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Unit 1: Metabolic Processes - Part 2 (8.5 hours) |
Students will describe the structure and function of the macromolecules necessary for the normal metabolic functions of all living things, and the role of enzymes in maintaining normal metabolic functions. Laboratory investigations will be conducted into the transformation of energy in the cell, including photosynthesis and cellular respiration, and into the chemical and physical properties of biological molecules. Ways in which knowledge of the metabolic processes of living systems can contribute to technology development and affect community processes and personal choices in everyday life will be explained.
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Ontario
Curriculum objectives: |
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Text: Biology 12, Nelson |
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Lesson One |
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Summary:(U3) |
Homework: |
ENZYMES
Enzymes
are organic catalysts.
Organic: contains C, H, O
Catalyst: lowers energy needed
for a reaction to take place
Catalysts are not permanently altered by these
chemical reactions
Enzymes
are involved in synthesis and degradation reactions in living things
An enzymes function
is
determined by it's three dimensional shape
There
are three basic structures of enzymes:
1.
Enzymes can be a protein
2.
Enzymes may be a protein with a non-protein organic part (vitamin, coenzyme)
3.
Enzymes may be a protein with a mineral (cofactor, activator ion)
Enzymes
may also contain protein, non-protein organic part and a mineral.
If
any part is missing the shape of the enzyme is altered. This will disrupt the
enzyme's function.
Vitamins
and Minerals are referred to as “Prosthetic Groups” when added to a protein.
An enzyme with both protein and prosthetic groups is called a “Holoenzyme”, and the protein in this case is referred to as an “Apoenzyme”.
Some information on Prosthetic groups…
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Vitamin |
Uses |
Deficiency |
Source |
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A |
makes visual
pigments |
night blindness |
liver, carrots |
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C |
maintains cell membranes |
scurvy |
citrus fruits |
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D |
used for Ca, P
metabolism |
rickets |
milk, fish oil, cereals |
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K |
used for clotting
factor |
blood clots poorly |
produced by
bacteria in intestines |
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Mineral |
Uses |
Deficiency |
Source |
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Ca |
bone formation,
muscle contraction |
rickets |
milk, cheese, rice, soy |
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Cu |
bone formation, hemoglobin production |
anemia |
potatoes |
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Fe |
blood function |
respiratory distress |
beef, bread |
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I |
thyroid function |
goiter |
cod, kelp |
pH
H2O
can degrade/ionize spontaneously into H+ + OH-
In
pure water, the concentration of H+ ions is 1 x 10-7 mol/L or pH 7
(from exponent –7)
ph 7 is called Neutral
Acids (sour, rough) have
a pH of less than 7
e.g. lemon juice, pH 2 is 100 000 more acidic than pure water (105 more
concentrated)
Bases (bitter, smooth) have a pH of more than 7
e.g. baking soda in water, pH 10 is 1000 more basic than pure water (103
less concentrated)
Enzyme
function may be affected by pH (see future classes)
View video on enzymes
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Lesson Two |
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Summary:(U6) |
Homework: |
TYPES OF CHEMICAL REACTIONS
Endothermic:
the chemical potential energy of the products is greater than that of the
reactants e.g. photosynthesis
Exothermic:
the chemical potential energy of the reactants is greater than that of the
products e.g. cellular respiration
Activation Energy is the energy required to start a reaction (greater in
endothermic reactions)
Draw
Chemical Potential Energy vs. Time graphs for endothermic and exothermic
reactions
-label
chemical potential energy of reactants, products, net energy change and
activation energy
Enzymes
act on these reactions by reducing the activation energy needed
to start the reaction
(draw
the effect of enzymes on the graph)
-this
allows reactions to occur at lower temperatures than would normally be required
-the speed of the actual reaction is not altered, just the energy needed to
start the reaction
Enzymes
bind to specific substrates (reactants) because they have a specific three
dimensional shape
-this
specific binding is called a “lock and key” mechanism
-in
the Active Site of the enzyme, pressure is exerted on chemical bonds in the
substrate
-this
pressure allows the chemical reaction to occur with less activation energy than
without the enzyme
-products
are released from the enzyme returning the enzyme to its initial form for reuse
Enzyme activity is affected by the following factors:
Temperature:
-in cooler temperatures, molecules move slowly resulting in reduced rates of reaction.
-the rate of reaction in human enzymes doubles with every increase in 10oC
up to approximately 40oC
-above
40oC the proteins may denature with H-bonds breaking. This change in
shape will inactivate the
enzyme.
Acidity
(pH):
-different enzymes work best in different conditions.
-changes in pH change how the amino acids in enzymes bind to form their three dimensional shape,
and inactivate the enzymes.
-e.g.
pepsin works best in acidic conditions like the stomach, trypsin works best in the alkaline (basic) conditions like
the intestines.
Concentration:
If there is a shortage of enzyme, substrate, cofactor or coenzyme the reaction
will not occur.
ENZYME POISONS
-Some
poisons (competitive inhibitors) act by binding to the active site of an enzyme
-these competitive inhibitors block the substrate from binding to the active
site.
-e.g. cyanide inhibits respiratory enzymes, carbon monoxide inhibits hemoglobin
-Other poisons (noncompetitive inhibitors) bind to another site on the enzyme
which changes the shape of the active site.
-this
shape change prevents substrate binding.
-e.g.
heavy metals like lead and mercury bind to S-H groups in enzymes altering the
active sites
Work on enzyme questions
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Lesson Three |
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Summary:(U3) |
Homework: |
CELL MEMBRANES (PLASMALEMMA)
-cell
membranes contain four main components
Phospholipids:
-phospholipids
are amphipathic (both polar and non-polar)
-the polar end contains glycerol with phosphate group, the Non-polar end contains
two fatty acids
-a
bilayer exists around cells
-extra cellular fluid around cells contacts the polar end of one layer of
phospholipids
-cytoplasm contacts the polar end of another layer of phospholipds
-non-polar
fatty acids from both layers are found between the two layers
-large molecules, polar molecules and charged molecules cannot fit through the
non-polar region inside the membrane.
-water is small enough to diffuse across this barrier, however.
-the
membrane is fluid as phospholipids move around within their layer
-unsaturated fatty acids are bent at double bonds, come in little contact with
each other and remain fluid (in plants)
-saturated
fatty acids are straighter and tend to stick where they make contact with each
other (Van der Waals forces)
-saturated fatty acids also have cholesterol between fatty acids to keep
membrane fluid
Transmembrane
Proteins (globular proteins):
-these
are proteins that pass through from one side of the membrane to the other
-the middle area is usually hydrophobic (non-polar) while the ends are
hydrophilic (polar), keeping it in the membrane
-these
proteins are used for transport of specific material across the membrane and
other functions
Supporting
Fibres (fibrous proteins):
-these
proteins hold material in place on the fluid membrane (e.g. other proteins)
Glycolipids,
Glycoproteins:
-carbohydrate chains attach to both lipids and proteins, and act as identity
markers for the cell (these distinguish cell types)
Label Diagrams
Finish Enzyme Questions
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Lesson Four |
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Summary: (D4,R1) |
Homework: |
-test on nucleic acids next class (lessons 18-28 of last unit)
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Lesson Five |
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Summary: |
Homework: |
TEST ON LESSONS 18- 28 OF LAST UNIT
-test on nucleic acids
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Lesson Six |
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Summary: (D4) |
Homework: |
ENZYME LAB CONTINUED
Finish write up of enzyme lab
Bring up DNA test
-quiz on membrane structure next class
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Lesson Seven |
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Summary: (D4) |
Homework: |
Do quiz on cell membranes
MOVEMENT ACROSS THE CELL MEMBRANE
Kinetic Molecular Theory (particle theory):
-all
matter is made of particles
-these
particles are constantly moving (faster when heated)
-there
is large space between the particles (relative to particle size)
-these
particles are attracted to each other
Terms used in this unit include:
Diffusion:
-spontaneous movement of materials from an area of high concentration to an area of low
concentration.
-diffusion stops when concentration is equal in all areas
Dialysis:
-diffusion of solute (dissolved material, e.g. salt) through a semipermeable
membrane
Osmosis:
-diffusion of solvent (material that does dissolving, e.g. water) through a
semipermeable membrane
The rate of
diffusion is affected by the following factors:
Temperature:
-the higher the temperature, the faster the molecules move by diffusion
Concentration:
-the greater the difference in concentration, the greater the rate of diffusion
down the gradient
-No
gradient = no diffusion
Particle Size:
-larger particles diffuse slower than small particles
Solubility:
-material that is less soluble diffuses slower than more soluble material
TYPES OF TRANSPORT
Passive
Transport:
-movement of material across a membrane using none of the cells energy
-energy
is provided by heat as material moves as described by the kinetic molecular theory
Active Transport:
-movement of material across a membrane using ATP energy provided by the cell
TYPES OF SOLUTIONS
Saturated
Solution:
-a solution which has dissolved the maximum amount of solute possible
Unsaturated Solution:
-a solution which can still dissolve more solute
Supersaturated Solution:
-a solution that contains more than the maximum amount of possible dissolved solute
-to supersaturate a solution, a saturated solution must be heated, and more
solute dissolved
-the heat allows a greater amount of dissolving to occur
-this solution is then cooled to its initial temperature and the
dissolved material stays dissolved
-the solute crystallizes when agitated
Isotonic
Solution:
-the concentration of solvent in extra-cellular fluid is the same as the
concentration of solvent in the
cytoplasm
Hypertonic Solution:
-the concentration of solvent in the extra-cellular fluid is less than the
concentration of solvent in the
cytoplasm
-osmotic pressure increases (pressure of water moving through the cell
membrane) as solvent moves out of the cell by osmosis
-solute moves in by dialysis
-this will result in plasmolysis (shrinking of cell membrane
e.g. a cell in salt water
Hypotonic Solution:
-the concentration of solvent in the extra-cellular fluid is more than the concentration of solvent in
the cytoplasm
-turgor pressure increases (pressure of water against the cell membrane) as solvent
moves in by osmosis to fill the cell (turgid)
-solute moves out by dialysis
-this will result in the cell growing in size and possibly bursting (in plant
cells this does not occur because of the cell wall)
e.g. a cell in fresh water
SELECTIVE MOVEMENT ACROSS THE CELL MEMBRANE
Selective
movement across a membrane (sheet from package of notes)
Material that is too large or charged/polar material (unable to move through
hydrophobic area of phospholipid bilayer) must cross the membrane through proteins.
Facilitated Diffusion:
Material
is in high concentration on one side of the membrane and low on the other
-it must fit into a protein, which has a specific shape, and then is transported across the
membrane by this protein
-the transmembrane
protein returns to the original form after this is done
-no cellular energy is expended for this process
-transport without use of cellular energy is called “passive transport”
Facilitated:
helped by protein (because of size/charge)
Diffusion:
movement from high to low concentration
Sodium-Potassium
Pump:
-the
cell uses ATP energy to transport 3 Na+ out of a cell and 2 K+ into a cell
through the same transmembrane protein.
-this can occur against a concentration gradient, and it requires cellular
energy it is
-transport
with use of cellular energy is called “active transport”
Coupled
Channel:
-if
the sodium-potassium pump builds up a high concentration of sodium on one side
of the membrane, sodium
will
try to move back through the membrane by diffusion
-this is only possible at a transmembrane protein because the sodium
has a + charge (unable to move through hydrophobic region of bilayer)
-the protein that
allows
Na+ to move across by facilitated diffusion only allows this movement if it is
also joined by a sugar
-the sugar and Na+ must
move across together
-this is called a “coupled channel”, as both chemicals are needed for this facilitated
diffusion
-the pull of the diffusion of sodium may be so great as to allow sugar to be
pulled into the cell
against a concentration gradient
Hydrogen Ion Pump (Proton Pump):
-hydrogen
ions are pumped across a membrane by active transport into an area of high
concentration as they
are
removed from NAD (a carrier of hydrogen ions)
-this transmembrane protein is called a “proton pump”, as each hydrogen ion is
a proton
-the hydrogen ions move back to the lower concentration through a transmembrane protein (because
they are charged)
-the energy from this process is used to assemble an ATP molecule.
-this
whole process of ATP production using transmembrane proteins is called “chemiosmosis”
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Lesson Eight |
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Summary:(D4) |
Homework: |
CELL ENVIRONMENT LAB
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Purpose: Observations: Discussion: 2. What percentage of salt concentration is found in the cytoplasm of potatoes? Explain how you determined this. |
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Lesson Nine |
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Summary: (D4) |
Homework: |
MOVEMENT ACROSS THE CELL MEMBRANES (CONTINUED)
Material
can move through the phospholipid bilayer if it is small and uncharged or small
and polar (e.g. water)
Charged particles are repelled by the hydrophobic interior of the bilayer and are unable to
cross except at protein channels
An
example of facilitated diffusion/coupled channels/sodium potassium pumps in
action is the absorption of sugar
into the blood from the intestine:
-sodium ions are actively pumped out of intestinal cells and into the blood
-this is done with
sodium
potassium pumps, and uses the ATP of the cell (active transport)
-now
the sodium concentration of the cell is low, sodium from the inside of the
intestine will diffuse into the
cell by facilitated diffusion
-this diffusion of sodium must occur through a coupled channel, and sugar is transported
in with the sodium
-the pull of the sodium diffusion is so great that sugar can be pulled into the
cell from low to high concentration
-sugar
inside the cell is now in high concentration and moves into the blood by
facilitated diffusion
Membrane
proteins may be held in place in a number of ways:
-integral
proteins (most often transmembrane proteins) are held in place by having a
non-polar region on the
interior of the membrane and polar regions on the outside of the membrane
-peripheral
proteins are found on the outside of the membrane only and held in place with
ionic bonds to the heads
of phospholipids or to nearby transmembrane proteins. These are easy to remove, as the ionic
bonds are relatively weak
-lipid
bound proteins are found on the exterior and interior of the membrane and are
held in place by covalent bonds to
the tails of the phospholipids
Other
functions of membrane proteins besides cell transport:
-membrane bound proteins could act as enzymes
-membrane bound proteins could act as receptors for hormones which are unable
to enter the cell themselves
-glycoproteins could act as identity markers for the cell
-membrane proteins could bind to neighboring membrane proteins in order to
allow cells to adhere to each other
-supporting fibres/cytoskeleton bound to the membrane proteins in many cases
Endocytosis: bulk cell ingestion of material using
active transport
Pinocytosis: small particles are ingested down narrow tubes in the cell
membrane
Phagocytosis: pseudopods (cell arms) reach out and engulf particles in vacuoles
e.g. white blood cells, amoebas
Exocytosis: vacuoles are emptied through cell membrane
using active transport
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Lesson Ten |
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Summary: (U5) |
Homework: |
REDOX REACTIONS
Oxidation/Reduction
reactions (redox reactions) involve the gain or loss of electrons
Electrons
are often carried together with protons in the form of H atoms
Oxidized:
loss of electrons (usually accompanied by loss of H, gain of O)…called reducing
agent
Reduced:
gain of electrons (usually accompanied by gain of H, loss of O)…called
oxidizing agent
e.g.
photosynthesis
6H2O
+ 6CO2 --> C6H12O6 + 6O2
… the reactant with C becomes product with C (CO2 becomes C6H12O6)
CO2
is reduced as it gains H, loses O (CO2 may be called the
oxidizing agent)
H2O
is reduced as it loses H, gains O (H2O may be called the
reducing agent)
e.g. cellular respiration
C6H12O6
+ 6O2 --> 6H2O + 6CO2 … (C6H12O6
becomes CO2)
O2
is reduced as it gains H, loses O (O2 may be called the oxidizing
agent)
C6H12O6
is oxidized as it loses H, gains O (C6H12O6 may
be called the reducing agent)
ELECTRON CARRIERS
Electron
carriers such as NAD (nicotinamide adenine dinucleotide) exist which pick up or
lose H atoms in redox reactions
e.g.
NAD + H2 <=> NADH2 shows how NAD can be
reduced
This
electron carrier consists of two nucleotides containing a phosphate, ribose and
base joined together
AMP
(adenosine monophosphate) group contains the adenine base, acts as a “core” and
joins an enzyme
NMP
(nicotinamide monophosphate) group contains the nicotinamide base, acts as a
“active site” and gains/loses Hydrogen atoms
-combined AMP and NMP groups make a molecule of the dinucleotide NAD
ATP
Energy
is required by all living things in the form of ATP (adenosine triphosphate)
Adenosine
triphosphate is a RNA nucleotide for adenine which contains two extra
phosphates
AMP
(adenosine monophosphate) + phosphate + energy <=> ADP (adenosine
diphosphate)
ADP
+ phosphate +energy (31 KJ/mol) <=> ATP
ATP
is used by organisms for chemical energy as it is easy to build/break down
Work on cellular respiration questions
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Lesson Eleven |
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Summary: (U2,U5,U6) |
Homework: |
ENERGY TRANSFERS
-nuclear
potential energy (on the sun) is converted via nuclear fusion into radiant
energy (light)
-radiant
energy is converted via photosynthesis into stored chemical energy (sugar)
-stored
chemical energy is converted via cellular respiration into stored chemical
energy (ATP)
-ATP
is used for the characteristics of life
The
first two laws of thermodynamics apply:
The
energy conversions occur as energy changes forms, and is not created or
destroyed
During
each energy conversion, heat is lost (a more random form of energy)
ATP is
made two ways…
Substrate level phosphorylation occurs in cytoplasm
Enzymes
are used to add a phosphate to ADP to make ATP
Chemiosmosis occurs in the mitochondrial membranes
Protons
from NAD are actively pumped between membranes, and as they diffuse back out
by
facilitated diffusion energy from this process is used to join a phosphate with
an ADP
CELLULAR RESPIRATION
Cellular
Respiration
C6H12O6
+ 6O2 + 36 ADP + 36 phosphate --enzymes--> 6H2O
+ 6CO2 + 36 ATP + heat
This reaction occurs in three steps
1. Glycolysis
This reaction occurs in cytoplasm
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Glycolysis
Glucose (C6H12O6 ) Summative
Equation The ATP made in this reaction are made by substrate level phosphorylation |
The text
book explanation is more detailed, involves H loss with condensation and other
differences
Ignore
the text and use the above explanation…see teacher if you wish to have a more
detailed explanation of the
text or read on...
Here
goes (you don't need to know this stuff)
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Glycolysis (actual)
Net
Equation: |
-start page 2 of fill in the blank
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Lesson Twelve |
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Summary: (U3,U5,D5) |
Homework: |
FAD
FAD is
another electron carrier like NAd
FAD is flavin adenine dinucleotide and carries electrons with less
energy than those carried by NAD
FAD + H2 --> FADH2 is the reaction by which this substance is reduced
MITOCHONDRIA
Mitochondria
are the eukaryotic organelles where the next two steps in aerobic cellular
respiration occur
These
organelles have two phospholipid bilayer membranes with the inner one folded to increase surface
area
The
fluid inside the mitochondria is called matrix and the folds are called cristae
CELLULAR RESPIRATION (continued)
After
glycolysis of a glucose molecule the two pyruvate produced move into the matrix
of the mitochondria
The pyruvate then go through a reaction called Kreb’s cycle (also called the citric acid cycle)
2. Kreb'c
Cycle (citric acid cycle)
This
reaction occurs in the matrix of the mitochondria
This cycle occurs twice per glucose metabolized as each glucose produces two
pyruvate
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Kreb's Cycle
Net
Equation (go around twice for each glucose) The ATP made in this reaction are made by substrate level phosphorylation |
Text
book explanation is more detailed, involves H loss with condensation and other differences
Ignore
the text and use the above explanation…see teacher if you wish to have a more
detailed explanation of the
text or read on...
Here
goes (you don't need to know this stuff)
|
Kreb's Cycle (actual) All reactions occur 2X (as you start with 2 pyruvate) |