Chapter 2: The Chemical Level of Organization Copyright 2009, John Wiley & Sons, Inc.
-
date post
23-Jan-2016 -
Category
Documents
-
view
237 -
download
5
Transcript of Chapter 2: The Chemical Level of Organization Copyright 2009, John Wiley & Sons, Inc.
Chapter 2: The Chemical
Level of Organization
Copyright 2009, John Wiley & Sons, Inc.
Biology based on principles of chemistry and physics
Living organisms are collection of atoms and molecules
Life’s processes dependent on Chemistry
All life composed of Matter (Anything that has mass and
occupies space)
Why Chemistry?
Matter consists of chemical elements in pure form and in combinations called compounds
• Organisms are composed of matter• Matter is anything that takes up space and has mass
• Since chemicals compose your body and all body activities are chemical in nature, it is important to become familiar with the language and fundamental concepts of chemistry.
• We are taking the approach that in order to understand living systems you have to understand what they are made of.
How Matter is Organized
Chemical Elements All forms of matter are composed of chemical
elements which are substances that cannot be split into simpler substances by ordinary chemical means.
Elements are given letter abbreviations called chemical symbols.
Trace elements are present in tiny amounts
Copyright 2009, John Wiley & Sons, Inc.
Periodic Table of the Elements
Structure of Atoms
Units of matter of all chemical elements are called atoms. An element is a quantity of matter composed of atoms of the same type.
Atoms contain: Nucleus: protons (p+) & neutrons (neutral
charge) Electrons (e-) surround the nucleus as a
cloud (electron shells are designated regions of the cloud)
Copyright 2009, John Wiley & Sons, Inc.
2 Representations of Atomic Structure
Atomic Number and Mass Number Atomic number is number of protons in the
nucleus. Mass number is the sum of its protons and
neutrons.
Copyright 2009, John Wiley & Sons, Inc.
Atomic Mass
Mass is measured as a dalton (atomic mass unit)
Neutron has mass of 1.008 daltons proton has mass of 1.007 daltons electron has mass of 0.0005 dalton
Atomic mass (atomic weight) is close to the mass number of its most abundant isotope.
Copyright 2009, John Wiley & Sons, Inc.
Atomic Number and Mass Number Atomic Mass
The atomic mass, also called the atomic weight, of an element is the average mass of all its naturally occurring isotopes and reflects the relative abundance of isotopes with different mass numbers.
The mass of a single atom is slightly less than the sum of the masses of its neutrons, protons, and electrons because some mass (less than1%) was lost when the atom’s components came together to form an atom.
Copyright 2009, John Wiley & Sons, Inc.
Ions, Molecules, Compounds, Free Radicals Ions - an atom that gave up or gained an electron
written with its chemical symbol and (+) or (-) Molecule - atoms share electrons (2 or more similar elements)
written as molecular formula showing the number of atoms of each element
■ Compound – 2 or more different elements
□ has characteristics different from those of its elements Free Radical - an electrically charged atom or group of atoms with
an unpaired electron in its outermost shell Unstable and highly reactive; can become stable by giving up an electron taking an electron from another molecule Antioxidants are substances that inactivate oxygen-derived free
radicals
Copyright 2009, John Wiley & Sons, Inc.
Chemical Bonds The atoms of a molecule are held together by forces of
attraction called chemical bonds (union between electron structures of atoms)
The likelihood that an atom will form a chemical bond with another atom depends on the number of electrons in its outermost shell, also called the valence shell.
Electrons:
-Carry a negative charge
-Repel one another but attracted to protons in the nucleus
- It takes energy to hold electrons in place
-Move in orbitals - volumes of space that surround the nucleus
Copyright 2009, John Wiley & Sons, Inc.
Electrons and Electron Shells
Only outer shell electrons can interact (form bonds)! If outermost shell is full, element is stable (He) If outermost shell is not full, unstable and can
bond The 1st shell can hold 2 electrons The 2nd shell can hold 8 electrons Stability is goal : by gaining, losing or sharing
electrons
Ionic Bonds When an atom loses or gains a valence electron, ions
are formed Charge difference attracts the two ions to each other
Positively and negatively charged ions are attracted to one another.
Cations are positively charged ions that have given up one or more electrons (they are electron donors).
Anions are negatively charged ions that have picked up one or more electrons that another atom has lost (they are electron acceptors).
Copyright 2009, John Wiley & Sons, Inc.
The Ionic Bond Formation
Covalent Bonds Covalent bonds are formed by the atoms of molecules sharing one,
two, or three pairs of their valence electrons. Covalent bonds are the most common and strongest chemical
bonds in the body. Single, double, or triple covalent bonds are formed by sharing
one, two, or three pairs of electrons, respectively. Covalent bonds may be nonpolar or polar.
Nonpolar covalent bond -atoms share the electrons equally; one atom does not attract the shared electrons more strongly than the other atom
Polar covalent bond- unequal sharing of electrons between atoms. In a water molecule, Oxygen has greater electronegativity & attracts the hydrogen electrons more strongly;
Copyright 2009, John Wiley & Sons, Inc.
Copyright 2009, John Wiley & Sons, Inc.
Polar Covalent Bond
Nonpolar Covalent Bond
fd
TEST YOURSELF!!
How many covalent bonds can each of these atoms form??
Copyright 2009, John Wiley & Sons, Inc.
Hydrogen Bonds An attraction between a
slightly positive hydrogen atom in one molecule and a slightly negative atom (usually oxygen) in another molecule
weak intermolecular bonds; serve as links between molecules.
help determine three-dimensional shape
give water considerable cohesion which creates a very high surface tension
Copyright 2009, John Wiley & Sons, Inc.
Chemical Reactions (Metabolism) When new bonds form or old bonds are broken
Metabolism is all the chemical reactions in the body Law of conservation of mass = total mass of reactants equals the total mass of the
products Require a source of energy and a catalyst (enzymes) Occur in liquid environment – water Influenced by: Temperature ; Concentration of reactants; Catalysts
Energy and Chemical Reactions Chemical reactions involve energy changes
Two principal classes of energy: potential energy = stored energy kinetic energy = energy of motion
Chemical energy is potential energy stored in the bond of molecules digestion of food releases that chemical energy so that it
can be converted to heat or mechanical energy Law of conservation of energy
energy can neither be created nor destroyed--just converted from one form to another
2-25
• Five Types of Energy
1. Mechanical - resulting from the position & movement of objects Ex. Moving a limb
2. Chemical – energy within chemical bonds Ex. ATP + H2O ADP + H2PO4 + E+
3. Heat - flows between objects that are different temperatures Ex. Human body’s chemical rxns release heat as a by-product
and this helps to maintain body temperature
4. Electric - ability of an electric current to produce work, heat, light, or other forms of energy. It is measured in kilowatthours.
5. Electromagnetic - reflected or emitted from objects in the form of electrical and magnetic waves that can travel through space
26
Energy Transfer in Chemical Reactions Forming new bonds releases energy & breaking old
bonds requires energy Chemical reactions usually involve both
exergonic reactions release more energy endergonic reactions absorb more energy than they
release Human metabolism couples exergonic and endergonic
reactions, so that the energy released from one reaction will drive the other. Glucose breakdown releases energy used to build
ATP molecules that store that energy for later use in other reactions
Activation Energy Atoms, ions & molecules are continuously moving & collidingActivation energy is the collision energy needed to break bonds & begin a reaction
Copyright 2009, John Wiley & Sons, Inc.
Factors that Cause a Collision and Chemical Reaction Concentration
Temperature Catalysts are chemical compounds that speed up chemical reactions
by lowering the activation energy needed for a reaction to occur. A catalyst does not alter the difference in potential energy between
the reactants and products. It only lowers the amount of energy needed to get the reaction started. A catalyst helps to properly orient the colliding particles of matter
so that a reaction can occur at a lower collision speed. The catalyst itself is unchanged at the end of the reaction; it is
often re-used many times.
Copyright 2009, John Wiley & Sons, Inc.
Catalysts and chemical reactions
Copyright 2009, John Wiley & Sons, Inc.
Types of Chemical Reactions
Synthesis Reactions--Anabolism -Two or more atoms, ions or molecules combine to form new
& larger molecules
-Anabolism - all the synthesis reactions in the body
-Usually endergonic→absorb more energy than they release
-Example combining amino acids → protein molecule
Decomposition Reactions—Catabolism-Large molecules are split into smaller atoms, ions or molecules
-Catabolism -all decomposition reactions in the body
-Usually are exergonic→release more energy than they absorb
Types of Chemical Reactions
Exchange Reactions Substances exchange atoms
consist of both synthesis and decomposition reactions Example: HCl + NaHCO3 → H2CO3 + NaCl
ions have been exchanged between substances
Reversible ReactionsReactants can become products or products can revert to the
original reactants
Indicated by the 2 arrows pointing in opposite directions between the reactants and the products
AB ↔ A + B
Oxidation-Reduction Reactions Oxidation is the loss of electrons from a molecule (decreases
its potential energy); acceptor of the electron is often oxygen Reduction is the gain of electrons by a molecule
increases its potential energy In the body, oxidation-reduction reactions are coupled & occur
simultaneously
Inorganic Compounds & Solvents Most of the chemicals in the body are
compounds Inorganic compounds
usually lack carbon & are structurally simple Exceptions: CO , CO2 , HCO3 Water, Oxygen, CO2, Salts, Acids & Bases
Organic compounds contain carbon & usually hydrogen always have covalent bonds
Water – most abundant & importantinorganic compound in living systems
Characteristics of H2O
1. Polar molecule:– b/c it is polar it forms H+ bonds
with other H2O molecules forming a lattice structure w/in the H2O
2. % of body’s weight– 50% in ♀ (> body fat than ♂)– 60% in ♂
3. % of blood plasma– 92% H2O
AP1: Ch. 2: Chemical Basis of Life 37
Polar Water Molecules
Copyright 2009, John Wiley & Sons, Inc.
H2O: Functions in living organisms1. Stabilizing Body Temp.
– H2O has a high specific heat (meaning it takes a large amount of e+ to raise its temperature)
– Thus it is resistant to temperature ’s
– H2O also evaporates (thus it can be sweat used to cool the body when it evaporates and takes the “heat” with it)
2. Protection– Acts as a lubricant to
prevent damage from friction
– It also forms a “fluid cushion” around the organs (ex. CSF)
3. Chemical Rxns– Reacting molecules must be
dissolved in H2O for many of the bodies chemical rxns
– **Hydrolysis– **Dehydration Synthesis
4. Mixing Medium– Mixture: combination of 2 or
more substances blended together but not chemically combined
a. Solutionb. Suspensionc. Colloid
39
3 Common MixturesA mixture is a combination of elements or compounds that are
physically blended together but are not bound by chemical bonds.
Solution: a substance called the solvent dissolves another substance called the solute. Usually there is more solvent than solute in a solution.
A colloid differs from a solution mainly on the basis of the size of its particles with the particles in the colloid being large enough to scatter light.
Suspension: the suspended material may mix with the liquid or suspending medium for some time, but it will eventually settle out.
Copyright 2009, John Wiley & Sons, Inc.
Concentration
The concentration of a molecule is a way of stating the amount of that molecule dissolved in solution.
Percent gives the relative mass of a solute found in a given volume of solution.
A mole is the name for the number of atoms in an atomic weight of that element, or the number of molecules in a molecular weight of that type of molecule, with the molecular weight being the sum of all the atomic weights of the atoms that make up the molecule.
Copyright 2009, John Wiley & Sons, Inc.
Acids & BasesAcid
A proton (H+) donor
Base
A proton (H+) acceptor OH- is what is usually found in
solution that will bind to free H+’s
42
Strong Acid/Base
• Either will completely dissociate when put into H2O, releasing all of the H+ or OH- in their make-up
• The rxn is not freely reversable
• Ex.• HCl H+ + Cl-
• NaOH Na+ + OH-
Weak Acid/Base
• A proton (H+) acceptor• OH- is what is usually
found in solution that will bind to free H+’s
• Rxn is reversible• Ex.
• H3COOH ↔ CH3COO- + H+
Dissociation of Acids, Bases, and Salts
Copyright 2009, John Wiley & Sons, Inc.
pHpH scale expresses hydrogen ion (H+) concentration in a solution.
scale range = 0-14
neutral = 7
Acids release H+
thus increasing [H+]
pH values < 7
Bases lower [H+]
bond up H+ or
Release OH-
pH values > 7
Why do we care about pH?
pH can affect:
Shapes and functions of molecules
Rates of many chemical reactions
Ability of two molecules to bind to each other
Ability of ions or molecules to dissolve in water
Organisms usually tolerate only small changes in pH
BLOOD pH MUST BE MAINTAINED AT 7.35-7.45
Buffers help to keep a relatively constant pH
Buffers act as a reservoir for hydrogen ions, donating or removing
them from solution as necessary.
Buffers- convert strong acids or bases→ weak acids or bases
Examples of buffers used by living systems include: Bicarbonate, Phosphates, Amino Acids, Proteins as Components
H2CO3 ↔ H+ + HCO3-
Carbonic Acid Proton Bicarbonate Ion Conjugate Acid (H+ donor) Conjugate Base (H+ acceptor)
b/c the rxn is reversible: In a [H+] flow in In a [H+] flow in Thus: H2CO3 and HCO3
- remain in constant equilibrium
The greater the buffer concentration the more resistant to , but pH may still just not as drastically as seen w/o the buffer
AP1: Ch. 2: Chemical Basis of Life 46
Oxygen
21% of earth’s atmosphere is O2
Essential to lives of most animals
Humans use it in the final step in a series of rxns in which e+ is extracted from food molecules
Carbon Dioxide
Byproduct of organic molecule metabolism
A small % is eliminated via exhalation
Accumulation of high amounts is toxic to cells
AP1: Ch. 2: Chemical Basis of Life 47
• Carbon is unique in that it can form covalent bonds w/ up to 4 other atoms allowing the formation of the large, diverse, complicated molecules required for life.
• These molecules are:1. Carbohydrates2. Lipids3. Proteins4. Nucleic Acids
• Carbon Backbone: series of C atoms bound together by covalent bonds
• CB allows for variation in length as well as highly varied combinations of atoms.
AP1: Ch. 2: Chemical Basis of Life 49
Carbohydrates Made up of C, H, O in a 1:2:1 ratio Glucose : C6-H12-O6• Carbo: Atom Hydrates: Hydrated
• Range from small to large in size1. Monosaccharide- Mono 1 Simple Sugar
2. Disaccharide- Di 2
3. Polysaccharide- Complex Sugar
• Functions:
A. Structural: ribose and deoxyribose (DNA, RNA, ATP)
B. Energy: simple sugars(monosaccharides) can be used as an immediate e+ source, complex sugars must be processed before use
• Glycogen (polysaccharide) - e+ storage molecule
C. Bulk: cellulose (polysaccharide) forms the bulk of feces
AP1: Ch. 2: Chemical Basis of Life 50
Monosaccharides = 1 (mono) sugar
Copyright 2009, John Wiley & Sons, Inc.
Disaccharides Combining 2 monosaccharides by dehydration
synthesis releases a water molecule. sucrose = glucose & fructose maltose = glucose & glucose lactose = glucose & galactose (lactose intolerance)
Copyright 2009, John Wiley & Sons, Inc.
Polysaccharides (PS) = many (poly) sugars
• Many MS’s bound together to form long chains (can be straight or branched)
• 3 major types:– In animals you find 1 type in plants 2 types
a) Glycogen: “animal starch”; used as an e+ storage molecule. When quickly metabolized it results in e+ for cells
b) Starch: long chains of glucose used for e+ storage in plants
• Humans can break it down & use it for e+
c) Cellulose• Long chains of glucose that fxn as a structural
molecule in plants• Humans can’t break it down & use it for e+,
thus it b/comes bulk of feces
53
Lipids (a.k.a. fats)• Major components: C, H, & O • Minor components: P & N• Compared to carb’s, lipids do not have 2:1 ratio of H
to O and have a lower ratio of O to C, this makes them less polar thus they can be dissolved in non-polar organic solvents (acetone, alcohol)
• 4 major groups:– Triglycerides– Phospholipids– Steroids– “Other”
AP1: Ch. 2: Chemical Basis of Life 54
• Fxns of lipids:A. Protection: surrounds and protects organsB. Insulation: fat under the skin prevents heat loss; myelin
sheaths electrically insulate axons of neuronsC. Regulation: steroids regulates physiological
processes prostaglandins regulate inflammationD. Vitamins: “fat soluble” vitamins do many things
• Vit A forms retinol req’d for night vision• Vit D Promotes Ca2+ uptake in bone tissue• Vit E Promotes healing• Vit K necessary to form clotting factors
E. Energy: can be broken down to yield more e+ than either carb’s or proteins
AP1: Ch. 2: Chemical Basis of Life 55
• Make-up 95% of fats in the human body
• 1- glycerol + 3 Fatty Acids (FA’s)• FA’s differ from each other by #
of C’s and degree of saturation– 2 types:
1. Saturated• Only single covalent bond btwn
C’s in the carbon backbone
2. Unsaturated• 1 or more double covalent bond
btwn C’s in the carbon backbonea) Monounsaturated
b) Polyunsaturated
AP1: Ch. 2: Chemical Basis of Life 56
Gly
cero
l
Fatty Acid
Fatty Acid
Fatty Acid
Triglycerides
Triglycerides
Copyright 2009, John Wiley & Sons, Inc.
Phospholipids (PL) Glycerol + 2 FA’s + phosphate
containing molecule Notice structurally similar to TG’s
Polar Molecule: Hydrophilic Head (Polar) Hydrophobic Tails (Non-polar)
Essential in the cell membrane’s structure
AP1: Ch. 2: Chemical Basis of Life 58
Chemical Nature of Phospholipids
2-59
head tails
Steroids
• Structurally they are a unique lipid, but their solubility characteristics are similar
• All composed of C’s bound together in a 4-ring-like structure
• Important Examples:– Cholesterol (building blocks for
other steroids)Ingest too much heart disease, but it is still essential to diet
– Bile Salts– Estrogen– Progesterone– Testosterone
AP1: Ch. 2: Chemical Basis of Life 60
• Eicosanoids– Group of important
molecules derived from FA’s
– Made in most cells – Important regulatory
molecules– Examples:a) Prostaglandins: implicated
in regulation of hormones for blood clotting, some reproductive fxns, and more (*Asprin*
b) Thromboxanesc) Leukotrienes
• Fat Soluble Vitamins– Structurally not similar to
one another but they are non-polar molecules essential to normal body fxn
AP1: Ch. 2: Chemical Basis of Life 61
Other Lipids
Proteins
Major components: C, H, O, & N Minor components: S, P, Fe, and I Protein’s molecular mass can be huge:
NaCl= 58 Glucose= 108 Proteins 1000 to several million
AP1: Ch. 2: Chemical Basis of Life 62
Fxns of proteins1. Regulation
– Enz’s control chem rxns and hormones regulate many physiological processes
2. Transport– Can help to transport things in the watery environment of the
blood & can control mvmt in & out of cell3. Protection
– Antibodies and complement system proteins protect against foreign invaders
4. Contraction– Actin and Myosin and proteins involved in muscle movement
5. Structure– Collagen fibers give structural framework– Keratin lends strength to hair, skin, nails
6. Energy– Can be broken down to produce e+ equals the same yield as
carb’s63
Protein Structure
The building blocks of proteins are amino acids(AA): These are made up of a central C with
an Amine group at one end and a carboxyl group at the other
The R-Group varies from AA to AA Btwn each AA the Amine and Carboxyl
groups bind to each other and form Peptide Bonds. Thus the reason proteins are often referred to as polypeptides.
64
All
20
Am
ino A
cid
S
tru
ctu
res
AP1: Ch. 2: Chemical Basis of Life 65
Formation of a Dipeptide Bond Dipeptides formed from 2 amino acids joined by a
covalent bond called a peptide bond dehydration synthesis
Polypeptides chains contain 10 to 2000 amino acids.
Copyright 2009, John Wiley & Sons, Inc.
4 Levels Protein Structure
1. Primary (1o)- Sequence of aa bound by peptide bonds
2. Secondary (2o) a-helix & b-pleated sheet
- Local structure that results from H-bonding
-If these bonds are broken by temperature
or pH the protein will unfold & become
non-functional
3. Tertiary (3o)- 3D structure-Caused by the interactions btwn the polypeptide and its immediate environment
4. Quaternary (4o)-Spatial relationships between individual subunits
AP1: Ch. 2: Chemical Basis of Life 67
Copyright 2009, John Wiley & Sons, Inc.
Proteins : Enzymes• Protein catalyst that increases the
rate of chemical rxn w/o being ed itself
• An enz’s 3-d shape is essential for its fxn
• Lock & Key Model (old name)– Lock: Active Site– Key: Reactants
• Induced fit model (new name)– more correct term– The enz can shape significantly to fit
reactants• Enz’s lower activation e+ b/c they
orient the reactant in such a way that chem rxn is more likely to occur
69
Enzyme binds reactants Combines reactants Releases reactant so that it can do it
all over again It is capable of catalyzing multiple
reactions Some enz’s require co-factors to fxn
or an organic molecule Co-factors: ions
Usually finalize the shape of the active site
Organic Molecule: co-enzymes
-ase …this suffix means enzyme
70
Enzyme and substratecome together at activesite of enzyme, forming anenzyme–substrate complex
Enzyme
SucraseActive siteof enzyme
Substrates
Sucrose andWater
H2O
Mechanism of enzyme action
1
Enzyme catalyzesreaction and transformssubstrate into products
Enzyme and substratecome together at activesite of enzyme, forming anenzyme–substrate complex Glucose
Fructose
Enzyme
SucraseActive siteof enzyme
Substrates
Sucrose andWater
Products
H2O
Mechanism of enzyme action
1
2When reaction is complete,enzyme is unchanged andfree to catalyze same reactionagain on a new substrate
Enzyme catalyzesreaction and transformssubstrate into products
Enzyme and substratecome together at activesite of enzyme, forming anenzyme–substrate complex Glucose
Fructose
Enzyme
SucraseActive siteof enzyme
Substrates
Sucrose andWater
Products
H2O
Mechanism of enzyme action
1
3 2
Nucleic Acids - Made-up of C,H,O,N & P
DNA- genetic code
Deoxyribonucleic Acid
Double Helix
RNA- mRNA, rRNA, tRNA
Ribonucleic Acid
Single stranded
•building blocks are called nucleotides
PhosphateGroup
Pentose Sugar
NitrogenousBase
Basic Nucleotide →
Nitrogenous Organic Bases- 2 types Purines
Guanine Adenine
Pyrimidines Cytosine Thymine Uracil
AP1
DNA bases• Adenine• Guanine• Cytosine• Thymine
RNA bases• Uracil• Guanine• Cytosine• Adenine
RNA (single stranded) DNA (Double Stranded)
AP1
DNA• DNA is a double helix
– “twisted ladder”• Vertically nucleotides are held together
via a covalent bond between the
phosphate group of 1 NA and the next• Horizontally, nucleotides are held
together via a H bond between
nitrogenous bases next to each other*NB’s must have to correct partner to bind to**
→ complementary base pairing
– DNA :T=A G=C – RNA: U=A G=C
DNA• The two opposing strands of DNA
also run antiparallel to each other.– Meaning the sugar phosphate
backbone of 1 strand runs the opposite direction of it’s partner• 5’ 3’• 3’ 5’
• Within DNA the sequence of bases is a “code” that stores information used to determine the structure and fxn of cells
• Gene: sequence of DNA that directs the synthesis of an RNA molecule that will become a protein
Adenosine Triphosphate (ATP)
Temporarymolecular storage ofenergy as it is beingtransferred fromexergonic catabolicreactions to cellularactivities
Copyright 2009, John Wiley & Sons, Inc.
Formation & Usage of ATP Hydrolysis of ATP (removal of terminal phosphate group by
enzyme -- ATPase) releases energy leaves ADP (adenosine diphosphate)
Synthesis of ATP enzyme ATP synthase catalyzes the addition of the
terminal phosphate group to ADP energy from 1 glucose molecule is used during both
anaerobic and aerobic respiration to create 36 to 38 molecules of ATP
Cyanide Poisoning: The way cyanide works is by impeding the production of
ATP within the mitochondria
Copyright 2009, John Wiley & Sons, Inc.