Sunday, March 6, 2011

Cellular Respiration

- Cellular respiration is the most efficient catabolic pathway
- It is a step-wise process (slowly releasing ATP)

There are 3 metabolic stages:
1. Glycolysis (occurs in cytoplasm) (breaks down glucose into 2 molecules of pyruvate)
2. Citric Acid Cycle (occurs in the matrix of mitochondria) (it completes breaking down glucose)
3. Oxidative posphorylation (occurs in the inner membrane of mitochondria)

Glycolysis has 2 major phases: Energy investment phase and Energy payoff phase
Oxygen is not required in either glycolysis or citric acid cycle



- In glycosis, 2 ATP was used, 4 was produced, so the net worth is 2 ATP

- In between glycolysis and citric acid cycle, carbon dioxide was lost (also known as dicarboxylation), so only 2 carbon remain. Coenzyme A joins in to form Acelyle CoA
- for each pyruvate, 1 carbon dioxide was lost, and 1 NADH was formed
- the only difference in transformation of NAD to NADH and FAD to FADH2 is that NAD to NADH uses more energy than FAD to FADH2
- NADH can make 3 molecules of ATP
- FADH2 can only make 2 molecules of ATP
- As each step progresses, 1 proton is lost and the electronegativity increases for each protein.

Saturday, February 26, 2011

Cell Membrane + Transport

- cell membrane controls what enters the cell and what leaves the cell
- cell membrane = 2 phospholipid + proteins
- cell membrane is semi-permeable (only allows small molecules through)
- cell membrane is impermeable to polar substances due to the fact that most of the bilayer is nonpolar and hydrophobic
- 4 components of the cell membrane are protein molecules, carbohydrates, cholesterol and phospholipid
- cholesterol is what holds the cell membrane together
- protein is polar on the two sides but nonpolar in the middle
- cytoskeleton holds the cell, move it, transfer material in and out, and help cell maintain its structure
- gatekeepers: open and close to let materials (ex.ions) in and out
- receptors (protein molecules) transport materials in and out

transport proteins: proteins that allow specific ions and polar molecules to pass through. It is specific to its type of substance.
There are 2 types of transport proteins:
1. channel proteins: certain molecules or atomic ions use it as a tunnel to get through to the membrane at a faster rate
2. carrier proteins: it change shape to allow their passengers to cross through.


There are 2 types of transports:
1. passive transport: movement of materials across cell membrane without spending energy

Diffusion is a type of passive transport where molecules go from an area of high concentration to an area of low concentration because of Brownian motion (random movement of molecules)

Osmosis is the movement of a solvent through semi-permeable barrier until an equilibrium is reached (diffusion). Water follows the concentration gradient (the difference in number of solute or ions in two adjoining regions).
There are 3 types of osmosis:
1. isotonic solution: solute and solvent inside the cell = solute and solvent outside the cell
2. hypertonic solution: solute inside < solute outside, solvent inside > solvent outside, solvent diffuses outward, shrinking the cell
3. hypertonic solution: solute inside > solute outside, solvent inside < solvent outside, solvent diffuses inward, expanding the cell (may burst)


- Tonicity, which is the ability of a surrounding solution to cause a cell to gain or lose water, it mainly depends on the concentration of solute from the two sides.
- Osmoregulation, the control of solute concentration and water balance.

Facilitated Diffusion is when molecules uses protein carrier molecules (for noncharged molcules) or channel proteins (for charged molecules) to diffuse in and out of a cell

2. active transport: movement of materials across cell membrane using energy (ATP)

active transport pump is a cell membrane protein that actively pumps ions across the membrane against their concentration gradient.

bulk transport is used when some materials are too large to pass in or out of the membrane on their own, so the membrane will actively engulf these materials, using energy in process.
An example would be endocytosis, where the membrane engulf the material found outside and traps it in a vesicle or a vacuole.
There are three types of endocytosis:
1. pinocytosis: cells take up solution with dissolved molecules
2. phagocytosis: solid particles are engulfed
3. Receptor-mediated endocytosis: engulfs receptors
Another example would be exocytosis, where the vesicles form inside the cell, fuse with the cell membrane and release its materials into the external environment


-membrane potential: voltage across a membrane
-There are 2 forces that drive diffusion of ions across a membrane
  1. chemical force (ion's concentration gradient)
  2. electrical force (effect of the membrane potential on the ion's movement)
-when these 2 forces combined together, it is called electrochemical gradient

- electrogenic pump: transport protein that generates voltage across a membrane
- proton pump: transports hydrogen ions (H+) out of cell
- cotransport: the simultaneous movement of two substances across a membrane

Saturday, February 19, 2011

Energy

- cells convert energy in many ways
- organism's metabolism transforms matter and energy, subject to the laws of thermodynamics

Thermodynamics: study of energy transformations
3 Laws of Thermodynamics:
- Energy cannot be created or lost
- It takes energy to keep randomness in place (spontaneous changes that do not require outside energy increase the entropy, or disorder of the universe)
- Absolute Zero

- Living systems increase the entropy of the universe
- energy is required to maintain order

Free energy: energy that can do work under cellular conditions
- organisms live at the expense of free energy

Spontaneous change: free energy decrease, stability of system increases
- maximum stability: equilibrium (closed system)
- cells of our body constantly flows materials in and out, prevents metabolic pathways from reaching equilibrium

Exergonic reaction:
- release of free energy and is spontaneous
Endergonic reaction:
- absorbs free energy from surroundings and is not spontaneous

Metabolism:
- organism's chemical reactions
- arises from interactions between molecules
- it starts with a molcule and ends with a product, performed by a few specific enzymes

Catabolic pathways:
- complex molecules --> simple compounds
- releases energy
Anabolic pathways:
- simple compounds --> complex molecules
- consume energy

- Energy is the capacity to cause change which can perform work
- Energy can be converted

Kinetic energy:
- energy associated with motion
Potential energy:
- stored in the location of matter
- chemical energy stored in molecular structure

ATP:
- powers cellular work by coupling exergonic reactions to endergonic reactions
- 3 main types of work: mechanical, transport, chemical

Energy coupling: key feature in the way cells manage their energy resources to do this work
Couple Reaction: one releases energy, which fuels another

Nucleic Acids

- Nucleic Acids are polymers formed for monomer called nucleotides
- Nucleotide contains nitrogenous base, 5 carbon pentose sugar, phosphate group
- The nitrogen bases in DNA are: adenine, thymine, guanine, cytosine
- In RNA, thymine is replaced by Uracil
- Single ring are pyramidines (cytosine, thymine, uracil)
- Two rings are purines (adenine, guanine)

DNA is short form for Deoxyribonucleic Acid
- it's the genetic code for proteins and life functions
- 2 nucleotide strands: A+T, C+G are linked by hydrogen bonds forming a double helix
- DNA are antiparallel



RNA is short form for Ribonucleic Acid
- RNA carries the protein code from nucleus to ribosome during PRO synthesis
- 1 nucleotide strand: A, U, C, G
- mRNA is messenger
- tRNA is transfer

ATP is short form for Adenosine Triphosphate
- it's a monomer
- it's a nucleotide
- its energy for molecule of cells
- ATP -> ADP + P + Energy

Nucleotide Coenzymes
- 3 types: NAD+, FAD, NADP+
- it moves H+ ions and electrons around
- drives chemical reactions

Neucleosome: structure responsible for the compactness of chromosome. each nucleosome consists of a sequence of DNA wrapped around a core of protein.

rRNA (Ribosomal RNA):
- molecular component of ribosome (cell's essential protein factory)
- it makes polypeptides which make up proteins

- Ribosomes are made of RNA + Proteins

Phosphodiester bond
- covalent bond joining 3' hydroxyl of sugar of ribonuleotide to 5' hydroxyl of the adjacent sugar

Protein

- Proteins account for more than 50% of dry weight of most cells

7 Classes of Proteins:
1. Structural Proteins (function in cell membrane)
2. Contractile Proteins (provide muscular movement)
3.Storage Proteins (a source of amino acid for developing embryos)
4. Defensive Proteins (antibodies carried in blood)
5. Transport Proteins (hemoglobin, transports oxygen from lungs)
6. Enzymes (regulate chemical reactions in cells)
7. Hormones (chemical messenger)

- proteins are made from 20 amino acids
- bonded together by peptide bonds (dehydration synthesis reaction)

- 9 amino acids are essential
1 amino acid = 1 amino acid monomer
2 amino acid = dipeptide molecule
many amino acid = polypeptide chain
1 or more polypeptide chains = a protein molecule

secondary structure:
- connected by hydrogen bonds
- 2 types (alpha helix and beta pleated sheet)
       1. alpha helix: flexible, coiled
       2.beta pleated sheet: strong, parallel

tertiary structure:
- folded
- hydrogen bond
- ionic bond
- di-sulfide bridges occur between neighbouring cysteine amino acids
- 2 types (fibrous and globular)
1. fibrous: strong, insoluble in water
2. globular: spherical, hydrophobic inside, hydrophilic outside, soluble in water

- reducing agent breaks down di-sulfide bridges
- oxidizing agent (H peroxide) helps reform bridges

Quaternary structure:
- 2 or more polypeptide chains linked together



Denatured Proteins:
- proteins that cannot perform properly
- chemicals and or heat disrupts the bonds within proteins

Friday, February 11, 2011

Fat

Fat is made of glycerol and fatty acids

fatty acids are linked to glycerol by ester linkage.
3 fatty acid + 1 glycerol = triacylglycerol / triglyceride
Saturated fat: contains only single bonds (molecule is linear). Animal fats (solid at room temperature)
Unsaturated fat: contain 2/3 bonds (molecule is "bent"). Plant and fish fats (liquid at room temperature)

Function of fat is for energy storage

Phospholipid = 2 fatty acid + phosphate group     attached to glycerol
fatty acid is hydrophobic
phosphate group is hydrophillic

Bilayer: when phospholipid is added to water, hydrophobic tails will point towards the interior, the shape is bilayer. It is found in cell membranes.

Steroids: lipids that consist of 4 fused rings.
Cholesterol: steroid found in animal cell membrane
Cardiovascular disease: too much cholesterol in blood

Carbohydrates

Carbohydrates: short-term energy storage

monosaccharide: 3-7 carbon atoms. Are broken down quickly for energy
disaccharide: 2 sugars bonded together (ex. glucose + fructose)
polysaccharide = complex carbohydrates: long chain of simple sugar grouped together

starch: polymer of monosaccharide glucose
glycogen: polysaccharide used by animals to store energy, also the main form of energy storage in liver and muscles. Excess glucose bonds together to form glycogen
glycogen packs more glucose unit into one cell than starch do

In starch, glucose are facing the same direction. In cellulose, glucose are facing in opposition direction for eachother.  This makes cellulose hard for us, humans to digest (since we don't have the enzymes that could digest that). Cellulose is also hard to break down and cannot dissolve in water like starch can.

Isomers and Funtional Groups

Isomer: same molecular formula, different structure and properties

3 types of isomers:
1. structural
2. geometric
3. enantiomer
Functional group: reactive part of a molecule
- hydroxyl
- carbonyl
- carboxyl
- amino
- sulfhydryl
- phosphate

Acid and Bases

Acid: more hydrogen, less hydroxide
Base: more Hydroxide, less hydrogen
Buffers: compounds used to maintain a constant pH within a system.

Water

water is solvent
sugar and tea are solute

cohesion: water molecule attracted to other water molecules (polar)
adhesion: water molecule attracted to other substances
surface tension: water together creating the smallest surface area
capillary action: cohesion and adhesion working together moving the water molecule

water has high heat capacity
water as gas: most dense
water as solid: least dense

Bonds

There are 2 types of bonds:
- covalent bond
- ionic bond

covalent bond is a bond between 2 non-metals
ionic bond is a bond between a metal and a non-metal

in ionic bond, the metal looses an electron to the non-metal while in covalent the non-metals share their valence electrons

cation: when an atom looses its electron (s), becoming positively charged
anion: when an atom gains electron (s), becoming negatively charged

Electronegativity: attraction between an atom and the bonding electron (s). It only occurs in covalent bonds not ionic bonds. When there is an unequal attraction between two bonding atoms, it is called the polar covalent bond. When it is equal, it is known as the non-polar covalent bond.

Hydrogen bond: attractive interaction of a hydrogen atom with an electronegative atom (also called the intermolecular bond).
There are 3 types of intermolecular bond (Van Der Waals Forces).
1. London forces
2. Dipole - dipole forces
3. Hydrogen bonds

Cell Theory

- cells are the basic unit of life
- organisms are composed of cells
- cells come from pre-existing cells