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Testing for Macromolecules in Foods lab activity.doc
Chemical Fundamentals and Macromolecules Sample Quiz
Chem Fundamentals and Macromolecules Quiz.doc
Jeopardy Review: Chemistry, Macromolecules and Enzymes
Chemistry,Macromolecules and Enzymes Jeopardy Review.ppt
Unit 1, Topic: Biochemistry
Text Refernce: Biology 12.
Idea: An introduction to biochemistry
- Organic Compounds:
..........- Compounds that contain carbon are called organic.
..........- Macromolecules are large organic molecules.
- Carbon (C):
..........- Carbon has 4 electrons in outher shell.
..........- Carbon can form covalent bonds with as many 4 others.
..........- Usually with C, H, O, N.
..........- Large organic molecules.
..........- Also called Polymers "Many sub-units".
..........- Made up of smaller "building blocks" called monomers.
..........- Examples: Carbohidrates, Lipids, Proteins, Nucleic Acids.
..........- How are they formed:
..................- Also called "condensation reaction".
..................- Form polymers by combinding monomers by "removing water".
.........- Separates monomers by "adding water".-
.........- Small sugar molecules to large sugar molecules.
.........- Examples: monosaccharide, disaccharide, polysaccharide.
.....................- One sugar unit: Glucose (C6H12O6), Galactose, Fructose, Ribose, Deoxyribose.
.....................- Sucrose (Gluctose + Fructose)
.....................- Lactose (Gluctose + Galactose)
.....................- Maltose (Gluctose + Glucose)
.....................- Many sugar units
.....................- Starch (bread, potatoes), glycogen (beed muscle), cellulose (lettuce, corn).
- Anabolic Reactions:
.........- Build up (produce larger molecules from small molecules).
- Catabolic Reactions:
.........- Break down larger molecules to smaller molecules.
.........- A molecule has the same number of atoms but differently arranged.
- Complete Stem Cells Application.
- Get a webpage for topic.
Welcome to Biochemistry!
Tuesday Feb 15, 2011
Lipids and Proteins
Compounds not soluble in water ( soluble in hydrophobic solvents)
Stores the most energy ( 9 calories per gram, carbs stores 4 calories per gram)
Six functions for Lipids
long term energy storage
protection against heat loss (insulation)
Protection from physical loss
Protection from water loss
chemical messengers (hormones)
Major component of membranes (phospholipids)
fatty acids (ester bonds /linkage)
2 types of fatty acids saturated (bad) and unsaturated (good)
Bilayer separates two water compartments.
Consists of 4 rings with atoms coming off them that make different hormones
Ex cholesterol, estradiol, testosterone, progesterone
Makes resistance coating on fruits like cherries
Linked to alcohol or carbon rings
Proteins ( Polypeptides)
20 different amino acids bonded by peptide bonds
Make of 50% of mass of dry cell
All amino acids have same structure but differ in their R group structure
The 8 essential amino acids are Isoleucine
, Leucine, Lysine,
Six functions of proteins
storage: albumin (egg white)
Structural: membranes, hair, nails
Enzymes: cellular reactions
Four levels of protein structure
Straight chain of amino acids bonded by peptide bonds
3D folding arrangement of primary structure into coils and pleats held together by hydrogen bonds
Secondary structures bent and folded into new arrangement
Bonds: H-bonds, ionic, disulfide bridges (S-S)
Called a “subunit”
Polypeptides’ final shape, determined by primary structure
Protein shape is essential for its duties to be completed
Not all polypeptides have Quaternary structure
Composed of 2 or more subunits
Wednesday, February 16, 2011
Macromolecules: Proteins (cont'd) and Nucleic Acids
Final shape of polypeptide (tertiary structure)
+ chemical and physical factors
However, changes in temperature, pH, ionic concentration, and/or other environmental factors may
of the polypeptide
this is called
there are good and bad consequences
ex/ cooking meat denatures protein in it and makes it chewy, easier to eat
(image created by: Jane Yang)
(Nelson Biology 12 Textbook, page 47)
more ex/s in textbook page 47, last paragraph
polypeptide “change” can be
if what changed is removed/reversed
AS LONG AS
structure of polypeptide remains intact (peptide bonds are not broken)
: assist in folding of growing polypeptide into the structure (into tertiary structure)
: Change of environment = change of shape = change of function = affects important roles in bodily functions, for instance.
composed of long chains of
linked by dehydration synthesis (phosphodiester bond)
5-carbon sugar (pentose sugar)
nitrogenous bases (Adenine (+) Thymine/Uracil ; Cytosine (+) Guanine)
Two main types:
(deoxyribonucleic acid): double stranded
(ribonucleic acid): single stranded
(adenosine triphosphate) [forgotten a lot as a nucleic acid]
: 2 adjacent nucleotide polymers running in opposite directions relative to one another
(Nelson Biology 12 Textbook, page 53)
Unit 1, Topic: Biochemistry
Text Refernce: Biology 12.
Energy obtained from other sources
ATP releases energy when its bonds are broken (energy storage molecules)
In living organism most catalysts are enzymes
Lock and Key:
Energy is the ability to do work and cannot be created or destroyed only transferred
Kinetic energy is the energy of motion or moving objects
Potential energy is stored energy
– ability to do useful work
– transfer of energy from one place to another
Hydrolysis of the terminal phosphate of ATP to create ADP +Pi 54 KJ/mol of energy, this can be used to drive energy requiring reactions
– Exergonic reaction (Bio) Exothermic reaction (Chem)
“Consuming” or Using energy –
Endergonic reaction (Bio) Endothermic Reaction (Chem)
Reaction coupling –
Mixing of Exergonic and Endergonic reactions
sum of all anabolic and catabolic (Like a cat shreds big to small) reactions in a cell and is therefore the sum of all living processes
randomness and disorder in a system, theory is that reactions/things go towards disorder
Anabolic increases entropy
Tuesday, March 1, 2011 – by Joel Tham
like a facilitator for speeding up reactions without being used up
Protein based catalysts
Do not get used up in a reaction - “recycled”
Lower the activation energy of a reaction
However, the energy levels of reactants and products stay the same (same amount of energy is released/absorbed)
Makes it easier to get to the transition state
Why do we need enzymes?
The reactions that occur in cells would happen too slowly to sustain life
The most common type of activation energy is
The problem is that heat can denature enzymes and cause cells to die
Enzymes lower EA (energy of activation) so heat is not needed
Reactants are called substrates
Substrates bind to a region on the enzyme called the active site
The active site is where the reaction occurs
Enzymes are very specific for the substrate they bind/catalyze
Usually one enzyme only binds one type of substrate
Enzyme + substrate must have a similar shape
A different enzyme is needed for each type of reaction
Same enzyme catalyzes the forward + reverse reaction (if they both exist)
ex) amylase in the following reaction: amylose + H2O
Lock and Key Theory
Old theory of enzymes
Explained the specificity of enzymes (only work for one type of reaction)
Implied that enzymes are static (they do not change)
However, enzymes do alter slightly in shape
More widely accepted model
The enzymes are similar in shape to the substrates
As the substrate enters the active site, the enzyme changes shape to better fit the substrate
The enzyme and substrate form an enzyme-substrate complex (ES complex)
Some enzymes require the presence of nonprotein cofactors (ex Zn+2) or organic coenzymes (ex NAD+) before they can work properly
Bind to the enzymes’ active site or to the substrate
Enzyme activity can be affected by several factors
3. Enzyme concentration
4. Substrate concentration
1. Enzyme Inhibition (preventing normal enzyme activity)
Similar in shape to the substrate
Compete for the active site and prevent the substrate from binding
ex) methanol and ethanol
(causes permanent damage to central nervous system)
provide ethanol (competes with methanol for enzymes, causing the methanol to leave the system)
Attach to a site (allosteric site) on the enzyme other than the active site
Cause a change in the enzyme’s shape so that the substrate cannot bind
If the substrate can still bind, the activity is reduced
Only binds after the enzyme has bound to substrate (ES complex)
Prevents the formation of product(s)
Allosteric sites are receptor sites away from the active site that bind substances that may activate or inhibit (ex. non-competitive enzyme activity)
This involves enzymes that have quaternary structure (each subunit has its own active site)
An activator binds to an allosteric site and helps to keep all active sites open/available to substrate
An inhibitor binds to an allosteric site and inactivates the enzyme (changes shape of active sites)
Nelson Biology 12 - page 73 figure 7
Used to control a series of reactions involving more than one enzyme
A product formed later in the sequence inhibits an enzyme involved in an earlier step of the process
ex. synthesis of amino acids (pg 74 figure 8)
Summary - Enzymes are Regulated By:
Inhibition (competitive, non-competitive, uncompetitive, feedback)
ex. enzymes produced in an inactive form and only activated when needed (ex. pepsinogen
A cell can control the amount of enzymes it makes
Amount of enzyme available can be regulated
reaction only occurs if enzyme is available
Examples of Industrial uses of enzymes – page 76
Production of ethanol
Dairy (removal/conversion of lactose in milk)
Detergents (harsher conditions are not needed to clean clothes)
Making leather “wearable” (treating the leather)
Making wine and juice
Cadbury Caramilk Secret?
Here is Margaret's theory for the Caramilk secret:
(same site I presented in class)
(another useful site for enzymes)
(the video we saw in class)
Enzyme Assignment (due Thursday, March 10, 2011)
Questions on page 77
Membrane Structure and Function Assignment
Independent Study Chapter:
Membrane Structure and Function
Section 1: (pg. 125-128)
Overview: Life at the Edge
The formation of a membrane to enclose a solution different from the surrounding solution was thought to be one of the earliest steps in evolution. This membrane still permitted the intake and output of nutrients and waste products
The plasma membrane is selectively permeable and controls the flow of substances in and out of the cell
It is selectively permeable: it allows some substances in and not others
The selectivity is made possible by the plasma membrane and its component molecules
The most important components of membranes are lipids and proteins, but carbohydrates are also important
Phospholipids are the most abundant lipids in most membranes
They are amphipathic molecules, meaning they have both a hydrophilic region and a hydrophobic region
Most of the proteins within membranes have both hydrophilic and hydrophobic regions as well
The phospholipids and proteins are arranged in the fluid mosaic model
The fluidity of Membranes
Membranes are not static
Membranes are mostly held together with hydrophobic interactions (weaker then covalent bonds)
most lipids and proteins are capable of lateral shifts in the membrane plane
it is rare for a molecule to flip transversely across the membrane switching between phospholipid layers - for this to happen the hydrophilic sections of the molecule must cross the hydrophobic membrane core
lateral movement of the phospholipids in the membrane is quick
adjacent phospholipids switch with each other about 10^7 times a second
phospholipids move 2mumetres in one second
proteins are larger then lipids and move much more slowly but some membrane proteins do shift
some proteins in the membrane appear to move in a very slow directed manner
it is thought that they are moved by cytoskeletal fibres by motor proteins that are connected to the membrane's protein cytoplasm regions
conversely some other proteins in the membrane are held all but immobile because of how they are attached to the cytoskeleton
membranes remain in a fluid form as the temperature decreases until finally the phospholipids arrange themselves in a closely packed formation and the membrane solidifys
temperature of the solidification depends on type of liqiuds
membrane remains fluid if at the low temperature if it is rich in phospholipids and unsaturated hydrocarbons
this is because unsaturated hydrocarbon tails have kinks in them where double bonds are located and because of this the phospholipids cannot pack themselves as single bond ones and therefore cannot become as solid
steroid cholesterol (found inbetween phospholipid molecules in the plasma membrane of animal cells) has different effects on the membrane
at fairly high temperatures (37 degrees celsius human body temperature for example)
cholesterol also lowers the temperature required to solidify membranes
cholesterol can be thought of as a temperature buffer becasuse it helps resist change in the fluidity caused by temperature changes
membranes must be fluid to work correctly
membranes are usually as fluid as salad oil
when a membrane solidifies its permeability changes and enzymatic proteins in the membrane can become inactive as a result
an example would be when the activity of enzymatic proteins require them to move laterally in the membrane
the lipid composition of cell membranes can change as an adjustment to changing temperatures
for example in plants that can tolerate extreme cold the percentage of unsaturated phospholipids increase in autumn, this keeps the membranes from solidifying during winter
Section 4: [7.3] Passive Transport – Diffusion
Molecules have a type of energy called thermal motion (heat).
One result of this is
Molecules of any substance move randomly and spread out evenly into available space, leading to a dynamic equilibrium
In the absence of other forces, a substance will diffuse from where it is more concentrated to its
where it is less concentrated
No work must be done in order to make this happen, as the concentration gradient itself represents potential energy and drives diffusion
The diffusion of a substance across a biological membrane is called
In a cell scenario, when a substance is more concentrated on one side of the permeable membrane, there is a tendency for it to diffuse across the membrane down to its concentration gradient, such as the uptake of oxygen by a cell performing cellular respiration.
To better understand this, imagine dye solutions to which a membrane is permeable.
Osmosis good copy.pptx
Biology Grade 12 - Membrane Lesson Summary.docx
Facilitated Diffusion: Passive Transport Aided by Proteins
Section 8: 7.5 Bulk Transport
: transportation of large molecules that cannot diffuse through plasma membrane
: fusion of vesicles with the plasma membrane
Used for exporting waste or products
Ex/ Neuron uses exocytosis to release neurotransmitters to signal other neurons or muscle cells
Ex/ Plant cell walls use exocytosis to deliver proteins and carbohydrates from Golgi vesicles to the outside of the cell
Vesicle comes off the Golgi apparatus
Moves along microtubules of cytoskeleton
Reaches plasma membrane. Lipid molecules (from vesicle membrane and plasma membrane)
rearrange and fuse together. Vesicle membrane becomes a part of the plasma membrane
Once fused, contents of vesicle spill to outside (extracellular fluid)
: transportation of larger particles into the cell
3 types of Endocytosis
Phagocytosis: transports large food particles
Pinocytosis: transports small amount of Extracellular fluid
Pseudopodium form from the plasma membrane
They act as little arms that 'engulf' a large particle
Food vacuole is formed and moves into the cell
Extracellular fluid has many little particles the cell may need
Plasma membrane pinches inward, creating a small 'pocket' for fluid
The pocket closes off. A vesicle is formed and shipped off into the cell
Purpose of this is to enable the cell to get large amounts of SPECIFIC substances (even if the substances are in a low concentration in the extracellular fluid)
In membrane, specific receptor sites (usually clustered in coated pits) are exposed to extracellular fluid
the substances specific to these receptors bind to the sites
vesicle formed with specific substance in it, and afterwards receptors are recycled into plasma membrane for more receptor-mediated endocytosis!
We used receptor-mediated endocytosis to take in cholesterol (low-density lipoproteins or LDLs) for further use in the body.
If the receptor sites for LDLs is defective or missing, cholestorol accumulates in the blood.
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