AP Biochemistry 11

8/13/2019 AP Biochemistry 11

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How Matter is Organized

Chemistry is the science of thestructure and interactions ofmatter. all living things consist of matter.

Matter is anything thatoccupies space. mass is the amount of matter in

any object. weight is the force of gravityacting on matter

Does air have matter?


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Chemical Elements

Elements are substances that can not be splitinto simpler substances by ordinary means. 112 elements ( 92 occur naturally )

26 of naturally occurring elements are in the body

represented by chemical symbols ( first 1-2 lettersof name )

4 elements form 96 % of the bodys mass hydrogen, oxygen, carbon and nitrogen

Trace elements are present in tiny amounts such as copper, tin, selenium & zinc


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Structure of Atoms Atoms are the smallest units of

matter that retain theproperties of an element

Atoms consist of 3 types ofsubatomic particles

protons, neutrons andelectrons

Nucleus contains protons (p+) &

neutrons (neutral charge) Electrons (e-) surround the

nucleus as a cloud (electronshells are designated regions of

the cloud)


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Atomic Number & Mass Number Atomic number is number of protons in the nucleus. .

Mass number is the sum of its protons and neutrons.


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Isotopes


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Molecule, Element, compound

Molecule= more than one atom existing in union Element= Molecule contains identical atoms

Compound: Molecule contains different atoms


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IONS: Charged particles

When an atom gains or loses electrons ions areformed

Positively charged= cation

Negatively charged = anion


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Chemical Bonds Bonds hold together the

atoms in molecules andcompounds An atom with a full outer

electron shell is stable andunlikely to form a bond with

another atom Octet rule states thatbiologically importantelements interact toproduce chemically stablearrangements of 8electrons in the valenceshell.

Whether electrons areshared, donated or acquireddetermines the types of

bonds formed


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Covalent Bonds Atoms share electrons

to form covalent bonds Electrons spend most of

the time between the 2

atomic nuclei single bond = share 1pair double bond = share 2 pair triple bond = share 3 pair


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Polar Covalent Bonds Unequal sharing of electrons between atoms.

In a water molecule, oxygen attracts thehydrogen electrons more strongly Oxygen has greater electronegativity as

indicated by the negative Greek delta sign.


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Ionic Bonds

Positively and negativelycharged ions attract eachother to form an ionic bond

In the body, ionic bondsare found mainly in teethand bones

An ionic compound that

dissociates in water into +and - ions is called anelectrolyte


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The Ionic Bond in Sodium Chloride

Sodium loses an electronto become Na+ (cation)

Chlorine gains an electron

to become Cl- (anion) Na+ and Cl- are attracted

to each other to form thecompound sodium chloride(NaCl) -- table salt

Ionic compounds generallyexist as solids


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Hydrogen bonds Hydrogen bonds are the most important inter

molecular force of attraction . Formed by the attraction between slightly positive

Hydrogen atom and a slightly negative atom ofanother element.

Too weak to create molecules but creates shapesand stabilizes large molecules like proteins ornucleic acids


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Chemical Reactions

When new bonds form or old bonds are broken

Metabolism is all the chemical reactions in the body


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Energy and Chemical Reactions

Chemical reactions involve energy changes

Law of conservation of energy energy can neither be created nor destroyed--just

converted from one form to another

Reactions that yield energy = Exergonic reactions(Larger to smaller molecules)

ABA + B

Reactions that require energy to occur= Endergonicreactions (smaller to larger molecules )

A + B AB


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Energy Transfer in ChemicalReactions

Chemical reactions usually involveboth

Human metabolism couplesexergonic and endergonicreactions, so that the energyreleased from one reaction will

drive the other. Glucose breakdown releases energy

used to build ATP molecules thatstore that energy for later use in

other reactions


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Activation Energy Atoms, ions & molecules

are continuously moving& colliding

Activation energy is thecollision energy needed

to break bonds & begin areaction

Increases in concentration & temperature, increase the

probability of 2 particles colliding more particles in a given space as concentration is raised

particles move more rapidly when temperature is raised


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Catalysts/Enzymes Normal body temperatures

and concentrations are too

low to cause chemicalreactions to occur

Catalysts speed up chemicalreactions by lowering the

activation energy needed toget it started Catalysts orient the

colliding particles properlyso that they touch at the

spots that make thereaction happen Catalyst molecules are

unchanged and can be usedrepeatedly to speed upsimilar reactions.


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Free Energy andActivation

Energy Tutorial

S th i R ti D iti R ti
http://www.wiley.com/college/boyer/0470003790/animations/catalysis_energy/catalysis_energy.htmhttp://www.wiley.com/college/boyer/0470003790/animations/catalysis_energy/catalysis_energy.htmhttp://www.wiley.com/college/boyer/0470003790/animations/catalysis_energy/catalysis_energy.htmhttp://www.wiley.com/college/boyer/0470003790/animations/catalysis_energy/catalysis_energy.htmhttp://www.wiley.com/college/boyer/0470003790/animations/catalysis_energy/catalysis_energy.htmhttp://www.wiley.com/college/boyer/0470003790/animations/catalysis_energy/catalysis_energy.htm


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Synthesis Reactions--Anabolism

Two or more atoms, ions or

molecules combine to formnew & larger molecules

All the synthesis reactionsin the body together are

called anabolism Usually are endergonic

because they absorb moreenergy than they release

Example combining amino acids to

form a protein molecule

Large molecules are split into

smaller atoms, ions ormoleculesAll decomposition reactionsoccurring together in the bodyare known as catabolismUsually are exergonic sincethey release more energy thanthey absorb

Decomposition Reactions--Catabolism


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Inorganic Compounds & Solvents

Most of the chemicals in the body arecompounds Inorganic compounds

usually lack carbon & are structurally simple water, salts, acids and bases

Organic compounds contain carbon & usually hydrogen

always have covalent bonds


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DissociationpH - measure or acidity/alkalinity pH = - log [H+]

acidic < 7 < basicAcids-raise H+ contentBases-lower H+ content:

release OH- or accepts H+

1pH unit = 10x difference1000 as many H+ in a pH of 5 as there are in 8

Buffer-takes up or releases H+ or OH- to preventchanges in pH. In the bicarbonate system, H2CO3H+base acceptor, HCO3- acid acceptor

What happens to shells in carbonated drinks?

Does Sea Ice Speed Up Ocean Acidification?How does the bicarbonate s stem work in a blood lasma? In the ocean?

O A idifi ti : 2 3
http://www.nrdc.org/oceans/acidification/aboutthefilm.asphttp://science360.gov/obj/video/e6d75961-f294-4936-b365-8cab109bbb57http://vimeo.com/9431503http://vimeo.com/9431503http://science360.gov/obj/video/e6d75961-f294-4936-b365-8cab109bbb57http://www.nrdc.org/oceans/acidification/aboutthefilm.asp


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Ocean Acidification: 2, 3
http://www.nrdc.org/oceans/acidification/aboutthefilm.asphttp://science360.gov/obj/video/e6d75961-f294-4936-b365-8cab109bbb57http://vimeo.com/9431503http://vimeo.com/9431503http://science360.gov/obj/video/e6d75961-f294-4936-b365-8cab109bbb57http://www.nrdc.org/oceans/acidification/aboutthefilm.asp


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Carbon dioxide


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Carbon dioxideconcentration inmetabolically active cells ismuch greater than incapillaries, so carbon

dioxide diffuses from thecells into the capillaries.About 7% of the CO2directly dissolves in theplasma. Another 23% bindsto the amino groups in

hemoglobin. The remaining70% is transported in theblood as bicarbonate ion.


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Concept of pH

pH scale runs from 0 to14 (concentration of H+in soln.)

pH of 7 is neutral(distilled water)

pH below 7 is acidic andabove 7 is alkaline
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What is more acid than lemon?

In a test of pH levels, a glass of milk was found to have a pH of 6.0. Aglass of grape juice had a pH of 3.0. What is the relationship betweenthe pH levels of the milk and grape juice?

A The milk is 100 times more acidic than the grape juiceB The grape juice is 3 times more acidic than the milk

C The milk is 3 times more acidic than the grape juice

D The grape juice is 1000 times more acidic than the milk

How many more H+s do tomatoes have than bananas? Lemons than milk?Bleach than soap?


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Inorganic Acids, Bases & Salts Acids, bases and salts always dissociate into ions

if they are dissolved in water acids dissociate into H+

and one or more anions

bases dissociate into OH-and one or more cations

salts dissociate into anionsand cations, none of whichare either H+ or OH-

Acid & bases react in the body to form salts Electrolytes are important salts in the body that

carry electric current (in nerve or muscle)


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Water & Its Properties Most important inorganic compound in living

systems, Medium of nearly all chemical reactions Polarity

uneven sharing of electrons makes it an excellent solvent for ionic or polar substances gives water molecules cohesion

allows water to moderate temperature changes Participates as a product or reactant in certainreactions in the body hydrolysis reactions

water is added to a large molecule to separate it intotwo smaller molecules

digestion of food dehydration synthesis reaction

two small molecules are joined to form a larger

molecule releasing a water molecule

l


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Water as a Solvent Most versatile solvent known

polar covalent bonds (hydrophilic vs hydrophobic) its shape allows each water molecule to interactwith neighboring ions/molecules

Water dissolves many substances


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Water has a high surface tension Water is wet

Water is attracted to itself, and this attraction,due to H bonds is stronger than the attraction tothe air above

Adhesion and cohesion allow for capillary actionwater transport in plants

Occurs as solid, liquid and gas within normaltemperature ranges on Earth
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Water = good evaporative coolant Heat of vaporization is also high

amount of heat needed to change from liquid to gas evaporation of water from the skin removes large amount of

heat

B/c it takes a lot of energy to change water from a liquid to

a gas, it takes energy with it Heat capacity is high

can absorb a large amount of heat with only a small increase inits own temperature

large number of hydrogen bonds in water bonds are broken as heat is absorbed instead of

increasing temperature of water

large amount of water in body helps lessen the impact of

environmental changes in temperature


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Chemical Reactions energy causes rearrangement of e-'s and new bonds, new

compounds are formed, E can be force of collision, heat,electricity etc.

reactants yield product(s) Balanced equations (energy cannot be created or

destroyed). Balance the following equations:CH4+ O2CO2+ H2OCuO + NH3Cu + H2O + N2NH3+ O2NO + H2O

CH4+ 2O2= CO2+ 2H2O3CuO + 2NH3= 3Cu + 3H2O + N24NH3+ 5O2= 4NO + 6H2O

f


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Mixtures-- combination of substances inwhich the individual components retaintheir own properties

solutions-- or more substances isdistributed evenly in another substance

solution=solvent(H2O)+solute(dissolvedparticles)

suspension-- particles of materials are

temporarily mixed together (blood)

colloid-- particles larger than solution,smaller than suspension (cytosol)


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Chemistry Tutorial

The Biology Project:http://www.biology.arizona.edu/biochemistry/tutorials/chemistry/main.html

Carbon & Its Functional Groups
http://www.biology.arizona.edu/biochemistry/tutorials/chemistry/main.htmlhttp://www.biology.arizona.edu/biochemistry/tutorials/chemistry/main.htmlhttp://www.biology.arizona.edu/biochemistry/tutorials/chemistry/main.htmlhttp://www.biology.arizona.edu/biochemistry/tutorials/chemistry/main.html


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Properties of carbon atoms

forms bonds with other carbon atoms produce large,

stable molecules with many different shapes (rings, straight or

branched chains)

Many functional groups can attach to carbon skeleton

esters, amino, carboxyl, phosphate groups (Table 2.5) Very large molecules called macromolecules (polymers if all

monomer subunits are similar)

Carbon & Its Functional Groups

The properties of different biological molecules


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The properties of different biological moleculesdepend on certain characteristic groupings ofatoms called functional groups.

If you know the properties of some of thefunctional groups, you will be able to quickly lookat many simple biological molecules and get someidea of their solubility and possible identity. The

names of the six most important functional groupsare:

Hydroxyl

Carbonyl Carboxyl Amino Sulfhydryl

Phosphate

d l


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Hydroxyl Two functional groups containing oxygen, the

hydroxyl and carbonyl groups, contribute towater solubility.

Hydroxyl groups have one hydrogen paired

with one oxygen atom (symbolized as -OH).Hydroxyl groups are not highly reactive, butthey readily form hydrogen bonds and

contribute to making molecules soluble inwater.Alcohols and sugars are "loaded" withhydroxyl groups.

Genistein and daidzein, two phytoestrogens from legumes


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p y g g

Notice that the only difference between these two moleculesis the additional hydroxyl (-OH) group on genistein. Bothare typical isoflavones. Genistein, however, is considerablymore estrogenic than daidzein; chemists attribute this tothe influence of the additional hydroxyl group. The hydroxylgroups are important for binding to estrogen receptors.

b l


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Carbonyl Carbonyl groups have one oxygen atom double-

bonded to a carbon atom (symbolized as -C=O).Like hydroxyl groups, carbonyl groups contributeto making molecules water-soluble.All sugarmolecules have one carbonyl group, in addition tohydroxyl groups on the other carbon atoms. Aldehyde groups, where the C=O group is at the end of

an organic molecule. A hydrogen atom is also located onthe same carbon atom.

Keto groups, where the C=O group is located within anorganic molecule. All sugars have either a keto or analdehyde group.


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Carbonyl -COH C3H6Oaldehyde = end (propanol)

ketone = inside (acetone)


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C b li A id


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Carboxylic Acids Carboxyl groups are weak acids, dissociating

partially to release hydrogen ions.The carboxylgroup (symbolized as COOH) has both a carbonyland a hydroxyl group attached to the same carbonatom, resulting in new properties.

Carboxyl groups frequently ionize, releasing the H from thehydroxyl group as a free proton (H+), with the remaining Ocarrying a negative charge. Molecules containing carboxyl

groups are called carboxylic acids and dissociate partiallyinto H+and COO.

Carboxyl groups are common in many biological molecules,

including amino acids and fatty acids.

A i G


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Amino Group Nitrogen in biological molecules usually occurs in

the form of basic amino groups.Nitrogen isanother abundant element in biological molecules.Having a valence of 3, nitrogen normally formsthree covalent bonds, either single, double, or

triple bonds.

Amino groups (-NH2) are common functional groupscontaining nitrogen. Amino groups are basic, andoften become ionized by the addition of a hydrogenion (H+), forming positively charged amino groups (-NH3

+).

S lfh d l


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Sulfhydryl Sulfur is found mainly in proteins in the form of

sulfhydryl groups or disulfide groups.Like oxygen,sulfur typically has a valence of 2, although it canalso have a valence of 6, as in sulfuric acid.

Sulfur is found in certain amino acids and proteinsin the form of sulfhydryl groups (symbolized as -SH). Two sulfhydryl groups can interact to form adisulfide group (symbolized as -S-S-).


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Importance of Functional Groups in


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Importance of Functional Groups inBiology

Function Groups Practice
http://www.execulink.com/~ekimmel/functional.htmhttp://www.execulink.com/~ekimmel/functional.htm


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Function Groups PracticeMatch the columns

1.

2.

3.

4.

5.

6.

Types of Organic compounds
http://www.execulink.com/~ekimmel/functional.htmhttp://www.execulink.com/~ekimmel/functional.htm


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Four major groups of organiccompounds, necessary for life are:

polymers monomers____

Carbohydrates monosacchrides Lipids fatty acids

Proteins amino acids

Nucleic acids nucleotides

Types of Organic compounds

Carbohydrates


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Carbohydrates

Diverse group of substances from C, H, and O

ratio of one carbon atom for each water molecule(carbohydrates means watered carbon)

glucose is 6 carbon atoms and 6 water molecules (H20)

Main function is to produce energy

3 sizes of carbohydrate molecules

monosaccharides

disaccharides

polysaccharides

Mono saccharides


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Mono saccharidesone sugar

Called simple sugars Contain 3 to 7 carbon atoms

(CH2O)n

We can absorb only 3 simple sugarswithout further digestion in our smallintestine

glucose found in syrup or honey fructose found in fruit

galactose found in dairy products

Disaccharides (two)


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Disaccharides ( two )

Formed by combining 2 monosaccharides bydehydration synthesis (releases a water molecule)

Name of bond= Glycosidic bond sucrose = glucose & fructose

Condensation Rxn & Dehydration


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Condensation Rxn & DehydrationSynthesis

2 Condensation & Hydrolysis QT Mov

Dis h id s f distin ti n
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Disacchrides of distinction

glucose + fructose = sucrose

glucose + glucose = maltose

glucose + galactose = lactose
http://hyperphysics.phy-astr.gsu.edu/hbase/organic/imgorg/fructose.gif


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Polysaccharide


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Polysaccharide

Lipids = fats oils steroids waxes


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Lipids = fats, oils, steroids, waxes Formed from C, H and O 18-25% of body weight

Hydrophobic fewer polar bonds because of fewer oxygen atoms insoluble in water

Combines with proteins for transport in blood

Lipoproteins Three functional classes:Storage lipid:-Triglycerides: Common body fat.Regulatory lipid:

- Steroids: act as hormone- Eicosanoids: hormonesStructural lipid: Phospholipids: Cell membrane

Glycolipids: Cell membrane

Triglycerides


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Triglycerides Fats composed of a single glycerol molecule and 3

fatty acid molecules three-carbon glycerol molecule is the backbone

Very concentrated form of energy 9 calories/gram compared to 4 for proteins &

carbohydrates

our bodies store triglycerides in fat cells if we eat

extra food

Triglyceride Formation


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Triglycerides =three fatty

acids attachedby dehydrationsynthesis to

one molecule ofglycerol by anester bond

Triglyceride Formation

Figure 2.15

Saturation of Triglycerides


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Saturation of Triglycerides Determined by the

number of single or

double covalent bondsin fatty acid

Saturated fats containsingle covalent bonds

and are covered withhydrogen atoms----lard Unsaturated are not

completely coveredwith hydrogen----

safflower oil, corn oil Polyunsaturated fats

contain even lesshydrogen atoms----oliveand peanut oil

Regulatory lipids: Steroids


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Regulatory lipids: Steroids Formed from 4 rings of

carbon atoms joinedtogether

Common steroids

sex hormones, bile salts,

vitamins & cholesterol Cholesterol found in animal

cell membranes

starting material for

synthesis of othersteroids

Which is most soluble inwater?

Eicosanoids
http://www.wiley.com/college/boyer/0470003790/animations/cholesterol/cholesterol.swfhttp://www.wiley.com/college/boyer/0470003790/animations/cholesterol/cholesterol.swf


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Eicosanoids Lipid type derived from a fatty

acid called arachidonic acid prostaglandins = wide variety of

functions modify responses to hormones

contribute to inflammatory response prevent stomach ulcers

dilate airways

regulate body temperature

influence formation of blood clots leukotrienes = allergy &

inflammatory responses

Structural lipids


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Structural lipidsPhospholipids: Glycerol+ fatty acids + phosphate

Part of cell membrane. Ex. Lecithin.

Glycolipid: Glycerol+ fatty acid+ sugar chain.

Part of cell membrane surface.

Chemical Nature of Phospholipids


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Chemical Nature of Phospholipidsamphi pathic

head tails

Lipid Behavior in Various
http://www.johnkyrk.com/cellmembrane.htmlhttp://www.johnkyrk.com/cellmembrane.html


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Lipid Behavior in VariousEnvironments

How do phospholipids behave

In an oil spill?

Submerged in water? In a living cell?

Lipoproteins
http://www.johnkyrk.com/cellmembrane.htmlhttp://www.johnkyrk.com/cellmembrane.htmlhttp://www.johnkyrk.com/cellmembrane.htmlhttp://www.johnkyrk.com/cellmembrane.htmlhttp://www.healthscout.com/animation/68/31/main.htmlhttp://www.healthscout.com/animation/68/31/main.html


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Lipoproteins

Whatdeterminesthe densityof

lipoproteins?

Nucleic acids are chains of nucleotides
http://www.healthscout.com/animation/68/31/main.htmlhttp://www.healthscout.com/animation/68/31/main.html


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Three types: DNA, RNA, ATP

Function: Storage of geneticinformation and energy

Nucleotides are composed of:

sugar, phosphate,nitrogenous base Sugar = deoxyribose (DNA) or ribose (RNA & ATP)

DNA Bases = adenine, thymine, cytosine, guanine

RNA bases = adenine, uracil, cytosine, guanine

Base Pairing: A-T, G-C or A-U. Held together byhydrogen bonds

Nucleic acids are chains of nucleotides


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DNA Structure


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DNA Structure

Huge molecules containing

C, H, O, N and phosphorus Each gene of our genetic

material is a piece of DNAthat controls the synthesis

of a specific protein A molecule of DNA is a

chain of nucleotides

Nucleotide = nitrogenous

base (A-G-T-C) + pentosesugar + phosphate group

RNA Structure


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RNA Structure

Differs from DNA single stranded ribose sugar not

deoxyribose sugar

uracil nitrogenous basereplaces thymine Types of RNA within the

cell, each with a specific

function messenger RNA ribosomal RNA transfer RNA

Adenosine Triphosphate (ATP)


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Adenosine Triphosphate (ATP) Temporary molecular storage of energy as it is

being transferred from exergonic catabolicreactions to cellular activities muscle contraction, transport of substances across cell

membranes, movement of structures within cells andmovement of organelles

Consists of 3 phosphategroups attached toadenine & 5-carbon

sugar (ribose)

Formation & Usage of ATP


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Formation & Usage of ATP Hydrolysis of ATP (removal of terminal phosphate

group by enzyme -- ATPase) releases energy

leaves ADP (adenosine diphosphate)

Synthesis of ATP enzyme ATP synthase catalyzes the addition of

the terminal phosphate group to ADP

energy from 1 glucose molecule is used duringaerobic respiration to create 36 to 38 moleculesof ATP

Amino Acid Structure


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Amino Acid Structure

Central carbon atom

Amino group (NH2)

Carboxyl group (COOH)

Hydrogen

Side chains (R groups) vary between amino acids

Proteins


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Contain carbon, hydrogen, oxygen, andnitrogen

Constructed from combinations of 20amino acids.

Levels of structural organization primary, secondary and tertiary

shape of the protein influences its ability to form

bonds

Which Amino Acidsare hydrophobic?


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are hydrophobic?How do you know?

Which AminoAcids arealkaline?Why?

Formation of a peptide Bond


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Formation of a peptide Bond

Dipeptides formed from 2 amino acids joined by acovalent bond called a peptide bond dehydration synthesis

Polypeptides chains formed from 10 to 2000 aminoacids.

Levels of Structural Organization
http://www.stolaf.edu/people/giannini/flashanimat/proteins/protein%20structure.swfhttp://www.stolaf.edu/people/giannini/flashanimat/proteins/protein%20structure.swf


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Primary is unique sequence of amino acids Secondary is alpha helix or pleated sheet folding

Tertiary is 3-dimensional shape of polypeptide chain

Quaternary is relationship of multiple polypeptide chains

L f g

The four levels of protein
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Primary is uniquesequence of amino acids

Secondary is alpha helixor pleated sheet folding

Tertiary is 3-dimensionalshape of polypeptidechain

Quaternary isrelationship of multiplepolypeptide chains

Protein Folding Tutorial:

Protein folding in Water

f f pconfiguration

Bonds of protein Structure
http://www.wiley.com/legacy/college/boyer/0470003790/animations/animations.htmhttp://www.stolaf.edu/people/giannini/flashanimat/proteins/hydrophobic%20force.swfhttps://mywebspace.wisc.edu/jonovic/web/proteins.htmlhttps://mywebspace.wisc.edu/jonovic/web/proteins.htmlhttps://mywebspace.wisc.edu/jonovic/web/proteins.htmlhttps://mywebspace.wisc.edu/jonovic/web/proteins.htmlhttp://www.stolaf.edu/people/giannini/flashanimat/proteins/hydrophobic%20force.swfhttp://www.wiley.com/legacy/college/boyer/0470003790/animations/animations.htm


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Bonds of protein Structure

Hydrogen bond formsthe secondary structure

Disulfide bonds stabilizethe tertiary structure of

protein molecules Disulfide bond between

2 polypeptide chains

create quaternarystructure

Protein Denaturation
http://www.sumanasinc.com/webcontent/animations/content/proteinstructure.htmlhttp://www.sumanasinc.com/webcontent/animations/content/proteinstructure.html


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Function of a protein dependson its ability to recognize andbind to some other molecule

Hostile environments such as

heat, acid or salts will changea proteins 3-D shape anddestroy its ability to function

raw egg white when cooked isvastly different

Protein Denaturation

Glycoprotein and Proteoglycan
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Glycoprotein and Proteoglycan

Proteins exist in combination with sugar.

Glycoprotein: Protein + sugar chain. Found in cellmembrane. Serve as surface proteins.

Proteoglycan: Protein + sugar chain. Also present in

cell membrane. Can have enzymatic activity.

Enzymes
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y Enzymes are protein molecules that act as

catalysts by lowering Activation Energy Enzyme = apoenzyme + cofactor Apoenzymes are the protein portion Cofactors are nonprotein portion

may be metal ion (iron, zinc, magnesium or calcium) may be organic molecule derived from a vitamin

Enzymes usually end in suffix -ase and are namedfor the types of chemical reactions they catalyze

How Enzymes Work Enzyme Tutorial Enzyme Catalysis
http://media.pearsoncmg.com/bc/bc_campbell_concepts_6/activities/eb1Lib/activities/03/3I/st01/frame.htmlhttp://www.mhhe.com/physsci/chemistry/essentialchemistry/flash/activa2.swfhttp://www.mhhe.com/physsci/chemistry/essentialchemistry/flash/activa2.swfhttp://highered.mcgraw-hill.com/sites/0072495855/student_view0/chapter2/animation__how_enzymes_work.htmlhttp://www.northland.cc.mn.us/biology/Biology1111/animations/enzyme.htmlhttp://bcs.whfreeman.com/thelifewire/content/chp06/0602001.htmlhttp://bcs.whfreeman.com/thelifewire/content/chp06/0602001.htmlhttp://www.northland.cc.mn.us/biology/Biology1111/animations/enzyme.htmlhttp://highered.mcgraw-hill.com/sites/0072495855/student_view0/chapter2/animation__how_enzymes_work.htmlhttp://www.mhhe.com/physsci/chemistry/essentialchemistry/flash/activa2.swfhttp://media.pearsoncmg.com/bc/bc_campbell_concepts_6/activities/eb1Lib/activities/03/3I/st01/frame.html


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Enzyme Structure Interactions
http://www.ryancshaw.com/Files/micro/Animations/Enzyme-Substrate/micro_enzyme-substrate.swfhttp://www.ryancshaw.com/Files/micro/Animations/Enzyme-Substrate/micro_enzyme-substrate.swf


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yLock and Key: shape and active

site of enz is only compatiblew/ substrate, formingsubstrate enzyme complex

-enz reused but are eventually

decomposed=constant synthesis-usually end in "ase" and takename of substrate

Factors Affecting Enzyme Action
http://www.ryancshaw.com/Files/micro/Animations/Enzyme-Substrate/micro_enzyme-substrate.swfhttp://www.ryancshaw.com/Files/micro/Animations/Enzyme-Substrate/micro_enzyme-substrate.swf


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g y

Temperature:

40oC, denaturationEnzyme Saturation

Concentration of substrate

pH pepsin ( gastric protease) pH2

trypsin (pancreatic protease)

pH 8
http://highered.mcgraw-hill.com/sites/0072943696/student_view0/chapter2/animation__protein_denaturation.htmlhttp://highered.mcgraw-hill.com/sites/0072943696/student_view0/chapter2/animation__protein_denaturation.html


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Saturation


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Saturation

Cofactors


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Cofactors can aid how enzymeworks. If they are organic, thenthey are coenzymes these areenzyme activators

Allosteric & Competitive

Cofactorsinhibitorsactivators

Pharmacological EnzymeInhibitorsAllosteric RegulationBiochemical PathwayCompetitive vs Noncompetitive

Inhibitors

Competitive vs Noncompetitive Inhibitors
http://www.wiley.com/college/pratt/0471393878/student/animations/enzyme_inhibition/index.htmlhttp://www.wiley.com/college/pratt/0471393878/student/animations/enzyme_inhibition/index.htmlhttp://bcs.whfreeman.com/thelifewire/content/chp06/0602002.htmlhttp://highered.mcgraw-hill.com/olc/dl/120070/bio09.swfhttp://bcs.whfreeman.com/thelifewire/content/chp06/0602001.htmlhttp://bcs.whfreeman.com/thelifewire/content/chp06/0602001.htmlhttp://bcs.whfreeman.com/thelifewire/content/chp06/0602001.htmlhttp://bcs.whfreeman.com/thelifewire/content/chp06/0602001.htmlhttp://highered.mcgraw-hill.com/olc/dl/120070/bio09.swfhttp://highered.mcgraw-hill.com/olc/dl/120070/bio09.swfhttp://bcs.whfreeman.com/thelifewire/content/chp06/0602002.htmlhttp://www.wiley.com/college/pratt/0471393878/student/animations/enzyme_inhibition/index.htmlhttp://www.wiley.com/college/pratt/0471393878/student/animations/enzyme_inhibition/index.htmlhttp://bcs.whfreeman.com/thelifewire/content/chp06/0602001.htmlhttp://bcs.whfreeman.com/thelifewire/content/chp06/0602001.html


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p p
http://bcs.whfreeman.com/thelifewire/content/chp06/0602001.htmlhttp://bcs.whfreeman.com/thelifewire/content/chp06/0602001.html


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In this animation, the enzyme is olive, the substrate is green,the competitive inhibitor is red and the products A & B are

yellow and blue. The enzyme has binding site into which eitherthe substrate or the competitive inhibitor may fit.

Which product, A or B, would most likely be a competitiveinhibitor?


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The enzyme has 2 binding sites, one for thesubstrate (the active site) and the other for theallosteric activator (the regulatory site). Allosteric

Activation Nerve gas permanently blocks pathways involved in nervemessage transmission, resulting in death.

Penicillin, the first of the "wonder drug" antibiotics,permanently blocks the pathways certain bacteria use to

assemble their cell wall components.

Examples of Enzyme function
http://bcs.whfreeman.com/thelifewire/content/chp06/0602s.swfhttp://bcs.whfreeman.com/thelifewire/content/chp06/0602s.swfhttp://bcs.whfreeman.com/thelifewire/content/chp06/0602s.swfhttp://bcs.whfreeman.com/thelifewire/content/chp06/0602s.swfhttp://bcs.whfreeman.com/thelifewire/content/chp06/0602s.swfhttp://bcs.whfreeman.com/thelifewire/content/chp06/0602s.swf


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p y

Ethylene levels cause changes in the production of differentenzymes, allowing fruits to ripen.

In eukaryotic cells the mRNA transcript undergoes a seriesof enzyme regulated modifications.

The enzyme RNA-polymerase reads the DNA molecule in the3' to 5' direction and synthesizes complementary mRNAmolecules that determine the order of amino acids in thepolypeptide.

ATP Synthase

DNA polymerase, ligase, RNA polymerase, helicase andtopoisomerase,

Positive Feedback


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Amplification occurs when the stimulus is furtheractivated, which in turn initiates an additional

response that produces system change

Lactation in mammals

Onset of labor in childbirth

Ripening of fruit Blood clotting

Estrogen & Progesterone in Female System

Negative Feedback/ FeedbackInhibition
http://health.howstuffworks.com/human-body/systems/circulatory/adam-200077.htmhttp://glencoe.mcgraw-hill.com/sites/9834092339/student_view0/chapter52/positive_and_negative_feedback.htmlhttp://glencoe.mcgraw-hill.com/sites/9834092339/student_view0/chapter52/positive_and_negative_feedback.htmlhttp://glencoe.mcgraw-hill.com/sites/9834092339/student_view0/chapter52/positive_and_negative_feedback.htmlhttp://glencoe.mcgraw-hill.com/sites/9834092339/student_view0/chapter52/positive_and_negative_feedback.htmlhttp://health.howstuffworks.com/human-body/systems/circulatory/adam-200077.htmhttp://highered.mcgraw-hill.com/olc/dl/120070/bio10.swfhttp://highered.mcgraw-hill.com/olc/dl/120070/bio10.swfhttp://highered.mcgraw-hill.com/olc/dl/120070/bio10.swfhttp://highered.mcgraw-hill.com/olc/dl/120070/bio10.swf


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Inhibition

When the product is in abundance,it binds competitively with itsenzyme's active site; as theproduct is used up, inhibition isreduced and more product can beproduced. In this way theconcentration of the product isalways controlled within a certainrange.

Operons in gene regulation

Temperature regulation in animals

Plants response to water

limitations
http://highered.mcgraw-hill.com/olc/dl/120070/bio10.swfhttp://highered.mcgraw-hill.com/olc/dl/120070/bio10.swf


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1

2

3

4

A

B

C

D

1 A


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2

3

4

5

6

B

C

D

E

F

Resources Animations:
http://africangreyparrott.com/bio.winona.edu/berg/ANIMTNS/c-inhban.htmhttp://africangreyparrott.com/bio.winona.edu/berg/ANIMTNS/c-inhban.htm


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n mat ons Microbiology: BioTopics Contents:

What is an Enzyme: Lipid Behavior in Various Environments Organic Molecules Interactive Animations for Biochemical Processes Biology Project Chemistry Tutorial Chemistry Target Practice

Importance of Functional Groups Functional groups Matching Identify the Biomolecules Matching "Hot Potatoes" Practice matching exercises Factors that affect the rate of Chemical Reactions with Alka Seltzer

Properties of Water Properties of Water & Transpiration Enzyme Specificity Tutorial Enzyme Kinetics Animation
http://africangreyparrott.com/bio.winona.edu/berg/ANIMTNS/c-inhban.htmhttp://student.ccbcmd.edu/courses/bio141/lecguide/unit6/http://www.biotopics.co.uk/conten.htmlhttp://www.northland.cc.mn.us/biology/biology1111/animations/enzyme.swfhttp://www.johnkyrk.com/cellmembrane.htmlhttp://www.biology.lsu.edu/introbio/tutorial/spotted/BioStudio/2ORGANICMOLE/1OrMo.htmlhttp://www.wiley.com/legacy/college/boyer/0470003790/animations/animations.htmhttp://www.biology.arizona.edu/biochemistry/tutorials/chemistry/main.htmlhttp://www.zerobio.com/target_practice_quiz/target_practice_quiz_chemistry.swfhttp://www.clickandlearn.org/Bio/Gr12Bio/lesson2Functional%20Groups%20Presentation_files/frame.htmhttp://www.tvcc.edu/depts/biology/HotPot/Biol%201406/functional_groups.htmhttp://www.tvcc.edu/depts/biology/HotPot/Biol%201406/biomolecule_structure.htmhttp://www.tvcc.edu/depts/biology/Study%20Resources/lecture/Hot%20Potatoes.htmhttp://www.alkaseltzerplus.com/asp/student_experiments_1.htmlhttp://www.health-benefit-of-water.com/properties-of-water.htmlhttp://www.brighthub.com/environment/science-environmental/articles/64900.aspxhttp://www.learnerstv.com/animation/animation.php?ani=171&cat=biologyhttp://www.kscience.co.uk/animations/enzyme_model.htmhttp://www.kscience.co.uk/animations/enzyme_model.htmhttp://www.learnerstv.com/animation/animation.php?ani=171&cat=biologyhttp://www.brighthub.com/environment/science-environmental/articles/64900.aspxhttp://www.health-benefit-of-water.com/properties-of-water.htmlhttp://www.alkaseltzerplus.com/asp/student_experiments_1.htmlhttp://www.tvcc.edu/depts/biology/Study%20Resources/lecture/Hot%20Potatoes.htmhttp://www.tvcc.edu/depts/biology/HotPot/Biol%201406/biomolecule_structure.htmhttp://www.tvcc.edu/depts/biology/HotPot/Biol%201406/functional_groups.htmhttp://www.clickandlearn.org/Bio/Gr12Bio/lesson2Functional%20Groups%20Presentation_files/frame.htmhttp://www.zerobio.com/target_practice_quiz/target_practice_quiz_chemistry.swfhttp://www.biology.arizona.edu/biochemistry/tutorials/chemistry/main.htmlhttp://www.wiley.com/legacy/college/boyer/0470003790/animations/animations.htmhttp://www.biology.lsu.edu/introbio/tutorial/spotted/BioStudio/2ORGANICMOLE/1OrMo.htmlhttp://www.johnkyrk.com/cellmembrane.htmlhttp://www.northland.cc.mn.us/biology/biology1111/animations/enzyme.swfhttp://www.biotopics.co.uk/conten.htmlhttp://student.ccbcmd.edu/courses/bio141/lecguide/unit6/http://africangreyparrott.com/bio.winona.edu/berg/ANIMTNS/c-inhban.htm

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AP Biochemistry 11