Unit 1: Metabolic Processes Are You Ready?

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Unit 1 Metabolic ProcessesAre You Ready?

• SBI4U1
• DAY 1

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Scanning electron micrographAnimationhttp//micr
o.magnet.fsu.edu/primer/java/electronmicroscopy/ma
gnify1/index.html
1.1 Chemical Fundamentals
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Atoms of the same element with the same number of
protons, but a different number of neutrons
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Uses of Isotopes

• Radioisotopes can be used to help understand
  chemical and biological processes in organisms.
• They can also be used in radiometric dating which
  is useful in determining the age of fossils
• They also have numerous medical applications

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• ExampleA solution of phosphate, containing
  radioactive phosphorus-32, is injected into the
  root system of a plant.
• Since phosphorus-32 behaves identically to that
  of phosphorus-31, the more common form of the
  element, it is used by the plant in the same way.
  
• A Geiger counter is used to detect the movement
  of the radioactive phosphorus-32 throughout the
  plant.
• This information helps scientists understand the
  detailed mechanism of how plants utilized
  phosphorus to grow and reproduce.

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• Brachytherapy is a form of radiation therapy
  where radioactive isotopes in the form of small
  pellets (called seeds) are inserted into
  cancerous tumours to destroy cancer cells while
  reducing the exposure of healthy tissue to
  radiation.
• It is currently approved for treatment of
  prostate cancer and cancers of the head and neck.
  There are also studies underway to see whether it
  can be used in the treatment of lung cancer.

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• In radioimmunotherapy, doctors inject antibodies
  that have isotopes attached.
• The antibodies flow through the bloodstream and
  deliver the radioactivity by seeking out and
  latching onto proteins on the cancerous cells.
• RIT is used the treatment of blood cell cancers,
  such as leukemia and lymphoma. It is also being
  looked at for treatment of prostate, colorectal
  and pancreatic cancers.

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Valence electrons are those electrons that are
available for bonding.The electrons in the
outermost s and p orbitals
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Orbitals volumes of space around the nucleus
where electrons are most likely found
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Ionic and Molecular Compounds

• Formation of sodium chloride

• Formation of hydrogen chloride

A metal and a nonmetal transfer electrons to form
an ionic compound. Two nonmetals share electrons
to form a molecular compound.
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Ionic Compounds

• Ionic compounds consist of a lattice of positive
  and negative ions.

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Covalent BondHow many electrons are involved in
each covalent bond?
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Double and Triple Bonds

• Atoms can share four electrons to form a double
  bond or six electrons to form a triple bond.

O2
N2

• The number of electron pairs is the
• bond order.

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Electronegativity is a measure of an atom's
ability to attract a shared electron pair when it
is participating in a covalent bond with another
atom By calculating the net Electronegativity of
the atoms, we can determine the distribution of
electrons and the nature of the molecule
The Pauling scale of electronegativity
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Electronegativity

• nonpolar bond electrons are shared equally

• polar bond electrons are shared unequally
  because of the difference in electronegativity.

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Electronegativity

• Number assigned to each element (En)
• Difference in En helps determine the nature of
  the bond ionic or covalent
• Covalent bonds can be either nonpolar covalent or
  polar covalent
• This difference has Biological Consequences

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Bond Polarity

• A polar bond can be pictured using partial
  charges

?
??
?? 0.9
2.1
3.0
Electronegativity Difference
Bond Type
0 - 0.5
Nonpolar
0.5 -1.7
Polar
?1.7
Ionic
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MOLECULAR SHAPE

• When atoms form a covalent bond, the valence
  electron pairs arrange themselves to be as far
  away from each other as possible.
• This change to the orientation of the valence
  electrons is Hybridization.
• Symmetry of shape will also determine polarity of
  molecule or functional group.

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• Methane CH4 tetrahedral shape equal 109.5
  angle between valence electrons symmetrical
  nonpolar

• Ammonia NH3 pyramidal shape equal 107 angle
  between valence electrons asymetrical shape
  polar molecule

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To determine if a molecule is polar or nonpolar,
must consider both electronegativity and shape
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Which of the following is the essential
characteristic of a polar molecule?a.Contains
double or triple bondsb.is formed at extremely
low temperaturesc.contains ions as part of the
structured.has an asymmetrical distribution of
electrical chargee.contains the element oxygen
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intermolecular forces of attractionExamples
London forces, dipole-dipole forces, hydrogen
bonds
Van der Waals forces
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London forces - weak/temporary/ random
charges-gases at room temperature- volatile
e.g. octaneDipole-dipole-between polar
molecules-stronger- e.g. HCl
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• London forces are weak because (1.) partial
  charges are involved and (2.) because they are
  temporary. They arise from the random movement of
  electrons in atoms and molecules.

a) small collection of nonpolar molecules b) a
nonpolar molecule may temporarily have a slight
excess of electrons in one portion of the
molecule c) During the brief interval that these
temporarily polar molecules exist, they are
attracted to each other
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• Hydrogen bonds strongest intermolecular bonds

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Properties of water are due to hydrogen bondsI.
They are responsible for the surface tension
properties of water.II. They are responsible for
the relatively high boiling point of water.III.
They are responsible for adhesion- cohesionIV.
The make water a good heat sink.V. The maximum
density of water occurs at 4C
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Solubility

• The solubility of many molecules is determined by
  their electronegativity and molecular structure.
• Sugars, such as glucose, have many hydroxyl (OH)
  groups, which tend to increase the solubility of
  the molecule.
• Molecules that lack polar covalent bonds, such as
  lipids, clump together in water because they are
  excluded from interacting with the polar groups.

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Hydrophobichttp//programs.northlandcollege.edu/b
iology/Biology1111/animations/hydrogenbonds.html
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and hydrophilic

• like dissolves like
• -polar nature excellent solvent
• http//programs.northlandcollege.edu/biology/Biolo
  gy1111/animations/dissolve.html

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Functional Groups

• Functional groups are clusters of atoms with
  characteristic structure and functions.
• Generally, they are polar covalent groups
• They increase the solubility of a substance in
  water.
• The hydroxyl (OH) groups in glucose are what make
  this sugar soluble

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Acids and Bases

• pH scale is used to measure
• Is an inverse logarithmic scale
• pH7 is neutral
• pH ? 7 means high H
• pH gt 7 means high OH-

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Conjugate Acids and Bases

• Weak/reversible
• Act to absorb protons or release proton to
  maintain constant pH

If an acid has the formula CH3COOH, then the
conjugate base would be
CH3COO-.
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Buffers are compounds that tend to neutralize the
pH of a solution by combining with either H ions
or OH- ions to keep the solution neutral. Buffers
play a very important role in most organisms, as
many organisms cannot live at pHs that are too
acidic or too basic.
CH3COOH    lt -------- gt    CH3COO-       H
The acetic acid molecule (CH3COOH) acts as a
store of base and acid ions. The acetate ion
(CH3COO-) acts like a base which accepts H and
neutralizes them. The hydrogen ion (H) acts
like an acid which accepts OH- and neutralizes
them.
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In living organisms, buffers maintain pH in the
cells within a narrow range, allowing enzymes to
functionBuffer Animation!http//www.mhhe.com/phy
ssci/chemistry/essentialchemistry/flash/buffer12.s
wf
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Review 1.1 Chemical FundamentalsAnswer p.23
4,6,7,8,10,12,14,15
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• What type of intermolecular forces of attraction
  must be overcome to melt each of the following
  solids?
• A) ice, H2O (s) B) iodine, I2 (s)

4 a) Hydrogen bonds must be broken to melt ice,
H2O (s) , into water H2O (l) . b) London forces
must be broken to melt I 2 (s) into I 2 (l) . -
the only intermolecular forces that hold nonpolar
molecules to one another
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Is carbon tetrachloride, CCl 4 , and ammonia, NH
3 , polar or nonpolar?

• 6. Based on VSEPR theory and electronegativity
  values, carbon tetrachloride, CCl 4 , is nonpolar
  due to the symmetrical arrangement of its polar C
  Cl bonds and ammonia, NH 3 , is polar due to
  the nonsymmetrical arrangement of its polar N-H
  bonds.

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Why is table salt, NaCl (s), soluble in ethanol,
CH 3 OH (l), but not soluble in gasoline, C 8 H
18 (l) ?

• 7. Table salt, NaCl (s), is soluble in ethanol,
  CH 3 OH (l) , because Na and Cl ions are
  attracted to polar ethanol molecules.
• Na and Cl ions are not attracted to nonpolar
  gasoline molecules (C 8 H 18 (l) ).

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What is the difference between a weak acid and a
dilute solution of a strong acid?

• 8. A weak acid only partially dissociates to
  release H ions, while a strong acid completely
  dissociates.

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Describe the components of a buffer and the role
each plays in helping maintain a constant pH.
10. A buffer is formed from a weak acid and a
weak base in approximately equal concentrations.
The weak acid will donate a hydrogen ion to a
base, neutralizing it, and its conjugate base
will accept a hydrogen ion form an acid,
neutralizing it.
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What is the difference between ionic and polar
covalent bonds?

• 12. Ionic bonds are formed because of a complete
  transfer of electrons from one element to another
  element.
• Polar covalent bonds result from the unequal
  sharing of electrons between two different
  elements.

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• Hydrophobic the tendency of nonpolar molecules
  to exclude water.
• Hydrophilic the tendency of polar and ionic
  substances to dissolve in water.

a) C6H 6 (l) is b) C2H5OH (l) is c) CCl
4 (l) is
hydrophobic
hydrophilic.
hydrophobic
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• 15. What property of water accounts for each of
  the following observations?

a) A steel sewing needle floats on water but a
large steel nail sinks.
A steel sewing needle floats on water because the
surface tension of the water holds it there,
while a large steel nail sinks because the force
of gravity on the nail is greater than the
surface tension of the water.
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b) Dogs pant on a hot summer day.

• Dogs pant to cool their bodies. The evaporation
  of water requires heat, due to its high latent
  heat of evaporation, which it gets from the dogs
  tongue.

c) Water creeps up the wall in a flooded room.
Water creeps up the walls of a flooded room due
to the cohesion of water molecules to molecules
in the wall because of hydrogen bonding.
d) Hands are usually washed in water.
Hands are usually washed in water because water
is considered the universal solvent and most
substances will be dissolved and washed away.
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1.2 The Chemicals of Life 
DAY 3 - Carbohydrates. Structure/function.
Biological importance. Model kits build
glucose, maltose, amylase, glycogen and
cellulose. Relate structure to properties to
function
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The following structural formula is
representative of which functional
group?a.sulfhydrylb.carboxylc.hydroxyld.
aminoe.carbonyl 
carboxyl
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The following structural formula is
representative of which functional
group?a.sulfhydrylb.carbonyld.hydroxyld.amino
e.carboxyl 
AMINO
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The following structural formula is
representative of which functional
group?a.sulfhydrylb.carbonylc.hydroxyld.amino
e.carboxyl 
CARBONYL
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Biological macromolecules

1. Carbohydrates
2. Lipids
3. Proteins
4. Nucleic acids

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Anabolic reactions

• Require energy endothermic reaction
• Produce big molecules
• By removing water and forming new covalent bonds
  (dehydration synthesis)
• Require enzymes

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Catabolic reactions

• Produce energy exothermic
• Break big molecules into smaller
• Adding water to break covalent bonds (hydrolysis
  reactions)
• Require enzymes

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CARBOHYDRATESCH2O n

• Monosaccharides 1
• Disaccharides 2
• Oligosaccharides 3 10
• Polysaccharides greater than 10

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Function

1. Energy glucose
2. Longer term energy needs/storage glycogen
   (animals) and starch (plants)
3. Structural cell wall of plants (cellulose)
4. Recognition communication (cell surface markers
   identification of self vs non-self
   glycoproteins)

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carbohydrates

• Classified based on
• Size of base carbon chain
• Number of sugar units
• Location of CO
• stereochemistry

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Monosaccharides (various isomers same chemical
formula different chemical and physical
properties)
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Some important monosaccharides

• D-glyceraldehyde simplest sugar
• D-glucose Most important in diet common names
  include dextrose, grape sugar, blood sugar
• D-fructose sweetest of all sugars
• D-galactose Part of milk sugar
• D-ribose used in RNA

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Glycosidic linkages (ether) covalent bonds
holding monosaccharides to one another
Dehydration synthesis (mostly 1-4 linkage) -
starch -glycogen -cellulose
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Several simple sugars attached to one another
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In humans the function of glycogen is to keep
glucose available.
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Glucose in Water Animation

• http//www.stolaf.edu/people/giannini/flashanimat/
  carbohydrates/glucose.swf

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Based on location of CO

• Aldose
• Aldehyde CO

• Ketose
• Ketone CO

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Steochemistry study of the spatial arrangement
of molecules

• Stereoisomers have
• The same order and type of bonds
• Different spatial arrangements
• Different properties
• Many biologically important chemicals, like
  sugars, exist in stereoisomers.

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Enantiomers molecules that have  opposite spatial
configuration and are optically active.
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Day 4 Lipids

• Lipids. Structure/model of fatty acid, glycerol,
  triglyceride. Saturated, unsaturated, cis/trans
  properties and function. Steroids, waxes and
  phospholipids.
• Homework
• Read and summarize proteins for next class.
• http//www.tvdsb.on.ca/westmin/science/sbioac/bioc
  hem/triglyc.htm
• Lipids Animations!
• http//www2.nl.edu/jste/lipids.htm

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Lipids Also called Fats and Oils

• Lipid Facts
•  Fat  Solid at room temperature
• Oil  Liquid at room temperature
• Contribute 30-50 of calories for Americans
• Soluble in organic solvents, i.e., not soluble in
  water (They are all hydrophobic)
• Lipids are primarily consumed for energy
• Diverse groups no basic sub-unit

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Function

• 1. Energy storage fats long-term (2x energy of
  CHOs)
• 2. Cushions/protects organs e.g. kidney,
  reproductive organs, etc.
• 3. Insulation helps maintain constant internal
  temperature
• 4. Structural cell membrane
• -phospholipid - cholesterol (fluidity to memb)
• 5. Vitamins and Hormones (regulation of
  biological processes)
• -steroids
• -testosterone, estrogen, progesterone
• -vit. D (co-enzyme)
• 6. Waxes waterproof/protective coating

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When a molecule of glycerol reacts with one or
more fatty acids an ester linkage results. The
formation of this linkage is a result of a
reaction between an alcohol and a carboxylic acid
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Formation of a triglyceride
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Fatty Acid Nomenclature

• Based on
• Number of carbons
• Number of double bonds
• Oleic Acid

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• Saturated
• No double bonds
• Solid at room temperature
• Implicated in coronary heart disease (CHD)
• Meats, dairy
• Unsaturated
• Has double bonds
• Fluid at room temperature
• Less stable to off flavor development
• Vegetables, legumes, fish

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LIPIDS
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Unsaturated double bonds between 1 or more
carbons
Saturated only single bonds
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• Polyunsaturated  2-5 double bonds
• Highly Unsaturated  gt5 double bonds
• Omega 3 Fatty Acids
• Good for reducing CHD
• High in fish
• Linolenic Acid, an Omega 3 Fatty Acid

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Micelle - fatty acids are the main component of
soaps, where their tails are soluble in oily dirt
and their heads are soluble in water to emulsify
and wash away the oily dirt(However, when the
head end is attached to glycerol to form a fat,
that whole molecule is hydrophobic)
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Phospholipids

• Modified fatty acid
• Two fatty acids tails and a choline-phosphate
  head
• Tails are hydrophobic
• Head is hydrophilic
• Cell membrane

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(4 ring compounds)
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Cholesterol

• Why is cholesterol important in the body?
• Hormone production
• Membranes
• Vitamin D
• Absorption of fats
• Foods high in cholesterol
• Organ meats
• Eggs
• Shellfish

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• Waxes
• Extremely hydrophobic
• Cutin cuticle of leaf

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When one fat molecule is broken down to glycerol
and fatty acids, the number of hydroxyl ions
consumed in order to neutralize the fatty acids
would be a.0, b.3, c.1, d.4,
e.2
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Fat uses in Foods

• Flavor
• Fried Foods
• Popcorn
• Texture
• Shortening (Flakiness)
• Moistness
• Stabilizers (emulfsifiers)
• Lecithin
• Mono and diglycerides

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• Relationship of Fat and Cholesterol on CHD
• CHD is No. 1 killer of Americans
• Approximately1 million deaths/year
• General Agreement
• Cholesterol and tryglycerides build up in
  arteries and reduce blood flow to heart.
• Hypothesis
• Reduce cholesterol and fat in diet and reduce CHD
  

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Issues w/ Fat and CHD

• Cholesterol not only Factor in CHD
• Heredity
• Stress
• Smoking

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Response from Industry

• Theory  Produce fat-like substance that has
  reduced metabolism
• Examples
• Olestra - sucrose polymer
• Expected for use in all types of foods
• Issues  Anal leakage and vitamin loss

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EXPERTS SAY...

• Lower fat intake to 30 of daily calories
• Consume proper amount of fatty acids in diet
• Have approximately 11.51 ratio of saturated,
  monounsaturated and polyunsaturated fats
• Dietary fiber may be of some benefit
• Some suggest increase intake of Omega 3 Fatty
  Acids
• May reduce blood cholesterol

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Day 5 Proteins

• Functions. Amino acid structure and properties of
  R groups. Primary, secondary, tertiary and
  quaternary structure and bonds.
• Homework
• Read and summarize nucleic acids
• http//www.tvdsb.on.ca/westmin/science/sbioac/bioc
  hem/amino.htm

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ProteinsNext to water, protein is the major
component of living cells!
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The 20 amino acids see pg. 42
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Polypeptide structure - Animationhttp//science.n
hmccd.edu/biol/dehydrat/dehydrat.html
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Essential Amino Acids

• Humans can not synthesize them they are dietary
  requirements (there are 8)

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Protein structures Animationhttp//www.stolaf.edu
/people/giannini/flashanimat/proteins/protein20st
ructure.swf
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Primary Structure "The sequence of amino acids
in the polypeptide chain."
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Secondary structure The ?Helix nature of wool is
what makes it shrink.
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The ?pleated sheet structure is often found in
many structural proteins, such as "Fibroin", the
protein in spider webs.
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Tertiary structure
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Globular proteins-spherical in nature-Common
globular proteins include egg albumin,
hemoglobin, insulin, and many enzymes.
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Quaternary Structure
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Proteins when heated can unfold or "Denature".
This loss of three dimensional shape will usually
be accompanied by a loss of the proteins
function. If the denatured protein is allowed to
cool it will usually refold back into its
original conformation.
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Dipeptide hydrolysis
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Day 6 Nucleic acids DNA and RNA structure and
differences. Bonds in DNA. Nucleoside,
nucleotide, purine pyrimidine. Other nucleic
acids ATP, NAD, NADP, FADp.56 1,3,4,5 ,6,9,10,
11,13,14, 16 ,17,18,19
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Base pairing in DNA anitiparallel
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Nucleotides (Both Sides of Double Helix)
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Adenosine triphosphate (ATP) major energy
carrier
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Coenzyme A (CoA)
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Flavin Adenine Dinucleotide (FAD)
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Nicotinamide Adenine Dinucleotide (NAD)
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Nicotinamide Adenine Dinucleotide Phosphate
(NADP)
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PRACTICE QUESTIONSA) Structurally, a
sulfhydryl group is most similar to which of the
following? 
a.carbonyl, b.hydroxyl, c.carboxyl, d.amino,
e.acetyl
B) A nitrogen atom would be found bonded to a
hydrogen atom in which of the following
functional groups?a.sulfhydryl, b.carbonyl,
c.hydroxyl, d.amino, e.carboxyl
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C) In terms of maintaining the shape of an
enzyme, the strongest bonds involved area.
covalent (disulfide) bonds, b.hydrogen bonds,
c.dipole-dipole interactions, d.hydrophobic
bonds, e.ionic interactions
D) Which of the following functional groups would
be found in a monosaccharide?a. carbonyl and
hydroxyl, b.carboxyl and carbonyl, c.glycosidic
and hydroxyl, d.hydroxyl and sulfhydryl,
e.carboxyl an amino
E) Of the following, which is not considered to
by a polymer?a. cellulose, b.protein, c.RNA,
d.fat, e.starch
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TEXT ANSWERS p.56

1. Why are hydrocarbons all nonpolar molecules?

Hydrocarbons are all nonpolar molecules because
of the symmetrical arrangement of their C-C and
C-H bonds.
2. List the elements found in all carbohydrates,
indicating the atomic ratio in which they are
found.
carbon, hydrogen, and oxygen in the ratio 121
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• 3. A) Define functional group.
• b) What advantage is conferred to biological
  molecules by having functional groups?

A) In organic chemistry, a functional group is a
reactive cluster of atoms attached to the carbon
backbone of organic molecules. B) Biological
molecules with functional groups are more
reactive than molecules without functional groups.
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• 4. Why are monosaccharides more soluble in water
  than are triacylglycerols?

Monosaccharides are more soluble in water than
triacylglycerols because of the large number of
asymmetrical polar bonds.
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Carbohydrate (or derivative) Main function
Glucose Primary source of energy in most living organisms
Starch (amylose) Energy storage in plant cells
Chitin Structural carbohydrate in insects, crustaceans, and mushrooms
Cellulose Plant cell wall component
glycogen Energy storage in animal cells
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• 6. Describe the difference between a condensation
  reaction and a hydrolysis reaction.

A condensation (dehydration synthesis) reaction
releases a water molecule in an anabolic
reaction, while a hydrolysis reaction adds a
water molecule across a chemical bond in a
catabolic reaction.
9. Why are glucose and galactose monomers?
Glucose and galactose are isomers because they
have the same chemical formula (C 6 H 12 O 6 )
but different arrangements of atoms.
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10. Why do animals use lipids instead of
carbohydrates as energy-storing molecules?
First, lipids contain more energy per gram than
carbohydrates. Secondly, lipids offer greater
thermal insulation than carbohydrates and allow
animals to survive in frigid environments.
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11. A) How many fatty acids are attached to a
glycerol molecule in a triacylglycerol? In a
phospholipid? b) What two functional groups
react when a fatty acied bonds to a glycerol
molecule?

• A) Three fatty acids are attached to a glycerol
  molecule in a triacylglycerol and two fatty acids
  are attached to a glycerol in a phospholipid.
• B) Hydroxyl and carboxyl groups react when a
  fatty acid molecule bonds to a glycerol molecule.

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13. Distinguish between a polypeptide and a
protein.
A polypeptide refers to a single chain of amino
acids with primary, secondary, or tertiary
structures, while a protein consists of one or
more polypeptide chains twisted and folded
together into a specific shape. The amino acid
sequence of a polypeptide chain determines the
three-dimensional shape of the protein.
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• 14. B) The functional group found on the R-group
  side chain is a carboxyl group.
• C) This amino acid is acidic because of its
  acidic functional group.

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16. State two similarities and two differences
between an alpha helix and a beta-pleated sheet.

• Similarities between alpha-helix and beta-pleated
• - they determine the secondary structure
• - they occur because of hydrogen bonding
• Differences
• - the type of structure formed (spiral helix vs.
  flat sheets)
• - alpha helix is formed by hydrogen bonding
  between successive amino acids along a
  polypeptide chain, while a beta-pleated sheet is
  formed from hydrogen bonds between two parallel
  polypeptide chains.

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17. A) List the four types of bonds that
stabilize a proteins tertiary structure. b)
Which of these bonds is the strongest?

• A) The four types of bonds that stabilize
  tertiary structure are
• - hydrogen bonds (a type of van der Waals
  force),
• - disulfide bridges (covalent bonds),
• - ionic bonds, and
• -hydrophobic interactions ( a type of van der
  Waals force).
• B) The strongest of the above are the disulfide
  bridges because they are the only covalent bond.

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18. Describe two differences between RNA and DNA
nucleotides.

• Two differences between RNA and DNA are the
  sugar found in the nucleotide, RNA has ribose and
  DNA has deoxyribose, and that RNA is single
  stranded while DNA is double.
• Also DNA contains the nitrogenous base thymine,
  (T) while RNA contains uracil (U) instead.

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19. State the rule for base pairing in DNA,
indicating the number of hydrogen bonds that
forms in each case.

• The rule for DNA base pairing is adenine with
  thymine, forming two hydrogen bonds, and cytosine
  with guanine, forming three hydrogen bonds.

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DAY 7 SEE HANDOUT1.3 An Introduction to
Metabolism (DAY 8)Read section 1.3 p.58-68
Answer 2,3,6,7,8Thermodynamics the science of
energy transformations (flow of energy through
living and non-living systems)
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All living things require ENERGY which is the
capacity for doing work

• Forms of energy
• thermal
• light
• chemical
• electrical

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KINETIC ENERGY

• Energy of motion
• Falling water
• Pistons in a car engine
• Skier going down a hill
• examples on a molecular scale include the energy
  of vibrations, random diffusion, and heat.

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POTENTIAL ENERGY

• stored energy
• Example Molecules of glucose have potential
  energy, stored in bonds

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FIRST LAW OF THERMODYNAMICS

• Energy can neither be created nor destroyed, but
  can be transformed from one form to another.
• E.g. during photosynthesis, light energy from
  the Sun is transformed into chemical energy
  stored in the bonds of glucose

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• During cellular respiration, the energy in the
  bonds of glucose is released and is transformed
  into new molecules, motion, and heat energy.

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The Second LAW OF THERMODYNAMICS Every energy
transformation increases the entropy of the
universe.

• There is ALWAYS some loss of useful energy.

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The second law of thermodynamicsIn all
processes or reactions, some of the energy
involved irreversibly loses its ability to do
work. orIn any reaction the amount of
molecular disorder always increases
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Entropy is a measure of the randomness or
disorder in a collection of objects

• Entropy increases
• when solids become liquids or gases
• Complex molecules react to form simpler molecules
  (catabolic reactions)
• During diffusion

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Living systems seem to break the second Law of
Thermodynamics

• Anabolic processes in cells build highly ordered
  structures (e.g. proteins and DNA) from a random
  assortment of molecules (amino acids and
  nucleotides) in the cell fluids.

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• On a large scale, living organisms build and
  maintain highly ordered structures such as cells,
  tissues, organs and systems, as well as nests,
  webs and homes.
• All of these changes cause the universe to become
  a little more ordered.

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But these anabolic processes are coupled to
catabolic processes

• Which release free energy and thermal energy and
  increase the entropy of the universe.
• Living organisms create order in a local part of
  the universe at the expense of greater a greater
  amount of disorder in the universe as a whole.

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Free energy       It is clear that we should be
concerned only with energy available to do useful
work, so-called free energy or Gibbs energy.
Josiah WillardGibbs(1839 - 1903)
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The relationship between energy change, entropy
change, and the temperature of a reaction is best
described in terms of free energy
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• Exothermic Reactions
• Produce energy (exergonic reactions)
• Tend to increase entropy (therefore, spontaneous)
• - delta G value
• E.g. cellular respiration

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Exothermic Reaction
178
During this part of the reaction the molecules
are said to be in a transition state.
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Activation Energy amount of energy needed to
strain and break the reactants' bonds in a
biochemical reaction
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• B) Endothermic Reactions
• Require energy (endergonic reactions)
• Tend to decrease entropy (because they create
  big/organized molecules)
• Are not spontaneous
• delta G values
• E.g. photosynthesis

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REDOX REACTIONS

• Biochemical reactions are essentially energy
  transfers.
• Often they occur together, "linked" in
  oxidation/reduction reactions.
• Reduction is the gain of an electron. Sometimes
  we also have H ions along for the ride, so
  reduction also becomes the gain of H.
• Oxidation is the loss of an electron (or
  hydrogen).
• In oxidation/reduction reactions, one chemical is
  oxidized, and its electrons are passed (like a
  hot potato) to another chemical.

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• OIL RIG (oxidation is loss, reduction is gain)
• Many metabolic processes (glycolysis, Kreb's
  Cycle, and Electron Transport Phosphorylation)
  involve the transfer of electrons by redox
  reactions.

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a.the synthesis of glucose in a plant
All but one of the following are
examples of oxidizing reactions. Which one is not
an oxidizing reaction? a.the synthesis of glucose
in a plant b.a log burning in a fireplace c.the
breakdown of glucose in a cell d.a newspaper
turning yellow as it ages e.the rusting of a nail
187
In the following chemical reaction, a
oxidation/reduction reaction is
occurring.C6H12O6 6 H2O 6 O2 ? 12 H2O 6
CO2because electrons are transferred from one
substance to another
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Chemical intermediates - NucleotidesSome
compounds contain high-energy bonds, e.g. the
bond between phosphate groups of tri- and
diphosphate nucleotides    
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Physical energy intermediates       An equally
common way of storing energy is in the form of
potential energy, as an electrical gradient
(potential), concentration gradient, or pH
gradient. Some proteins (e.g. cotransporters)
are able to utilize the flow of ions directly to
power their endergonic reactions.
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ANSWERS - p.58-68 1.3 An Introduction to
Metabolism
2. Identify each of the following activities as
either anabolic or catabolic.

• A) protein synthesis is anabolic
• b) Digestion is catabolic
• c) DNA synthesis is anabolic
• d) Photosynthesis is anabolic
• e) Cellular respiration is catabolic.

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• 3. Metabolism represents the sum of all anabolic
  and catabolic reactions in a cell or organism.
• 6. A) an arm raised a decrease in entropy
  because potential energy is increased.
• b) Protein is digested into amino acids in the
  duodenum an increase in entropy, because a large
  number of amino acids ae more randomly arranged
  than in a protein molecules in which the amino
  acids are attached to one another in a particular
  sequence.
• c) Chromosomes move along spindle fibres the
  cells free energy is used to move chromosomes
  into a more ordered arrangement entropy
  decreases as organization increases.

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• 6. D) oxygen diffuses into alveoli in the lungs
  an increase in entropy as oxygen molecules
  trapped in alveoli diffuse into capillaries and
  move randomly through the circulatory system.
• e) A cell divides an increase in entropy as the
  system is becoming more random, and much of the
  cells free energy is used in cell division two
  cells represent a more random arrangement of
  objects than a single cell

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• 7. Gibbs free energy represents energy that can
  do useful work.
• 8. A) Heat death of the universe refers to the
  state where all the particles and energy of the
  universe will move randomly, unable to do useful
  work. All energy will still be present, but it
  will be uniformly distributed and unable to apply
  a push or pull to anything.
• b) Heat death of the universe is related to the
  death of an organism because a dead organism is
  unable to do work. Energy is still present, but
  it cannot perform the work that is necessary to
  keep the organism alive.

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1.4 ENZYMESAn enzyme is a biological
protein-based catalyst
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Enzyme nomenclature Enzymes are divided into 6
groups based on the chemical reactions they
catalyze.

1. Oxidoreductases
2. Transferases
3. Hydrolases
4. Lyases
5. Isomerases
6. Ligases (synthetases)

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Enzymes online tutorial

• Excellent animations
• http//www.lewport.wnyric.org/jwanamaker/animation
  s.htm
• http//www.northland.cc.mn.us/biology/Biology1111/
  animations/enzyme.html
• http//highered.mcgraw-hill.com/sites/0072437316/s
  tudent_view0/chapter8/animations.html

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Substrate the reactant that an enzyme acts on
when it catalyzes a chemical reaction
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The Induced-fit model of enzyme-substrate
interaction describes a protein as a dynamic
molecule that changes its shape to better
accommodate the substrate
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Factors Affecting Enzyme Activity

1. Temperature
2. pH
3. Substrate Concentration

200
37?C is the optimum temperature in most living
systems(at high/temperatures enzyme function is
altered denatured enzyme)
201
- most enzymes work best at pH 7 (narrow
range) - however, some such as pepsin have a
pH of 3 - changing the pH will alter the
enzymes 3D shape
pH
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Substrate Concentration

• As concentration increases, the rate of reaction
  increases
• Maximum occurs when all the enzymes are working

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cofactors

• Inorganic atoms (Zn, Ca, Fe,) which bind
  temporarily to enzyme

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coenzyme

• Organic molecules
• E.g. vitamins
• Necessary to activate enzyme and allow it to bind
  to substrate
• Also can help weaken bonds in substrates

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Controlling Enzyme Activity

• 1. Regulating transcription/translation .
• By regulating transcription/translation,
  production of enzymes can be turned off/on.
• Some end products can act as transcription
  factors and inhibit the transcription/translation
  of enzymes

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• 2. Competitive Inhibition A substrate mimic
  (molecule that has the same configuration as the
  substrate) can enter into ACTIVE SITE and block
  enzyme action.
• Some antibiotics are competitive inhibitors
• E.g. HIV (protease inhibitors)
• Penecillin (inhibits a bacteria transpepsidase
  cell wall is not built properly)
• When bind permanently (poisons or toxins)
• When bind temporarily (can be disloged by
  increasing concentration of substrate)

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Inhibitors
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• 3. Allosteric Inhibition (Feedback inhibition).
  Allows an enzyme to be temporarily inactivated.
• Binding of an allosteric inhibitor changes the
  shape of the enzyme, inactivating it while the
  inhibitor is still bound.
• This mechanism is commonly employed in feedback
  inhibition. Often one of the products of a series
  of reactions act as an allosteric inhibitor and
  blocks the pathway.
• AKA non-competitive inhibition

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3.
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Regulation of Enzyme Action4. Allosteric
Activators

• Substances bind to an allosteric site on enzyme
  and increase efficiency

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a) Substrate and enzymeb) Competitive
Inhibitorc) Non competitive inhibitor
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a. starch hydrolysis for the food industryb.
proteases to coagulate milk for the manufacture
of cheesec. removal of lactose from dairy
products for lactose intolerant peopled.
proteases added to detergents to remove
protein-based stains
Applications of enzymes for commercial or
industrial use!
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Enzymes are _________________________ catalysts,
and as such they _________________________ a
chemical reaction without being
_________________________ in the process. Enzymes
work by reducing the _________________________.
The _________________________ is the reactant
that an enzyme act on. This reactant binds to a
particular spot on the enzyme known as the
_________________________. Enzymes are very
_________________________ for the reactant to
which they bind. The names of enzymes usually end
in _________________________. 
ANS protein, speed up, consumed, activation
energy, substrate, active site, specific, ase
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Temperature and pH affect enzyme activity. As
with all other reactions, enzyme-catalyzed
reactions _________________________ in speed with
an increase in temperature. However, as the
temperature increases beyond a critical point,
the protein structure begins to get disrupted ,
resulting in _________________________ and loss
of enzyme function. Every enzyme has a(n)
_________________________ temperature at which it
works best and activity tends to decrease on
either side of this temperature. Most human
enzymes work best at around ______________________
___. Some enzymes require nonprotein
_________________________, such as zinc and
manganese ions. Other enzymes may require organic
_________________________ such as NAD and NADP.
A variety of substances inhibit enzyme activity.
___________________________________ are so
similar to the enzyme's substrate that they are
able to enter he enzyme's active site and block
the normal substrate from binding. This process
is reversible and can be overcome be increasing
the concentration of the enzyme's substrate.
Another class of inhibitors does not affect an
enzyme at its' active site, they are called
___________________________________ and their
effect cannot be overcome by adding more
substrate.
ANS increase, denaturation, optimal, 37?C,
cofactors, coenzymes, Competitive inhibitors,
non-competitive inhibitors
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Practice!1. Define catalyst

• A chemical that speeds up the rate of reaction
  without being consumed in the reaction.

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• 2. Draw a labeled free-energy diagram to
  illustrate the effect of an enzyme on the
  activation energy of a hypothetical reaction.
  (Assume it is an exergonic reaction.)
• 3. What is meant by the statement, an enzyme
  cannot affect the free-energy change of a
  reaction?

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• 5. How does an enzyme lower the activation energy
  of a biochemical reaction?

The enzymes do this by bringing the substrates
into the correct geometry and by putting stress
on the necessary chemical bonds.
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• 6. How do competitive enzyme inhibition and
  noncompetitive enzyme inhibition differ?

A competitive inhibitor binds to the active site
of an enzyme, preventing the substrate(s) from
binding. In this case, the inhibitor competes
with the substrate for the active site. A
noncompetitive inhibitor attaches to an enzyme at
a binding site other than the active site. This
causes a conformational change in the enzymes
protein structure that causes a loss of affinity
of the active site for its substrate.
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• 8. What happens to an enzyme after it has
  catalyzed a reaction?

After an enzyme catalyzes a reaction, it will
catalyze the same reaction again.
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For an exothermic reaction, ?H is negative.For
an endothermic reaction, ?H is positive.