Chapter 2
Chemistry of
Living Systems
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Chemistry of Atoms
Atom: smallest possible unit of matter that
retains properties of its element
Three components of an atom include:
Electrons: -1 electrostatic charge
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orbit around nucleus
Protons: +1 electrostatic charge
found in nucleus
Neutrons: no charge (neutral)
found in nucleus
More notes on atoms…
Electrically neutral atoms have an equal number of protons and
electrons
Atomic number: number of protons in an atom (written 11Na)
Atomic weight: equal to number of protons and neutrons
Isotopes – atoms having the same # of protons & electrons but
different # of neutrons (e.g. 12C and 14C)
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Elements Essential To Life
Element: a substance that cannot be broken down into other
substances by chemical reactions
About 25 elements are essential to life:
C, O, H, N: make up 96% of living matter
Ca, P, K, S, Na, Cl, Mg, Fe, I: make up most of remainder
Trace elements: required by an organism in extremely minute
quantities
e.g.. B, Mn, Zn and others
C HOPKINS CaFe
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Electron Configuration
Electrons orbit around the nucleus, are involved in chemical reactions
Orbital: three-dimensional space where an electron will most likely
be found 90% of the time
Electron Configuration
First energy level: holds up to 2 electrons
Second energy level and higher levels: each holds up to 8 electrons
NOTE: stated that each can hold up to 8 (or 2) electrons
All except outer level usually full – outer level determines
how many bonds the atom may form
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Electrons & Chemical Bonds
Electrons & Chemical Bonds
Remember first shell can only hold 2, others can hold up to 8
shells fill from inside out…
Valence electrons: electrons in outermost energy shell (valence shell)
Chemical properties of an atom depend on the number
of valence electrons present
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Count the electrons!
# of electrons in outer shell gives vital clues
4 or more in outer shell tends to accept electrons
Less than 4 in outer shell tends to donate electrons
Provides hints as to how many bonds can be formed
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Chemical Bonds
Chemical bonds: attractive forces that hold atoms together in a
molecule
Bonds form when electrons are shared OR transferred
between atoms
Covalent bonds – sharing electrons
Ionic bonds – transferring electrons between atoms
Metallic bonds – sharing electrons
Hydrogen bonds – weak attractions between molecules (work through
H on one molecule and a negative atom (e.g. O, N, F) on the other
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Nonpolar Covalent Bonds
Form between atoms by sharing one
or more pairs of valence electrons
“Nonpolar” because the electrons are
shared equally
These share a single pair of electrons
so this is said to be a ‘single bond’
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Nonpolar Covalent
(another example)
Since TWO pairs of electrons are shared
this is referred to as a ‘double bond’
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Covalent bonds that make
Polar Molecules
Share electrons as in other covalent bonds, but the nucleus
of one atom attracts the electrons more strongly
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Hydrogen Bonds
formed by the charge attraction when a hydrogen atom covalently
bonded to one electronegative atom is attracted to another
electronegative atom
Slightly positive hydrogen attracted to an electronegative atom
Example – water molecules attracted to each otherweak attraction:
20X weaker than covalent bonds
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Hydrogen Bonds In Action
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Walking On Water - Possible?
Yeah, but you
gotta walk
really fast!
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Surface tension is due to hydrogen bonding
Ionic Bond
formed after the complete transfer of an electron from a donor atom
to an acceptor
The resulting positive and negative ‘ions’ are then attracted to each
other by the ‘electrostatic’ force (positive to negative)
Terminology:
Ion: charged atom or molecule
Anion: a negatively charged ion
Cation: a positively charged ion
In ionic bonding one atom is an electron donor while
the other is an electron acceptor
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Ionic Bonding…
Ionic Bonding - Animation
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Example of Ionic Bonding
Sodium has one lone electron in its outer shell
Chlorine has seven (lacks 1 to have 8)
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Ionic Solids
Ionic compounds are called salts (e.g. NaCl or table salt)
Ionic solids tend to form in regular arrays called crystals
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Solubility & Dissociation
Solubility – the ability of one substance
to dissolve in another
Dissociation – separation of ionic
compounds into individual
anions & cations when placed in solution
Water treats anions and
cations differently…
Electrolytes – dissociated ions in
a solution: So called because they
have the ability to conduct an
electric current
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Chemical Reactions
Chemical Reactions
The making and breaking of chemical bonds
Some reactions are energy requiring - endergonic
Some are energy releasing - exergonic
Reactants - substances beginning a chemical reaction
Products – substances made by the reaction
A-P-P + Pi
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(ADP)
A-P-P-P
(ATP)
Types Of Reactions
Synthesis Reactions– new bonds formed
Decomposition Reactions – bonds broken
Anabolic – synthesis reactions taking place within the body
(e.g. synthesizing new proteins)
Catabolic – decomposition reactions taking place within
the body (e.g. digestion of foodstuff into smaller products)
Metabolism – All of the anabolic and catabolic reactions
of the body (anabolism + catabolism = metabolism)
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Oxidation & Reduction
Oxidation – the process of loosing an electron
Reduction – the process of gaining an electron
The transfer of electrons can be complete  ionic bonds
Transfer can be incomplete (sharing)  covalent bonds
This process is usually a partnership with one atom donating
and one accepting – termed Oxidation-Reduction Reactions
These reactions can either MAKE new molecules (synthesis reactions)
or BREAK APART existing molecules (decomposition reactions)
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Reversibility & Equilibrium
of Reactions
in theory all reactions are reversible
In actuality not all reactions tend to behave this way
When they do, they are said to be reversible and can proceed from
reactants to products or from products back to reactants
When the rate of forward to reverse direction reaction is equal the
reaction is said to be in equilibrium
For a reaction in equilibrium the ratio of reactants to products remains
constant
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Factors Affecting Reaction Rate
Reactants – some are more active than others
Concentration – usually greater concentration of reactants will increase rate –
due to increasing chance they bump into one another (must contact each other
to react)
Temperature – greater temperature increases motion (speed) and thus
increases chance of contact with other reactants
Catalyst – a substance that increases reaction rate without being changed or
used up itself
A biological catalyst is usually protein based and is called an enzyme
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Activation Energy
Sometimes a reaction requires an initial input of energy to start the
reaction – this amount is referred to as the Activation Energy
Catalysis (enzyme) - lowers activation energy, in addition to speeding
up the overall reaction rate
In a biological setting specialized proteins called ENZYMES function as
biological catalysts
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Some Important Molecules
in Living Systems
Water – the ‘universal solvent’
Organic compounds – meaning those things that have carbon and
hydrogen
Acids/Bases & Buffers – where we examine the ions H+ and OH-
protons/hydrogen ions
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hydroxide ions
Water
most abundant constituent of cells
important solvent
Lubrication and shock absorption – e.g. tears and CSF
Temperature regulation:
High specific heat – it takes a lot of heat energy in order to raise
the temperature of water. (largely due to hydrogen bonding)
Evaporation – liquid to gas requires heat (uses up body heat)
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Acids/Bases and Buffers
Acid: substance which dissociates into hydrogen ions (H+)
and negative anions
e.g. HCl to H+ & ClBase: dissociates into hydroxide ions (OH-) and positive cations
e.g. NaOH
to Na+ & OHThe ratio of H+ to OH- determines the pH of the solution
More H+ = acid
More OH- = basic (alkaline)
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Buffers
Buffers – compounds which keep pH constant/stable
Two chemicals work together, one acid & one base
called a conjugate acid/base pair
The conjugate acid can come apart into a H+ and the
conjugate base e.g H2CO3
H+ & HCO3Excess H+ added is ‘absorbed’ by the conjugate base
Excess OH- is combined with a H+ from the buffer
becoming water
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Organic Compounds
Organic compounds – contain Carbon & Hydrogen
Four major classes of biomolecules:
Carbohydrates
Lipids (fats & oils)
Proteins
Nucleic Acids
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Organic Molecules …
Many of these are polymers – long chains made of small
units
Each of the four groups of biomolecules has its own type
of monomer building blocks…
Monomers – single ‘building block’ molecules that are
assembled into polymers.
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Carbohydrates
Monomers are simple sugars = Monosaccharides
Can be assembled into various sized pieces
Two monosaccharides = a disaccharide
Polysaccharide = ‘lots of sugars’ = long chains
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More on Carbohydrates
Long chains of carbohydrates can be branched or straight
Glycogen (animal starch) – long branched carbohydrate
used to store energy in animals –made of glucose monomers
Glycogen is stored in liver & muscle and glucose is
released as needed from these stores
Other examples include plant starch (digestible) and
cellulose (non-digestible) = plant fiber
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Lipids
Fats & Oils
Triacylglycerols make up about 95% of all lipids in the body
Two major components of a triacylglycerol are:
Glycerol
Fatty Acid
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Phospholipids – major portion
of cell membranes
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Additional Lipids
Some types that are derived from fatty acids include:
Prostaglandins, leukotriens & thromboxanes
roles include: blood clotting, release of some hormones
Aspirin inhibits production of prostaglandin
Fat Soluble vitamins are also lipid based
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Proteins
Monomer = Amino Acid
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Table 2.4 (1 of 4)
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Table 2.4 (2 of 4)
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Table 2.4 (3 of 4)
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Table 2.4 (4 of 4)
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Making of a Peptide Bond
Individual amino acids within a protein are linked by bonds
called peptide bonds.
These bonds are formed when the OH from a carboxyl group
joins with an H from an Amine group of another amino acid
C from one amino acid & N (from another) bond together
and a water is lost – dehydration reaction
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Rules to identify peptide bonds
1. Bond between carbon & nitrogen
2. Carbon in this bond must also have a double bonded oxygen
Which of the following is a peptide bond?
B
D
A
_
_
=
_
_
=
_
_
_
_
_
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_
H
E
H O H H O H H O H H
O
_ _ _ _ _ _ _ _ _ _
N_ C C N C C N C C N C C
H
H
H
H
H
=
_
H
C
Other peptide bonds in this molecule…
Levels of Protein Structure
Primary Structure – the order of amino acids (the sequence)
Secondary Structure – local bending/folding due often to
hydrogen bonding: includes helix & pleated sheet forms
Tertiary Structure – Overall shape of a single polypeptide.
Due largely to interactions such as cross-linking between
distant portions of the molecule (see image – next slide)
Quaternary Structure – shape due to interactions between
different polypeptides making up a larger protein
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Enzymatic Structure
Enzymes have binding sites which attach substrate molecules. These
fit in a lock-and-key fashion. Thus, enzymes are specific and generally
only work with their own specialized reactions.
Enzymes typically reduce the activation energy so less energy is
required to run the reaction. This makes the reaction far more efficient
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Nucleic Acids - DNA & RNA
Monomers are called nucleotides
Each nucleotide has three parts
5-carbon sugar (ribose or deoxyribose)
phosphate group
Nitrogen containing base
without the phosphate
the sugar/base combination
is called a nucleoside
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Bases
Purine bases – double ring structure
Adenine (A)
Guanine (G)
Pyrimidine bases – single ring structure
Thymine (T)
Cytosine (C)
Uracil (U) – found in RNA instead of thymine
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Nucleic Acid Polymer Structure
Similar to a ladder
Bases form the rungs
( G C , A=T or A=U)
Sides of ladder alternate
Sugar-Phosphate-Sugar-Phosphate…
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Base Pairing Rules
Always pair a purine with a pyrimidine
G always pairs with C (DNA and RNA)
A always pairs with T (DNA)
A always pairs with U (when making RNA)
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ATP – Energy Molecule!
High energy bond
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ATP – Energy Molecule!
ATP stores energy in high energy phosphate bonds
This energy can be released in the presence of water
ATP is an adenine nucleotide (adenine monophosphate)
which has two extra phosphates
When hydrolyzed (broken by water) this bond releases its
energy for use. ATP becomes ADP (diphosphate)
The cell can add another inorganic phosphate to ADP
using energy to recreate/recharge ATP
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ATP – Energy Molecule!
Adenosine - P
Adenosine - P
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P + H2O
P
P
+
Pi
+ energy
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