BIOCHEMISTRY

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BIOCHEMISTRY

• The chemical
• basis of life

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ATOMS

• Basic unit of matter
• Two regions
• Nucleus
• Electron cloud

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Subatomic Particles

• Protons ?
• Positively charged particles
• Located in the nucleus
• Neutrons ?
• Neutral particles
• Located in the nucleus
• Electrons ?
• Negatively charged particles
• Located in the electron cloud
• These are the particles involved when atoms bond
  with other atoms

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• Electrons orbit the nucleus.
• An atom is only about 0.0000000001 meters big.
  It would take 10 BILLIONS atoms lying side by
  side to equal 1 meter!

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Atomic Number

• The number of protons distinguishes an atom of
  one type from another.
• All atoms of the same element have the same
  number of protons.
• This unique number is
• called the atomic number.

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Atomic Mass

• The atomic mass is equal to
• the total number of protons
• plus neutrons in an atom.
• Atomic Mass P N

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Mass Number

• The mass number can be written as a superscript
  above the symbol and the atomic number as a
  subscript below the symbol.

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Elements Isotopes

• Elements Simplest Pure Substance
• Elements of Life
• 96 ? Carbon (C), Hydrogen (H), Oxygen (O), and
  Nitrogen (N)
• 3 ? P, S, Ca, K, Na, Mg, Fe, Cl
• 1 ? other trace elements
• Isotopes
• Atoms of the same element that contain a
  different number of neutrons
• Radioactive isotopes will breakdown at a specific
  rate and are used in determining the age of
  various things (i.e. fossils rocks)

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Isotopes

• Atoms of the same element can have different
  numbers of neutrons.
• These different forms of the same element are
  called isotopes.
• The atomic mass is the average mass of all the
  known isotopes of the element.

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Atoms

• All atoms are neutral they have the same number
  of electrons as protons.
• Example An atom of 42He has an atomic number
  of 2 and a mass of 4.
• Therefore, it has 2 protons and 2 neutrons in
  its nucleus.
• Since it has 2 positive protons (neutrons are
  neutral) it must have 2 negative electrons to
  make the total charge neutral.

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How are electrons arranged?

• Electrons are located in different energy levels.
• The farther away from the nucleus the electron is
  found, the higher the energy.
• As electrons move from a lower level to a higher
  level energy is absorbed.
• As electrons move from a higher level to a lower
  level energy is release in the form of light.

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Periodic Table
Group
Period

• The elements are listed in order of increasing
  atomic number.
• By looking at the row (period) number you can
  determined how many energy levels an atom has.
• By looking at the column (group) number you can
  determine how many electrons are in the outermost
  level.

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Comparing Atoms
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How does one kind of atom differ from another?

• Number of protons determines an element.
• Even if atoms bond or break apart, the number of
  protons will always be the same.

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Chemical Compound

• Pure substance formed by two or more
  elements chemically combined.
• Ex water H2O, sodium chloride NaCl

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Types of Bonds

• Ionic The TRANSFER of electrons between a metal
  and a nonmetal
• Covalent The SHARRING of electrons between two
  or more nonmetals
• Two Types Polar and Nonpolar
• Metallic A sea of electrons around two or more
  metals
• Animations http//ithacasciencezone.com/chemzone/
  lessons/03bonding/mleebonding/covalent_bonds.htm

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Bonding by Analogy

• Sometimes it helps to think of bonds (which you
  can't see) in terms of familiar things you can
  see.  This is called an analogy.  Let's use the
  natural attraction between dogs and bones as an
  analogy to the attraction between opposite
  charges and atomic or intramolecular bonds.

http//ithacasciencezone.com/chemzone/lessons/03bo
nding/dogbonds.htmIonic20Bonding
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• A neutral atom contains an equal number of
  positive and negative charges. 
• In a sense, the atoms fight over the available
  electrons in much the same way two or more dogs
  will fight over bones. 
• The bone and the electron are very similar. 
• The Dog - Bone analogy works quite well for three
  of the four types of atomic bonds.  (van der
  Waal's forces are the only one which cannot be
  represented with this analogy)
• http//ithacasciencezone.com/chemzone/lessons/03bo
  nding/dogbonds.htmIonic20Bonding

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• Ionic bonds One big greedy thief dog!
• Covalent bonds  Dogs of equal strength.
• Polar Covalent bonds Unevenly matched but
  willing to share.
• Metallic bonds  Mellow dogs with plenty of bones
  to go around.

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Ionic Bonds
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Covalent Bonds

• Sharing of electrons
• These are stronger bonds than either of the other
  two types because the electrons are shared.
• Your body is based upon carbon bonding.
• So the covalent bond is considered the most
  important bond with regards to life.
• Interestingly, Si, just above C in the periodic
  table, with its covalent bonding, is the basis
  for the computer industry.

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Metallic Bonds
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Van der Waals Bonds

• When molecules are close together an attraction
  can develop between oppositely charged regions of
  nearby molecules
• Example water molecules

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Geckos and Van der Waals

• Geckos can stick to so many surfaces in a
  seemingly impossible manner.
• Specifically, the tiny hairs on the gecko's feet
  (called setae) are split at the microscopic level
  into as many as 1,000 branches.

As a result, even though the Van der Waals forces
acting on an individual tip is small, the
adhesion of a billion or so tips
adds up to enough force to let
the gecko stick to basically
anything.
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Water (H2O)

• Most abundant compound in
  organisms
• Water is polar
• Unequally shares electrons between hydrogen
  oxygen atoms
• Makes it possible for
  other compounds to
  dissolve in water

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Water has Hydrogen Bonds

• Adhesion the attraction of unlike molecules to
  one another
• Cohesion the attraction of
  like molecules to one another

Cohesion causes water to form drops, surface
tension causes them to be nearly spherical, and
adhesion keeps the drops in place.
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Property Meaning Importance
1. Transparency Light passes through water Light reaches chloroplast in cells and aquatic plants
2. Universal Solvent Many compounds dissolve in water Dissolved compounds can be brought to cells (via sap or blood) or move about cell cytoplasm.
3. Cohesion 4. Adhesion Water molecules stick together due to H bonds. Water molecules stick to other molecules Small animals may walk on water. Capillary action. Water pulled to top of trees
5. Heat Capacity Large amounts of energy are needed to raise temp of water Water bodies have stable temperatures. Body temps can be maintained. Transfer of heat from warm to cool body parts
6. Heat Point Capacity 7. Density of Ice Much energy needed to pull water molecules apart. Ice is less dense than water so it floats In nature, water rarely boils so life is spared. Ice insulates organisms living beneath
8.Evaporation Evaporation (boiling) requires much energy. Evaporation can cool warm cells
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Properties of Water

• Solutions and suspensions
• Mixtures are composed of 2 or more elements or
  compounds that are physically mixed, but not
  chemically combined
• There are two types of mixtures that can be made
  with water
• Solutions
• suspensions
• Solutions made of a solute and a solvent

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Properties of Water

• Solutions
• Made of a solute and a solvent
• Usually water acts as a solvent
• Polar water molecules are able to pull apart the
  solute to form a solution
• Water is known as the universal solvent
• Many biological fluids are solutions
• Solutions are also known as homogeneous mixtures

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Properties of Water

• Suspensions
• Particles do not dissolve in H2O and remain
  suspended
• Colloids are a type of suspension
• Examples of suspensions smoke, fog, jello, blood

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pH scale and buffers

• The pH of substances ranges from 0-14
• 7 neutral
• 0 - 6.9 acid
• 7.1 - 14 base
• Buffers
• Prevent sharp, sudden changes in pH so that the
  body can maintain homeostasis
• pH of most fluids in the body 6.5 - 7.5

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Acidic (acid) 0 - 7
Basic (base) 7 - 14
Neutral
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Acids, Bases and the pH scale

• H concentration of hydrogen ions
• OH- concentration of hydroxide ions
• The pH scale measures the concentration of H
  ions (how acidic something is)
• Ranges from 0-14
• At 7 H ions and OH- ions are equal so it is
  neutral
• 0-7 acidic, has more H ions
• 7-14 basic, has more OH- ions

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• ACIDS release H when mixed with water
• Sour, corrosive
• Ex HCl, H2SO4
• Always have H at front of formula
• BASES release OH- when mixed with water
• Bitter, slippery, usually in cleaners
• NaOH, CaOH
• Always have OH at end of formula

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What is a buffer?

• Buffers are weak acids or bases that react with
  strong acids and bases to prevent sharp changes
  in pH
• Helps to neutralize
• Help to control pH in blood, digestive tract,
  etc. to maintain homeostasis
• Ex Antacids buffer the stomach from the
  Hydrochloric Acid (HCl)

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Organic vs. Inorganic

• All compounds can be separated into two groups
• Inorganic
• Does not contain carbon
• Non-living (never alive)
• Examples Oxygen gas, metals, rocks, water
• Organic
• Contains carbon
• Living (or dead once was alive)
• Examples wood, grass, diamonds, petroleum

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Inorganic Compounds

• Usually do not contain CARBON (except good old
  CO2)
• WATER-- a very curious material
• salts, compounds in our bones, etc. but none as
  numerous as the ORGANIC compounds in living things

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Why Carbon Compounds?

• Carbon (C) forms strong, stable COVALENT bonds
• Carbon forms almost infinite chains when bonded
  to other C atoms
• Chains may form as ring structures with single or
  double bonds
• Ex Polymerization

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We eat polymers!

• Hey, come on over here and have a big slice of
  POLYMER pizza. It's not as strange as it sounds.
  French fries are loaded with a polymer called
  starch, which your body
  digests into sugar to use
  as fuel.

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Polymerization

• Monomers (small)
• One unit of a compound
• Polymers
• Many monomers combine to make a polymer
• Macromolecules (huge)
• Many large molecules combined
• Polymers are everywhere http//pslc.ws/macrog/pau
  l/

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Containers

• Fast food often comes in
  boxes made of polystyrene foam.
• Cup lids are made of polystyrene, but in plastic
  form instead of foam.
• Napkins are made of paper, which is made from
  wood pulp, and that wood pulp has an awful lot of
  the polymer cellulose.
• The trays are made of polyethylene. Most of the
  prizes in the kids' meals are made from
  polystyrene and polyethylene or polyvinyl
  chloride.

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Clothing

• The polymers in clothes can be everything from
  plant materials, to synthetics, to proteins like
  silk and wool.
• Sweaters are also made out of acrylics, like
  polyacrylonitrile.
• Spandex is a special kind of polyurethane that's
  very stretchy. Spandex is also used in bicycle
  pants, swim suits, and other items of
  stretchwear.

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Carbohydrates

• Made of C, H, O
• Functions
• Main energy source in organisms
• Structural component in plants
• Types
• Sugars
• gives off energy when broken down
• Cellulose ? twisted chain of sugars, not
  digestible by humans
• Chitin ? hard cellulose found in the exoskeletons
  of invertebrates
• Ex. Sucrose, fructose, glucose
• Starches
• used as a storage molecule for sugars
• Many athletes eat these before events
• Ex. Bread, rice, pasta, corn

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Lipids

• Made of C, H, O
• in the form of glycerol and fatty acid chains
• Commonly called fats, oils, waxes
• Functions
• Storage of energy
• Parts of biological membranes
• Water proof coverings
• Chemical messengers (steroids)
• Insoluble in water
• Ex. Lard, butter, oil, hormones, steroids

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Steriods

• Steroids occur in animals in something called
  hormones. The basis of a steroid molecule is a
  four-ring structure, one with five carbons and
  three with six carbons in the rings.
• Many body builders and athletes use anabolic
  steroids to build muscle mass. The steroids make
  their body want to add more muscle than they
  normally would be able to.
• The body builders wind up stronger and bulkier
  (but not faster). Never take drugs to enhance
  your body. Those body builders are actually
  hurting their bodies. They can't see it because
  it is slowly destroying their internal organs and
  not the muscles. When they get older, they can
  have kidney and liver problems. Some even die!

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Lipids...

• Saturated fats
• all Carbons attached by single bonds with the
  maximum H atoms
• meats, dairy
• Unsaturated fats
• C atoms joined by double bond, not with the
  maximum H atoms (more double
  bondspolyunsaturated)
• liquid fats at room temp.--sesame, peanut, canola
  oils

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Fats

• There are two kinds of fats, saturated and
  unsaturated.
• Unsaturated fats have at least one double bond in
  one of the fatty acids.
• A double bond happens when two electrons are
  shared or exchanged in a bond. They are much
  stronger than single bonds.
• Saturated fats have no double bonds. Fats have
  a lot of energy stored up in their molecular
  bonds. That's why the human body stores fat as an
  energy source. When it needs extra fuel, your
  body breaks down the fat and uses the energy.
• One molecule of sugar only gives a small amount
  of energy, a fat molecule gives off many times
  more.

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Trans Fats

• Trans fats are unsaturated fats
• Found in partially hydrogenated oils
• Have recently been removed from many foods due to
  health concerns
• N.Y restaurants
• Frito Lay
• Krispy Kreme
• Girl Scout Cookies
• Wendys
• etc

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and more fats

• Sterols
• cholesterol (HDL, LDL)
• build cells, chemical messengers
• Phospholipids
• molecules that have parts that dissolve in water
  and parts that do not
• cell membrane structure--bilayers

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Nucleic acids

• Made of C, H, O, N, P
• Monomers are called nucleotides
• Nucleotides are made up of a 5-carbon sugar,
  phosphate group and a nitrogen base
• Functions
• Store hereditary information
• Transmit hereditary information
• Two types
• RNA (ribonucleic acid)
• DNA (deoxyribonucleic acid)

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Proteins

• Made of C, H, O, N
• Monomers of proteins are amino acids
• There are 20 different amino acids that combine
  in different ways to make millions of proteins
• The most diverse macromolecules
• Functions
• Control the rates of chemical reactions (enzymes)
• Regulate cell processes
• Used to form bone muscles
• Transport substances into or out of cells
• Help fight disease

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Protein

• Burgers are full of proteins,
  
• which your body uses to
  
• build and repair itself.
• The pepperoni and the cheese on this pizza are
  also loaded with proteins.
• And popcorn is formed from starch, while a hot
  dog is yet another source of protein. (Of course,
  buttery popcorn and hot dogs also contain a lot
  of fat. Fat molecules are big, but they're not
  polymers.)

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Proteins Digestion
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Polymer OR Protein

• As we discussed earlier, sweaters can be made
  from polymers.
• Sweaters can also be made from wool, which is a
  protein called keratin.
• So is your hair and fingernails, by the way.

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Those fabulous proteins...

• Organics of C-H-O-N
• Build structures, carry out metabolism
• made up of AMINO ACIDS
• 20 common amino acids
• an amino group (NH2) on one end
• an acid or carboxyl group (-COOH) on the other
• a Hydrogen (H) atom
• a fourth compound - which determines the nature
  of the amino-acid

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Amino Acid
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• Amino Acids form covalent bonds (PEPTIDE BONDS)
  and may form EXTREMELY long chains

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Protein structure

• One or more polypeptide chains
• enzymes
• Catalysts decrease start up energy of RXN
• may accelerate RXN by 1010 times
• regulate chemical pathways,
  release energy, transfer info
• involved in all life processes,
• even in enzyme production!

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Enzymes

• They usually speed up the rate of a reaction by
  lowering the
  amount of activation
  energy needed to
  start the reaction.
• end with -ase.
• Ex. lactase

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Chemical reactions

• Chemical reactions involve the making and
  breaking of chemical bonds.
• Chemical bonds store energy.
• When a bond is broken, energy is released (heat,
  light, sound)

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Exothermic Reaction

• Energy is Released
• Ex. Fireworks, cellular respiration, digestion
• These reactions involve the breaking of polymers
  into monomers

http//www2.uni-siegen.de/pci/versuche/english/v4
1-1.html
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• Endothermic Reaction is one in which energy is
  absorbed (stored in bonds)
• The joining of monomers into polymers.
• Ex. Photosynthesis, making proteins, etc.

http//www.chemistry-videos.org.uk/chem20clips/KS
320Endothermic/enothermic.html
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Exothermic ExergonicEndothermic Endergonic
http//www2.uni-siegen.de/pci/versuche/english/ka
pitel4.html
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Summary