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Bio 106 Chapter 2
Chapter 2 Vocabulary
143
Biology
Undergraduate 1
05/29/2010

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Term
Biochemistry
Definition

the study of the molecules that compose living organisms

        Carbohydrates

        Fats

        Proteins

        Nucleic acids

Term
Element
Definition
simplest form of matter to have unique chemical properties
Term
• Atomic number
Definition
of an element - number of protons in its nucleus
Term
– 24 elements have biological role
Definition
• 6 elements = 98.5% of body weight
– oxygen, carbon, hydrogen, nitrogen, calcium, and phosphorus
• trace elements in minute amounts
Term
• Minerals--
Definition
--Inorganic elements like Ca, P, Cl, Mg, K, Na, I, Fe, Zn, Cu, and S
– constitute about 4% of body weight
– structure (teeth, bones, etc)
– enzymes
Term
– Electrolytes
Definition
needed for nerve and muscle function are mineral salts
Term
– Atomic Mass
Definition
of an element is equal to its total number of protons and neutrons
Term
Electrons
Definition
clouds that surround the nucleus
Term
– valence electrons
Definition
in the outermost shell
• determine chemical bonding properties of an atom
Term
• Isotopes –
Definition
varieties of an element that differ only in the number of neutrons
– same chemical behavior, differ in physical behavior
– breakdown (decay) to more stable isotope by giving off radiation
Term
– Radioisotopes
Definition
unstable isotopes that give off radiation
Term
– Radioactivity
Definition
radioisotopes decay to stable isotopes releasing radiation
Term
• Ionization
Definition
transfer of electrons from one atom to another
Term
• Electrolytes--
Definition
--Salts that ionize in water and form solutions capable of conducting an electric current
Term
Electrolytes important in
Definition
– chemical reactivity
– osmotic effects (influence water movement)
– electrical effects on nerve and muscle tissue
– Imbalances have ranging effects from muscle cramps, brittle bones, to coma and cardiac arrest
Term
• Molecules
Definition
– chemical particles composed of two or more atoms united in a chemical bond
Term
– Compounds
Definition
– molecules composed of two or more different elements
Term
• Isomers
Definition
molecules with identical molecular formulae but different arrangement of their atoms
Term
• Chemical bonds
Definition
bonds – forces that hold molecules together, or attract one molecule to another
Term
• Ionic Bonds
Definition
• The attraction of a positive ion(cation) to a negative ion.(anion)
• electron donated by one and received by the other
• Relatively weak attraction that is easily disrupted in water, dissolves
Term
• Single Covalent Bond--
Definition
One pair of electrons are shared
Term
– Nonpolar covalent bond
Definition
• shared electrons spend approximately equal time around each nucleus
• strongest of all bonds
Term
– polar covalent bond
Definition
• if shared electrons spend more time orbiting one nucleus than they do the other, they lend their negative charge to the area they spend most time
Term
• Hydrogen bond
Definition
a weak attraction between a slightly positive hydrogen atom in one molecule and a slightly negative oxygen or nitrogen atom in another.
• Water molecules are weakly attracted to each other by hydrogen bonds
Term
• Mixtures
Definition
consists of substances physically blended, but not chemically combined
• body fluids are complex mixtures of chemicals
– each substance maintains its own chemical properties
– Most mixtures in our bodies consist of chemicals dissolved or suspended in water
• Water 50-75% of body weight
– depends on age, sex, fat content, etc.
Term
• Water’s polar covalent bonds and its V-shaped molecule
Definition
gives water a set of properties that account for its ability to support life.
Term
• Solvency
Definition
ability to dissolve other chemicals
• water is called the Universal Solvent
Term
– Hydrophilic
Definition
– substances that dissolve in water
• molecules must be polarized or charged
Term
– Hydrophobic
Definition
substances that do not dissolve in water
• molecules are non-polar or neutral (fat)
• Virtually all metabolic reactions depend on the solvency of water
Term
• Water as a Solvent
Definition
• Polar water molecules overpower the ionic bond in Na+ Cl-
– forming hydration spheres around each ion
– water molecules: negative pole faces Na+, positive pole faces Cl-
Term
• Adhesion
Definition
– tendency of one substance to cling to another
Term
• Cohesion
Definition
tendency of like molecules to cling to each other
– water is very cohesive due to its hydrogen bonds
Term
– surface film
Definition
on surface of water is due to molecules being held together by a force called surface tension
Term
– water ionizes
Definition
into H+ and OH-
– water ionizes other chemicals (acids and salts)
– water involved in hydrolysis and dehydration synthesis reactions
– Thermal Stability of Water
Term
• heat capacity
Definition
the amount of heat required to raise the temperature of 1 g of a substance by 1 degree C.
Term
– calorie (cal)
Definition
the amount of heat that raises the temperature of 1 g of water 1 degree C.
• hydrogen bonds inhibit temperature increases by inhibiting molecular motion
• water absorbs heat without changing temperature very much
Term
– effective coolant
Definition
1 ml of perspiration removes 500 calories
Term
• Solution
Definition
consists of particles of matter called the solute mixed with a more abundant substance (usually water) called the solvent
Term
• Solute
Definition
can be gas, solid or liquid
– solute particles do not scatter light
– will not separate on standing
Term
• Colloids
Definition
• Most common colloids in the body are mixtures of protein and water
• Many can change from liquid to gel state within and between cells
– scatter light and are usually cloudy
– particles remain permanently mixed with the solvent when mixture stands
Term
• Suspension
Definition
– defined by the following physical properties
• cloudy or opaque in appearance
• separates on standing
Term
• Emulsion
Definition
– suspension of one liquid in another
• fat in breast milk
Term
acid
Definition
is proton donor (releases H+ ions in water)
Term
base
Definition
is proton acceptor (accepts H+ ions)
– releases OH- ions in water
Term
– pH
Definition
a measure derived from the molarity of H+
– a pH of 7.0 is neutral pH (H+ = OH-)
– a pH of less than 7 is acidic solution (H+ > OH-)
– a pH of greater than 7 is basic solution (OH- > H+
Term
• pH
Definition
measurement of H+
Term
change of one number
Definition
on the pH scale represents a 10 fold change in H+ concentration
– a solution with pH of 4.0 is 10 times as acidic as one with pH of 5.0
Term
– Our body uses buffers
Definition
to resist changes in pH
– slight pH disturbances can disrupt physiological functions and alter drug actions
– pH of blood ranges from 7.35 to 7.45
– deviations from this range cause tremors, paralysis or even death
– pH Scale
Term
• Energy
Definition
capacity to do work
– to do work means to move something
– all body activities are a form of work
Term
– Potential energy
Definition
energy contained in an object because of its position or internal state
Term
– chemical energy
Definition
potential energy stored in the bonds of molecules
Term
• Kinetic energy
Definition
- energy of motion; energy that is actively doing work
– moving water flowing through a dam
Term
– heat
Definition
kinetic energy of molecular motion
Term
• chemical reaction
Definition
a process in which a covalent or ionic bond is formed or broken
Term
• chemical equation
Definition
symbolizes the course of a chemical reaction
– reactants (on left) ® products (on right)
Term
– classes of chemical reactions
Definition
– decomposition reactions
– synthesis reactions
– exchange reactions
Term
• Decomposition Reactions
Definition
• Large molecule breaks down into two or more smaller ones
• AB ® A + B
Term
• Synthesis Reactions
Definition
• Two or more small molecules combine to form a larger one • A + B ® AB
Term
• Exchange Reactions
Definition
• Two molecules exchange atoms or group of atoms
• AB+CD ® ABCD ® AC + BD
Term
• Reaction Rates
Definition
reactions occur when molecules collide with enough force and the correct orientation
Term
• Reaction Rates affected by:
Definition
– concentration
• reaction rates increase when the reactants are more concentrated
– temperature
• reaction rates increase when the temperature rises
Term
– catalysts
Definition
–substances that temporarily bond to reactants, hold them in favorable position to react with each other, and may change the shapes of reactants in ways that make them more likely to react.
• speed up reactions without permanent change to itself
• holds reactant molecules in correct orientation
• catalyst not permanently consumed or changed by the reaction
Term
• Enzymes
Definition
most important biological catalysts
Term
• Metabolism
Definition
All the chemical reactions of the body
Term
• Oxidation
Definition
– any chemical reaction in which a molecule gives up electrons and releases energy
– molecule oxidized in this process
– electron acceptor molecule is the oxidizing agent
• oxygen is often involved as the electron acceptor
Term
• Reduction
Definition
– any chemical reaction in which a molecule gains electrons and energy
– molecule is reduced when it accepts electrons
– molecule that donates electrons is the reducing agent
Term
oxidation-reduction (redox) reactions
Definition
– oxidation of one molecule is always accompanied by the reduction of another
– Electrons are often transferred as hydrogen atoms
Term
• 4 categories of carbon compounds
Definition
– carbohydrates
– lipids
– proteins
– nucleotides and nucleic acids
Term
4 valence electrons
Definition
– binds with other atoms that can provide it with four more electrons to fill its valence shell
Term
– carbon atoms bind readily with each other – carbon backbones
Definition
– forms long chains, branched molecules and rings
– forms covalent bonds with hydrogen, oxygen, nitrogen, sulfur, and other elements
Term
– carbon backbone
Definition
carries a variety of functional groups
Term
• Functional Groups --
Definition
small clusters of atoms attached to carbon backbone
• determines many of the properties of organic molecules
Term
• Macromolecules
Definition
very large organic molecules
– very high molecular weights
• proteins, DNA
Term
– Polymers
Definition
molecules made of a repetitive series of identical or similar subunits (monomers)
Term
• Monomers
Definition
an identical or similar subunits
Term
• Polymerization--
Definition
joining monomers to form a polymer
Term
• Dehydration Synthesis
Definition
• Monomers covalently bond together to form a polymer with the removal of a water molecule
– A hydroxyl group is removed from one monomer and a hydrogen from the next
Term
• Hydrolysis--Splitting a polymer
Definition
(lysis) by the addition of a water molecule (hydro)
– a covalent bond is broken
– All digestion reactions consists of hydrolysis reactions
Term
• Organic Molecules:
Definition
Carbohydrates
• hydrophilic organic molecule
• general formula
– (CH2O)n n = number of carbon atoms
– for glucose, n = 6, so formula is C6H12O6
– 2:1 ratio of hydrogen to oxygen
Term
• names of carbohydrates often built from
Definition
– word root ‘sacchar-’
– the suffix ’-ose’
– both mean ‘sugar’ or ‘sweet’
• monosaccharide or glucose
– Monosaccharides
Term
• Simplest carbohydrates
Definition
– simple sugars
– 3 important monosaccharides
– glucose, galactose and fructose
– same molecular formula - C6H12O6
• isomers
– produced by digestion of complex carbohydrates
• glucose is blood sugar
• Disaccharides
• Sugar molecule composed of 2 monosaccharides
Term
• 3 important disaccharides
Definition
– sucrose - table sugar
• glucose + fructose
– lactose - sugar in milk
• glucose + galactose
– maltose - grain products
• glucose + glucose
Term
• Polysaccharides
Definition
• long chains of glucose
Term
• 3 polysaccharides of interest in humans
Definition
– Glycogen: energy storage polysaccharide in animals
– Starch: energy storage polysaccharide in plants
• only significant digestible polysaccharide in the human diet
– Cellulose: structural molecule of plant cell walls
• fiber in our diet
• Glycogen
Term
• Carbohydrate Functions
Definition
• quickly mobilized source of energy
– all digested carbohydrates converted to glucose
– oxidized to make ATP
Term
• • hydrophobic organic molecule
Definition
– composed of carbon, hydrogen and oxygen
– with high ratio of hydrogen to oxygen
– Less oxidized than carbohydrates, and thus has more calories/gram
Term
• Five primary types in humans (lipids)
Definition
– fatty acids
– triglycerides
– phospholipids
– eicosanoids
– steroids
Term
– carboxyl (acid) group
Definition
on one end, methyl group on the other and hydrogen bonded along the sides
Term
– saturated
Definition
carbon atoms saturated with hydrogen
Term
– unsaturated
Definition
contains C=C bonds without hydrogen
Term
– polyunsaturated
Definition
many C=C bonds
Term
– essential fatty acids
Definition
– obtained from diet, body can not synthesize
Term
• Triglycerides
Definition
(Neutral Fats)
Term
Oil
Definition
liquid at room temperature• often polyunsaturated fats from plants
Term
Fat
Definition
solid at room temp.
saturated fat came from animals
Term
• Primary Function
Definition
storage, insulation and shock absorption (adipose tissue)
Term
• Phospholipids
Definition
• similar to neutral fat except that one fatty acid replaced by a phosphate group
• structural foundation
of cell membrane
Term
• Amphiphilic
Definition
– fatty acid “tails” are hydrophobic
– phosphate “head” is hydrophilic
Term
• Eicosanoids
Definition
– role in inflammation, blood clotting, hormone action, labor contractions, blood vessel diameter
Term
• Steroid
Definition
a lipid with 17 of its carbon atoms in four rings
Term
• Cholesterol
Definition
the ‘parent’ steroid from which the other steroids are synthesized
– cortisol, progesterone, estrogens, testosterone and bile acids
• Cholesterol
– synthesized only by animals
• especially liver cells
• 15% from diet, 85% internally synthesized
– important component of cell membranes
– required for proper nervous system function
Term
– HDL –
Definition
high-density lipoprotein – “good” cholesterol
– lower ratio of lipid to protein
– may help to prevent cardiovascular disease
Term
– LDL
Definition
low-density lipoprotein – “bad” cholesterol
– high ratio of lipid to protein
– contributes to cardiovascular disease
Term
• Organic Molecules: Proteins
Definition
• Representative Amino Acids
• Note: they differ only in the R group
Term
• peptide
Definition
– any molecule composed of two or more amino acids joined by peptide bonds
Term
• peptide bond
Definition
joins the amino group of one amino acid to the carboxyl group of the next
– formed by dehydration synthesis
– Dipeptide Synthesis
Term
• (protein) Primary structure
Definition
– protein’s sequence amino acid which is encoded in the genes
Term
(Protein)• Secondary structure
Definition
– coiled or folded shape held together by hydrogen bonds
– hydrogen bonds between slightly negative C=O and slightly positive N-H groups
– most common secondary structure are:
• alpha helix – springlike shape
• beta helix – pleated, ribbonlike shape
Term
• Tertiary structure
Definition
– further bending and folding of proteins into globular and fibrous shapes
Term
• globular proteins
Definition
compact tertiary structure well suited for proteins embedded in cell membrane and proteins that must move about freely in body fluid
Term
• fibrous proteins
Definition
slender filaments better suited for roles as in muscle contraction and strengthening the skin
Term
• Quaternary structure
Definition
– associations of two or more separate polypeptide chains
– functional conformation – three dimensional shape
Term
• Conformation
Definition
unique three dimensional shape of protein crucial to function
– ability to reversibly change their conformation
• enzyme function
• muscle contraction
• opening and closing of cell membrane pores
Term
• Denaturation
Definition
– extreme conformational change that destroys function
• extreme heat or pH
• Primary Structure of Insulin
Term
– keratin
Definition
tough structural protein
• gives strength to hair, nails, and skin surface
Term
– collagen
Definition
durable protein contained in deeper layers of skin, bones, cartilage, and teeth
Term
– Communication
Definition
– some hormones and other cell-to-cell signals
– receptors to which signal molecules bind
Term
• ligand
Definition
any hormone or molecule that reversibly binds to a protein
Term
• Membrane Transport
Definition
– channels in cell membranes that governs what passes through
– carrier proteins – transports solute particles to other side of membrane
– turn nerve and muscle activity on and off
Term
• Catalysis
Definition
– enzymes
Term
– Recognition and Protection
Definition
– immune recognition
– antibodies
– clotting proteins
Term
– – motor proteins
Definition
molecules with the ability to change shape repeatedly
Term
– Cell adhesion
Definition
– proteins bind cells together
– immune cells to bind to cancer cells
– keeps tissues from falling apart
Term
• Enzymes
Definition
proteins that function as biological catalysts
– permit reactions to occur rapidly at normal body temperature
– Substrate - substance an enzyme acts upon
Term
• Naming Convention
Definition
– named for substrate with -ase as the suffix
• amylase enzyme digests starch (amylose)
Term
• Lowers activation energy
Definition
energy needed to get reaction started
– enzymes facilitate molecular interaction
Term
• Substrate binds to active site forming enzyme-substrate complex
Definition
– highly specific fit –’lock and key’
Term
– Astonishing speed
Definition
one enzyme molecule can consume millions of substrate molecules per minute
Term
– Factors that change enzyme shape
Definition
– pH and temperature
– alters or destroys the ability of the enzyme to bind to substrate
– enzymes vary in optimum pH
• salivary amylase works best at pH 7.0
• pepsin works best at pH 2.0
– temperature optimum for human enzymes – body temperature (37 degrees C)
Term
• Cofactors
Definition
inorganic partners (iron, copper, zinc, magnesium and calcium ions)
– some bind to enzyme and induces a change in its shape, which activates the active site
Term
– Coenzymes
Definition
– organic cofactors derived from water-soluble vitamins (niacin, riboflavin)
– they accept electrons from an enzyme in one metabolic pathway and transfer them to an enzyme in another
Term
– nitrogenous base
Definition
single or double carbon-nitrogen ring)
Term
– sugar
Definition
monosaccharide)
Term
– ATP
Definition
best know nucleotide
Term
– adenine
Definition
nitrogenous base
Term
– ribose
Definition
sugar
Term
• Adenosine Triphosphate (ATP)
Definition
• body’s most important energy-transfer molecule
• briefly stores energy gained from exergonic reactions
• holds energy in covalent bonds
– 2nd and 3rd phosphate groups have high energy bonds ~
– most energy transfers to and from ATP involve adding or removing the 3rd phosphate
Term
– Adenosine triphosphatases (ATPases)
Definition
hydrolyze the 3rd high energy phosphate bond
– separates into ADP + Pi + energy
– Phosphorylation
– addition of free phosphate group to another molecule
– carried out by enzymes called kinases (phosphokinases)
• Sources and Uses of ATP
Term
• Overview of ATP Production
Definition
• ATP consumed within 60 seconds of formation
• entire amount of ATP in the body would support live for less
than 1 minute if it were not continually replenished
• cyanide halts ATP synthesis
Term
• Guanosine triphosphate (GTP)
Definition
– involved in energy transfer
– donates phosphate group to other molecules
Term
– Cyclic adenosine monophosphate (cAMP)
Definition
– cAMP becomes “second messenger” within cell
– activates metabolic effects inside cell
Term
• DNA (deoxyribonucleic acid)
Definition
• – constitutes genes instructions for synthesizing all of the body’s proteins
• transfers hereditary information from cell to cell and generation to generation
Term
• RNA (ribonucleic acid) – 3 types
Definition
– messenger RNA, ribosomal RNA, transfer RNA
– carries out genetic instruction for synthesizing proteins
– assembles amino acids in the right order to produce proteins
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