BIOCHEMISTRY

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BIOCHEMISTRY
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• Focus
• How are molecules assembled?
• How is form and function related in molecules?

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INORGANIC - Water

• Polar molecule

Figure 2.4a
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• Water
• Solvent
• Polar substances dissociate, forming solutes

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SOLUBLE?
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Properties of Water

• 1.Cohesion due to H bonds ie surface tension,
  transpiration
• 2.Adhesion due to H bonds with other substances
  capillary action movement in xylem

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• 3.High specific heat capacity high energy
  required to raise temp. of water thus
  temperature doesnt fluctuate as much ? why? H
  bonds can absorb a lot of energy
• 4.Evaporative cooling water can remove a lot
  of energy when it evaporates this is important
  in thermoregulation high humidity hinders
  evaporative cooling

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• Q1 WHAT COULD HAPPEN IF YOU WORKED OUT HEAVILY
  AND THREW YOURSELF IN A HOT TUB?
• Q2 WHY WOULD IT NOT BE A GOOD IDEA TO CONSUME ICE?

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• 5.Water expands when freezes - at 0C H bonds
  create crystal lattice arrangement that pushes
  water molecules farther apart thus reducing
  density

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• 6.Water acts as a solvent polar or ionic
  substances can dissolve in water hydrophobic
  substances wont dissolve while hydrophilic
  substances will

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ORGANIC MACROMOLECULES

• Carbon in rings or chains

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Macromolecules I

• 1. The four major types of organic macromolecules
  are carbohydrates, lipids, proteins, and nucleic
  acids.

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• ASSEMBLY (condensation-dehydration) VS
  DISASSEMBLY (hydrolysis) OF MACROMOLECULES

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• ISOMERS same formula but different arrangement
• STRUCTURAL atoms rearranged
• GEOMETRIC arrangements around CC bond as cis
  or trans

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• C) ENANTIOMERS
• Mirror images L vs D
• ie L DOPA (effective vs parkinsons) vs D DOPA

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• Geometric and Enantiomers are known as
  STEREOISOMERS where bond relationships are the
  same but different spatial arrangements

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• LIVING THINGS USE L-AMINO ACIDS AND D-SUGAR

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Macromolecules (polymers) are formed from smaller
building blocks called monomers.
Polymer Monomer carbohydrate
monosaccharides protein amino acid
nucleic acids nucleotide
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CARBOHYDRATES
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• 1. Carbohydrates generally have molecular
  formulas that are some multiple of CH2O
• - have CO and OH functional groups

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• b.Functions - energy source, recognition or
  signaling, and/or structural.

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ALDOSES VS KETOSES

• LOCATION OF CO
• If on 1st C ? aldose
• If on 2nd C ? ketose

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of CARBON ATOMS

• TRIOSE
• PENTOSE
• HEXOSE

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ALPHA
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• MONOSACCHARIDE 1 MONOMER
• DISACCHARIDE 2 MONOMERS
• OLIGOSACCHARIDE 2-20
• POLYSACCHARIDE - MANY

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1-4 alpha
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• Storage Polysaccharides starch/glycogen-
  polymers of glucose
• - simplest form is amylose unbranched starch
• amylopectin branched polymer of starch
• glycogen more extensive than amylopectin

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• Amylase is used to break down amylose (starch)
  into sugar. Which type of animal would lack
  amylase?

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1-4 Beta-linkages
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• B) Structural polysaccharides
• Cellulose polymer of glucose
• Starch alpha vs cellulose beta
• parallel cellulose molecules held together by H
  bonds arranged as microfibrils
• also known as fibre (can be used as energy source
  if beta bonds broken)

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• Chitin exoskeleton component which changes from
  leathery to hard in presence of calcium
  carbonate. Also found in fungi. Structural
  component is glucose nitrogen group.

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CHITIN
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• RECOGNITION/SIGNALING
• - Carbohydrates can be used as identifying
  molecules on the surface of cells
• ie glycocalyx (sticky oligosaccharides) attached
  to proteins/lipds can be used as glue between
  cells

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LIPIDS

• Energy source and storage
• Nerve functioning
• Insulation/cushioning
• Steroids and many hormones
• Main Cell membrane component

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• MONO, DI and TRIGLYCERIDES ? number of fatty acid
  chains

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• Bond Ester linkage
• HO ratio greater than 21
• Insoluble (non-polar) ? hydrophobic

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SAT VS UNSAT

• Saturated fats ? max of H bonds
• Monounsaturated 1 CC
• Polyunsaturated 2 CC
• Unsats are oils at room temp

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• Monounsat ? reduces cholesterol
• Sat ? raises cholesterol
• Polyunsat ? inc. cancer rates

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• HYDROGENATION INVOLVES MAXIMIZING C-H BONDS

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WHICH HAS THE LOWEST MP?
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WHICH OIL IS BETTER?

• Which oil would you choose? Oil from plants in
  cooler or hotter climates?

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• Why do you think TRANS FATS (which are
  unsaturated) are bad for you?
• HINT THINK OF THE NAME!!!!

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• CAN YOU HAVE FAT FREE TURKEY?

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• LECITHINS ARE PHOSPHOLIPIDS USED IN EMULSIFYING
  FATS

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• Phospholipids are amphipatic (polar and non-polar
  ends)
• Amphipatic molecules spontaneously form micelles
  in water

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Phospholipids in Water
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SPONTANEOUS ARRANGMENT

• HYDROPHILIC FACES WATER VS HYDROPHOBIC FACING
  HYDROPHOBIC

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• Cholesterol is used for
• To produce vitamin D proper bone/teeth dev.
• Keeping cell membrane fluid
• Making bile acids

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PROTEINS
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• 8 functional classes
• 1) structural proteins 2) contractile
  proteins 3) storage proteins 4) defense
  proteins 5) transport proteins 6) hormones 7)
  enzymes 8) receptors

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THE AMINO ACID
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CAN ACT AS BUFFERS

• CAN DONATE H AT HIGH pH
• CAN ACCEPT H AT LOW pH
• HELPS REGULATE pH

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• The specific shape that determines a protein's
  function comprises four (4) successive levels of
  structure, each determined by the previous level.
  

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• The primary structure is the sequence of amino
  acids forming the polypeptide chain.
• - PEPTIDE BONDS FORMED BETWEEN AMINO ACIDS

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Primary Protein Structure
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• b. The secondary structure consists of coiling
  or folding of a polypeptide chain usually
  resulting in one of two repeating structures,
  either an alpha-helix or a beta-pleated sheet.

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• Tertiary structure - overall 3-d shape of a
  polypeptide tertiary structure is maintained by
• - hydrogen, ionic and covalent disulfide
  bridges) bonds and hydrophobic or hydrophilic
  interactions between the "R" groups

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• d.Quaternary structure is produced by the
  bonding interactions of two (2) or more
  polypeptide subunits. Quaternary structure is
  maintained by hydrogen bonding, ionic
  interactions, and hydrophobic interactions.

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• Q. What would be symptoms from someone suffering
  from scurvy?

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• Prosthetic groups ? Non-amino acid components
  that assist in function

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• A PROTEINS FUNCTION IS TIED TO ITS FORM
• - Either fibrous (primarily alpha ie Keratin) or
  globular (ie enzymes)

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IMPORTANCE OF CHANGING SHAPE

• Conformational changes of proteins used in many
  biological processes (ie pumps, movement)

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• Conformation (Shape) depends upon environment.
• pH, Salt, Temperature can alter shape a
  denatured proteins is one that has completely
  lost is structural integrity.

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• Glu glutamic acid ? polar
• Val valine ? non-polar

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DOMAINS

• Distinct regions with distinct functions
• Ie DNA binding sites

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Universal Proteins Conserved Domains
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Effects of Altered Protein Structure on Function


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Section of DNA Polymerase
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NUCLEIC ACIDS

• Common association ? DNA (stores genetic
  information) and RNA (converting DNA into
  polypeptides)
• Can also be used in energy transfer and signalling

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DNA OR RNA

• DNA contains genes which code for polypeptides.
  DNA is transcribed into RNA so that information
  can be translated into a polypeptide.

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NUCLEOTIDES

• 3 PARTS
• PHOSPHATE GROUP
• PENTOSE (RIBOSE OR DEOXYRIBOSE)
• DNA ? NITROGEN BASES (ADENINE, GUANINE, THYMINE,
  CYTOSINE) AS PURINES AND PYRIMIDINES

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DNA

• ANTIPARALLEL MOLECULE
• COMPLEMENTARY BASE PAIRING (AT, GC)
• STRANDS RUN 5 ? 3
• NUCLEOTIDES LINKED BY PHOSPHODIESTER LINKAGES
• BASES LINKED BY H BONDS

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RNA (URACIL REPLACES THYMINE)
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RNA IS DIFFERENT

• HAS RIBOSE SUGAR ? Extra O at 2 end
• Uracil replaces thymine
• Single stranded
• Encodes gene only

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Adenosine triphosphate (ATP)
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• The evil witch Purple-a has cast a spell over
  MorrowLand and has abolished all hydrogen bonds.
  What affect would this have?

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• ASPARTAME
• Phenylalanine
• Aspartic acid
• Methanol
• Is it safe?