Biochemistry


 * Macromolecules Lab**


 * Chemical Fundamentals and Macromolecules Sample Quiz**

- 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. - Macromolecules: ..........- 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". - Hydrolysis: .........- Separates monomers by "adding water".- - Carbohydrates: .........- Small sugar molecules to large sugar molecules. .........- Examples: monosaccharide, disaccharide, polysaccharide. ................Monosaccharide: .....................- One sugar unit: Glucose (C6H12O6), Galactose, Fructose, Ribose, Deoxyribose. ................Disaccharide: .....................- Sucrose (Gluctose + Fructose) .....................- Lactose (Gluctose + Galactose) .....................- Maltose (Gluctose + Glucose) ................Polysaccharide: .....................- 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. - Isomers: .........- A molecule has the same number of atoms but differently arranged.
 * Jeopardy Review: Chemistry, Macromolecules and Enzymes**
 * February 10,2011**
 * Marco Becerril**
 * Unit 1, Topic: Biochemistry**
 * Text Refernce: Biology 12.**
 * Idea: An introduction to biochemistry**

Homework: - Complete Stem Cells Application. - Get a webpage for topic.

media type="youtube" key="zKNZjP9BdCw" height="390" width="480" []

Welcome to Biochemistry! media type="youtube" key="itWLaLat8LU" height="390" width="640" []


 * Tuesday Feb 15, 2011**
 * Niles** **Lawrence**
 * Lipids and Proteins**


 * __ Lipids: __**
 * Compounds not soluble in water ( soluble in hydrophobic solvents)
 * Stores the most energy ( 9 calories per gram, carbs stores 4 calories per gram)
 * Examples:
 * 1) Fats
 * 2) Phospholipids
 * 3) Oils
 * 4) Waxes
 * 5) Steroid hormones
 * 6) Triglycerides
 * Six functions for Lipids
 * 1) long term energy storage
 * 2) protection against heat loss (insulation)
 * 3) Protection from physical loss
 * 4) Protection from water loss
 * 5) chemical messengers (hormones)
 * 6) Major component of membranes (phospholipids)

http://4.bp.blogspot.com/_P3QbBrepTgI/THEsTvimfwI/AAAAAAAAA0o/aECf3y64DOQ/s400/fatty+acid.jpg
 * Triglycerides:**
 * **1** glycerol and **3** fatty acids (ester bonds /linkage)
 * 2 types of fatty acids saturated (bad) and unsaturated (good)


 * Phospholipids**
 * Bilayer separates two water compartments.

http://www.bioteach.ubc.ca/Bio-industry/Inex/


 * Steroid Hormones**
 * Consists of 4 rings with atoms coming off them that make different hormones
 * Ex cholesterol, estradiol, testosterone, progesterone
 * Waxes**
 * 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, Methionine , Phenylalanine , Threonine, Tryptophan and Valine.

http://www.bothbrainsandbeauty.com/wp-content/uploads/2009/12/aminoacidstructure.jpg
 * Six functions of proteins
 * 1) storage: albumin (egg white)
 * 2) Transport: hemoglobin
 * 3) Regularity: hormones
 * 4) Movement: muscles
 * 5) Structural: membranes, hair, nails
 * 6) Enzymes: cellular reactions
 * Four levels of protein structure
 * 1) Primary Structure
 * 2) Secondary Structure
 * 3) Tertiary Structure
 * 4) Quaternary Structure
 * Primary Structure**


 * Straight chain of amino acids bonded by peptide bonds


 * Secondary Structure**


 * 3D folding arrangement of primary structure into coils and pleats held together by hydrogen bonds


 * Tertiary Structure**


 * 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


 * Quaternary Structure**

http://www.contexo.info/DNA_Basics/images/proteinstructuresweb.gif
 * **Not all polypeptides have Quaternary structure**
 * Composed of 2 or more subunits
 * Ex enzymes

media type="youtube" key="lijQ3a8yUYQ" height="390" width="480" http://www.youtube.com/watch?v=lijQ3a8yUYQ


 * Wednesday, February 16, 2011**
 * Macromolecules: Proteins (cont'd) and Nucleic Acids**
 * Jane Yang**

Proteins (cont’d)


 * Final shape of polypeptide (tertiary structure) **determined by** primary structure + chemical and physical factors
 * However, changes in temperature, pH, ionic concentration, and/or other environmental factors may **CHANGE** the 3D structure of the polypeptide
 * this is called **Denaturation**

(image created by: Jane Yang)
 * there are good and bad consequences
 * ex/ cooking meat denatures protein in it and makes it chewy, easier to eat

(Nelson Biology 12 Textbook, page 47)


 * more ex/s in textbook page 47, last paragraph


 * polypeptide “change” can be **reversed** if what changed is removed/reversed AS LONG AS structure of polypeptide remains intact (peptide bonds are not broken)
 * **Chaperone protein**: assist in folding of growing polypeptide into the structure (into tertiary structure)


 * Remember **: Change of environment = change of shape = change of function = affects important roles in bodily functions, for instance.

__** Nucleic Acids **__
 * composed of long chains of **nucleotides** linked by dehydration synthesis (phosphodiester bond)

//Nucleotide includes//:
 * phosphate group
 * 5-carbon sugar (pentose sugar)
 * nitrogenous bases (Adenine (+) Thymine/Uracil ; Cytosine (+) Guanine)

media type="youtube" key="Cb1Fh5M4jI0" width="425" height="350"

Two main types: 1. **DNA** (deoxyribonucleic acid): double stranded 2. **RNA** (ribonucleic acid): single stranded

--> 3. **ATP** (adenosine triphosphate) [forgotten a lot as a nucleic acid]

DNA—double helix —**anti-parallel**: 2 adjacent nucleotide polymers running in opposite directions relative to one another

(Nelson Biology 12 Textbook, page 53)

**Bre Klarenbeek ** **Unit 1, Topic: Biochemistry ** **Text Refernce: Biology 12. ** **Idea: Enzymes **
 * 28.02.11 **

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: media type="youtube" key="EiMBsgNZh-M" height="390" width="480" 

Induced Fit: media type="youtube" key="VXNsr6Rc6ok" height="390" width="480" 

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 Free energy – ability to do useful work 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 Releasing energy – Exergonic reaction (Bio) Exothermic reaction (Chem)

“Consuming” or Using energy – Endergonic reaction (Bio) Endothermic Reaction (Chem)

Reaction coupling – Mixing of Exergonic and Endergonic reactions Metabolism – 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 Entropy – randomness and disorder in a system, theory is that reactions/things go towards disorder Anabolic increases entropy [] [] [] [] [] . []

=Enzymes=

Tuesday, March 1, 2011 – by Joel Tham
__Catalyst:__ like a facilitator for speeding up reactions without being used up

__Enzymes:__ Ø Protein based catalysts Ø Do not get used up in a reaction - “recycled” Ø 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 \ faster reactions

__Why do we need enzymes?__ Ø The reactions that occur in cells would happen too slowly to sustain life The most common type of activation energy is __heat__ Ø The problem is that heat can denature enzymes and cause cells to die · Enzymes lower EA (energy of activation) so heat is not needed

__Enzyme Activity__ Ø Reactants are called substrates Ø Substrates bind to a region on the enzyme called the active site · The active site is where the reaction occurs Ø 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) Ø ex) amylase in the following reaction: amylose + H2O « maltose  Ø 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   Ø Induced-Fit Theory   · 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   Ø Bind to the enzymes’ active site or to the substrate   Ø Enzyme activity can be affected by several factors  2. pH  3. Enzyme concentration  4. Substrate concentration   Ø __Enzyme regulation__ 1. Enzyme Inhibition (preventing normal enzyme activity) Ø __Competitive Inhibitors__ · Similar in shape to the substrate · Compete for the active site and prevent the substrate from binding · ex) methanol and ethanol  § Methanol poisoning ® alcohol dehydrogen__ase__ (causes permanent damage to central nervous system)   § Cure ® provide ethanol (competes with methanol for enzymes, causing the methanol to leave the system)   Ø __Non-competitive Inhibitors__   · 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   Ø __Uncompetitive Inhibitors__   · Only binds after the enzyme has bound to substrate (ES complex)   · Prevents the formation of product(s)  2. __Allosteric Regulation__   Ø Allosteric sites are receptor sites away from the active site that bind substances that may activate or inhibit (ex. non-competitive enzyme activity)  Ø This involves enzymes that have quaternary structure (each subunit has its own active site)   Ø An activator binds to an allosteric site and helps to keep all active sites open/available to substrate   Ø An inhibitor binds to an allosteric site and inactivates the enzyme (changes shape of active sites)   Ø Nelson Biology 12 - page 73 figure 7  3. __Feedback Inhibition__   Ø Used to control a series of reactions involving more than one enzyme   Ø A product formed later in the sequence inhibits an enzyme involved in an earlier step of the process   Ø ex. synthesis of amino acids (pg 74 figure 8)
 * 1) Temperature

__Summary - Enzymes are Regulated By:__ Ø Inhibition (competitive, non-competitive, uncompetitive, feedback) Ø Allosteric activated/inhibited · ex. enzymes produced in an inactive form and only activated when needed (ex. pepsinogen ® pepsin) Ø A cell can control the amount of enzymes it makes Ø 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 · Baking · 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: 

__Links:__ [] (same site I presented in class) [] (another useful site for enzymes) [] (the video we saw in class)

__Homework:__

 Ø Enzyme Assignment (due Thursday, March 10, 2011)  Ø Questions on page 77  Ø 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 (page 132)
Molecules have a type of energy called thermal motion (heat). One result of this is ** diffusion ** 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.
 * 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 ** concentration gradient ** 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 ** passive transport. **

To better understand this, imagine dye solutions to which a membrane is permeable.

OSMOSIS





Facilitated Diffusion: Passive Transport Aided by Proteins


 * Section 8: 7.5 Bulk Transport **(pages 138-139)

**Bulk Transport**: transportation of large molecules that cannot diffuse through plasma membrane **Exocytosis**: fusion of vesicles with the plasma membrane 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 []
 * Used for exporting waste or products

**Steps** > <span style="direction: ltr; font-size: 110%; margin-bottom: 0in; margin-left: 0.375in; margin-top: 0in; unicode-bidi: embed; vertical-align: middle;">rearrange and fuse together. Vesicle membrane becomes a part of the plasma membrane
 * 1) <span style="direction: ltr; font-family: Calibri; font-size: 11pt; margin-bottom: 0in; margin-left: 0.375in; margin-top: 0in; unicode-bidi: embed; vertical-align: middle;">Vesicle comes off the Golgi apparatus
 * 2) <span style="direction: ltr; font-family: Calibri; font-size: 11pt; margin-bottom: 0in; margin-left: 0.375in; margin-top: 0in; unicode-bidi: embed; vertical-align: middle;">Moves along microtubules of cytoskeleton
 * 3) <span style="direction: ltr; font-family: Calibri; font-size: 11pt; margin-bottom: 0in; margin-left: 0.375in; margin-top: 0in; unicode-bidi: embed; vertical-align: middle;">Reaches plasma membrane. Lipid molecules (from vesicle membrane and plasma membrane)
 * 1) <span style="direction: ltr; font-family: Calibri; font-size: 11pt; margin-bottom: 0in; margin-left: 0.375in; margin-top: 0in; unicode-bidi: embed; vertical-align: middle;">Once fused, contents of vesicle spill to outside (extracellular fluid)

**Endocytosis**: transportation of larger particles into the cell

**3 types of Endocytosis**
 * 1) <span style="direction: ltr; font-family: Calibri; font-size: 11pt; margin-bottom: 0in; margin-left: 0.375in; margin-top: 0in; unicode-bidi: embed; vertical-align: middle;">Phagocytosis: transports large food particles
 * 2) <span style="direction: ltr; font-family: Calibri; font-size: 11pt; margin-bottom: 0in; margin-left: 0.375in; margin-top: 0in; unicode-bidi: embed; vertical-align: middle;">Pinocytosis: transports small amount of Extracellular fluid
 * 3) <span style="direction: ltr; font-family: Calibri; font-size: 11pt; margin-bottom: 0in; margin-left: 0.375in; margin-top: 0in; unicode-bidi: embed; vertical-align: middle;">Receptor-mediated Endocytosis

<span style="font-family: arial,helvetica,sans-serif; font-size: 13px; line-height: 19px; margin: 0in;"> []

**Phagocytosis** ("Cellular Eating") **Pinocytosis** ("Cellular Drinking") **Receptor-Mediated Endocytosis**
 * <span style="direction: ltr; font-family: Calibri; font-size: 11pt; margin-left: 0.375in; margin-top: 0in; unicode-bidi: embed; vertical-align: middle;">Pseudopodium form from the plasma membrane
 * <span style="direction: ltr; font-family: Calibri; font-size: 11pt; margin-left: 0.375in; margin-top: 0in; unicode-bidi: embed; vertical-align: middle;">They act as little arms that 'engulf' a large particle
 * <span style="direction: ltr; font-family: Calibri; font-size: 11pt; margin-left: 0.375in; margin-top: 0in; unicode-bidi: embed; vertical-align: middle;">Food vacuole is formed and moves into the cell
 * <span style="direction: ltr; font-family: Calibri; font-size: 11pt; margin-left: 0.375in; margin-top: 0in; unicode-bidi: embed; vertical-align: middle;">Extracellular fluid has many little particles the cell may need
 * <span style="direction: ltr; font-family: Calibri; font-size: 11pt; margin-left: 0.375in; margin-top: 0in; unicode-bidi: embed; vertical-align: middle;">Plasma membrane pinches inward, creating a small 'pocket' for fluid
 * <span style="direction: ltr; font-family: Calibri; font-size: 11pt; margin-left: 0.375in; margin-top: 0in; unicode-bidi: embed; vertical-align: middle;">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!
 * Example:
 * 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.