Transcript Week 10 notesx

Biology 20
Biochemistry
Explain how the human digestive and
respiratory system exchange energy and
matter with the environment
• Describe the chemical nature of
carbohydrates, lipids, and proteins and
their enzymes.
Biochemistry
Element - A substance consisting entirely of one
type of atom, for instance, carbon, hydrogen or
oxygen. Elements can combine into compounds
to form other substances.
Ion – an atom or group of atoms that have
a charge
Compound - A substance consisting of more
than one atom or one type of element, e.g.
carbon dioxide is a compound.
Biochemistry
pH scale - scale is commonly used over a
range 0 (acidic) to 14 (basic).
• Acid - Substances that have a pH of lower
than 7 (neutral) that can dissolve in water.
Base - Substances that have a pH of higher
than 7 (neutral) that can dissolve in water.
Metabolism
• Metabolism: All the chemical reactions
that occur within the cells.
• Monomer: Basic subunit used to build
larger molecules. Eg. Amino acids
• Polymer: Molecules composed of many
basic subunits bonded together
– Eg. Many amino acids bond together to form
on protein.
Polymer:
Protein
Monomer:
Amino acid
Chemistry Review
• Isomer - A chemical with the same
number and types of atoms as
another chemical, but possessing
different properties.
Catabolic Reactants
• Complex chemicals broken down into
smaller units
• Eg. Breaking down food
Anabolic Reactions
• Small units combine to make larger
molecules
• Eg. Plants and photosynthesis
Dehydration Synthesis
• The process by which larger molecules
are formed by the removal of water from
two smaller molecules.
+
H20
Hydrolysis
• The process by which a larger molecule
is broken down into two smaller
molecules. Water is taken up at the
broken bond site.
+
H2 0
Chemistry Review
• Organic Compounds
– contain carbon atoms that are linked together
• Inorganic Compounds
– do not contain linked carbon atoms.
4 Types
• There are 4 major types of organic molecules
important in biology.
– Carbohydrates
• monosaccharides, disaccharides, polysaccharides
– Lipids
• Triglycerides, Phospholipids, Waxes, Steroids
– Proteins
• Primary, Secondary, Tertiary, Quaternary
– Nucleic Acids (Study these in Bio 30)
• DNA, RNA
What I need to know about Biochem
• Metabolic reactions
– Catabolic
• Hydrolysis
– Anabolic
• Dehydration synthesis
• Monomers make up Polymers
• Isomers have the same formula but a
different shape
Biochemistry
Carbohydrates
Types of Carbohydrates
Monosaccharides
Disaccharides
Polysaccharides
Carbohydrates
• Characteristics
– A Carbohydrate can be a single sugar or a
polymer of many sugars.
– Carbohydrates contain CHO
• Carbon, Hydrogen, Oxygen
– Ratio of carbon, hydrogen, oxygen = 1:2:1
• Purpose
– Source of energy for cellular respiration
– Structural material
Purposes of Carbohydrates
Structural
Energy
Major structural
component of cell
organelles,
membranes and
cytoplasm
Produced by
photosynthesis,
carbohydrates are
the major energy
source for cells.
Energy is released
through cell
respiration
Monosaccharides
Types of Monosaccharides
• Monosaccharides
– Single sugar = C6H12O6
– Three common isomers
• (**You don’t have to know the differences in their bonding sites, just that they are the
same chemical formula**)
• Glucose
– blood sugar
• Fructose
– fruit, honey, twice as sweet as glucose
• Galactose
– milk sugar, rarely found alone.
Types of Monosaccharides
Three Monosaccharides
Glucose
Fructose
Galactose
Three Monosaccharides
Disaccharides
Disaccharides
• Formed by the joining of 2
monosaccharides
– Process called DEHYDRATION SYNTHESIS
Disaccharides
Dehydration Synthesis
Dehydration Synthesis
Disaccharides
• Formed by the joining of 2
monosaccharides
– Process called DEHYDRATION SYNTHESIS
– The reverse process is called HYDROLYSIS
Disaccharides
• Three Common Isomers
– Sucrose
• Glucose + Fructose
• sugar cane, table sugar
– Maltose
• Glucose + Glucose
• found in seeds of germinating plants
– Lactose
• Glucose + Galactose
• Found in milk
• Lactose Intolerance is common
Polysaccharides
Complex Carbohydrates
Important Polysaccharides
Pronounced
kite-in
Polysaccharides
• Formed by the union of may monosaccharides
by dehydration synthesis
• Types:
– Starch
• Multiple sub-units of glucose
• Storage form of energy in plants
– Glycogen
• Branched chains of glucose
• Storage of of glucose in animals
– liver and muscle cells
• High Blood Glucose -- Glycogen formed in the liver
• Low Blood Glucose -- Glycogen converted to glucose
Cellulose
• Structural material found in plant cell walls
• glucose is linked together differently
compared to starch and therefore only
organisms with cellulase can digest it.
– Microbes in cow’s first stomach cleave the bonds
with cellulase
– The cow regurgitates (vomits into his own mouth)
– chews again (gross!)
– swallows into second stomach (yummy)
• What is it good for??
– Roughage -- retains water in feces = soft poo
What I need to know about Carbs
• Function
– Energy storage (Glycogen/Starch) or structure
(Chitin/Cellulose)
• Types
– Monosaccharides: Glucose, Galactose, Fructose
(C6H12O6)
– Disaccharides: Lactose, Sucrose, Maltose (and
which monosaccharides they’re each made of) (C12H22O11)
– Polysaccharides: Mostly Starch will be discussed
in Digestion
Biochemistry
Lipids
Lipids
• Structure
– Contains CHO
– Ratio of H to O is greater than 2 to 1
• Purpose
– Long Term Energy Storage
• 1 gram of lipids contains > twice the calories
compared to carbohydrates or proteins
– Structural Material
• cell membranes
• cushion for organs
• carriers for vitamins
• raw material for synthesis
of some hormones
• insulator
Classification of Lipids
Types of Lipids
• Triglycerides
– Formed from 1 glycerol and 3 fatty acids
– formed by dehydration synthesis
Classification of Lipids
Triglyceride Formation
Triglyceride Formation
Types of Lipids
• Triglycerides
– Formed from 1 glycerol and 3 fatty acids
– formed by dehydration synthesis
1) FAT
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•
usually from animals
saturated fatty acids only contain single bonds
Very Stable -- hard to break down
solid or semi-solid at room temperature
Example: Butter
Types of Lipids
2) Oil
• usually from plants
• polyunsaturated fatty acids have some double
bonds between carbon atoms
• more reactive than fats therefore more easily
broken down
• liquid at room temperature
• Example: Canola oil
Types of Lipids
• Phospholipids
– Have a phosphate molecule attached to a
glycerol backbone
Classification of Lipids
Types of Lipids
• Phospholipids
– Have a phosphate molecule attached to a
glycerol backbone
– Polarized molecule
• one side is relatively hydrophilic, other side
hydrophobic
– Major component of membranes
• Waxes
– Very stable
– Insoluble in water
– valuable waterproof coatings for plant
leaves, animal feathers and fur
Types of Lipids
• Steroids
– structure = four fused carbon rings
Classification of Lipids
Types of Lipids
• Steroids
– structure = four fused carbon rings
– Made from cholesterol
What I need to know about Lipids
• Function
– Energy storage (Triglycerides) or structure (Phospholipids – Cell
membranes)
• Types
– Triglycerides (made of 1 glycerol and 3 fatty acid chains)
• Saturated
– Only single bonds, as many H as possible
• Unsaturated
– Some double bonds, possible spots to add H
– Steroids
– Waxes
– Phospholipids
• Made of C, H, O in varying ratios
Biochemistry
Proteins
Proteins
• After water, protein is the most abundant
molecule in body
– 17% of body weight
• 1000’s of types: species specific and individual
specific
Proteins
• Purpose
1) Cell Structure
• Major part of muscle, skin, nerves …
• Required for the building, repair and maintenance of cell
structure.
2) Cell Function
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•
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Chemical messenger -- hormones
Transport -- hemoglobin
Movement -- contractile proteins
Catalysis of cell reactions -- enzymes
Defence against foreign substances -- antibodies
Proteins
• Structure
– Contains CHON
– Carbon, Hydrogen, Oxygen, NITROGEN
• Terms
– Protein
• A large molecule made of one or more
polypeptide chains folded and coiled into a
specific shape.
– Polypeptide Chains
• polymers of amino acids arranged in a specific
order and linked by peptide bonds
Proteins
– Peptide Bond
• Covalent bond between adjacent amino acids
– Amino Acids
• The structural subunit of proteins
• 20 Different types
• 8 are “essential”
– Cannot be manufactured by the body
– Must be obtained from food
• Structure...
Levels of Protein Structure
• Primary protein structure
– linear arrangement of amino acids in the
polypeptide (like beads on a string)
– exact sequence of amino acids determines
overall protein structure
(analogy: different arrangements of letters
spell out words with different meanings)
– all proteins have primary structure
Primary Protein Structure
Levels of Protein Structure
• Secondary Protein Structure
– The coiling and folding of amino acid chains
(polypeptides)
• coils are like springs
• folding produces sheet-like structure
• this type of structure is held together by hydrogen
bonding between amino acids
– Some proteins have lots of secondary
structure, some have none
Secondary Structure
Levels of Protein Structure
• Tertiary Protein Structure
– The coiled and folded polypeptide is further
twisted into n overall 3-D shape
• Shape held together by hydrogen bonds,
covalent bonds, ionic bonds
– Refers to the polypeptide as a whole
– Polypeptides may have an overall shape
(tertiary structure) that is either
• Globular (like a big blob), or
• Helical (like a long, coiled spring)
Tertiary Structure
Levels of Protein Structure
• Quaternary Protein Structure
– arrangements of polypeptide subunits,
when a protein is made up of more than
one polypeptide
– Held together by hydrogen bonds, ionic
bonds, covalent bonds
• Example: hemoglobin, many enzymes
Quaternary Structure
• (a) The primary structure of a
protein is the sequence of
amino acids in the
polypeptide strand.
• (b) Hydrogen bonds that form
with nearby amino acids coil
and fold the polypeptide into
α-helices and β-pleated
sheets; these constitute the
polypeptide’s secondary
structure.
• (c) The polypeptide folds
further to form its tertiary
structure. These folds are
stabilized by R-group
interactions.
• (d) The clustering of two or
more polypeptides in a
tertiary structure generates
the quaternary structure of a
protein.
Protein Changes
• Denaturation
– Changes in the shape of the protein by physical or
chemical factors such as heat, radiation or pH
changes.
– Protein may uncoil or assume a new shape.
– Protein’s physical properties and biological
properties are changed.
• Coagulation
– Permanent change in the shape of the protein
• e.g. boiling and cooling egg white
What I need to know about Proteins
• Function
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Structure -- muscles
Chemical messenger -- hormones
Transport -- hemoglobin
Movement -- contractile proteins
Catalysis of cell reactions -- enzymes
Defence against foreign substances – antibodies
Made of CHON (only one with nitrogen)
Monomer: Amino Acids
Polymer: Polypeptide Chain/Protein
Too many kinds to name!
Biochemistry
Vitamins and Minerals
Vitamins
• Characteristics:
– Organic molecules
– Cannot be synthesized from food
– Needed in small amounts for bodily functions
Inorganic Molecules
• Minerals
– building materials for cell structures and
hormones -- calcium, iron, iodine
– coenzymes -- magnesium activates enzymes
in protein synthesis
– regulating body’s acid-base balance -potassium
– regulates the body’s water balance -- sodium
Inorganic Molecules
• Water
– Most abundant molecule in the body
– 60% of adult weight
– Functions:
• excellent solvent
• involved in chemical reactions
– hydrolysis
• maintains constant body temperature
Biochemistry
Chemical Tests
Chemical Test
• Chemical tests are used to determine the
presence of different types of organic
molecules.
• Some important tests include:
Benedicts Reagent
Iodine Test
Biuret
Sudan IV Dye
Benedicts Reagent
• Tests for the presence of simple sugars
• Negative test: After heating the benedict
solution remains blue
• Positive test: After heating the blue
benedict solution turns yellow  to
orange.
Benedicts Test
Negative Test: Blue
Positive Test: Orange
No simple sugar is
present
Simple sugar is present
Iodine Test
• Test for Starch
• Negative Test: The iodine solution
remains amber when no starch is present
• Positive Test: The iodine solution turns
blue black when starch is present
Iodine Test for Starch
Negative Test: Solution
remains amber
Positive Test: Solution turns
blue black
No starch in present
Starch is present
Biuret Test for Protein
• Biuret solution is blue
• Negative Test: When added to a
substance not containing protein, the
solution remains blue
• Positive Test: When added to a
substance containing protein, the
substance turns purple
Biuret Test for Protein
Negative Test: Solution
remains blue
Positve Test: Solution
turns violet
Sudan IV & translucence test
• Test for fats
• If fat is present in the sample tested, a red
or pink colour will result
Translucence test
• The presence of fats can be detected by
rubbing samples on a piece of unglazed
paper
What I need to know about
Chemical Tests
• We will use these results to complete a lab
report later in the unit
• You don’t have to memorize the indicators
Video Review
• Crash Course
• Good Cartoon
Enzymes
What is it??
• Enzymes are PROTEIN molecules.
• Protein molecules are composed of one or
more amino acid chains, folded into
uniquely shaped globs.
 Enzymes act as CATALYSTS!
 Catalysts are chemicals that regulate the
rate of chemical reactions.
 Are not consumed or altered during the
reaction
Activation Energy
 Activation Energy is the energy input required to
initiate any reaction.
Activation Energy
 Activation Energy is the energy input required
to initiate any reaction.
 Enzymes regulate cell activities (metabolism)
by lowering the activation energy
 reactions, therefore, occur more rapidly and at
lower temperatures.
Activation Energy
Activation Energy
Activation Energy
FUNCTION vs. SHAPE
TWO THEORIES
1) LOCK & KEY THEORY
• Each chemical reaction requires its own enzyme
therefore “one reaction = one enzyme” concept
• The enzyme forms a temporary bond with a
special molecule called a SUBSTRATE
• substrate a molecule on which an enzyme works
– A substrate is always…
» the substance acted upon
» the substance which is changing
• Active Site the area of an enzyme that
combines with the substrate
Get’in Together
• When the substrate and the enzyme
combine or “join” at the active site, the
tandem is called an Enzyme-Substrate
Complex.
Lock & Key (Con’t)
– The ENZYME-SUBSTRATE COMPLEX then
separate into product(s) and enzyme
Important
• Note that:
– The enzyme remains unchanged and ready to react
again with a new substrate.
Important
• The substrate has been turned into
products.
INDUCED FIT MODEL
• Improved Theory – 1973
– suggests that the shape of the active site
does NOT exactly fit the shape of the
substrate
– The substrate forces its way into the
enzyme
– This makes for a tighter fit
– The orientation of the substrate molecules
in the ENZYME-SUBSTRATE COMPLEX
helps speed up the chemical reaction by
 adding stress to bonds more easily
 bringing reactive sites physically closer
together
Induced Fit (Cont’d)
 Once a bond is formed (or broken) in
substrate(s) then products are released and the
ENZYME REMAINS UNCHANGED and may be
REUSED!
 A single enzyme can catalyze several million
reactions in one minute
 The same enzyme may also catalyze the reverse
reaction
 The net result is that a one step reaction is
converted into a multi-step reaction, therefore,
lowering the activation energy – the minimum
amount of energy required to initiate a chemical
reaction.
Naming Enzymes
 Enzymes are named after the substrate which it acts
upon
 To name an enzyme, usually, the suffix “ase” is
added to the end of the substrate name.
 For example:
Substrate
Sucrose
Lactose
Peptide Bonds
-Ketoglutarate ...
Enzyme
Sucrase
Lactase
Peptidase
?????
-Ketoglutarase
Regulation of Enzyme Activity
 METABOLIC PATHWAYS
 cellular processes that involve many steps are
controlled by enzymes
 one enzyme for each step.
Allosteric Activity
a change in an enzyme caused by the binding
of a molecule
 Some enzyme’s shape may be altered by a
“moderator molecule”.
 can be a cofactor (mineral)
 Coenzymes (organic molecules)
 sometimes even the product molecule.
A Moderator Molecule
Cofactors
Regulation of Enzyme Activity
 FEEDBACK INHIBITION
***Super Important concept in Biology – also called Negative Feedback**
 Stops a metabolic pathway
 the product of an metabolic pathway acts as
a moderator on an enzyme in the series,
thereby altering its shape (active site)
 the enzyme cannot combine with the
substrate
 Once the moderator molecule is removed
from the moderator site, the active site
snaps back to its original shape.
Feedback Inhibition
Glucose
Glucose
Glucose
Glucose
Glucose
Glucose
Glucose
Glucose
feedback inhibition
• feedback inhibition the inhibition of an
enzyme in a metabolic pathway by the
final product of that pathway
feedback inhibition
Factors Affecting Enzyme
Reactions
• There are four factors that affect the rate
at which an enzyme can work.
1) Temperature
2) pH
3) Substrate Concentration
4) Competitive Inhibitor Molecules
TEMPERATURE
in order for a reaction to occur
molecules must collide
 as temperature increases,
collisions increase
DOES RATE OF REACTION
INCREASE WITH
TEMPERATURE???
• NOT NECESSARILY!!
Enzymes have an optimal
temperature at which the reaction
is fastest.
 Beyond this temperature, the rate of reaction
decreases
 This is because at high temperatures, the unique
shape begins to change – denaturation.
 This results in a loss of the active site
 Each enzyme has its own optimal temperature
 Human body approx. = 370C
 Sperm producing enzymes = 340C
 This explains why fevers and colds are dangerous
pH
 acidity or alkalinity
 the lower the number the more acidic
 the higher the number the more alkaline
 Enzymes have an optimal pH at which the
reaction is fastest
 Just like with temperature, pH’s out of
the optimal range will cause a decrease
in rate of reaction
 shape changes = enzyme denatures.
CONCENTRATION
 Since molecules must collide for a reaction to
occur, it is only logical that the more substrates
you have, the greater the chance the enzyme will
have of combining and reacting with it.
 The rate does not continue to rise as you add
more and more substrate.
 There is a limit to the amount of enzyme available
 A substrate cannot join with the active site of an
enzyme until it is free.
 Therefore, once the number of substrate molecules
exceeds the number of enzyme reaction sites, the
reaction rate levels off.
Competitive Inhibitor Molecules
 Competitive Inhibitor molecules interfere
with the enzyme combining with its
substrate.
– Competitive Inhibitor
 shaped like substrate
 COMPETES for active site
 fits into active site
 = physically blocks substrate from entering active
site
 enzyme becomes useless
Competitive
Inhibition
Competitive Inhibitor Molecules
 Examples:
 Cyanide – binds to enzyme in the Electron
Transport Chain preventing formation of
ATP.
 Carbon Monoxide – binds to hemoglobin
irreversibly, therefore, no oxygen can be
carried
 Penicillin – binds to enzyme that allows
bacteria to make its protective covering,
therefore, bacteria becomes susceptible to
the immune system and other drugs
Video Review
• In Depth Review
• Cute Cartoon