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I. Basic chemistry
A. Matter vs energy
1. Matter -substance or mass in form of gasses, liquids or solidsB. Composition of matter
2. Energy -ability to do work in form of heat, light or sound
can be stored as chemical energy in chemical bonds
1. Atoms -smallest unit of matterC. Bonds (attractions between atoms)
different atoms (=elements) each have unique characteristics because of structure
Structure determines which other atoms an atom will combine (=bond) with to form molecules
ex. C,H,O,N, Na, K, Cl2. Atomic structure - cloud around a nucleus
a. Proton (P) large and in nucleus
positive charge
b. Neutron (N) large and in nucleus
no charge
c. Electron (e) very small and forms clouds in layers (=shells)
negative charge3. Electrons and bonds
a. Atoms are most stable when outermost electron cloud has 8 electrons (or 2 for H and He)
b. In isolation in labs -Atoms are electrically neutral (P=e)
c. In real world -most atoms do not have 8 electrons in outer shell (except inert gas atoms)
therefore, most atoms will give/take away or share electrons with other atoms to be stable
d. Electrons (in outermost orbit) shared or given/taken between atoms is basis for forming molecular bonds.
Describe an atom and the atomic components responsible for forming bonds.
1. Ions and ionic bonds
Ions are charged atoms or electrolytes which are formed when ionic bonds are broken.
a. Atom in which an electron has been lost becomes more stable but P>e so positively charged ion
ex. Na with outer shell of 1 e
b. Atom in which an electron has been gained becomes more stable but P< e so negatively
charged ion ex. Cl with outer shell of 7 e1) Ionic bondc. Ions important because
results from opposite charges attracting each other
ex Na+ to C- to form NaCL, K+ to Cl- to form KCl, , Ca++ to CO3-- to form CaCO32) Ionic bonds easily broken in water so ionic molecules not often found in body
exception is CaCO3 in bones1) They are most responsible for moving water in the body. Increased ions (and all solutes) increases osmotic pressure (a tendency for water to move towards the solution with highest solute concentration). Hence, if cells move ions then water follows.2. Covalent bonds2) they provide electrochemical signals in excitable cells (neurons and muscles)
3) affect pH of solutions (hydrogen or H ion)
a. Result from sharing of electrons -strong bonds not broken by water
example: C to O to form CO2, O to H to form H2O, O to O to form O2, C to H and C to O to form organics.
b. Polar molecules
one side (=pole) has more electrons (O) than other (=unequal sharing of electrons) making molecules more easily dissolved in water
example: water, monosaccharides, amino acids, nucleic acids
c. Non-polar molecules (= equal sharing of electrons )making molecules less easily dissolved in water
example: lipids
d Covalent bonds important because they form the backbone of all organic molecules, water and gasses.
3. Hydrogen bond
a. Result from attraction of H with (usually) O or N -weak bond between adjacent water molecules or within very large (=proteins and DNA) moleculesb. Important because
1) Stick water molecules together allow water to flow2) Maintain globular shape of proteins and staircase shape of DNA
Desribe how each bond is formed, its role in the body and give examples of molecules formed. Distinguish between polar and non-polar covalently bonded molecules in terms of solubility in water.
D. Chemical reactions
making or breaking of bonds in molecules
way of transfering energy from one chemical to another
1. Equation
symbolic sentence telling what is happening to reactants
arrows show which way reaction is proceeding
may be reversible as in following examplesa) H20 (water) and CO2 (carbon dioxide) <=> H2CO3 (carbonic acid)
b) H2CO3 (carbonic acid)<=> H + (postiviely charged hydrogen ion) and HC03- (negatively charged Bicarbonate ion)
2. Factors affecting reaction rate
a. Enzymes
protein catalysts that increase the reaction rate but do not change themselves
all useful biochemical reactions have a unique enzyme to accelerate the rateb. Molecule concentration
more reactants on one side make the reaction flow faster and in a certain direction
ex. high CO2 and H2O> H2CO3
ex. CO2 and H2O<high H2CO3c. Temperature
increasing temp increases reaction rate due to increased enzyme activity.d. Molecule size
smaller molecules (H2O) react faster than largere. pH of solution
high H ion concentration (acidic) competes with H in proteins thereby breaking H bonds in protein enzymes. Changed enzyme shape(denaturation) reduces effectiveness of the enzyme.
Describe the factors that affect reaction rate.
3. Reaction types
a. Synthesis (dehydration) -building larger molecules1) Requires energy to make bonds between moleculesb. Hydrolysis -breaking molecules
reaction used to make larger, energy-storage molecules (e.g., fats and glycogen)
also used to make other molecules that are needed2) Water molecule is released
1) Energy is released when bond is broken
example: fat burning
energy used to fuel metabolism and for synthesis reactions to build other molecules2) Water is used to break molecule hence the name
Describe each reaction as to its function and define the role of water and energy is in reaction type. give examples.
II. Biochemistry (molecules important in living systems) A. Inorganic molecules
1. Water functions
a)important solvent (because of polarity) that dissolves and transports substances (solutes)b) Important reactant in reactions, especially hydrolysis reactions, where water is inserted between molecules to break them
c) important for lubrication-particularly synovial and serous membranes.
d) evaporation of water cools body surfaces.
Describe the roles of water in the body.
2. Ions
a) electrically charged atoms (electrolytes) can produce electrical current then they are moved (e.g. Na+, Cl-, K+)b) ions used to move water (e.g. Na+, Cl-)
c) trigger muscle contraction (e.g. Ca++)
d) form ATP (e.g. P04--)
3. Acids/bases/buffers
H+ concentration, [H+], measured on pH scale where:
a larger [H+] represented by a smaller pH value (acidic)
a smaller [H+] represented by a larger pH value (basic)a. Weak Acids
acid releases H+ into solution tending to increase [H+] of solution
H2CO3 = H+ and HCO3-
b. Bases
accepts H+ (proton acceptor) tending to increase [H+] of solution
HCO3 and H+ = H2CO3
c . Buffers
buffers have ability of releasing or binding to H+ therefore resisting large abrupt changes in pH therefore maintain pH homeostasis-high [H+] can be damaging to protein structures
example: carbonic acid/bicarbonate ion
H20 (water) and CO2 (carbon dioxide) <=> H2CO3 (carbonic acid)<=> H + (hydrogen ion) and HC03- (Bicarbonate ion)
Determine whether a solution's given pH value is high or low in H ion concentration and whether that solution is acidic or basic.4. Gases
Oxygen needed to combust fuel molecules (cell respiration or ATP production). Carbon dioxide is waste product of cell respiration (ATP production)
Glucose and Oxygen = Carbon dioxide and Water and ATP molecules.B. Organic molecules-all based on chains or rings of carbon atoms (e.g., carbon backbone) modified with functional groups
1. Carbohydrates
sugars and starches (2-3% of body) -rings of carbon with hydrogen and oxygen (CHO) therefore tend to be polar and therefore soluble in watera. Function2. Lipids (> 20% of body)
primarily fuel for cellular respiration, i.e., broken down by cells to get energy in bonds to run cellular metabolismb. Structure
1) Monosaccharide (= simple sugar = monomer)
6C = glucose,in ring -used as immediate source of energy for cell respiration or metabolism
5C = ribose and deoxyribose sugars used as basis of RNA and DNA nucleic acids
2) Disaccharides
assembled from 2 monosaccharides (sucrose) via synthesis reaction -used to build larger carbohydrates
3) Polysaccharide (= complex carbohydrates) long chains of simple sugars are partially soluble and are used as moderate term energy storage molecules, (e.g., glycogen in muscles & liver)
a. Lipid type and functions 3. Proteins - (15% of body). CHO but also nitrogen and sulfur1) triglycerides -composed of glycerol and 3 fatty acids (energy carrying builiding blocks) b. Structure of large chains or rings of carbons, hydrogen with little oxygen so tend to be non-polar therefore insoluble in water
long term energy storage -over 30 minute of sustained activity.
surrounds organ to cushion from damage
thermal insulation in skin
2) phospholipids -large molecule with non-polar end and phosphate polar end-forms
basis of cell membrane
3) cholesterol- ring forms
important in maintaining cell membrane fluidity and integrity4) steroid hormones -cholesterol-based molecules
used to signal other cells (i.e., Testosterone and estrogen)
a. Protein functions
enzymes * most important* -hydrolyzing or synthesizing molecules
contractile proteins in muscle -movement and heat production
antibodies -disease resistance
hormones and neurotransmitters -signalling chemicals
hemoglobins-gas transport
membrane proteins-transport, identification, tissue formation,
structural fibers -collagen and elastic fibers
b. Protein structure-most diverse of biomolecule categories
1) Amino acids or monopeptides (20 types) basic building block of proteins
has acid or carboxyl group (COOH) and a basic or amine group ( NH2), rarely used for energy production2)Dipeptide - 2 amino acids synthesized together, used as building block for polypeptides, some are used as neurotransmitters
3) Polypeptides or Proteins - many amino acids and/or several polypeptides
sequence of amino acids along with intramolecular hydrogen bonds between amino acids create globular 3-D structure. High concentrations of H ions in a solution break hydrogen bonds in proteins (denaturation) thereby destroying protein function
Determine effect of pH has on protein structure and function.c. Enzymes
1) Act as reaction catalyst by bringing molecules into more advantageous position to undergo chemical changes (make or break bond). Enzyme must move, change shape, to work.
2) usual globular structure (nature) can change (denature) depending on conditions (e.g. temperature, pH). A change in structure (denatured by breaking hydrogen bonds) thereby reduces function
3) Enzymes are highly specific controlling only 1 reaction,
(e.g., sucrose to glucose + fructose)
4) Substrate and product
substrate is altered by enzyme (reaction occurs) to form product
enzyme releases substrate and changes back to normal5) Enzymes control cell function and appearance by making or modifying other molecule concentrations
Describe the function of enzymes. Identify substrate, enzyme and product in a given reaction and be able to write equation for reaction. Identify the effect that acids have on protein structure and function.
4. Nucleic Acids
These are long chain chemicals are formed into structures called genes. As such, "genetic material" is a description of structure, not function.a. nucleotides -basic building block of nucleic acids
b. polynucleotides-sequence of many nucleotides
5. ATP (adenosine triphosphate) 1)RNA (oxyribonucleic acid) Function - information transfer molecule involved in the mechanics of the synthesis of protein
Structure - one stranded polynucleotide
2) DNA (deoxyribonucleic acid)
Structure - double stranded polynucleotide of nucleotide pairs, strands held together by hydrogen bonds
Function - inherited, information molecule that provides template for the production of proteins, especially enzymes (sequence of nucleotides codes for sequence of amino acids forming the polypeptide)
Describe the structure of each of the four major categories of organic molecules. Give specific function of named chemicals. Describe the sequence of construction of each category of organic molecule naming the building block molecules.
molecule that carries and then transfers energy to enzymes so they can affect reactions
This energy molecule is usable in all cells unlike larger fuel molecules (glucose, glycogen and triglycerides)Describe the function of ATP.
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Professor Thomas M. Lancraft
Human Anatomy and Physiology Courses
at St. Petersburg College
St. Petersburg/Gibbs Campus7/2008