BIOCHEMISTRY

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BIOCHEMISTRY
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THE ATOM

• Just like cells are the basic unit of life, the
  ATOM is the basic unit of matter.
• They are very small. If placed side by side one
  million would stretch a distance of 1cm.
• The atom is made up of 3 particles.

Particle Charge
PROTON
NEUTRON NEUTRAL
ELECTRON -
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ISOTOPES

• atoms of the same element that HAVE A DIFFERENT
  NUMBER OF NEUTRONS
• Some isotopes are radioactive. This means that
  their nuclei is unstable and will break down at a
  CONSTANT RATE over time.
• There are several practical uses for radioactive
  isotopes
• CARBON DATING
• TRACERS
• KILL BACTERIA / CANCER CELLS

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COMPOUNDS

• a substance formed by the chemical combination of
  2 or more elements in definite proportions
• Ex water, salt, glucose, carbon dioxide

H20
CO2
NaCl
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• The cell is a COMPLEX CHEMICAL FACTORY containing
  some of the same elements found in the nonliving
  environment.
• carbon (C), hydrogen (H), oxygen (O), and
  nitrogen (N) are present in the greatest
  percentages

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TWO TYPES OF COMPOUNDS

• Organic - Contain C, H, and O in some ratio
  (usually referred to as chemicals of life)
• Carbohydrates, Proteins, Lipids, Nucleic Acids
• Inorganic - usually "support" life - no specific
  ratio of C, H, and O
• Water (H2O), Carbon Dioxide (CO2)

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CHEMICAL BONDS

• Chemical bonds hold the atoms in a molecule
  together.
• There are 2 types of chemical bonds IONIC and
  COVALENT

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MIXTURES

• Water is not always pure. It is often found as
  part of a mixture.
• A mixture is a material composed of TWO OR MORE
  ELEMENTS OR COMPOUNDS THAT ARE PHYSICALLY MIXED
• Ex salt pepper mixed, sugar and sand can be
  easily separated

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SOLUTION

• Two parts
• SOLUTE SUBSTANCE THAT IS BEING DISSOLVED (SUGAR
  / SALT)
• SOLVENT - the substance in which the solute
  dissolves
• Materials that do not dissolve are known as
  SUSPENSIONS.
• Blood is the most common example of a suspension.
  
• Cells other particles remain in suspension.

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FORMULA

• The chemical symbols and numbers that compose a
  compound ("recipe")
• Structural Formula Line drawings of the
  compound that shows the elements in proportion
  and how they are bonded
• Molecular Formula the ACTUAL formula for a
  compound

C2H5OH
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ACIDS BASES

• Acids always (almost) begin with "H" because of
  the excess of H ions (hydrogen)
• Ex lemon juice (6), stomach acid (1.5), acid
  rain (4.5), normal rain (6)
• Facts about Acids
• Acids turn litmus paper BLUE and usually taste
  SOUR.
• You eat acids daily (coffee, vinegar, soda,
  spicy foods, etc)

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ACIDS BASES

• Bases always (almost) end with -OH because of
  the excess of hydroxide ions (Oxygen Hydrogen)
• EX oven cleaner, bleach, ammonia, sea water,
  blood, pure water
• Facts about Bases
• Bases turn litmus BLUE.
• Bases usually feel SLIPPERY to touch and taste
  BITTER.

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Neutralization Reactions

• When an acid reacts with a base to produce a salt
  and water.

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pH SCALE

• measures degree of substance alkalinity or
  acidity
• Ranges from 0 to 14
• 0 5 strong acid
• 6-7 neutral
• 8-14 strong base

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• The goal of the body is to maintain HOMEOSTASIS
  (neutrality) to do this when pH is concerned,
  we add weak acids bases to prevent sharp
  changes in pH.
• These are called BUFFERS

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Tying in Inorganic Chemistry

• Radiation effects on living things
• For therapy and safety reasons
• Molecular bonding/ligands and functional groups

• Technology based on biomimicry
• Mixtures and solutions in drug design and
  homeostasis
• Acid base reactions and how they affect the body

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Tying in Organic Chemistry

• Life uses organic chemistry to create more
  complex molecules/rxns
• Two major reactions in organic chemistry occur in
  living organisms condensation and hydrolysis

• Designing drugs that affect living things
• Mixtures and solutions in drug design and
  homeostasis

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Biology Review

• Parts of a cell (animal) most other eukaryotes
  are similar to this type (e.g. protists)

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http//www.youtube.com/watch?vGigxU1UXZXo

• http//www.youtube.com/watch?vRrS2uROUjK4

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Biology Review

• Parts of a cell (plant)

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Biology Review

• Parts of a cell (bacteria)

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Biology Review

• Parts of viruses

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Biology Review

• Parts of viruses

NOT LIVING
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Biology Review

• Cell theory (definition of life)

All known living things are made up of one or
more cells. All living cells arise from
pre-existing cells by division. The cell is the
fundamental unit of structure and function in all
living organisms. The activity of an organism
depends on the total activity of independent
cells. Energy flow (metabolism and biochemistry)
occurs within cells. Cells contain hereditary
information (DNA) which is passed from cell to
cell during cell division. All cells are
basically the same in chemical composition in
organisms of similar species.
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Biology Review

• Cell theory (definition of life)

All known living things are made up of one or
more cells. All living cells arise from
pre-existing cells by division. The cell is the
fundamental unit of structure and function in all
living organisms. The activity of an organism
depends on the total activity of independent
cells. Energy flow (metabolism and biochemistry)
occurs within cells. Cells contain hereditary
information (DNA) which is passed from cell to
cell during cell division. All cells are
basically the same in chemical composition in
organisms of similar species.
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Biology Review

• Cell theory (definition of life)

All living cells arise from pre-existing cells by
division. (sexual vs asexual)
Asexual
Sexual
Asexual (e.g. bacteria)
Budding (Yeast) Asexual
(SEX)
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Biology Review

• Cell theory (definition of life)

All living cells arise from pre-existing cells by
division. (sexual vs asexual)
Spores mostly sexual (e.g. plants/fungi)
Sexual
Male plant (Pollen) Usually tossed Into wind
or Carried by animals to female plants (e.g.
bees) Once spores meet partner, sex occurs
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Biology Review

• Cell theory (definition of life)

All living cells arise from pre-existing cells by
division. (sexual vs asexual)
Spores mostly sexual (e.g. plants/fungi)
Sexual
Humans, helping plants have sex since we thought
it looked cool.
Male plant (Pollen) Usually tossed Into wind
or Carried by animals to female plants (e.g.
bees) Once spores meet partner, sex occurs
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Biology Review

• Cell theory (definition of life)

The cell is the fundamental unit of structure and
function in all living organisms. The activity
of an organism depends on the total activity of
independent cells. Energy flow
(metabolism and biochemistry) occurs within
cells. Cells contain hereditary information
(DNA) which is passed from cell to cell during
cell division. All cells are basically the same
in chemical composition in organisms of similar
species.
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Biology Review

• Cell theory (definition of life)

The activity of an organism depends on the total
activity of independent cells (e.g. animals)
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Biology Review

• Cell theory (definition of life)

Energy flow (metabolism and biochemistry) occurs
within cells. (Tens of thousands in humans alone
all sped up by enzymes) Cells contain hereditary
information (DNA) which is passed from cell to
cell during cell division. All cells are
basically the same in chemical composition in
organisms of similar species.
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Biology Review

• Cell theory (definition of life)

Energy flow (metabolism and biochemistry) occurs
within cells. (Tens of thousands in humans alone
all sped up by enzymes) Cells contain hereditary
information (DNA) which is passed from cell to
cell during cell division. All cells are
basically the same in chemical composition in
organisms of similar species.
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Biology Review

• Cell theory (definition of life)

Cells contain hereditary information (DNA) which
is passed from cell to cell during cell
division. All cells are basically the same in
chemical composition in organisms of similar
species.
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Biology Review

• Cell theory (definition of life)

Cells contain hereditary information (DNA) which
is passed from cell to cell during cell
division. All cells are basically the same in
chemical composition in
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Biology Review

• Cell theory (definition of life)

All cells are basically the same in chemical
composition in organisms of similar species. (All
animal cell membranes have the structure below
actual structures slightly differ)
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Biology Review

• Cell theory (definition of life)

All cells are basically the same in chemical
composition in organisms of similar
species. (This is where genetics comes into play
how does our DNA change the structure?)
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Biology Review

• What is evolution?
• A single mutation is not evolution
• The most important mutations occur in sex cell
  (gamete mutations during meiosis cause changes in
  offspring from parents)
• If multiple mutations occur, creating enough
  differences from an ancestor, a new species is
  born
• Requires multiple generations (gt 50-100)

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Biology Review

• What is evolution?
• If multiple mutations occur, creating enough
  differences from an ancestor, a new species is
  born
• If youre talking about humans, with 60-100 yr
  lifespans and only having kids a few times if at
  all, then evolution could take tens of thousands
  of years
• If youre talking about bacteria that reproduce
  every 30 minutes or so, they can evolve in a
  matter of months

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Schedule

• Topic 1 Evolution and Genetics
• Basic genetic events and reproduction
• DNA mutations and consequences
• Evolution of early earth to dinosaurs, mammals to
  humans, and evolution today
• Topic 2 Bioenergetics metabolism and catabolism
• Energy usage, Biosynthesis, Catabolism and waste
• Immunology
• Topic 3 Microbiology
• Bacteria, Fungi, Viruses, Parasites
• Topic 4 Human physiology
• Neuroanatomy and physiology
• Cardiovascular Physiology

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But first lets cover the basic Biochemistry
portion of things.
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ORGANIC COMPOUNDS
LIPIDS
PROTEINS
NUCLEIC ACIDS
CARBOHYDRATES
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CARBOHYDRATES

• Living things use carbohydrates as a key source
  of ENERGY!
• Plants use carbohydrates for structure
  (CELLULOSE)
• include sugars and complex carbohydrates
  (starches)
• contain the elements carbon, hydrogen, and oxygen
  (the hydrogen is in a 21 ratio to oxygen CH2O)

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Monosaccharides (simple sugars)

• all have the formula C H2 O
• all have a single ring structure
• (glucose is an example C6H12O6)

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Disaccharides (double sugars)

• all have the formula C12 H22 O11
• sucrose (table sugar) is an example

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Polysaccharides

• Formed of three or more simple sugar units
• Glycogen - animal starch stored in liver
  muscles
• Cellulose - indigestible in humans - forms cell
  walls
• Starches - used as energy storage

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How are complex carbohydrates formed and broken
down?
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Dehydration Synthesis

• Combining simple molecules to form a more complex
  one with the removal of water (dehydration)
• ex. monosaccharide monosaccharide ----gt
  disaccharide water
• (C6H12O6 C6H12O6 ----gt C12H22O11 H2O
• Polysaccharides are formed from repeated
  dehydration of water
• They are the stored extra sugars known as starch

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Hydrolysis

• Addition of WATER to a compound to SPLIT it into
  smaller subunits
• (also called chemical digestion)
• ex. disaccharide H2O ---gt monosaccharide
  monosaccharide
• C12 H22 O11 H2 O ---gt C6 H12 O6 C6 H12 O6

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Lipids (Fats)

• Fats, oils, waxes, steroids
• Chiefly function in energy storage, protection,
  and insulation
• Tend to be large molecules -- an example of a
  neutral lipid is below

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• Neutral lipids are formed from the union of one
  glycerol molecule and 3 fatty acids
• Fats -- found chiefly in animals
• Oils and waxes -- found chiefly in plants
• Oils are liquid at room temperature, waxes are
  solids
• Lipids along with proteins are key components of
  cell membranes
• Steroids are special lipids used to build many
  reproductive hormones and cholesterol

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PROTEINS

• contain the elements carbon, hydrogen, oxygen,
  and nitrogen
• composed of MANY amino acid subunits
• It is the number and sequence of the amino acids
  that forms primary structure.
• The basic amino acid form has a carboxyl group on
  one end, a methyl group that only has one
  hydrogen in the middle, and a amino group on the
  other end.
• Attached to the methyl group is a R group.

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AN R GROUP IS ANY GROUP OF ATOMS THIS CHANGES
THE PROPERTIES OF THE PROTEIN!
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FUNCTIONAL GROUPS

• There are certain groups of atoms that are
  frequently attached to the organic molecules we
  will be studying, and these are called functional
  groups.
• These are things like hydroxyl groups which form
  alcohols, carbonyl groups which form aldehydes or
  ketones, carboxyl groups which form carboxylic
  acids, and amino groups which form amines.

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Major Protein Functions

• Growth and repair
• Energy
• Buffer -- helps keep body pH constant

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Dipeptide

• formed from two amino acid subunits
• Formed by the process of Dehydration Synthesis
• amino acid amino acid ----- dipeptide water

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Hydrolysis of a dipeptide

• Breaking down of a dipeptide into amino acids
• dipeptide H2O ---gt aminoacid amino acid

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Polypeptide (protein)

• composed of three or more amino acids linked by
  synthesis reactions
• Examples of proteins include insulin, hemoglobin,
  and enzymes.
• There are an extremely large number of
  different proteins.
• The bases for variability include differences in
  the number, kinds and sequences of amino acids in
  the proteins

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NUCLEIC ACIDS

• in all cells
• composed of NUCLEOTIDES
• store transmit heredity/genetic information
• Nucleotides consist of 3 parts
• 1. 5-Carbon Sugar
• 2. Phosphate Group
• 3. Nitrogenous Base

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DNA (deoxyribonucleic acid)

• contains the genetic code of instructions that
  direct a cell's behavior through the synthesis of
  proteins
• found in the chromosomes of the nucleus (and a
  few other organelles)

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RNA (ribonucleic acid)

• directs cellular protein synthesis
• found in ribosomes nucleoli

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Enzymes and Enzyme Action

• catalyst inorganic or organic substance which
  speeds up the rate of a chemical reaction without
  entering the reaction itself
• enzymes organic catalysts made of protein
• most enzyme names end in -ase
• enzymes lower the energy needed to start a
  chemical reaction. (activation energy)
• begin to be destroyed above 45øC. (above this
  temperature all proteins begin to be destroyed)

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• It is thought that, in order for an enzyme to
  affect the rate of a reaction, the following
  events must take place.
• The enzyme must form a temporary association with
  the substance or substances whose reaction rate
  it affects. These substances are known as
  substrates.
• The association between enzyme and substrate is
  thought to form a close physical association
  between the molecules and is called the
  enzyme-substrate complex.
• While the enzyme-substrate complex is formed,
  enzyme action takes place.
• Upon completion of the reaction, the enzyme and
  product(s) separate. The enzyme molecule is now
  available to form additional complexes.

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How do enzymes work?

• substrate molecules upon which an enzyme acts
• the enzyme is shaped so that it can only lock up
  with a specific substrate molecule
• enzyme
• substrate -------------gt product

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"Lock and Key Theory"

• each enzyme is specific for one and ONLY one
  substrate (one lock - one key)
• this theory has many weaknesses, but it explains
  some basic things about enzyme function

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Factors Influencing Rate of Enzyme Action

• 1. pH - the optimum (best) in most living things
  is close to 7 (neutral)
• high or low pH levels usually slow enzyme
  activity
• A few enzymes (such as gastric protease) work
  best at a pH of about 2.0

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• 2. Temperature - strongly influences enzyme
  activity
• optimum temperature for maximum enzyme function
  is usually about 35-40 C.
• reactions proceed slowly below optimal
  temperatures
• above 45 C most enzymes are denatured (change in
  their shape so the enzyme active site no longer
  fits with the substrate and the enzyme can't
  function)

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• 3. Concentrations of Enzyme and Substrate
• When there is a fixed amount of enzyme and an
  excess of substrate molecules -- the rate of
  reaction will increase to a point and then level
  off.