BIOCHEMISTRY

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BIOCHEMISTRY
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Macromolecules

• Building Blocksof Life

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first a little review
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Macromolecules

• Smaller organic molecules join together to form
  larger molecules
• macromolecules
• 4 major classes of macromolecules
• carbohydrates
• lipids
• proteins
• nucleic acids

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Polymers

• Long molecules built by linking repeating
  building blocks in a chain
• monomers
• building blocks
• repeated small units
• covalent bonds

Dehydration synthesis
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How to build a polymer

• Synthesis
• joins monomers by taking H2O out
• 1 monomer provides OH
• other monomer provides H
• together these form H2O
• requires energy enzymes

Dehydration synthesis
Condensation reaction
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How to break down a polymer

• Digestion
• use H2O to breakdown polymers
• reverse of dehydration synthesis
• cleave off one monomer at a time
• H2O is split into H and OH
• H OH attach to ends
• requires enzymes

Hydrolysis
Digestion
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Bonding

• Covalent Bonds
• atoms share electrons.
• 2 kinds

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• Nonpolar covalent bonds
• electrons shared evenly between similar atoms
• bond is strong
• Ex O2, N2

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• Polar covalent bond
• Electrons shared unevenly between dissimilar
  atoms
• one atom pulls electrons more
• Gives a slightly negative charge
• Ex H20

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• Hydrophilic (polar) molecules
• have polar covalent bonds
• dissolve in water
• dissociate easily
• Ex glucose, amino acids

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• Hydrophobic (nonpolar) molecules
• mainly nonpolar covalent bonds
• do not dissolve in water (have few charges).
• Ex Lipids (fats)

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• Ionic Bonds
• Electrons not shared
• one or more electrons are transferred from one
  atom to another.

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• Transferring atom ()
  cation
• Receiving atom (-) anion
• NaCl is an example

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• Ionic bonds
• weaker than covalent
• dissociate when dissolved in H2O.
• Form hydration spheres

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Note orientation of water molecules
H2O
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• Hydrogen bonds
• weak bonds
• account for
• shape (due to folding) of large proteins
• holds DNA ladders together
• physical properties of water (like surface
  tension and capillary action).

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• Disulfide bonds
• found in proteins
• cause shape of proteins (folding and twisting of
  protein shapes).

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Chemical Reactions

• Synthesis
• results in the formation of new bonds
• requires energy
• wound healing, tissue growth
• Decomposition
• results in bond breakage
• energy is released as heat or captured for
  storage digestion

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Types of Rxns
Synthesis Reaction more complex chemical
structure is formed requires energy (wound
healing, tissue growth) A B AB
Decomposition Reaction chemical bonds are
broken to form a simpler chemical structure rls
energy (digestion) AB A B
Exchange Reaction chemical bonds are broken and
new bonds are formed AB CD AD CB
Reversible Reaction the products can change
back to the reactants A B n AB
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Organic vs. Inorganic
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• Organic compounds
• contain covalently bonded carbon atoms
• include macromolecules
• carbohydrates
• Lipids
• Proteins
• nucleic acids

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• Most macromolecules include a carbon core with
  functional groups attached.
• arrangements of atoms giving carbon core unique
  chemical properties

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• Inorganic compounds
• required, but not made by, living things
• contain no carbon
• include acids, bases, water, salts, minerals

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Inorganic Compounds

• Water
• accounts for 60 80 of cell contents
• very versatile and vital

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• Universal solvent (because it is a polar
  molecule)
• No chemical reactions unless in solution
• Dissolved compounds can be brought to cells (via
  blood) or move about cell cytoplasm

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• Exhibits cohesion water molecules stick together
  due to the hydrogen bonds.

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• Exhibits adhesion
• water molecules stick to other molecules thereby
  keeping things dissolved
• Polarity of water causes hydration layers with
  other molecules as (-) ends of water surround and
  enclose the () ends of other molecules and vice
  versa.

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• Has a high heat capacity
• large amounts of heat are needed to raise the
  temperature of water, so water bodies have stable
  temperatures
• Body temps can be maintained
• transfer of heat from warm to cool body parts.

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• Has a high boiling point
• Much energy is needed to pull water molecules
  apart
• since water rarely boils in nature, living
  systems are spared.

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• Major transport medium of body blood
• Major component of body lubricants synovial
  fluid, mucus, etc.
• Cushioning cerebrospinal fluid, amniotic fluid

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• Salts ionic compounds consisting of () and (-)
  ions other than H and OH-
• become electrolytes in body when dissolved
• conduct electricity in bodily functions such as
  muscle contraction and nerve conduction.

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• Important to bone and teeth hardness.
• Forms parts of hemoglobin molecule of RBCs.

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• Acids
• Taste sour
• React with metals
• Concentration of H ions that determine acidity
• Proton () donors produced by the body (gastic
  acid) or produced as a by-product (hydrogen
  peroxide)

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• Bases
• Taste bitter
• Feel slippery
• Proton acceptor, produced by the body
  (bicarbonate) or as a by-product of metabolism
  (ammonia)

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• Buffers
• Substances that maintain the pH constancy of body
  fluids
• Act as a H reservoir add or remove excess H

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Organic Compounds

• Contain carbon which is a unique molecule.
• Carbon bonds with itself and/or other molecules,
  covalently.
• Often found in chains (straight or branched),
  rings, folded sheets, etc..

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• makes carbon versatile
• The way carbons are bonded together determines
  type of organic compound
• carbohydrate, lipid, protein, nucleic acid, etc.

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Carbohydrates

• Known as sugars, CH2O
• classified by size
• named according to the number of carbons in the
  molecule (triose, tetrose, pentose, hexose, etc.)
  monomer monosaccharide (Latin sacchron means
  sugar)
• major energy source for the human body

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• Disaccharides (C12H22O11) known as double
  sugars
• formed when 2 monosaccharides are joined together
  by dehydration synthesis
• done so sugars can be transported.

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• for example
• sucrose (table sugar)
• lactose (milk sugar)
• maltose (grain sugar)
• created through dehydration synthesis of pairs of
  monosaccharides.

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• Polysaccharides
• known as complex sugars
• formed when many monosaccharides are joined
• act as
• fuel for cells
• structural components of DNA
• cell membranes
• cell surface receptors).

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• examples
• glycogen (animal starch stored in the liver and
  muscles)
• cellulose (structural polysaccharide of plant
  cell walls)
• starch (plant polysaccharide

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• When body needs energy, it looks to the liver to
  hydrolize glycogen (stored starch) and release
  the resulting monosaccharide to the cells.

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• the cells, in turn, release energy from bonds of
  monosaccharide
• energy that is released is converted to another
  energy compound called ATP.

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Lipids

• Commonly called fats
• insoluble in polar solvents (like water)
• soluble in nonpolar organic solvents like
  alcohol, ether, gasoline
• commonly attached to proteins in the bloodstream
  so they can travel in the aqueous plasma even
  though they are hydrophobic

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• composed of CHO but with a lower oxygen ratio
  than carbohydrates
• classified by their solubility.
• Ex include fats, oils, and waxes

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• Triglycerides (fats)
• composed of 3 fatty acids (carbon-hydrogen chain)
  and 1 glycerol (sugar) through
• dehydration synthesis into an E shape.
• large molecule which must be broken down in order
  to release the large amount of stored energy.

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• usually stored under the skin as fat
• can also collect in the lining of blood vessels
  and cause blockages
• act as good cushions, insulators and a
  concentrated source of energy

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• Fatty acids are classified as
• saturated (originating from animals and having
  all available hydrogens atoms which make them
  harder to metabolize)
• unsaturated lacking some hydrogen atoms
  contains double bonds

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• polyunsaturated (originating from plants)
• Hydrogenating oils makes them saturated and solid

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• Phospholipids
• complex lipids
• modified triglycerides composed of 2 fatty acids
  and a phosphorus chain
• used to build cell membranes.

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• Steroids
• lipid composed of ringed hydrocarbons
• Examples
• cholesterol which is the precursor for many
  hormones (like estrogen, progesterone, and
  testosterone)
• vitamin D
• bile salts.

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• Prostaglandins
• tissue hormone
• lipid responsible for
• blood vessel diameter
• Ovulation
• uterine contraction
• inflammation reactions
• blood clotting

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• Proteins
• 10 30 of cell mass composed of CHONPS
• monomers amino acids (20 commonly known)
• linked together by peptide bonds to form
  polypeptides.
• Strings of polypeptides protein.
• Average proteins are 50,000 aa long

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• protein versatility results from the various
  combinations and numbers of amino acids as well
  as the structural shape they take on (primary,
  secondary, tertiary, quaternary) shape confers
  properties.

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• Structural proteins
• primary and secondary structures
• linear or helical
• Insoluble
• Stable
• form body parts like collagen, keratin, elastin,
  bones, tendons, ligaments, cartilage, hair,
  nails, etc.

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• Functional proteins
• tertiary, quaternary structures
• water soluble
• Mobile
• chemically active
• include antibodies, hormones, enzymes

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• Denaturing of proteins functional proteins are
  highly susceptible to heat and pH (due to the
  weakness of the hydrogen bonds holding together
  their structure)

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• heat denaturation is irreversible once the
  arrangement of the molecule (and its composing
  atoms) is disrupted, it is no longer active.

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• Enzymes
• proteins
• act as biological catalyst
• Lower activation energy of the substrate
• Not destroyed or used up

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• some are proteins needing activation (cofactor)
  from a vitamin or mineral
• named according to substrate it catalyzes ex
  maltase hydrolyzes maltose most enzymes have an
  ase ending.

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• Operate in a very narrow pH, temperature and
  ionic range.
• can vary from enzyme to enzyme ex enzymes in
  the stomach vs. enzymes in the blood

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• Enzymes are substrate specific one enzyme for
  each type of substrate
• Enzymes are reusable

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• Enzymes have an activation site to which the
  substrate bonds. Any change in this site will
  render the enzyme inactive denaturation

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• Naming Enzymes
• Name of substrate affected with ase on the end
  ex sucrase, lactase, protease
• According to kind of chemical reactions catalyzed

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Factors Influencing Enzyme Activity

• Temperature
• pH
• Ionic concentration
• Substrate concentration?
• Enzyme concentration?
• Competitive inhibitors
• Noncompetitive inhibitors