Biochemistry

__**Chemical Fundamentals and Macromolecules Quiz**__ __**Enzyme Quiz**__

__**Jeopardy Review**__

__**Resources**__ [|Cell Membrane (fluid mosaic)]

__**Enzymes**__
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 * http://www.bbc.co.uk/schools/gcsebitesize/science/add_aqa/enzymes/
 * http://www.bbc.co.uk/schools/gcsebitesize/science/add_gateway/living/ [DNA and Enzymes section]
 * http://www.bbc.co.uk/schools/gcsebitesize/ [General site; useful for many subjects]

__**Macromolecules**__


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__**Testing for Macromolecules Lab**__

__**Cell Organelles and their Function**__ []


 * Oct 12, 2010**


 * __Macromolecules__**

- LARGE organic compounds - Also called polymers

- Made up of ‘building blocks’ called monomers

- contain Carbon → has 4 e¯ in outer shell → form covalent bonds with 4 other elements (C, H, O, N) → forms chains and rings

4 main macromolecules

1. Carbohydrates

2. Lipids

3. Proteins

4. Nucleic Acids


 * 1) Carbohydrates

- small sugar molecules to large sugar molecules


 * 1) monosaccharides

Ex. Glucose, ribose, fructose ribose, deoxyribose


 * 1) __ disaccharides __

Ex. Sucrose → glucose + fructose

Lactose → glucose + galactose

Maltose → glucose + glucose


 * 1) __ Polysaccharides __

Ex. Starch (bread, potatoes) *→* storage form of glucose in plants

Starch → Amylose + Amylopectin

↓ ↓

straight chain branched chain branches ά 1-6

O attached with 1- carbon from one glucose and 4 carbon from another glucose

below plane; ά 1-4 glycosidic linkage

- Glycogen (beef muscle)

- Cellulose (lettuce, corn)

Monomers with 5 or more carbons are LINEAR when DRY

Monomers are RING when WET

**__ 2 versions of glucose __** **__ α – glucose __** ** __β__ __– glucose__ **
 * -OH above plane -OH below plane **


 * __ Dehydration Synthesis / Synthesis Reaction __**

- Rxn by removing H2O (forms polymers by combining monomers) - Covalent bonds in different molecules have different names

**__ Hydrolysis __**

- To separate/digest macromolecule - Separate monomers by adding H2OHere is a (very) short video on Dehydration Synthesis[]

=**Macromolecules cont. ** = October 13th/2010 By: Clinton D'Silva

Interesting lesson on Carbohydrates that shows a visual representation all about Carbohydrates media type="youtube" key="_qf_r5EVP6U?fs=1" height="385" width="640" Video from []

Lipids

 * since it hates water it is only soluble in HYDROPHOBIC liquids
 * LIPIDS STORE THE MOST ENERGY
 * 6 types of Lipids:
 * 1) Fats
 * 2) Phospholipids
 * 3) Oils
 * 4) Waxes
 * 5) Steroids (hormones)
 * 6) Tryglycerides

TRIGLYCERIDES Triglycerides photos from []

Saturated Fatty Acids (bad for you) have no double bonds Unsaturated Fatty Acids (not so bad for you) have double bonds.

PHOPHOLIPIDS Hydrophobic - Water HATING Hydrophilic - Water LIKING

photos from [] [|http://www.biologycorner.com/APbiology/cellular/(notes)cell_membrane.html]

HORMONES use this link to get a clear cut understanding of how lipids form hormones []

Waxes interesting link on the formation of waxes and the fatty acids that surround us in the form of waxes []

6 Funct ions of Lipids

 * 1) Long term energy source
 * 2) Protection against heat loss (insulation)
 * 3) Protection against physical shock
 * 4) Protection against Water loss
 * 5) Chemical Messengers (hormones)
 * 6) Major component of membranes (phospholipids)

Proteins

 * Amino Acids (20 different AA) are bonded with PEPTITE BONDS (polypeptides)

Functions of Proteins
Storage albumin (egg white) Transport hemoglobin Regulatory hormones Movement muscles Structural membranes, hair, nails Enzymes cellular reactions

(only some have quatinary)
 * All POLY PEPTIDES HAVE PRIMARY SECONDARY AND TERTIARY *

THERE ARE 4 LEVELS OF PROTEIN STRUCTURE
this is shown in the following video If you want a written explanation read the from section 1.2 in the textbook or open up the PowerPoint at the top of the page media type="youtube" key="lijQ3a8yUYQ?fs=1" height="385" width="480" video from []

__Oct 19, 2010__ __Enzymes__ __Tom Parr__
 * Here is a good video to help explain the basics of enzymes.**
 * []**

__Defintions__
 * Enzymes - protein catalysts that lower activation energy for a reaction**
 * Energy - the ability to do work**
 * Exergonic (exothermic)- release of energy/heat (for reactions)**
 * Endergonic (endothermic) - require energy (for reactions)**
 * Activation Energy - energy used to reach transition state**
 * Substrate- the reactant that an enzyme acts on when it catalyzes a chemical reaction**
 * Active Site - the region binding enzymes to substrates**

__Lock and Key vs Induced Fit__
 * Two general explanations are given of how an enzyme binds to and acts upon a substrate. The induced fit is more accurate but the Lock and Key still emphasizes a key point. In the lock and key explantion it is explained how a specific enzyme act on a specific substrate rather then just whichever substrates are nearby (mcuh like how a key only fits the lock it is made for). This is a key point but fails to recognize that there is slight 3D movement in the enzyme to allow it to bing well with the enzyme at the active site.**


 * If you wwant more information visit:**
 * []**

__Factors that Affect Enzyme Activity__
 * 1. Temperatue - as the termperature rises the enzyme activity does well (reactions happen fast in higher temperatures) but after a certain point the temperature is so high that proteins denature and lose enzyme function. An example of this high termperature is when you have a bad fever, which causes your enzymes to be less functional. (Stead increase to reach peak then sudden plummet graph)**
 * 2. pH level - The pH level affects the 3D conformation of the enzyme. Unike temperature, the pH level does not suddenly cross a limit after reaching its optimum point and lower enzyme activity. It operates just as well slightly above optimum pH level as it would slightly below. (Steady increase to reach peak, steady decline graph)**
 * 3. Substrate Concentration - Obviously, the number of enzymes present result in the ability to work on more substrates at the same time. Therefore; the more enzumes, the higher enzyme activity (productivity).(Linear constant increase graph)**
 * 4. Substrate Concentration- When there are more substrates for enzymes to work on enzyme activity is increases. But after a certain point the activity will not increase anymore since there are more substrates then the available enzymes can work on. (Arc graph)**


 * This website explains it very well:**
 * []**

__Inhibition__
 * Different kinds of inhibition stop enzymes from catalyzing reactions and interacting with substrates at the activiation site. There kinds of inhibition are:**
 * 1. Competitive - competes for active site of the enzyme; similar in shape to substrate; prevents substrate from binding**
 * 2. Noncompetitive - do not compete for active site; they bind to another site causing change in enzyme configuration; the enzyme loses affinity for substrate**
 * 3. Uncompetitive - binds to the ES complex only and prevents conversion of substrate to complex**


 * This website helps explain inhibiton but please note that it calls the kinds of inhibition different things. The visuals are very effective for explaing enzyme inhibitiors.**
 * []**

__Regulation__
 * There are also two kinds of regulation which help keep enzyme levels at appropriate amounts. These two kinds of regulation are:**
 * 1. Allosteric - enzymes can have active and inactive forms; allosteric sites are sites on the enzyme to which allosteric activators stabilize the active form of the enzyme or allosteric inhibitors promote the inactive form of enzymes**
 * cooperativity- for enzymes with multiple subunits (therefore multiple active sitees) when a substrate binds to one active site it stabilizes the other substrates so other substrates can bind.**
 * 2. Feedback Inhibition -an enzyme produced through different reactions involving other enzymes will inhibit the other enzymes when enough of that specific enzyme have been produced**

Here is an appropriate site to help explain regulation: []

Hope my note helps! Tom Parr

CHAPTER 7. FLUID MOSAIC MODEL! Selective permeability of the cellular membrane depends on two things: the discriminating layer of lipid bilayer and the specific channel proteins that speed up the rate at which specific substances are able to travel though the lipid bilayer!
 * 7.2: Membrane Structure results in selective permeability!**

All nonpolar molecules are hydrophobic and can therefore dissolve in the lipid bilayer allowing them faster passing! But polar hydrophilic molecules have difficulty passing through the bilayer.

The lipid bilayer promotes the passage of non-polar molecules and prohibits the passage on polar molecules; even smaller polar molecules have great difficulty in their passing through the bilayer. This is when the channel proteins come in; they increase the rate of passage of a specific polar molecule through the lipid bilayer. An example of this is aquaporin a channel protein specific to water that allows for 3 billion water molecules to travel through the membrane per second! Transport proteins are very specific for the substance that they transport through the membrane. Another example, glucose, which is carried in red blood cells, enters through a channel protein that is so specific that it rejects fructose which is an isomer of glucose.

Fed and Tom!!!

=__7.3__=

**__ Diffusion: passive transport with no energy investment __**

  Concentration gradient à diffusion à dynamic equilibrium

-**concentration gradient**: unequal density of a substance on either sides of a membrane

- **diffusion** : product of thermal motion, spontaneous process of random movement of molecules (together becomes directional), all the while lowering the concentration gradient

- **dynamic equilibrium**: as many crossing one direction as the other (therefore same concentration of that substance on both sides of the membrane)

- rates of diffusion is based on membrane permeability

- concentration gradient of one substance will NOT affect the concentration gradient of another

- Here is an animation: []

- polar molecules/ions are able to diffuse with the help of transport proteins
 * Facilitated Diffusion: Eva and Chris **

2 types of transport proteins: - Pathways for specific molecules/ions to cross the membrane -> much faster than regular phospholipids
 * __ 1. Channel Proteins __**


 * Aquaporin:** Water channel protein that allows water to diffuse fast like in kidneys


 * Ion Channel Proteins:** Can be gated channel. -> open and close with chemical or electrical stimulus

- Change shape to move solute across membrane
- Some diseases don’t have transport proteins = failed transport = buildup of bad things= BAD THINGS HAPPEN

** Effects of Osmosis on Water Balance **

** Osmosis: ** The movement of water through a selectively permeable membrane · Goes from low concentration to high concentration

** Tonicity: ** The effect of a solution on a cell to gain or lose water · Dependant on non-penetrating solutes

** Types: ** · Isotonic: No net movement between cell and environment · Hypertonic: Cell loses water to environment · Hypotonic: Cell gains water from environment


 * ** Tonicity ** ||||  ** Type of Cell **  ||
 * || ** No cell wall (animal) **  ||  ** Cell Wall (plant, fungi…) **  ||
 * ** Isotonic ** || Normal  ||  Flacid (limp)  ||
 * ** Hypotonic ** || Lysed  ||  Turgid (Firm)  ||
 * ** Hypertonic ** || Shriveled  ||  Plasmolysis  ||

** Plasmolysis: ** Membrane pulls away from cell wall. Plants may wilt and die due to plasmolysis.

Biology Summary: Membrane Structure & Function (section 1) Sarah Dunn, Drew MacNeil, Sangitha Mensingh

__ Life at the Edge __
 * __ Selective permeability __ : allows some substances to cross the membrane more easily than others

7.1 Cellular membranes are fluid mosaics of lipids and proteins:


 * Lipids and proteins make up cell membranes, mostly lipids called phospholipids
 * Phospholipids are **amphipathic** (have both a hydrophilic and hydro phobic regions)
 * __ Fluid mosaic model __ : the membrane is a fluid structure with various proteins scattered throughout attached to a bilayer of phospholipids
 * About 10 million times per second, the phospholipids switch spots laterally; once a month they flip-flop (switch from the inside of the bilayer to the outside)
 * Proteins, much larger than the phospholipids, move within the membrane very slowly or not at all (if attached to the cytoskeleton)
 * The bilayer moves slower at lower temperatures and can solidify (stop flowing); unsaturated phospholipids create a membrane that remains fluid to a lower temperature (the unsaturated lipids are not packed as closely)
 * __ Example of previous point: __ Cholesterol can enter the bilayer and push the phospholipids further apart, causing the temperature of solidification to decrease. Too much cholesterol, however, can cause the membrane to become rigid.
 * To work optimally, membranes must be fluid; if they are not, enzymes within the proteins can become inactive. [[image:72398_10150299105300094_568695093_15321132_6190738_n.jpg]]

=7.5: Bulk Transport=


 * allows large molecules to enter the cell and requires energy
 * Exocytosis:
 * large molecules are packaged in vesicles by Golgi apparatus
 * vesicles attach to cell membrane inside cell, then large molecules are released outside and the vesicle becomes part of the cell membrane
 * Endocytosis:
 * opposite of exocytosis, molecules are absorbed into the cell; there are 3 types:
 * phagocytosis: cell sends out pseudopodiums to wrap around macromolecules and encases it in a food vacuole
 * pinocytosis: cell engulfs droplets of extracellular fluids into a vesicle
 * receptor-mediated endocytosis: substances attach to receptors on the outer cell membrane, and the cell engulfs the receptors and substance

For animation of bulk transport please check out []

Membrane Proteins and Their Functions
- A membrane is a collage of different proteins in the fluid mosaic model <span style="font-family: Times New Roman; margin: 0cm 0cm 0pt 36pt; tabstops: list 36.0pt; text-indent: -18pt;">- Protein determines the membrane’s function

__ 2 Types of Proteins __

Integral- penetrate the hydrophobic core of the lipid bilayer <span style="font-family: Times New Roman; margin: 0cm 0cm 0pt 36pt; tabstops: list 36.0pt; text-indent: -18pt;">- may be transparent proteins → span the membrane <span style="font-family: Times New Roman; margin: 0cm 0cm 0pt 36pt; tabstops: list 36.0pt; text-indent: -18pt;">- have hydrophilic parts on the outside → hydrophobic in the inside of membrane

Peripheral – loosely bound to the lipid bilayer/exposed integral proteins

(picture)

__ 6 Major Functions of Protein __

<span style="font-family: Times New Roman; margin: 0cm 0cm 0pt 36pt; tabstops: list 36.0pt; text-indent: -18pt;">1) Transport → a channel for a particular solute across the membrane <span style="font-family: Times New Roman; margin: 0cm 0cm 0pt 36pt; tabstops: list 36.0pt; text-indent: -18pt;">2) Enzymatic activity → may be an enzyme with its active site exposed on the outside <span style="font-family: Times New Roman; margin: 0cm 0cm 0pt 36pt; tabstops: list 36.0pt; text-indent: -18pt;">3) Signal transduction → a receptor of chemical messenger (hormone) <span style="font-family: Times New Roman; margin: 0cm 0cm 0pt 36pt; tabstops: list 36.0pt; text-indent: -18pt;">4) Cell-cell recognition → identification tags for recognition by other cells <span style="font-family: Times New Roman; margin: 0cm 0cm 0pt 36pt; tabstops: list 36.0pt; text-indent: -18pt;">5) Intercellular joining → Proteins adjacent cells hook together <span style="font-family: Times New Roman; margin: 0cm 0cm 0pt 36pt; tabstops: list 36.0pt; text-indent: -18pt;">6) Attachment to the cytoskeleton/extracellular matrix → microfilaments noncovalently bound to proteins, maintaining cell shape, often carbohydrates protein locations

__ Membrane Carbohydrates and Cell-Cell Recognition __

<span style="font-family: Times New Roman; margin: 0cm 0cm 0pt 36pt; tabstops: list 36.0pt; text-indent: -18pt;">- cells recognize other cells by binding to surface molecules, often carbohydrates, on the membrane

__glycolipids__ – carbohydrates covalently bonded to lipids

__Glycoproteins__ – carbohydrates covalently bonded to proteins

__ Synthesis and Sidedness Membrane __

- lipds acqure carbohydrates = glycolipids
 * membrane proteins and lipids are synthesized with in the ER
 * carbohydrates added to proteind = glycoproteins
 * glycoproteins travel from ER to Golgi apparatus via vesicles
 * Glogi Apparaatus- undergo further modification of carbohydrates
 * transported to the transmembrane through vesicles
 * vesicles fuse with the membrane, releasing the protein

7.4 Active transport uses energy to move solutes against their gradients

diffusion – passive transport (moving down concentration gradient – from high concentration to low concentration)

active transport requires ATP to move against concentration gradient – from low concentration to high concentration

sodium potassium pump – exchange of Na+ for K+ across the plasma membrane of animal cells (Figure 7.16 in package). Also look at the video on You tube video for further information []

Ion Pumps Maintain Membrane potential

-All cells have voltages, as cytoplasm is negative in comparison to extra-cellular fluid which is positive.

-Two forces drive diffusion of ions across membrane, chemical force of ion’s concentration gradient and electrochemical force of electrochemical gradient (cations in, anions out)

-Some membrane proteins actively pump ions to add to membrane potential, so that it is stored and can be used later for processes such as ATP synthesis and cotransport. The main electrogenic pump is animal cells is the sodium potassium pump, while in fungi and bacteria it is the proton pump, which uses H+.

Cotransport

A single ATP powered pump that uses a specific solute to transport several other solutes through active transport Hydrogen ions generated by proton pumps drive the active transport of amino acids, sugars and other nutrients.(the hydrogen ion has to accompany a solute for this to occur) This is how plants transport nutrients around its structure. GATORADE WORKS!!!