Ch.2 Biochem. Notes Ellis Version

8/14/2019 Ch.2 Biochem. Notes Ellis Version

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Basic Chemistry of Biology

Matter

Matter anything that occupies space and has mass.

Mass the quantity of matter an object has.

Elements

Elements pure substances that cannot be broken down

chemically into simpler kinds of matter.

- 90 naturally occurring elements.

-25 are essential to living things.

-of these 25, 4 make up 96% of the human body.1.) C carbon 2.) H hydrogen

3.) O oxygen 4.) N nitrogen

Atoms the simplest particle of an element that retains all of

the chemical properties of that element.

2

He4

Atomic Number(No. of Protons)

Chemical Symbol

Atomic Mass

Electrons (-)

Protons (+)

Neutrons

The Nucleus


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CompoundsIon an atom or molecule with an electric charge.

Chemical bond force holding two atoms or ions together.

Compound - a pure substance that is made up of atoms of two

or more elements (Ex: Water, contains hydrogen

& oxygen; Salt, contains sodium & chlorine

atoms).

Physical & chemical properties of compounds

differ from the physical & chemical properties ofthe individual elements that compose it.

Ionic bond the force of attraction between oppositely

charged ions.

One atom loses one or more electrons so that it

has full outer energy level. The other atominvolved in bonding gains one or more electrons

so that it too has a full outer energy level.

Na Cl


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By losing its outermost electron, a Sodium atom becomes an

Na+ion. By gaining one electron, a chlorine atom becomes a

Cl-ion. Because of their opposite charges, the Na

+andCl

-

ions are attracted to each other and form an ionic bond.

Another view:


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Covalent bond forms when two atoms share one or more

pairs of electrons. (Ex: Water, composed of

hydrogen & oxygen atoms, is held together by

covalent bonds.)

Two atoms of hydrogen and one atom of oxygen share electronsin covalent bonds to become stable. Covalent bonds result in

the formation of molecules.

O

H H

H

O

HAll organisms are

made up from70-95% water!

O

H H

Water theUniversal Solvent!


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Polarity

An oxygen atom has eight protons (+) in its nucleus and

therefore eight positive charges to attract electrons (-),

whereas a hydrogen atom has only one proton and therefore

one positive charge. With its greater positive charge, the

nucleus of the oxygen atom pulls the shared electrons toward

its nucleus and away from the nucleus of the hydrogen atom.

As a result, the electrical charge is unevenly distributed.

This uneven distribution of electrical charge causes the water

molecule to have a bent formation, making it a polarcompound.

H H

O

Structural Formula

Electron-energy-level Model


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Molecules of Life

Carbohydrates organic compounds composed of

carbon, hydrogen and oxygen in a ratio of

about two hydrogen atoms to one oxygenatom. The number of carbon atoms in a

carbohydrate varies. Carbohydrates exist as

monosaccharides, disaccharides or

polysaccharides.

Monosaccharides - a simple sugar. Contains carbon,

hydrogen, and oxygen in a ratio of 1:2:1.

1.) Glucose main source of energy for cells.

2.) Fructose found in fruits & the sweetest ofmonosaccharides.

3.) Galactose found in milk & is usually combined

with glucose & fructose.


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Disaccharides a double sugar; two monosaccharides

combined. (Ex: sucrose, common table sugar)


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Polysaccharide complex molecule composed of three or more

monosaccharides.


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Animals store glucose in the form of the polysaccharide

glycogen. Plants store it as starch (cellulose in cell walls)!


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AMINO ACIDS & PROTEINS

Macromolecules- large molecules, consist of several small

molecules joined together.

In proteins (which are macromolecules) thesesmall units are called amino acids

Proteins have the following characteristics:

Contain Carbon, Hydrogen, Oxygen &

Nitrogen

Have a carboxyl group (COOH) Have an R group that is different for each

amino acid.

Have an Amine group (NH2)

Use covalent bonds called peptide bonds to

connect amino acids together

Monomer- small unit that can join together with other monomers

to make polymers (EX: monosaccharide in carbohydrates, Amino

Acid in protiens

Polymer- larger unit made up by monomers linked together (Ex:

polysaccharide in carbohydrates, protein)

Amino Acid monomer, smaller building blocks of proteins

20 different molecules commonly occur in

proteins


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Each have the same chemical backbones, but

different R groups


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Amino Acid - monomer building blocks of proteins that share


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a basic structure.

Amino Acid Basic Structure


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Two amino acids form a covalent bond, call a

peptide bond.

Dipeptide bond two amino acids joined by a

bond.

Polypeptide bond many amino acids joined

together forming a chain.

Protein Structure

Primary Structure the unique sequence of amino

acids in a protein.

Secondary Structure - when proteins have


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segments of their polypeptide chain

repeatedly coiled or folded . A result

of hydrogen bonding along the

backbone of the polypeptide (can be

helix or pleated).

Tertiary Structure irregular contortions from

interactions between side chains (R

groups) of the various amino acids,

which are superimposed on the patterns

of secondary structure.

Quaternary Structure - the overall protein

structure that results from the

aggregation of two or more

polypeptide chains .


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Lipids

Lipids - large, nonpolar organic molecules that do

not dissolve in water (fats & oils).

Fatty Acids unbranched carbon chains that makeup most lipids. The two ends of the

fatty acid have different properties.


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Hydrophilic water loving

Hydrophobic water fearing

O

C

OH

C

C

C

C

C

C

C

C

C

C

C

C

C

C

C

HH

HH

HH

HH

HH

HH

HH

HH

HH

HH

HH

HH

HH

HH

HH

H

O

C

OH

C

C

C

C

C

C

C

C

C

C

C

C

C

C

C

HH

HH

HH

HH

HH

HH

HH

H

H

HH

H

H

HH

HH

HH

C HH

HH C

H

Linoleic Acid

Carbon atoms are

not bonded to the

maximum numberof atoms that they

can bond to.

Instead they have

formed double

bonds within the

carbon chain.

This type of fattyacid is said to be

unsaturated.

Unsaturated fats

are found in

vegetables!

Palmatic Acid

Each carbon atom

is covalently

bonded to fouratoms. The

carbon atoms are

in effect full, or

saturatedfatty

acid.

Saturated fats arefound in meat

products.


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Complex Lipids

Phospholipids have two,

rather than

three, fattyacids joined by

a molecule of

glycerol.

Triglyceride - composed of three molecules of fatty

acid joined to one molecule of the

alcohol glycerol. Saturated

triglycerides are composed of

saturated fatty acids.

Phospholipids have two, rather than

three, fatty acids

joined by a molecule oglycerol.

Cell membranes are composed of two

layers of phospholipids, which are

referred to as the lipid bilayer.


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Cell membranes are composed of two layers of

phospholipids, which are referred to as the

lipid bilayer. Lipids cannot dissolve in water

therefore they form a barrier between the

inside and outside of the cell.


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Nucleic Acids very large & complex organic

molecules that store important in

the cell.

DNA Deoxyribonucleic acid; forms chromosomes& contains genetic code!

Ribonucleic acid - RNA; stores and transfers

information that is essential for

the manufacturing of proteins.


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The Double Helix

ATP (Adenosine Triphosphate) a compound that

stores large amounts of energy that

can be made available to the cells of

the body. The energy currency of

the body.

DNA


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Chemical Reactions

Exothermic Reaction chemical reactions that

involve a net release of free enrgy (ex:

heat, light, etc.)

Endothermic Reactions reactions that involve a ne

absorption of free energy.

Activation Energy the amount of energy needed

to start a reaction.


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Enzymes proteins; biological catalysts. Organisms

have thousands of different enzymes,

each one tailor-made for a different

chemical reaction.

Catalysts reduces the amount of activation energy

that is needed for a chemical reaction.


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Enzyme Inhibition

controlling enzymes

Feedback inhibition- a

method of metabolic

control in which the end

product of a metabolic

pathway acts as an

inhibitor of an enzyme

with in that pathway.


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Solutions

Solution is a mixture in which one or more

substances are uniformly distributed in

another substance (ex: plasma theliquid part of blood).

Solute is the substance dissolved in the solution.

(ex: sugar water sugar is the solute)

Solvent is the substance that is doing the

Dissolving (ex: sugar water; solvent =

water).

Saturated solution is one in which no more solute

can dissolve.

Aqueous solution solutions in which water is the

solvent; universally important to

living things.

Ex: Salt water


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Acids & Bases

Dissociation of Water the breaking apart of the

water molecule into two ions

of opposite charge.Dissociation: H2O H

+ + OH-

Hydroxide ion - OH-

The free H+ from the dissociation of water can react

with another water molecule .

H+ + H2O H3O+

H3O+ ion is known as the hydronium ion.

Pure water (distilled) contains equal numbers of

hydronium ions (H3O+) and hydroxide (OH-)ions

and is therefore a neutral solution.

Acids a solution is an acid when the number of

hydronium ions (H3O+) in a solution is

greater that the number ofhydroxide ions

(OH-).


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Bases -a base is a solution that contains more

hydroxide ions (OH-) than hydronium ions

(H3O+).

pH a measure of hydrogen ion concentration

equal to log[H+] and ranging from 0 to 14.

The pH Scale


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Buffer a substance that consists of an acid and

base; used to control the pH in living

systems (ex: Carbonic Acid in the blood).

Properties of Water!

Hydrogen bonding a type of weak chemical bond

formed when the

slightly positive

hydrogen atom of a

polar covalent bond in

one molecule is

attracted to the

slightly negative atomof a polar covalent

bond in another

molecule.

Cohesion due to hydrogen bonding, neighboring

water molecules cling to one another.

This is why water beads up on a surface.


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Allows water columns in plants to hold

together for transport up to the leaves.

Adhesion the attraction of water molecules toother molecules or substances.

Water adhering to the walls of

conducting vessels within a plant allows

water to counteract the effects of gravity

and move up into the plant.

Surface tension a result from hydrogen bonding.

At the interface of water and air is an

ordered arrangement of water molecules

hydrogen bonded to one another and tothe water below.


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This makes the water behave as though

coated with an invisible film.

Other properties of water:

High Specific heat

Evaporative Cooling - sweating

Ice Floats this prevents oceans & lakes from

freezing solid

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Ch.2 Biochem. Notes Ellis Version