46 terms

The Chemistry of Life

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Matter
Matter - anything that has mass and occupies space; can exist in three states: solid, liquid, or gas

Chemistry - study of matter and its interactions
Atoms & Atomic Structure
Atom - smallest unit of matter that retains original properties

Subatomic particles:

Protons (p+) - found in central core of atom (atomic nucleus); positively charged

Neutrons (n0) - found in atomic nucleus; slightly larger than protons; no charge.

Electrons (e-) - found outside atomic nucleus; negatively charged

Atoms are electrically neutral - they have no charge; number of protons and electrons are equal, cancelling each other's charge; number of neutrons does not have to equal number of protons
Atoms & Atomic Structure (2)
Electron shells - regions surrounding atomic nucleus where electrons exist; each can hold a certain number of electrons:

1st shell (closest to nucleus) can hold 2 electrons

2nd shell can hold 8 electrons

3rd shell can hold 18 electrons but "satisfied" with 8

Some atoms may have more than 3 shells
Elements
Number of protons that an atom has in its nucleus is its atomic number

Atomic number defines every element:

Element - substance that cannot be broken down into simpler substance by chemical means

Each element is made of atoms with same number of protons
Elements in the Periodic Table and the Human Body
The human body is made up of four major elements: Hydrogen, Oxygen, Carbon, Nitrogen

Also 7 mineral elements and 13 trace elements
Isotopes and Radioactivity
Mass number - equal to sum of all protons and neutrons found in atomic nucleus

Isotope - atom with same atomic number (same number of protons), but different mass number (different number of neutrons)

Radioisotopes - unstable isotopes; high energy or radiation released by radioactive decay; allows isotope to assume a more stable form
Nuclear Medicine
Cancer radiation therapy - radiation damages structure of cancer cells; interferes with functions

Radiotracers - injected into patient and detected by camera; image analyzed by computer; shows size, shape, and activity of organs and cells

Treatment of thyroid disorders - high doses of iodine-131 treat overactive or cancerous thyroid tissue; radioisotope accumulates and damages cells
Matter Combined
Matter can be combined physically to form a mixture - atoms of two or more elements physically intermixed without changing chemical nature of atoms themselves

There are 3 basic types of mixtures:

Suspensions, colloids, and solutions
Mixtures
Suspension - mixture containing two or more components with large, unevenly distributed particles; will settle out when left undisturbed

Colloids - two or more components with small, evenly distributed particles; will not settle out

Solutions - two or more components with extremely small, evenly distributed particles; will not settle out; contain a solute dissolved in a solvent:

Solute - substance that is dissolved

Solvent - substance that dissolves solute
Chemical Bonds
Matter can be combined chemically when atoms are combined by chemical bonds.

A chemical bond is not a physical structure but rather an energy relationship or attractive force between atoms

Molecule - formed by chemical bonding between two or more atoms of same element

Compound - formed when two or more atoms from different elements combine by chemical bonding
Chemical Bonds (2)
Chemical bonds are formed when valence electrons (in outermost valence shell) of atoms interact

Valence electrons determine how an atom interacts with other atoms and whether it will form bonds with a specific atom

The octet rule states that an atom is most stable when it has 8 electrons in its valence shell (as in CO2)
The Duet Rule
The duet rule (for atoms with 5 or fewer electrons) states that an atom is most stable when its valence electron shell holds 2 electrons
Ions & Ionic Bonds
Ionic bond - formed when electrons are transferred from an atom to another atom; results in formation of ions: cations and anions

Cation - positively charged ion; forms when an atom loses one or more electrons

Anion - negatively charged ion; forms when an atom gains one or more electrons

The attraction between opposite charges bonds ions to one another forming a compound
Covalent Bonds
Covalent bonds - strongest bond; form when two or more atoms share electrons

Two atoms can share one (single bond), two (double bond), or three (triple bond) electron pairs

All elements have protons that attract electrons; property known as electronegativity:

The more electronegative an element the more strongly it attracts electrons, pulling them away from less electronegative elements

Example: oxygen is very electronegative
Nonpolar Covalent Bonds
Nonpolar covalent bonds result when two atoms in a molecule with similar or identical electronegativities pull with equal force; therefore share electrons equally

Nonpolar molecules occur in 3 situations:

Atoms sharing electrons are of the same element

Arrangement of atoms makes one atom unable to pull more strongly than another atom (as in CO2)

Bond is between carbon and hydrogen
Polar Covalent Bonds
Polar covalent bonds form polar molecules when nonmetals with different electronegativities interact resulting in an unequal sharing of electrons

Atom with higher electronegativity becomes partially negative (δ) as it pulls shared electrons close to itself

Atom with lower electronegativity becomes partially positive (δ+) as shared electrons are pulled toward other atom

Polar molecules with partially positive and partially negative ends are known as dipoles
Hydrogen Bonds
Hydrogen bonds - weak attractions between partially positive end of one dipole and partially negative end of another dipole

Hydrogen bonds are responsible for a key property of water—surface tension

Polar water molecules are more strongly attracted to one another than they are to nonpolar air molecules at surface
Chemical Reactions
A chemical reaction has occurred every time a chemical bond is formed, broken, or rearranged, or when electrons are transferred between two or more atoms (or molecules)

Reversible reactions can proceed in either direction as denoted by two arrows that run in opposite directions (as below)

Irreversible reactions proceed from left to right as denoted by a single arrow
Energy & Chemical Reactions
Energy is defined as capacity to do work or put matter into motion or fuel chemical reactions; two general forms of energy:

Potential energy is stored; can be released to do work at some later time

Kinetic energy is potential energy that has been released or set in motion to perform work; all atoms have kinetic energy as they are in constant motion; the faster they move the greater that energy
Energy & Chemical Reactions (2)
Energy is found in 3 forms in the human body; chemical, electrical, and mechanical, each of which may be potential or kinetic depending on location or process

Chemical energy - found in bonds between atoms; drives nearly all chemical processes

Electrical energy - generated by movement of charged particles or ions

Mechanical energy - energy directly transferred from one object to another
Energy & Chemical Reactions (3)
Energy, inherent in all chemical bonds, must be invested any time a chemical reaction occurs:

Endergonic reactions require input of energy from another source; products contain more energy than reactants because energy was invested so reaction could proceed

Exergonic reactions release excess energy so products have less energy than reactants
Homeostasis and Types of Chemical Reactions
Catabolic reactions (decomposition reactions) - when a large substance is broken down into smaller substances

Usually exergonic because chemical bonds are broken

Anabolic reactions (synthesis reactions) occur when small simple subunits and united by chemical bonds to make large more complex substances

These reactions are endergonic; fueled by chemical energy
Homeostasis and Types of Chemical Reactions (2)
Exchange reactions occur when one or more atoms from reactants are exchanged for one another

Oxidation-reduction reactions (redox reactions) - special kind of exchange reaction; occur when electrons and energy are exchanged instead of atoms

Reactant that loses electrons is oxidized

Reactant that gains electrons is reduced

Redox reactions are usually exergonic reactions capable of releasing large amounts of energy
Reaction Rates & Enzymes
For a reaction to occur atoms must collide with enough energy overcome the repulsion of their electrons- this energy required for all chemical reactions is called the activation energy (Ea)

Activation energy must be supplied so that reactants reach their transition states in order to react and form products

The following factors increase reaction rate by reducing activation energy or increasing likelihood of strong collisions between reactants:

Concentration of reactants

Temperature- raising the temperature of the reactants increases kinetic energy of their atoms- more collisions

Reactant properties- size and phase (solid, liquid, or gas) influence reaction rates

Presence or absence of a catalyst
Reaction Rates
Catalyst - substance that increases reaction rate by lowering activation energy without being consumed or altered in reaction

Enzymes - biological catalysts; most are proteins with following properties:

Speed up reactions by lowering the activation

Highly specific for individual substrates (substance that can bind to the enzyme's active site)

Do not alter the reactants or products

Not permanently altered in reactions catalyzed
Reaction Rates & Enzymes (2)
Induced-fit mechanism - describes enzyme's interaction with its substrate(s)

Binding of substrate causes a small shape change that reduces energy of activation
Biochemistry
Biochemistry - the chemistry of life

Inorganic compounds generally do not contain carbon bonded to hydrogen; include water, acids, bases, and salts

Organic compounds - those that do contain carbon bonded to hydrogen
Water
Water (H2O) makes up 60-80% of mass of human body and has several key properties vital to our existence

High heat capacity - able to absorb heat without significantly changing temperature itself

Carries heat with it when it evaporates (when changing from liquid to gas)

Cushions and protects body structures because of relatively high density

Acts as a lubricant between two adjacent surfaces (reduces friction)
Water (2)
Water serves as body's primary solvent; often called the universal solvent because so many solutes will dissolve in it entirely or to some degree

Water is a polar covalent molecule:

Oxygen pole - partially negative (δ)

Hydrogen pole - partially positive (δ+)

Allows water molecules to interact with certain solutes, surround them, and keep them apart
Water (3)
Water is only able to dissolve hydrophilic solutes (those with fully or partially charged ends); "like dissolves like", so water dissolves ionic and polar covalent solutes

Solutes that do not have full or partially charged ends are hydrophobic; do not dissolve in water; includes uncharged nonpolar covalent molecules such as oils and fats
Acids & Bases
Acid - hydrogen ion or proton donor; number of hydrogen ions increases in water when acid is added

Base (alkali) - hydrogen ion acceptor; number of hydrogen ions decreases in water when base is added

pH scale - ranges from 0-14

Simple way of representing hydrogen ion concentration of a solution

Literally the negative logarithm of the hydrogen ion concentration:

pH = - Log [H+]
Acids & Bases (2)
Buffer - chemical system that resists changes in pH; prevents large swings in pH when acid or base is added to a solution

Blood pH must remain within its narrow range to maintain homeostasis

Most body fluids are slightly basic:

Blood pH is 7.35-7.45

Intracellular pH is 7.2
Salts & Electrolytes
Salt - any metal cation and nonmetal anion held together by ionic bonds

Salts can dissolve in water to form cations and anions called electrolytes which are capable of conducting electrical current
Organic Compounds
Organic compound in body (e.g. carbohydrate, protein, nucleic acid) consists of polymers built from monomer subunits:

Monomers are single subunits that can be combined to build larger structures called polymers by dehydration synthesis (anabolic reaction that links monomers together and makes a molecule of water in process)

Hydrolysis is a catabolic reaction that uses water to break up polymers into smaller subunits
Carbohydrates
Carbohydrates, composed of carbon, hydrogen, and oxygen, function primarily as fuel; some limited structural roles

Monosaccharides - consist of 3 to 7 carbons; monomers from which all carbohydrates are made; glucose, fructose, galactose, ribose, and dexoyribose are most abundant monosaccharides

Disaccharides are formed by union of two monosaccharides by dehydration synthesis

Polysaccharides consist of many monosaccharides joined to one another by dehydration synthesis reactions

Glycogen is the storage polymer of glucose; mostly in skeletal muscle and liver cells

Some polysaccharides are found covalently bound to either proteins or lipids forming glycoproteins and glycolipids; various functions in body
Lipids
Lipids - group of nonpolar hydrophobic molecules composed primarily of carbon and hydrogen; include fats and oils

Fatty acids - lipid monomers consisting of 4 to 20 carbon atoms; may have none, one, or more double bonds between carbons in hydrocarbon chain

Saturated fatty acids - solid at room temperature; have no double bonds between carbon atoms so carbons are "saturated" with maximum number of hydrogen atoms

Monounsaturated fatty acids - generally liquid at room temperature; have one double bond between two carbons in hydrocarbon chain

Polyunsaturated fatty acids - liquid at room temperature; have two or more double bonds between carbons in hydrocarbon chain
The Good, the Bad, and the Ugly of Fatty Acids
The Good: Omega - 3 Fats

Found in flaxseed oil and fish oil but cannot be made by humans; must be obtained in diet

Polyunsaturated; positive effects on cardiovascular health

The Bad: Saturated Fats

Found in animal fats; also in palm and coconut oils

Overconsumption associated with increased cardiac disease risk

The Ugly: Trans Fats

Produced by adding H atoms to unsaturated plant oils ("partially hydrogenated oils")

No safe consumption level; significantly increase risk of heart disease
Lipids (2)
Triglyceride - three fatty acids linked by dehydration synthesis to glycerol; storage polymer for fatty acids (also called a neutral fat)

Phospholipids - composed of a glycerol backbone, two fatty acid "tails" and one phosphate "head"

A molecule with a polar group (phosphate head) and a nonpolar group (fatty acid tail) is called amphiphilic

This amphiphilic nature makes phospholipids vital to the structure of cell membranes

Steroids - nonpolar and share a four-ring hydrocarbon structure called the steroid nucleus

Cholesterol - steroid that forms basis for all other steroids
Proteins
Proteins are macromolecules that:

Function as enzymes

Play structural roles

Are involved in movement

Function in the body's defenses

Can be used as fuel
Proteins (2)
Twenty different amino acids (monomers of all proteins); can be linked by peptide bonds into proteins & polypeptides

Peptides - formed from two or more amino acids linked together by peptide bonds through dehydration synthesis

Two basic types of proteins classified according to structure: fibrous and globular

Fibrous proteins - long rope-like strands; link things together and add strength and durability to structures e.g. collagen

Globular proteins - spherical or globe-like; composed mostly of polar amino acids; function as enzymes, hormones
Proteins (3)
Proteins consist of one or more polypeptide chains folded into distinct structures which must be maintained to be functional

Complex structure of a complete protein is divided into four levels:

Primary structure - amino acid sequence of polypeptide chain

Secondary structure - one or more segments of primary structure folded in specific ways; held together by hydrogen bonds

Alpha helix - coiled spring

Beta-pleated sheet - Venetian blind

Tertiary structure - three-dimensional shape that peptide chain assumes (twists, folds, and coils including secondary structure); stabilized by hydrogen bonding
Proteins (4)
Quaternary structure - linking together more than one polypeptide chain in a specific arrangement; critical to function of protein as a whole

Protein denaturation - process of destroying a protein's shape by heat, pH changes, or exposure to chemicals (unfolding of proteins)

Disrupts hydrogen bonding and ionic interactions that stabilize structure and function.
Nucleotides and Nucleic Acids
Nucleotides - monomers of nucleic acids; named because of abundance in nuclei of cells; make up genetic material

Nucleotide structure:

Nitrogenous base

Five-carbon pentose sugar, ribose or dexoyribose

Phosphate group
DNA
DNA composed of two long chains that twisted around each other to form a double helix

Pentose sugar deoxyribose forms backbone of strand; alternates with phosphate group

Bases: adenine, guanine, cytosine, and thymine

DNA exhibits complementary base pairing;

A always pairs with T, and G always pairs with C by hydrogen bonding
RNA
RNA - single strand of nucleotides; can move between nucleus of cell and cytosol; critical to making proteins

RNA contains the pentose sugar ribose

RNA contains uracil instead of thymine; still pairs with adenine, (A = U)

Three types:

mRNA, tRNA, rRNA
ATP
Adenosine triphosphate (ATP)

Adenine attached to ribose and three phosphate groups; main source of energy in body

Synthesized from adenosine diphosphate (ADP) and a phosphate group (Pi) using energy from oxidation of fuels (like glucose)