Download Matter—anything that has mass and occupies space Weight—pull of

Matter—anything that has mass and occupies space
Weight—pull of gravity on mass
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3 states of matter
Solid—definite shape and volume
Liquid—changeable shape; definite volume
Gas—changeable shape and volume
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Capacity to do work or put matter into motion
Types of energy
Kinetic—energy in action
Potential—stored (inactive) energy
Energy can be transferred from potential to kinetic energy
Capacity to do work or put matter into motion
Types of energy
Kinetic—energy in action
Potential—stored (inactive) energy
Energy can be transferred from potential to kinetic energy
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Chemical energy
Stored in bonds of chemical substances
Electrical energy
Results from movement of charged particles
Mechanical energy
Directly involved in moving matter
Radiant or electromagnetic energy
Travels in waves (e.g., visible light, ultraviolet light, and x-rays)
Energy may be converted from one form to another
Energy conversion is inefficient
Some energy is “lost” as heat (partly unusable energy)
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Elements
Matter is composed of elements
Elements cannot be broken into simpler substances by ordinary
chemical methods
Each has unique properties
Physical properties
Detectable with our senses, or are measurable
Chemical properties
How atoms interact (bond) with one another
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Atoms
Unique building blocks for each element
Give each element its physical & chemical properties
Smallest particles of an element with properties of that element
Atomic symbol
One- or two-letter chemical shorthand for each element
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Four elements make up 96.1% of body mass
Element
Carbon
Hydrogen
Oxygen
Nitrogen
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9 elements make up 3.9% of body mass
Element
Calcium
Phosphorus
Potassium
Sulfur
Sodium
Chlorine
Magnesium
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Iodine
Iron
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Very minute amounts
11 elements make up < 0.01% of
body mass
Many are part of, or activate,
enzymes
Chromium
Copper
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Fluorine
Manganese
Silicon
Zinc
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Atoms are composed of subatomic particles
Protons, neutrons, electrons
Protons and neutrons found in nucleus
Electrons orbit nucleus in an electron cloud
Nucleus almost entire mass of the atom
Neutrons
Carry no charge
Mass = 1 atomic mass unit (amu)
Protons
Carry positive charge
Mass = 1 amu
Electrons in orbitals within electron cloud
Carry negative charge
1/2000 the mass of a proton (0 amu)
Number of protons and electrons always equal
Planetary model—simplified; outdated
Incorrectly depicts fixed circular electron paths
But useful for illustrations (as in the text)
Orbital model—current model used by chemists
Probable regions of greatest electron density (an electron cloud)
Useful for predicting chemical behavior of atoms
Different elements contain different numbers of subatomic particles
Hydrogen has 1 proton, 0 neutrons, and 1 electron
Lithium has 3 protons, 4 neutrons, and 3 electrons
Atomic number = Number of protons in nucleus
Written as subscript to left of atomic symbol
Ex. 3Li
Mass number
Total number of protons and neutrons in nucleus
Total mass of atom
Written as superscript to left of atomic symbol
Ex. 7Li
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Isotopes
Structural variations of atoms
Differ in the number of neutrons they contain
Atomic numbers same; mass numbers different
Atomic weight
Average of mass numbers (relative weights) of all isotopes of an atom
Atomic number, mass number, atomic weight
Give “picture” of each element
Allow identification
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Heavy isotopes decompose to more stable forms
Spontaneous decay called radioactivity
Similar to tiny explosion
Can transform to different element
Can be detected with scanners
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Valuable tools for biological research and medicine
Share same chemistry as their stable isotopes
Most used for diagnosis
All damage living tissue
Some used to destroy localized cancers
Radon from uranium decay causes lung cancer
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A molecule is formed when two or more atoms join together chemically.
A compound is a molecule that contains at least two different elements.
All compounds are molecules but not all molecules are compounds.
Textbook:
Most atoms chemically combined with other atoms to form molecules and
compounds
Molecule
Two or more atoms bonded together (e.g., H2 or C6H12O6)
Smallest particle of a compound with specific characteristics of
the compound
Compound
Two or more different kinds of atoms bonded together (e.g.,
C6H12O6 , but not H2)
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Most matter exists as mixtures
Two or more components physically intermixed
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Three types of mixtures
Solutions
Colloids
Suspensions
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Homogeneous mixtures
Most are true solutions in body
Gases, liquids, or solids dissolved in
water
Usually transparent, e.g.,
atmospheric air or saline solution
Solvent
Substance present in greatest
amount
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Usually a liquid; usually water
Solute(s)
Present in smaller amounts
Ex. If glucose is dissolved in blood,
glucose is solute; blood is solvent
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Can be expressed as
Percent of solute in total solution (assumed to be water)
Parts solute per 100 parts solvent
Milligrams per deciliter (mg/dl)
Molarity, or moles per liter (M)
1 mole of an element or compound = Its atomic or molecular
weight (sum of atomic weights) in grams
1 mole of any substance contains 6.02  1023 molecules of that
substance (Avogadro’s number)
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Colloids (AKA emulsions)
Heterogeneous mixtures, e.g., cytosol
Large solute particles do not settle out
Some undergo sol-gel transformations
e.g., cytosol during cell division
Suspensions
Heterogeneous mixtures, e.g., blood
Large, visible solutes settle out
Mixtures
No chemical bonding between components
Can be separated by physical means, such as straining or filtering
Heterogeneous or homogeneous
Compounds
Chemical bonding between components
Can be separated only by breaking bonds
All are homogeneous
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Chemical bonds are energy
relationships between electrons
of reacting atoms
Electrons can occupy up to seven
electron shells (energy levels)
around nucleus
Electrons in valence shell
(outermost electron shell)
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Have most potential energy
Are chemically reactive electrons
Octet rule (rule of eights)
Except for the first shell (full with two
electrons) atoms interact to have eight
electrons in their valence shell
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Stable and unreactive
Valence shell fully occupied or contains eight electrons
Noble gases
Valence shell not full
Tend to gain, lose, or share electrons (form bonds) with other atoms to
achieve stability
Three major types
Ionic bonds
Covalent bonds
Hydrogen bonds
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Ions
Atom gains or loses electrons and
becomes charged
# Protons ≠ # Electrons
Transfer of valence shell
electrons from one atom to
another forms ions
One becomes an anion (negative
charge)
Atom that gained one or more electrons
One becomes a cation (positive
charge)
Atom that lost one or more electrons
Attraction of opposite charges
results in an ionic bond
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Most ionic compounds are salts
When dry salts form crystals instead of individual molecules
Example is NaCl (sodium chloride)
Formed by sharing of two or more valence shell electrons
Allows each atom to fill its valence shell at least part of the time
Nonpolar Covalent Bonds
Electrons shared equally
Produces electrically balanced, nonpolar molecules such as CO2
Polar Covalent Bonds
Unequal sharing of electrons produces polar (AKA dipole) molecules such as
H2O
Atoms in bond have different electron-attracting abilities
Small atoms with six or seven valence shell electrons are electronegative,
e.g., oxygen
Strong electron-attracting ability
Most atoms with one or two valence shell electrons are electropositive,
e.g., sodium
Attractive force between electropositive hydrogen of one molecule and an
electronegative atom of another molecule
Not true bond
Common between dipoles such as water
Also act as intramolecular bonds, holding a large molecule in a threedimensional shape
Chemical Reactions
Occur when chemical bonds are
formed, rearranged, or broken
Represented as chemical
equations using molecular
formulas
Subscript indicates atoms joined by
bonds
Prefix denotes number of unjoined
atoms or molecules
Chemical equations contain
Reactants
Number and kind of reacting substances
Chemical composition of the
product(s)
Relative proportion of each reactant
and product in balanced equations
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Synthesis (combination) reactions
Decomposition reactions
Exchange reactions
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A + B  AB
Atoms or molecules combine to form larger, more complex molecule
Always involve bond formation
Anabolic
AB  A + B
Molecule is broken down into smaller molecules or its constituent
atoms
Reverse of synthesis reactions
Involve breaking of bonds
Catabolic
AB + C  AC + B
Also called displacement reactions
Involve both synthesis and decomposition
Bonds are both made and broken
Are decomposition reactions
Reactions in which food fuels are
broken down for energy
Are also exchange reactions
because electrons are exchanged
between reactants
Electron donors lose electrons and
are oxidized
Electron acceptors receive
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electrons and become reduced
C6H12O6 + 6O2  6CO2 + 6H2O + ATP
Glucose is oxidized; oxygen
molecule is reduced
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All chemical reactions are either exergonic or endergonic
Exergonic reactions—net release of energy
Products have less potential energy than reactants
Catabolic and oxidative reactions
Endergonic reactions—net absorption of energy
Products have more potential energy than reactants
Anabolic reactions
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All chemical reactions are theoretically reversible
A + B  AB
AB  A + B
Chemical equilibrium occurs if neither a forward nor reverse reaction is
dominant
Many biological reactions are essentially irreversible
Due to energy requirements
Due to removal of products
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Affected by
 Temperature   Rate
 Concentration of reactant   Rate
 Particle size   Rate
Catalysts:  Rate without being chemically changed or part of product
Enzymes are biological catalysts
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Study of chemical composition and reactions of living matter
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All chemicals either organic or inorganic
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Inorganic compounds
•Water, salts, and many
acids and bases
•Do not contain carbon
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Organic compounds
•Carbohydrates, fats,
proteins, and nucleic acids
•Contain carbon, usually
large, and are covalently
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bonded
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Both equally essential for life
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Most abundant inorganic compound
–
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60%–80% volume of living cells
Most important inorganic compound
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Due to water’s properties
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High heat capacity
–
Absorbs and releases heat with little temperature change
–
Prevents sudden changes in temperature
High heat of vaporization
–
Evaporation requires large amounts of heat
–
Useful cooling mechanism
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Polar solvent properties
–
Dissolves and dissociates ionic substances
–
Forms hydration layers around large charged molecules, e.g.,
proteins (colloid formation)
–
Body’s major transport medium
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Reactivity
–
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Necessary part of hydrolysis and dehydration synthesis reactions
Cushioning
–
Protects certain organs from physical trauma, e.g., cerebrospinal
fluid
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• Both are electrolytes
– Ionize and dissociate in water
• Acids are proton donors
– Release H+ (a bare proton) in
solution
– HCl  H+ + Cl–
• Bases are proton acceptors
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– Take up H+ from solution
•NaOH  Na+ + OH–
–OH– accepts an available proton (H+)
–OH– + H+  H2O
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• Ionic compounds that
dissociate into ions in water
– Ions (electrolytes) conduct
electrical currents in solution
– Ions play specialized roles in
body functions (e.g., sodium,
potassium, calcium, and iron)
– Ionic balance vital for
homeostasis
• Contain cations other than H+
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and anions other than OH–
• Common salts in body
– NaCl, CaCO3, KCl, calcium
phosphates
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pH = negative logarithm of [H+] in moles per liter
•
pH scale ranges from 0–14
•
Because pH scale is logarithmic
–
–
A pH 5 solution is 10 times more acidic than a pH 6 solution
Relative free [H+] of a solution measured on pH scale
–
As free [H+] increases, acidity increases
•[OH–] decreases as [H+] increases
•pH decreases
–
As free [H+] decreases alkalinity increases
•[OH–] increases as [H+] decreases
•pH increases
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• Acidic solutions
 [H+],  pH
– Acidic pH: 0–6.99
• Neutral solutions
– Equal numbers of H+ and OH–
– All neutral solutions are pH 7
– Pure water is pH neutral
•pH of pure water = pH 7: [H+] = 10–7 m
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• Alkaline (basic) solutions
 [H+],  pH
– Alkaline pH: 7.01–14
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Results from mixing acids and bases
–
Displacement reactions occur forming water and a salt
–
Neutralization reaction
•Joining of H+ and OH– to form water neutralizes solution
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Acid-base Homeostasis
•
pH change interferes with cell function and may damage living tissue
•
Even slight change in pH can be fatal
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pH is regulated by kidneys, lungs, and chemical buffers
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• Acidity reflects only free H+ in solution
– Not those bound to anions
• Buffers resist abrupt and large swings in pH
– Release hydrogen ions if pH rises
– Bind hydrogen ions if pH falls
• Convert strong (completely dissociated) acids
• Carbonic acid-bicarbonate system (important
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Molecules that contain carbon
–
Except CO2 and CO, which are considered inorganic
–
Carbon is electroneutral
•Shares electrons; never gains or loses them
•Forms four covalent bonds with other elements
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Unique to living systems
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Carbohydrates, lipids, proteins, and nucleic acids
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Many are polymers
–
Chains of similar units called monomers (building blocks)
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Synthesized by dehydration synthesis
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Broken down by hydrolysis reactions
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Sugars and starches
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Polymers
•
Contain C, H, and O [(CH20)n]
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Three classes
•
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Monosaccharides – one sugar
–
Disaccharides – two sugars
–
Polysaccharides – many sugars
Functions of carbohydrates
–
Major source of cellular fuel (e.g., glucose)
–
Structural molecules (e.g., ribose sugar in RNA)
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Simple sugars containing three to seven C atoms
(CH20)n – general formula; n = # C atoms
Monomers of carbohydrates
Important monosaccharides
– Pentose sugars
•Ribose and deoxyribose
– Hexose sugars
•Glucose (blood sugar)
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Double sugars
•
Too large to pass through cell membranes
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Important disaccharides
–
Sucrose, maltose, lactose
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Polymers of monosaccharides
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Important polysaccharides
–
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Starch and glycogen
Not very soluble
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Contain C, H, O (less than in carbohydrates), and sometimes P
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Insoluble in water
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Main types:
–
Triglycerides or neutral fats
–
Phospholipids
–
Steroids
–
Eicosanoids
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Called fats when solid and oils when liquid
•
Composed of three fatty acids bonded to a glycerol molecule
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Main functions
–
Energy storage
–
Insulation
–
Protection
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• Saturated fatty acids
– Single covalent bonds between C
atoms
•Maximum number of H atoms
– Solid animal fats, e.g., butter
• Unsaturated fatty acids
– One or more double bonds
between C atoms
•Reduced number of H atoms
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– Plant oils, e.g., olive oil
– “Heart healthy”
• Trans fats – modified oils –
unhealthy
• Omega-3 fatty acids – “heart
healthy”
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Modified triglycerides:
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Glycerol + two fatty acids and a phosphorus (P) - containing group
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“Head” and “tail” regions have different properties
•
Important in cell membrane structure
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Steroids—interlocking four-ring structure
•
Cholesterol, vitamin D, steroid hormones, and bile salts
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Most important steroid
–
Cholesterol
•Important in cell membranes, vitamin D synthesis, steroid hormones, and bile s
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Many different ones
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Derived from a fatty acid (arachidonic acid) in cell membranes
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Most important eicosanoid
–
Prostaglandins
•Role in blood clotting, control of blood pressure,
inflammation, and labor contractions
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Other fat-soluble vitamins
–
•
Vitamins A, D, E, and K
Lipoproteins
–
Transport fats in the blood
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• Contain C, H, O, N, and sometimes S an
• Proteins are polymers
• Amino acids (20 types) are the monom
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–
–
–
Joined by covalent bonds called peptide b
Contain amine group and acid group
Can act as either acid or base
All identical except for “R group” (in green
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Fibrous (structural) proteins
–
Strandlike, water-insoluble, and stable
–
Most have tertiary or quaternary structure (3-D)
–
Provide mechanical support and tensile strength
–
Examples: keratin, elastin, collagen (single most abundant protein
in body), and certain contractile fibers
Globular (functional) proteins
–
Compact, spherical, water-soluble and sensitive to environmental
changes
–
Tertiary or quaternary structure (3-D)
–
Specific functional regions (active sites)
–
Examples: antibodies, hormones, molecular chaperones, and
enzymes
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Quaternary multiple separate polypeptides
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Denaturation
–
Globular proteins unfold and lose functional, 3-D shape
•Active sites destroyed
–
Can be cause by decreased pH or increased temperature
•
Usually reversible if normal conditions restored
•
Irreversible if changes extreme
–
e.g., cooking an egg
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Globular proteins
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Ensure quick, accurate folding and association of other proteins
•
Prevent incorrect folding
•
Assist translocation of proteins and ions across membranes
•
Promote breakdown of damaged or denatured proteins
•
Help trigger the immune response
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Stress proteins
–
Molecular chaperones produced in response to stressful stimuli,
e.g., O2 deprivation
–
Important to cell function during stress
–
Can delay aging by patching up damaged proteins and refolding
them
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Enzymes
–
Globular proteins that act as biological catalysts
•Regulate and increase speed of chemical reactions
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Lower the activation energy, increase the speed of a reaction (millions of reactions per minute!
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Some functional enzymes (holoenzymes) consist of two parts
– Apoenzyme (protein portion)
– Cofactor (metal ion) or coenzyme (organic molecule often a
vitamin)
Enzymes are specific
– Act on specific substrate
Usually end in -ase
Often named for the reaction they catalyze
–
Hydrolases, oxidases
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Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)
–
Largest molecules in the body
•
Contain C, O, H, N, and P
•
Polymers
–
Monomer = nucleotide
•Composed of nitrogen base, a pentose sugar, and a phosphate
group
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• Utilizes four nitrogen bases:
– Purines: Adenine (A), Guanine (G)
– Pyrimidines: Cytosine (C), and Thymine (T
– Base-pair rule – each base pairs with its co
•A always pairs with T; G always pairs with C
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Double-stranded helical molecule (dou
Pentose sugar is deoxyribose
Provides instructions for protein synthe
Replicates before cell division ensuring
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Four bases:
– Adenine (A), Guanine (G), Cytosine (C), and Uracil (U)
Pentose sugar is ribose
Single-stranded molecule mostly active outside the nucleus
Three varieties of RNA carry out the DNA orders for protein synthesis
– Messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA
(rRNA)
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Chemical energy in glucose captured in this important molecule
•
Directly powers chemical reactions in cells
•
Energy form immediately useable by all body cells
•
Structure of ATP
–
Adenine-containing RNA nucleotide with two additional phosphate groups
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Phosphorylation
–
Terminal phosphates are enzymatically transferred to and energize other molecules
–
Such “primed” molecules perform cellular work (life processes) using the phosphat
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