BIOCHEMISTRY

1
BIOCHEMISTRY
2
CHEMISTRY OF LIFE

• Elements simplest form of a substance - cannot
  be broken down any further without changing what
  it is
• Atom the actual basic unit - composed of
  protons, neutrons, and electrons

3
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 -
4

• Electrons are not present within the atom,
  instead THEY REVOLVE AROUND THE NUCELUS OF THE
  ATOM FORM THE ELECTRON CLOUD
• Draw a helium atom. Indicate where the protons,
  neutrons and electrons are.

NEUTRONS
PROTONS
-
ATOMIC 2 (PROTONS) ATOMIC MASS 4 (PROTONS
NEUTRONS)


ELECTRONS
-
5
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

6
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
7

• 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

8
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)

9
CHEMICAL BONDS

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

10
IONIC BONDS

• Occur when 1 or more electrons are TRANSFERRED
  from one atom to another.
• When an atom loses an electron it is a POSITIVE
  charge.
• When an atom gains an electron it is a NEGATIVE
  charge
• These newly charged atoms are now called IONS
• Example NaCl (SALT)

11
(No Transcript)
12
COVALENT BONDS

• Occur when electrons are SHARED by atoms.
• These new structures that result from covalent
  bonds are called MOLECULES
• In general, the more chemical bonds a molecule
  has the more energy it contains

SHARING IS CARING!
13
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

14
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.

15
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

C2H6O
16
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 red and usually taste
  SOUR.
• You eat acids daily (coffee, vinegar, soda,
  spicy foods, etc)

17
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.

18
Neutralization Reactions

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

19
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

20

• 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

21
And now for the Biochemistry portion of things.
22
ORGANIC COMPOUNDS
LIPIDS
PROTEINS
NUCLEIC ACIDS
CARBOHYDRATES
23
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)

24
Monosaccharides (simple sugars)

• all have the formula C6 H12 O6
• all have a single ring structure
• (glucose is an example)

25
Disaccharides (double sugars)

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

26
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

27
How are complex carbohydrates formed and broken
down?
28
Dehydration Synthesis

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

29
(No Transcript)
30
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

31
(No Transcript)
32
Lipids (Fats)

• Fats, oils, waxes, steroids
• Chiefly function in energy storage, protection,
  and insulation
• Contain carbon, hydrogen, and oxygen but the HO
  is not in a 21 ratio
• Tend to be large molecules -- an example of a
  neutral lipid is below

33

• Neutral lipids are formed from the union of one
  glycerol molecule and 3 fatty acids
• 3 fatty acids glycerol ----gt neutral fat
  (lipid)
• 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

34
PROTEINS

• contain the elements carbon, hydrogen, oxygen,
  and nitrogen
• composed of MANY amino acid subunits
• It is the arrangement of the amino acid that
  forms the primary structure of proteins.
• 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.

35
AN R GROUP IS ANY GROUP OF ATOMS THIS CHANGES
THE PROPERTIES OF THE PROTEIN!
36
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.

37
(No Transcript)
38
Major Protein Functions

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

39
Dipeptide

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

40
Hydrolysis of a dipeptide

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

41
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

42
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

43
(No Transcript)
44
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)

45
RNA (ribonucleic acid)

• directs cellular protein synthesis
• found in ribosomes nucleoli

46
CHEMICAL REACTIONS

• a process that changes one set of chemicals into
  another set of chemicals
• REACTANTS elements or compounds that enter into
  a chemical reaction
• PRODUCTS elements or compounds that are
  produced in a chemical reaction
• Chemical reactions always involve the breaking of
  bonds in reactants and the formation of new bonds
  in products.

47

• In a reaction, energy is either TAKEN IN
  (ENDOTHERMIC) or GIVEN OFF (EXOTHERMIC)
• Can you think of an everyday example of each type
  of reaction?

48
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)

49

• 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.

50
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

51
"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

52
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

53

• 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)

54
(No Transcript)
55

• 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.