Ch 2 - Chemistry of Life 2013

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Chapter 2: The ChemicalLevel of Organization



Matter

• Matter – anything that has weight andtakes up space.– Includes solids, liquids, and gases

• All matter is composed of elements.– There are 112 known elements

• Ex. Iron, copper, silver, aluminum, carbon,hydrogen, oxygen



Matter and Living Organisms

• Living organisms require about 20elements.

• Of these, oxygen, carbon, hydrogenand nitrogen make up more than 95%of the human body.



Atoms• Elements are composed of

tiny particles called atoms.

• Atoms are the smallestcomplete units of elements.

• Atoms vary in size, weight,

and the ways they interactwith each other.• Protons (+) and neutrons

(neutral) are found on the

atom’s nucleus, while electrons (-) circle the nucleus.• Atomic number - # of protons

Nucleus

Atoms with the same atomic number belong to the same

element, and thus have the same inherent properties.



Atoms



Atomic Weight

• Mass refers to the amount of a substance.• Weight refers to the force exerted on a

substance by gravity.• Atomic mass of an atom refers to the sum of

the masses of protons and neutrons.

– 1 Proton– –1 Neutron– 1 Electron – 1/1840 of that size - negligible



Isotopes• Isotopes - Atoms of an element that possess

a different number of neutrons. Have thesame atomic # b/c # of protons stays thesame– Radioactive isotopes - Spontaneously decay into

elements of lower atomic number.• emit energy and/or subatomic particles

– Half-life refers to the amount of time necessary to decayhalf the atoms of a given sample.





Electrons and Atomic Behavior• Orbital refers to the area around a nucleus

where an electron is most likely found.– Chemical behavior of an atom is determined by

the number and arrangement of its orbitals.• Electrons are attracted to the positively charged

nucleus, thus it takes energy to hold electrons in place.– potential energy of position



Atomic Energy Levels (Orbitals)Electrons can absorb energy and release energy

8e 8e 2e



Electrons of various atoms

Elements?





Electrons and Atomic Behavior• During some chemical reactions, electrons

are transferred between atoms, while stillretaining their energy of position.– Oxidation - loss of an electron– Reduction - gain of an electron



Kinds of Atoms• ~112 Known elements

• Ninety-two naturally occurring– Periodic table arranged by grouping atoms based

on valence electrons (electrons in the outer energy

levels).• Russian chemist Dmitri Mendeleev in 1869.• Octet rule

– Most atoms important to life can contain no more

than 8 electrons– Inert atoms have outer level filled.– Reactive atoms do not have outer level filled.

http://en.wikipedia.org/wiki/Dmitri_Mendeleev

http://en.wikipedia.org/wiki/Dmitri_Mendeleev



Periodic Table of the Elements



Elements in the Human Body

Table 2 –1



Chemical Bonds

• A molecule refers to a group of atoms heldtogether by energy in a stable association. O 2

• Compound is composed of two or moredifferent types of atoms bond together. NaCl

• Atoms in a molecule are joined by chemicalbonds .



Chemical Bonds

• Ionic bonds areformedbecause ions ofoppositecharge attractone another.– table salt– Sodium Na+– Chlorine Cl-



• Covalent bonds are formed when

two or moreatoms share pairsof valenceelectrons.– Strength depends

on number ofshared electrons.

Share one = singlebond, share two =double bond =share three =

triple bond



Hydrogen Bonding• In a water molecule, both the oxygen and

hydrogen atoms attract the sharedelectrons in the covalent bond(electronegativity).

– Oxygen atom is more electronegative than thehydrogen atoms.



Chemical Reactions• A chemical reaction occurs during the

formation or breaking of chemical bonds.

• Chemical reactions can be influenced by:

– temperature– concentration of reactants and products– catalysts



Energy • Energy - the power to do work• Work - a change in mass or distance

Energy exists in 2 forms • Kinetic energy - energy of motion

• Potential energy - stored energy

• Chemical energy - potential energy stored in

chemical bonds. ATP• Electrical energy – movement of charged particles• Mechanical energy – moving matter

• Radiant energy – electromagnetic (energy in waves)



Break Down, Build Up• Decomposition reaction (catabolism) :

AB A + B• Synthesis reaction (anabolism) :

A + B -> AB• Exchange reaction (reversible) :

AB A + B

Water In, Water Out

• Hydrolysis :A—B—C—D—E + H2O A—B—C—H + HO—D—E

• Dehydration synthesis (condensation) :A—B—C—H + HO—D—E A—B—C—D—E + H

2O



Wh i h diff b



What is the difference betweenorganic and inorganic compounds?

Organic and Inorganic Molecules• Organic:

– molecules based on carbon and hydrogen

• Inorganic:– molecules not based on carbon and hydrogen

Essential Molecules • Nutrients :

– essential molecules obtained from food

• Metabolites :

– molecules made or broken down in the body



Why is water so important to life?Properties of Water

• Solubility:– water’s ability to dissolve a solute in a solvent to

make a solution

• Reactivity:– most body chemistry uses or occurs in water

• High heat capacity :– water’s ability to absorb and retain heat

• Lubrication :– to moisten and reduce friction



KEY CONCEPT

• Most of our body weight is water – 2/3• Water is the key structural and functional

component of cells and their control

mechanisms, the nucleic acids



Aqueous Solutions

Figure 2 –8

• Polar water molecules form hydration spheresaround ions and small polar molecules to keepthem in solution

El t l t



Electrolytes • Inorganic ions which conduct electricity in

solution• Electrolyte imbalance seriously disturbs vital

body functions

M l l d W t



Molecules and Water • Hydrophilic :

– hydro = water, philos = loving

– reacts with water• Hydrophobic :

– phobos = fear– does not react with water

Solutions • Concentration :

– the amount of solute in a solvent ( mol/L , mg/mL )

Wh t i H d h d d b ff ?



What is pH and why do we need buffers?• pH:

– the concentration of hydrogen ions (H+) in asolution

• Neutral pH:– a balance of H+ and OH —

– pure water = 7.0Acids and Bases• Acid (acidic) : pH lower than 7.0

– high H+

concentration,low OH— concentration

• Base (basic) : pH higher than 7.0– low H+ concentration,

hi h OH— concentration

H S l



pH Scale

Figure 2 –9

• Has an inverse relationship with H +

concentration:– more H + ions meanlower pH, less H + ions mean higher pH

• pH of body fluids measures free H + ions in solution• Excess H + ions (low pH):

– damages cells and tissues

– alters proteins– interferes with normal physiological functions

• Excess OH — ions (high pH) also cause problems, butrarely

Acid and Alkaline



Acid and Alkaline • Acidosis :

– excess H + in body fluid (low pH)

• Alkalosis :– excess OH — in body fluid (high pH)

Controlling pH • Salts :– positive or negative ions in solution– contain no H + or OH — (NaCl)

• Buffers :– weak acid/salt compounds– neutralizes either strong acid or strong

base

What kinds of organic compounds ar



What kinds of organic compounds ar there, and how do they work?



Functional Groups • Molecular groups which allow molecules to

interact with other molecules

Carbohydrate Functions



Carbohydrate Functions

Table 2 –5

• Monosaccharides: simple sugars with 3 to 7

carbon atoms (glucose)• Disaccharides: 2 simple sugars condensed by

dehydration synthesis (sucrose)

• Polysaccharides: Chains of many simple sugars(glycogen )

• Carbohydrates are quick energy sources and

components of membranes

Lipids



Lipids • Mainly hydrophobic molecules such as fats,

oils, and waxes• Made mostly of carbon and hydrogen atoms• Lipids have many functions, including

membrane structure and energy storage

Classes of Lipids

• Fatty acids may be:



• Fatty acids may be:– saturated with hydrogen (no

covalent bonds)

– unsaturated (1 or more doublebonds)

• Types of Eicosanoids– Leukotrienes : active in immune system– Prostaglandins : local hormones, short-chain fatty

acids

• Glycerides : are the fatty



Figure 2 –15

• Glycerides : are the fattyacids attached to aglycerol molecule– Triglyceride : are the 3 fatty-

acid tails, fat storagemolecule

• Steroids– Cholesterol : component of

cell membranes– Estrogens and

testosterone : sex hormones– Corticosteroids and

calcitrol : metabolicregulation

– Bile salts : derived fromsteroids

• Phospholipids and Glycolipids



• Phospholipids and Glycolipids – Have hydrophilic heads and hydrophobic tails– Are structural lipids, components of cell

membranes

Protein Structure



Protein Structure • Proteins are the most abundant and important

organic molecules• Basic elements: carbon (C), hydrogen (H), oxygen

(O), and nitrogen (N)• Basic building blocks: 20 amino acids

Protein Functions• 7 major protein functions:

– support: structural proteins – movement: contractile proteins – transport: transport proteins– buffering: regulation of pH– metabolic regulation: enzymes – coordination and control: hormones

– defense: antibodies

Amino Acid Structure



Amino Acid Structure

1. central carbon2. hydrogen3. amino group (—NH2)

4. carboxylic acidgroup (—COOH)5. variable side chain

or R group

P id B d



Peptide Bond • A dehydration

synthesis between:– the amino group of 1

amino acid– and the carboxylic

acid group ofanother amino acid

– producing a peptide

Primary Structure



Figure 2 –20a

Primary Structure • Polypeptide : a long chain of amino acids

Secondary Structure • Hydrogen bonds form spirals or pleats



Figure 2 –20c

Tertiary Structure• Secondary structure foldsinto a unique shape

QuaternaryStructure • Final protein shape:

several tertiarystructures together



Shape and Function • Protein function is based on shape • Shape is based on sequence of amino acids• Denaturation : loss of shape and function due to heat

or pH

Protein Shapes• Fibrous proteins : structural sheets or strands• Globular proteins : soluble spheres with active

functions

Enzymes



Enzymes • Enzymes are catalysts :

– proteins that lower the activation energy of a chemicalreaction

– are not changed or used up in the reaction• How Enzymes Work

– Substrates : reactants in enzymatic reactions– Active site : a location on an enzyme that fits a particular

substrate

How do enzymes control metabolism?



How do enzymes control metabolism?

Activation Energy• Chemical reactions in cells cannot start without help• Activation energy gets a reaction started

Materials in Reactions• Reactants :

– materials going into areaction

• Products :– materials coming out of a

reaction• Enzymes :

– proteins that lower theactivation energy of a

reaction

Enzyme Helpers



Enzyme Helpers • Cofactor :

– an ion or molecule that binds to an enzyme beforesubstrates can bind

• Coenzyme :– nonprotein organic cofactors ( vitamins )

• Isozymes :

– 2 enzymes that can catalyze the same reactionEnzyme Characteristics

• Specificity :– one enzyme catalyzes one reaction

• Saturation limits :– an enzyme’s maximum work rate

• Regulation :

– the ability to turn off and on

Nucleic Acids



Nucleic Acids • Large organic molecules, found in the nucleus, which

store and process information at the molecular level

• DNA and RNA

Deoxyribonucleic Acid (DNA)

• Determines inherited characteristics• Directs protein synthesis• Controls enzyme production• Controls metabolism

Ribonucleic Acid (RNA) • Codes intermediate steps in protein synthesis



Complementary Bases• Complementary base pairs :

– purines pair with pyrimidines :• DNA: adenine (A) and thymine (T) and cytosine

(C) and guanine (G)

• RNA: uracil (U) replaces thymine (T)

The Bases



Nucleotides • Are the buildingblocks of DNA• Have 3 molecular

parts:

– sugar(deoxyribose)– phosphate group– nitrogenous base

(A, G, T, C)

High Energy Compounds - ADP and ATP



High Energy Compounds - ADP and ATP • adenosine

diphosphate (ADP):– 2 phosphate groups

• adenosinetriphosphate (ATP) :– 3 phosphate groups

Phosphorylation

• Adding a phosphate group to ADP with a high-energybond to form the high-energy compound ATP

• ATPase : the enzyme that catalyzes phophorylation

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Ch 2 - Chemistry of Life 2013