Transcript Unit I

Chapter 2
The Chemical Level of
Organization
Atom & element defined

________= smallest unit of matter
– ____________:
• Protons- positively charged particles
• Neutrons- uncharged particles
– ____________:
• Electrons- tiny, negatively charged particles
• Electron shells- regions e- are likely to move about

________ = substance that cannot be split
into a simpler substance by ordinary chemical
means
Main chemical elements in body

Table 2.1
 96% of body’s mass:
–
–
–
–

____________
____________
____________
____________
3.8%: Calcium, Phosphorus, Potassium,
Sulfur, Sodium, Chlorine, Magnesium, Iron
 0.2%: 14 trace elements
Some trace elements important
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Aluminum
Boron
Chromium
Cobalt
Copper
Fluorine
Iodine
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Manganese
Molybdenum
Selenium
Silicon
Tin
Vanadium
Zinc
Atoms of each element…

Can lose, gain or share electrons with
other atoms
– To achieve stability- wants 8 outer shell e– Form ions or molecules
• _____________ - gain or lose e• _____________ - share e– Polar
– Nonpolar
• ______________ not strong enough to create a
molecule but contributes to structure
Ions
______ = atom having + or – charge
because of unequal # of protons & e ______________= process of giving up
or gaining electrons

– Ex.) Ca 2+ = calcium ion has 2 positive
charges due to losing 2 electrons
– Consult periodic table of elements
Molecules and compounds

____________ -- 2 or more atoms sharing
electrons
– 2 atoms of the same kind: O2 , O3
– OR, 2 or more different kinds: H2O , CH4

____________ -- atoms of 2 or more different
elements
– H2O, NaCl

All compounds are molecules, not all
molecules are compounds
Free radicals

Electrically charged atom or group of atoms
w/ unpaired e _____________ make it unstable, highly
reactive, & destructive to nearby molecules
– gives up e- or takes another e- from another
molecule
• May break apart other molecule
– Consuming ____________ may slow the damage
of free radicals
• Oxidation is removal of electrons
Chemical bonds

Determined by e- in outermost shell
– Octet=8 e- in outer shell= _____________
– When chemically stable, atom unlikely to
form chemical bond

Most biologically important atoms DO
NOT have a full outer shell
Types of chemical bonds

____________ - force of attraction holding
ions of opposite charge together
– Cations & anions

____________ - 2 atoms sharing electrons
– Single, double, triple
– Nonpolar- equal sharing, polar- non-equal sharing

______________ - polar, covalent bonds,
form between hydrogen atoms & other atoms
– Weak
– Partial positive, partial negative
Importance of Ionic bonds
Ionic cmpds usually exist as ______,
with orderly repeating arrangement
 Can be _____________

– NaCl
Mainly in teeth & bones for _________
 Other ions dissolved in body fluids

– ____________

Table 2.2= most common ions in body
Importance of covalent bonds
Most common chemical bonds in body
 __________________- one atom will
attract e- more strongly = greater
electronegativity

– VERY important in living systems
– __________ is polar covalent, allowing
many important molecules to dissolve
Non-polar covalent - equal sharing
Importance of hydrogen bonds

Establish links between:
– ______________
• H and O in water
– Occur in different parts of a large molecule
• Protein or nucleic acid
– Neighboring water molecules = ___________
• Creates high surface tension – measure of difficulty of
stretching or breaking surface of liquid

Weak but provide considerable strength &
___________
– hundreds in one molecule
Water - polar covalent bond
Hydrogen bonds between five water
molecules
Potential vs. Kinetic Energy
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Chemical reactions involve energy changes
____________ - capacity to do work
____________ energy – energy stored by
matter due to its position
– Water behind dam
– person poised to jump down

___________ energy – energy associated
with matter in motion
– Gates of dam open
– person jumps
Figure 2.9

_____________ (AE)- collision energy
to ________ chemical bonds in
reactants
– Initial energy needed to start rxn
•
•
•
•
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Reactants absorb energy
become unstable
make valence e- form new combinations
new bonds form, energy RELEASED
___________- speeds up rxn by  AE
– Itself remains unchanged
– Many in body are enzymes
Activation energy
Activation energy with & without a
catalyst
Water is SO important!
Most abundant __________ cmpd in all
living systems
 Nearly all bodily chemical rxns occur in
____________ environment
 _________ makes water an excellent
solvent for ionic or polar substances

– Cohesion
– Minimize temp changes
Water as solvent

Most versatile but not universal
– Solutes containing polar covalent bonds: _______
• Salt, sugar
– Solutes containing non-polar covalent bonds:
___________
• Animal fats, vegetable oils

NaCl dissolves in water- figure 2.11
 ___________ for metabolic rxns
– dissolved reactants collide & form products
– dissolves wastes & flush out in urine
Water in chemical reactions

Serves as reactant or product
– _____________= breakdown water
• during digestion enables dietary nutrients to be
absorbed– break down large nutrients into
smaller molecules
– _________________ = water molecule is
formed & removed from rxn as other
molecules join
• Protein synthesis
Water as a lubricant

Major ingredient of mucus & other lubricants
 Lubricants important in chest & abdomen
– Internal organs need to slide over one another

In joints
– to prevent bones, ligaments, & tendons rubbing

GI tract
– Moisten food and aid in passage
Dissociation is…
fig 2.12

Separation into ions
 _______= dissociates into one or more H+
ions & one or more anions
– H+ is a single proton, acid = proton donor

_______= dissociates into one or more OHions & one or more cations
– OH- strong attraction for proton, proton acceptor

_______= dissolved in water dissociates into
cations & anions NEITHER being H+ or OH– Are electrolytes
Acid, base, and salt
pH scale
figure 2.13
Expression of solution’s __________ or
___________
 Scale from 0 to 14

– Based on concentration of H+ in moles/L
– pH 7: solution contains one ten-millionth
(0.0000001=1x 10-7)of a mole of H+ /liter
•
•
•
•
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Midpoint of scale
equal amount of H+ & OHNeutral
Pure water
More H+ is acidic, more OH- is basic
pH scale
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pH 0 is most acidic possible
– pH 0 = 10 0 mol/L H+
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pH 14 is most basic or alkaline
– pH 14 = 10 -14 mol/L H+
– 10 -14 means 0.00000000000001 mol/L H+
Table 2.4 selected substances pH
pH of body fluids differ
 Normal limits are narrow
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– blood pH 7.35-7.45
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__________- function to convert
strong acids or bases to weak acids
or bases
– For blood: <7.35 is acidosis
– >7.45 is alkalosis
Strong & weak acids and bases
_______ acids- ionize easily, contribute
many H+ to a solution
 What is a strong base?
 _______ acids- do not ionize as much,
contribute few H+

– So, a weak base is?
Organic & inorganic acids and bases

_____________- convert strong acids
or bases into weak acids or bases
– Carbonic acid-bicarbonate buffer
– Phosphate buffer system
– Protein buffer system
Organic
vs.

Always contain
carbon, usually
hydrogen.
 Always have
covalent bonds.
 2 inorganic cmpds
that contain carbon:
– CO2 and bicarbonate
ion HCO3-
Inorganic
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Lack carbon
 Structurally simple
 Ex.) water, salts,
acids, bases
 Ionic or covalent
bonds
Major bio-organic cmpd groups
Carbohydrates
 Lipids
 Proteins
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– Enzymes
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Nucleic acids
– DNA, RNA
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ATP
Carbohydrates
table 2.6
Sugars, starches, glycogen & cellulose
 2-3% of body mass
 Carbon: hydrogen: oxygen (1:2:1)
 Characterized by size

– _____saccharide- monomer of carb, 3-6 C
– ___saccharide- 2 monosac bound together
– _____saccharide- 10s or 100s of monosac
bound by dehydration synthesis
Carbs (2)
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Source of chemical energy- generate ATP
Few for structural building units
– Deoxyribose in DNA
– Ribose in RNA
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Polysaccharides- not sweet, usually not water
soluble
– Main in humans: ____________= long chains of
glucose, stored in liver
– _________ = polymer of glucose -by plants
– Most poly- & di- can be broken down to mono- by
hydrolysis
– ____________ = build cell walls, non-digestible by
humans
Lipids (fats)
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table 2.7
18-25% of body mass in lean adults
Carbon, hydrogen, oxygen
most insoluble in water  hydrophobic
To be more soluble in blood combine with
protein  ____________ (HDL, LDL, VLDL)
Triglycerides, steroids, eicosanoids, fatty
acids, fat soluble vitamins (A,D,E,& K), and
lipoproteins
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__________- most plentiful lipid in body
– RT: solid or liquid
– Body’s most [highly] form of energy
• 2x energy/gram as carb or protein
– Body has unlimited capacity to store
Excess dietary carbs, proteins, fats, &
oils all have same fate
 2 building blocks of triglycerides:
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– 1 glycerol- backbone
– 3 fatty acids- bound by dehydration syn.
Saturation
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___________ fats- only single covalent
bonds between C in f. a. chain.
– Saturated w/ hydrogen
– Usually solid at RT
– Animal fat, cocoa butter, palm & coconut oil
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Monounsaturated fats- f. a. w/ only one
double covalent bond between 2 C
– Olive oil, peanut oil
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Polyunsaturated fats- more than one double
covalent bond between C of f.a.
– Canola, corn, safflower, sunflower, & soybean oils
Phospholipids
fig 2.18
Glycerol backbone, 2 f.a. chains, PO4 3 Phosphate group = _____________
 ___________ = f.a. chains
 Amphipathic molecule is ____________
 In cell membranes, tails line up to form
a phospholipid bilayer
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Steroids
fig 2.19
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4 rings of C atoms
 Synthesized by body cells from cholesterol
 Common in body: cholesterol, estrogens,
testosterone, cortisol, bile salts, & vitamin D
are all classified as sterols because have at
least one alcohol group
– Weakly amphipathic
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______________ needed for cell membrane

__________- esters of long chain
saturated and unsaturated f.a. w/
long chain alcohols
– Water repellent properties
– firm consistency
– certain skin glands secrete to protect
hair & skin
Nucleic Acids
fig 2.24
1st discovered in nuclei of cells
 Huge organic molec: C,H,O,N,and P

– Deoxyribonucleic acid = ______- inherited genetic
material inside cell
• determine traits & control protein synthesis
• ___________= one segment of DNA
• DNA stays in the nucleus
– Ribonucleic acid = ______- relays instruction from
genes to guide synthesis of protein from amino
acids
• Communicates between nucleus and ribosome
Nucleic Acids figure 2.24

Consists of:
1. _______________:
• purines= A,G – larger, double ring
• pyrimidines = C,T – smaller, single ring
In RNA have U instead of T
2. _______________
• DNA=deoxyribose
• RNA=ribose
3. _______________
ATP= Adenosine Triphosphate

Energy currency
 Transfers energy liberated catabolism to
cellular activities that require energy
– muscle contraction, movement of chromosomes,
movement of cell structures, transport across cell
membrane & synthesis of larger molecules

3 phosphates, adenine, & ribose
 Removal of 3rd P group & addition of water
results in energy liberation, ATP  ADP
Proteins
Large molecule
 Monomers are ___________
 contain C,H,O,N, some S
 12-18% body mass
 Much more _______ than carbs or lipids
 4 levels of structural organization
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Proteins
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Have many roles, largely responsible for
structure of body tissue
– ____________ speed up chemical rxns
– Motors to drive muscle contraction
– ____________ defend against invaders
– ____________ regulate homeostasis
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See table 2.8 for more details
Proteins
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fig 2.20-22
_____ amino acids, each has 3 groups
• Amino group (-NH2)
• Carboxyl group (-COOH)
• Side chain(-R), distinctive, gives each identity
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Synthesis of protein = stepwise
process, a.a. linked by ____________:
– Between C of carboxyl group on one a.a.
to N of amino group on another a.a
Polypeptide = 10-2000 a.a.
 small protein = 50 a.a.
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Peptide bond
Levels of organization of protein
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_______ structure- unique sequence of a.a.
– Genetically determined
– Figure 2.22 (a)

_________ structure- repeated twisting or
folding of neighboring a.a.
– Figure 2.22 (b)
– stabilized by H bonds at regular intervals
• Alpha helix= clockwise spiral
• pleated sheet

_________ structure- 3-D shape of
polypeptide chain
– Figure 2.22 (c)
– each protein has unique 3D - determines function
• Disulfide bridges- S-S bonds, strong but less common

___________ structure- arrangement of
individual polypeptides chains relative to one
another
– Bonds are similar to those that create tertiary struc
– Figure 2.22 (d)
When proteins break down

_____________ - process in which a
protein encounters an altered
environment, it may unravel, and lose
its characteristic shape
– No longer functional protein
• frying an egg
Enzymes

Most _________ are protein molecules called
___________
– Some are 2 parts: apoenzyme (a protein portion)
and cofactor (nonprotein portion- can be a metal
ion, or a coenzyme- organic molec, often derived
from vitamins)
Names usually end in –ase
 Grouped according to type: oxidase- adds O,
kinase adds P, phosphatase removes P
 Catalyze __________ reactions

Enzymes are:

1. ________________
– Each particular enzyme binds only to
specific substrates for specific rxn
– >1000 known, each has specific 3D shape

2. ________________
– Rxn goes 100 million to 10 billion x faster

3. Subject to variety of _____________
– Rate of synthesis & concentration
controlled by genes
Enzymes are specific to:
__________________
 Optimum ________

– Salivary amylase works at neutral pH
– Most peptidases work in stomach at pH 2

Optimum ___________
– Body temperature = 37 °C
E + S  ES complex P + E

____________: surface of enzyme that binds
substrate
 Lock and key /induced fit: Δ in conformation
of enzyme in response to substrate binding
rendering it catalytically active
 ____________: a small molecule that binds
to a larger one
 Allosteric regulation: catalytic activity is
modulated by non-covalent bonding of a
specific molec to site different from active site