in the course of energy conversions, the universe becomes more disordered (greater entropy)

Gibb's free energy equation: ΔG = ΔH-TΔS

ΔG = free energy change

ΔH = change in heat

T = absolute temperature

ΔS = entropy

Reactions with -ΔG are energy releasing (exergonic/exothermic)

Reactions with +ΔG are energy absorbing (endergonic/endothermic)

The sum of all chemical reactions that take place in cells.

Catabolism: break down molecules

anabolism: build up molecules

Takes place in a series (pathways), each of which serves a specific function

Controlled by enzymes, enable cells to carry out chemical activities

Globular proteins that exhibit tertiary structures

Substrate specific (as the substrate enters the active site, it induces the enzyme to alter its shape slightly so the substrate fits better)

Remain unchanged in a reaction and are reused

Named after their substrate

Catalyze reactions in both directions

Often require assistance from cofactors or coenzymes

Efficiency of enzyme is affected by temperatures and pH

Some compounds resemble the normal substrate molecule and compete for the same active site on the enzyme.

These mimics or competitive inhibitors reduce the productivity of enzymes by preventing the substrate from combining wth the enzyme.

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The enzyme contains more than one active site and the substrates do not resemble each other. The binding of one substrate prevents the other from binding to the enzyme.

Which substrate binds is random

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Involves two active sites, one for a substrate and the other for an inhibitor. Enzyme oscillates between two conformations, one active and one inactive.

When inhibitor binds to allosteric site, the enzyme undergoes a conformational change and the active site for the substrate is altered, and the enzyme cannot catalyze the reaction. (Feedback inhibition)[image]

Substrates stimulate an enzyme with quaternary structure to be more effective.

Ex: hemoglobin, once hemoglobin binds to one oxygen atom, it can very rapidly bind to three more oxygen atoms.

*All living things are composed of cells (Schleiden & Schwann)

*Cells are the basic unit of all organisms (Schleiden & Schwann)

*All cells arise from preexisting cells (Virchow)

*No internal membranes; no nuclear membrane, E.R., mitochondria, vacuoles, or other organelles

*Citcular DNA

*Ribosomes are very small

*Metabolism is aerobic or anerobic

*Mainly unicellular

*Cells are very small, 1-10μm

*Contain distinct organelles

*DNA wrapped with histone proteins into chromosomes

*Ribosomes are larger

*Metabolism is aerobic

*Cytoskeleton present

*Mainly multicellular with differentiation of cell types

*Cells are larger, 10-100μm

Magnification = enlarging

Resolution = clarity

Antoine van Leeuwenhoek: first microscope in 17th century

Robert Hooke: cork cells

Use light passing through living or dead specimen to form an image

Cells and tissue can be stained to make organelles easier to see (most stains kill cells)

Use electrons passing through a specimen to form an image

Have superior resolving power, magnification over 100,000x

Cannot be used to view live specimens, preparation kills cells

Transmission Electron: (TEM) Used for studying the interior of cells

Images appear flat and two dimensional

Scanning Electron: (SEM) Used for studying the surface of cells

Images have three dimensional appearance

Used to examine unstained, living cells

Often used to examine cells growing in tissue culture

Uses ultracentrifuge to spin liquid samples at high speed, separates them into layers based on density.

Tisues/cells mashed into homogenate, then spun in centrifuge. Densest particles settle to the bottom of tube.

Liquid layer poured off, proess repeated until desired layer is isolated.

Nuclei > mitochondria > ribosomes

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(Freeze etching)

Multistep techniques used to prepare detailed cast of the membrane. Tissue digested away, leaving only cast of the tissue.

Cast is then examined under electron microscope.

Contains chromosomes which are wrapped with proteins into a chromatin network.

Surrounded by selectively permeable nuclear membrane that contains pores to allow for transport of molecules (such as mRNA) which are too large to diffuse through the membrane.

Where components of ribosomes are synthesized.

Not membrane bound structures, actually a tangle of chromatin and unfinished ribosome precursors.

Site of protein synthesis.

Found free in the cytoplasm or attached to ER

Membranous system of channels and flattened sacs that traverse the cytoplasm. Two types:

*Rough ER: site of protein synthesis resulting from attached ribosomes

*Smooth ER: assists in synthesis of steroid hormones and other lipids, connects rough ER to the Golgi Apparatus, carries out detoxification

Lies near nucleus, consists of flattened membranuos sacs stacked next to one another and surrounded by vesicles.

Package substances produced in rough ER and secrete them to other cell parts, or surface of cell

Sacs of hydrolytic (digestive) enzymes surrounded by single membrane.

Principal site of intracellular digestion.

Helps cell renew itself by breaking down and recycling cell parts.

*Generally not found in plant cells

Found in plant and animal cells

Contain catalas which converts hydrogen peroxide (waste product of respiration) into water with release of oxygen.

Detoxify alcohol in liver cells

Site of cellular respiration, all cells have mitochondria

Have outer double membrane and inner series of membranes (Cristae).

Contain their own DNA

Single, membrane-bound structures for storage.

Vesicles = tiny vacuoles

Double membrane, found only in plants and algae. Three types:

*Chloroplasts: site of photosynthesis. In addition to double outer membrane, have inner membrane that forms grana (consisting of thylakoids). Grana lie in stroma. Contain own DNA

*Leucoplasts: store starch, found in roots like turnips

*Chromoplasts: store carotenoid pigmets, responsible for red-orange-yellow of carrots, tomatoes, and daffodils

Complex network of protein filaments, extends throughout cytoplasm, gives cell shape, enables it to move, anchors organelles to plasma membrane.

*Microtubules: hollow tubes made of tubulin (protein), make up cilia, flagella (both 9 pairs + 2 singlets), and spindle fibers (9 triplets)

*Microfilaments: (actin filaments) help support shape of cell. Enable animal cells to form cleavage furrow, amoeba to move using psuedopods, skeletal muscles to contract

*Not found in animal cells

Plants & algae = cellulose

fungi = chitin

When plant cell divides, thin gluey layer is formed between two cells (middle lamella)

Selectively permeable membrane that regulates what enters and leaves the cell.

S.J. Singer: fluid mosaic model.

*Phospholipid Bilayer with proteins throughout the layers

Amphipathic: has both a hydrophilic and hydrophobic region

Integral proteins: non polar regions, span the hydrophobic interior of the membrane

Peripheral proteins: loosely bound to the surface of the membrane

Proteins in plasma membrane have many functions:

*Transport molecules, electrons, and ions through channels, pumps, carriers, and electron transport chains

*Act as enzymes

*Act as receptors

*Cell to cell attachments

The movement of molecules down a concentration gradient from a region of high concentration to a region of low concentration

Requires no energy

*Diffusion: Simple - does not involve protein channels (countercurrent exchange )

Facilitated - requires hydrophilic protein channel to passively transport substances across the membrane

*Osmosis: diffusion of water across a membrane

Having greater concentation of solute than another solution

Water will flow out of the cell causing the cell to shrink (plasmolysis)

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Having lesser concentration of solute than another solution

Water will flow into the cell causing the cell to swell or burst.

Plant cell wall prevents cell from bursting

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Two solutions containing equal concentration of solutes

Water diffuses in and out, but there is no net change in the size of the cell

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Water will move across a membrane from the solution with the higher water potential to the solution with the lower water potential.

Addition of solutes lowers water potential to a value less than zero.

Water potential for pure water is zero.

Special water channel proteins that facilitate the diffusion of massive amounts of water across a cell membrane.

Don't affect water potential gradient or direction of water flow, just the rate at which water diffuses

Can also function as gated channels that open and close in response to variables

The movement of molecules against a gradient

*Requires energy (ATP)

Pumps or carries: ex- plastoquinone in thylakoid membrane, sodium potassium pump, electron transport chain

Contractile vacuole in freshwater protista

Exocytosis in nerve cells

Pinocytosis (cell drinking)

Phagocytosis (engulfing of large particles by psuedopods)

Receptor mediated endocytosis

Enables a cell to take up large quantities of specific substances

Extracellular substances bind to receptors on the cell membrane, once the ligand binds to the receptor endocytosis begins. The receptors migrate and cluster, turn inward and become a coated vesicle that enters the cell.

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The overall movement of a fluid in one direction in an organism

(Blood in humans, sap in trees)

Bulk flow movement is always away from source (where it originates) to sink (where it is used)

Tight Junctions: belts around epithelial cells that line organs and serve as barrier to prevent leakage into or out of organs

Desmosomes: "spot welds", consist of cytoskeletal filaments from adjacent cells that are looped together

Gap Junctions: permit passage of materials directly from cytoplasm of one cell to cytoplasm of adjacent cell

Plasmodesmata: connect one plant cell to the next. Analogouls to gap junctions in animal cells.

Reception: signal molecule binds to specific receptor on cell surface, causeing receptor molecule to undergo conformational change. Change in conformation leads to Transduction: a change in signal form where receptor relays message to secondary messenger

Secondary messenger includes response within cell

The means by which cells extract energy stored in food and transfer that energy to molecules of ATP

Oxidative process

Complete aerobic respiration of one molecule of glucose is highly exergonic

C₆H₁₂O₆ + 6O₂ → 6CO₂ + 6H₂O + energy

Anaerobic respiration (oxygen not present): glycolysis followed by fermentation

Aerobic respiration (oxygen present): glycolysis followed by Krebs Cycle, electron transport chain and oxidative phosphorylation

(Adenosine triphosphate)

Consists of adenosine (adenine plus ribose) and three phosphates

Unstable because the 3 phosphates are all negatively charged and repel one another

When one phosphate is removed by hydrolysis, a more stable molecule results

The change from a less stable molecule to a more stable molecule always releases energy

ATP provides energy for all cell activities by transferring phosphates from ATP to another molecule

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Process that breaks down 1 molecule of glucose (6 C molecule) into 2 3C molecules of pyruvate/pyruvic acid and releases 4 molecules of ATP.

Energy of activation for glycolysis is 2 ATP, so net gain = 2 ATP

2 ATP + 1 Glucose → 2 Pyruvate + 4ATP

Occurs in cytoplasm, produces ATP without using oxygen

Each step is catalyzed by a different enzyme

End product (Pyruvate) is raw material for Krebs cycle (next step in aerobic respiration)

During glycolysis, ATP is produced by substrate level phosphorylation (direct enzymatic transfer of a phosphate to ADP)

PFK (phosphofructokinase) allosteric enyzme, inhibits glycolysis when the cell has enough ATP and does not need to produce any more

An anaerobic, catabolic process that consists of glycolysis plus alcohol or lactic acid fermentation

*Facultative anaerobes: can tolerate presence of oxygen, but do not use it

*Obligate anaerobes: cannot live in an environment containing oxygen

Can generate ATP during anaerobic respiration as long as there is a mechanism to convert NADH back to NAD⁺.

The process by which certain cells convert pyruvate from glycolysis into ethyl alcohol and carbon dioxide in the absence of oxygen.

Oxidize NADH back to NAD⁺

(Making bread, beer, wine)

Pyruvate from glycolysis is reduced to form lactic acid or lactate.

NADH gets oxidized back to NAD⁺

(Human skeletal muscles- lactic acid causes fatigue and burning, continues to build up until blood can supply muscles with adequate oxygen)

Oxygen is present

Highly efficient, produce a lot of ATP

Consists of anaerobic phase (glycolysis) and aerobic phase (Krebs cycle and oxidative phosphorylation)

(Citric acid cycle)

Takes place in matrix of mitochondria, requires pyruvate

Each molecule of glucose is broken down to 2 molecules of pyruvate during glycolysis, respiration of each molecule of glucose causes Krebs cycle to turn 2 times.

Pyruvate must first combine with coenzyme A to form acetyl co-A, which produces 2 molecules of NADH, 1 for each pyruvate.

Each turn of Krebs cycle releases 3NADH, 1ATP, 1FADH and waste product CO₂

Enclosed by double membrane. Outer membrane is smooth, inner membrane (cristae) is folded.

Inner membrane divides mitochondria into two internal compartments: outer compartment and the matrix

Krebs cycle takes place in the matrix

Electron Transport Chain takes place in cristae membrane

Both are required for normal cell respiration, coenzymes that carry protons or electrons from glycolysis and the Krebs cycle to the electron transport chain

Dehydrogenase form of both facilitates transfer of hydrogen atoms from a substrate to its coenzyme

NAD: (nicotinamide adenine dinucleotide)

FAD: (flavin adenine dinucleotide)

A proton pump in the mitochondria that uses energy released from exergonic flow of electrons to pump protons from the matrix to the outer compartment.

Results in proton gradient inside mitochondria

Makes no ATP directly, sets stage for ATP production

Embedded in cristae membrane

Thousands of copies in every mitochondrion

Highly electronegative oxygen pulls electrons through the ETC

NAD delivers electrons to a higher energy level than FAD

Each NAP produces 3ATP, each FAD produces 2ATP

How most of the energy is produced during cell respiration

Uses potential energy stored in the form of a proton gradient to phosphorylate ADP and produce ATP

Powered by redox reactions of electron transport chain

 NAD and FAD lose protons (become oxidized) to the electron transport chain, which pumps them to the outer compartment of the mitochondria, creating a proton gradient.

The process by which light energy is converted to chemical bond energy and carbon is fixed into organic compounds.

6CO₂ + 12H₂O → C₆H₁₂O₆ + 6H₂O + 6O₂

*Light dependent reactions use light energy directly to produce ATP that powers the light-independent reactions

*Light independent reactions consist of Calvin cycle, which actually produces sugar.

Both reactions occur only when light is present

Absorb light energy and use it to provide energy to carry out photosynthesis.

*Chlorophylls: chlorophyll a and b are green and absorb all wavelengths of light in red, blue, and violet range

*Caratenoids: yellow, orange and red. Absorb light in blue, green, and violet range.

Chlorophyll a is pigment that participates directly in the light reactions of photosynthesis

grana: where the light reactions occur

stroma: where light independent reactions occur

 Grana consist of layers of membranes called thylakoids (site of photosystems I and II)

light harvesting complexes in the thylakoid membranes of chloroplasts.

Few hundred photosystems in each thylakoid.

Each photosystem contains a reaction center (containing chlorophyll a and a region containg several hundred antenna pigment molecules that funnel energy into chlorophyll a)

PSI: absorbs light best in 700 nm range (operates second)

PSII: absorbs light best in 680 nm range (operates first)

Electrons enter two transport chains, and ATP and NADPH are formed.

*Energy is absorbed by P680, electrons from chlorphyll a become energized and move to higher energy level. (captured by primary electron acceptor)

*Water gets split apart, providing electrons to replace those lost from chlorophyll a in P680.

*Electrons from P680 pass along electron transport chain and end up in P700. This flow is exergonic and provides energy to produce ATP by chemiosmosis. (Called photophosphorylation because it is powerd by light)

*Protons released from water during photolysis  pumped by thylakoid membrane from stroma into the thylakoid space through ATP synthase channels and into stroma. ATP produced here powers Calvin cycle.

*NADP becomes reduced when it picks up the two protons released from water in P680. Newly formed NADPH carries hydrogen to Cavin cycle to make sugar in light independent reactions.

*Energy absorbed by P700, electrons from chlorophyll a become energized and are captured by primary electron receptor. Ends with production of NADPH.

Sole purpose is to produce ATP, no NADPH is produced, no oxygen released

Chloroplast carries out when running low on ATP.

Cyclic electron flow takes photoexcited electrons from P680 ETC to P700, to primary electron acceptor and then back to P680.

Main business of light-independent reactions. Produces 3C sugar PGAL (phosphoglyceraldehyde).

Carbon enters stomates of leaf in form of CO₂ and becomes incorporated into PGAL.

Carbon fixation, reduction reaction

* CO₂ enters Calvin cycle, becomes attached to 5C sugar (ribulose biphosphate) RuBP, forming 6C molecule. 6C molecule breaks down (it is unstable) into two 3C molecules of 3PGA. Enzyme that catalyzes is rubisco.

*Calvin cycle does not depend on light, uses products of light reactions (ATP and NADPH)

*Occurs only in the light