Transcript Introduction to Biochemistry

I. Matter and Energy
 A. Matter
 Matter is anything that takes up space and has
mass
 Three states of matter exist (solid liquid and
gas)
 The fundamental units of matter are elements
which are composed of atoms that are
subdivided into subatomic particles.
B. Elements
 Elements are substances that cannot be broken
down into other substances by ordinary chemical
means
 Each element is represented by letters (e.g. H =
hydrogen, C = carbon, etc...)
 There are six elements that frequently occur in
organic matter: CHNOPS = Carbon, Hydrogen,
Nitrogen, Oxygen, Phosphorus, and Sulfur.
 Elements are organized into compounds and
molecules:
Molecules - two or more of the same element held
together by chemical bonds. (e.g. O2)
 Compounds - two or more different kinds of elements
held together by chemical bonds. (e.g. NaCl)

C. Organization of Matter



Atoms are the smallest possible amount of an
element.
Atoms of the same element share similar
chemical properties.
Atoms are composed of subatomic particles:



Electrons (e-, negatively charged) high energy, low
mass
Protons (p+, positively charged) low energy, high
mass
Neutrons (n0, neutral charge) low energy, high mass




Protons and neutrons are packed into a dense
core called a nucleus
Positively charged protons are attracted to
negatively charged electrons, but electrons
have high amounts of energy, defying
attraction to protons and spins around the
nucleus.
The three dimensional space, where electrons
are found around the nucleus, is called an
orbital.
Carbon, Hydrogen, Oxygen, and Sulfur atoms

Elements are defined by the atomic number and
mass number.
Atomic number = the number of protons in an atom
 Mass number = the number of protons and neutrons in
an atom


Examples - helium represented as He
Atomic number = 2 (two protons)
 Mass number = 4 (two protons and 2 neutrons)


Isotopes - atoms of an element that have the same
atomic number but different mass number.
(therefore different number of neutrons)
II. Energy and Energy Levels
 Energy is the ability to do work (types =
mechanical, chemical, thermal, and electrical)
 Energy is defined as being either potential or
kinetic:


Kinetic energy - energy of motion which is directly
proportional to the speed of that motion. (e.g.
electrons moving within an orbital)
Potential energy - energy stored by matter as a
result of its location or spatial arrangement. Different
states of potential energy of electrons in an atom is
referred to as an energy level. The more an energy
an electron possesses, the further away (thus high
energy level) the electron will be from the nucleus
Element's Chemical Properties and Chemical Bonds
 Chemical behavior of an atom is determined by the
electron configuration of the outermost electron
energy level.
 Electron configuration is the distribution of
electrons in each atom's energy level.
 Electron configuration rules:
Electrons must first occupy lower electron levels before
the higher levels can be occupied.
 The first energy level of an atom has only two electrons
and all higher energy levels have eight electrons.
 If an atom doesn't have enough electrons to fill all energy
levels, the outermost level will be the only one partially
filled with valence electrons (electrons in outermost
energy level).
 Octet Rule - with the exception of the first energy level,
the valence level is complete when it contains eight
electrons.



As a result of incomplete valence levels, atoms
fill those levels by interacting with each other
forming chemical bonds (attractions that hold
molecules together)
There are three general types of chemical
bonds: ionic, covalent, and hydrogen.

Covalent bonds - chemical bond between atoms
formed by sharing a pair of electrons.
 Covalent bonds may be single, double, or triple.
 example --> hydrogen gas
 H2 (molecular formula = # and types of elements)
 H-H (structural formula = # of elements &
bonding)
methane

Ionic bonds - bond formed by the attraction
after the complete transfer of an electron from a
donor atom to an acceptor.


Such a relation ship forms an ion (charged
atom). Clinically, we call these electrolytes.
There are two types of ions:
 Anion - an atom that has gained one or more electrons
from another atom and has become negatively charged.
 Cation - an atom that has lost one or more electrons
and has become more positively charged.
Na
Sodium atom (Na)
(11p+; 12n0; 11e–)
Cl
Chlorine atom (Cl)
(17p+; 18n0; 17e–)
(a)
+
–
Na
Cl
Sodium ion (Na+)
Chloride ion (Cl–)
Sodium chloride (NaCl)
CI–
Na+
(b)
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by Elaine Marieb & Katja Hoehn
Copyright © 2007 Pearson Education, Inc.,
publishing as Benjamin Cummings.
Ions in
solution
Salt
crystal
Na+
Na+
Cl–
Cl–
H+
–
Human Anatomy and Physiology, 7e
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O
H
+
Water
molecule
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publishing as Benjamin Cummings.

Hydrogen bonds – weak bonds formed between a
slightly positive hydrogen and a slightly negative
atom.
IV. Chemical Reactions
 Chemical Equation: Reactant + Reactant ---------Product(s)
May be reversible
 Tends toward equilibrium


Types of Reactions:
Synthesis reactions (A + B --> AB), usually anabolic,
requires energy (endergonic) to build compounds.
 Decomposition reaction (AB --> A + B), usually catabolic,
releases energy (exergonic) to break down compounds.
 Exchange/displacement reaction (AB + CD ---> AD +
CB), may or may not require\release energy.
 Redox reactions - compounds may gain or lose electrons:
 oxidized - reactant loses an electron
 reduced - reactant gains an electron


Chemical reactions are effected by particle size,
temperature, concentration, catalysts, etc...
V. Inorganic and Organic Compounds
Inorganic compounds
 Compounds that contain no carbon or if containing
carbon, may also contain elements other than HNOPS
 Examples: water, salts, acids, and bases

Water and Its Properties:
 High heat capacity - absorb/release large amounts of heat
energy without changing in temperature itself.
 High heat of vaporization - heat energy to cause
transformation (disrupt hydrogen bonds) of water from
liquid to gas.
 Polarity - unequal distribution of electrons causing slightly
positive hydrogens and slightly negative oxygens.
 Solvent - water dissolves solutes (therefore compounds are
dissociated in water).
 Reactant - involved in hydrolysis reactions and dehydration
synthesis reactions.
 Cushion/shock absorber (e.g. joints and cerebral spinal
fluid)


Salts are ionic compounds consisting of cations other
than H+. The dissociation of salts with water forms
electrolytes which are ions that conduct electrical
current in solution.
Acids and bases...
 Acids - hydrogen ion (H+ = proton) donors
 Bases - hydrogen acceptors
 pH - measure of protons in solution. (scale 0.014.0)
 Neutralization - reacting acids with bases yielding
a water and a salt.
Ions in
solution
Salt
crystal
Na+
Na+
Cl–
Cl–
H+
–
Human Anatomy and Physiology, 7e
by Elaine Marieb & Katja Hoehn
O
H
+
Water
molecule
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Concentration in moles/liter
[OH–]
[H+] pH
Examples
100
0
10–13
10–1
1
10–2
10–4
2 Lemon juice; gastric
juice (pH 2)
3 Grapefruit juice (pH 3)
Sauerkraut (pH 3.5)
4 Tomato juice (pH 4.2)
10–9
10–5
5 Coffee (pH 5.0)
10–8
10–6
10–9
6 Urine (pH 5–8)
Saliva; milk (pH 6.5)
7 Distilled water (pH 7)
Human blood; semen (pH 7.4)
8 Egg white (pH 8)
Seawater (pH 8.4)
9
10–10
10
10–11
10–12
11 Household ammonia
(pH 11.5–11.9)
12 Household bleach (pH 12)
10–13
13
10–14
14
10–12
10–11
10–10
Increasing acidity
10–14
10–3
10–7
Neutral
[H+] = [OH–]
10–6
10–8
10–5
10–4
10–3
10–2
10–1
Increasing alkalinity (basicity)
10–7
Milk of magnesia (pH 10.5)
Oven cleaner (pH 13.5)
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


Organic compounds
Compounds containing carbon but may also
contain hydrogen and oxygen
Biologically organic compounds may contain
(in addition to C,H,O) nitrogen, phosphorus,
and sulfur.
Types of organic compounds (Biological):




Carbohydrates - composed of units called
saccharides
Lipids - composed of units called fatty acids
Proteins - composed of units called amino acids
Nucleic acids - composed of units called nucleotides



A. Carbohydrates
Compounds containing carbon, hydrogen, and
oxygen in exact ratios (CnH2nOn)
Carbs are divided into two classes called simple
sugars (monosaccharides and disaccharides) and
complex sugars (oligosaccharides and
polysaccharides).

-
-
Monosaccharides - one saccharide, made up of 5
(pentose) or 6 (hexose) carbons.
Ribose (pentose) is component of RNA and DNA
Glucose
Fructose
Galactose
all hexoses are biologically important in the production of
energy.



Disaccharides - two saccharides formed from a
synthesis (dehydration/synthesis) reaction. egs.
sucrose (glu + Fru), lactose (glu + gala), and maltose
(glu + glu).
Polysaccharides - starches (in plants) and glycogen
(in animals), both composed of many glucoses.
Carbohydrates provide cellular fuel; glucose is
oxidized in body cells and bond energy released
during oxidation is transferred and trapped in the
bonds of ATP molecules (adenosine triphosphate).
ATP is then used in subsequent endergonic
(energy requiring reactions).
CH2OH
O H
H
H
OH H
OH
HO
HOCH2
HO
O
H
H
HO
OH
H
OH
Glucose
CH2OH
H
CH2OH
O OH
HO
H
OH H
H
H
H
Fructose
HOCH2
H
OH
Galactose
O
HOCH2
OH
H
H
OH
H
H
H
Deoxyribose
O
OH
H
H
OH
OH
H
Ribose
(a) Monosaccharides
CH2OH
O H
H
H
+
H
OH
OH
HO
HOCH2
HO
OH
H
Glucose
HO
H
H
OH
H
HO
CH2OH
H
Hydrolysis
H2O
H2O
CH2OH
O H
H
H
OH H
HO
H
O
HOCH2
H
O OH
H
OH H
H
H
Glucose
OH
Glucose
Maltose
HOCH2
O
H
O
OH
OH
Fructose
O H
H
OH
H
OH
HOCH2
H
O
Dehydration
synthesis
H
HO
CH2OH
H
Sucrose
HOCH2
HO
H
O
H
OH H
H
O
H
HOCH2
H
O OH
H
OH H
H
OH
H
Galactose
OH
Glucose
Lactose
(b) Disaccharides
Human Anatomy and Physiology, 7e
by Elaine Marieb & Katja Hoehn
Copyright © 2007 Pearson Education, Inc.,
publishing as Benjamin Cummings.



B. Lipids
Lipids are composed of fatty acids and glycerol.
Fatty acids are compounds containing long chains
of carbons and glycerol is a compound containing
a small chain of three carbons
Lipids are divided into three classes: Triglycerides,
Phospholipids, and Sterols.
Triglycerides - considered the most usable form of energy
in the body and is composed of three fatty acids bound to
one glycerol by dehydration synthesis. Triglycerides may
be saturated or unsaturated.
 Phospholipids - component of cell membranes and is
composed of one glycerol, two fatty acids. and a
phosphate.
 Sterols (steroids) - isoprene units (rings of carbon) egs.
cholesterol and sex hormones.

C. Proteins
 Proteins are composed of long chains of amino
acids.
 Peptide - short chain of amino acids (10-20?)
 Polypeptide - long chain of amino acids
 Structural Levels:
Primary = sequence of amino acids
 Secondary = coiling of primary due to hydrogen bonding
 Tertiary = folding of secondary due to hydrogen and
sulfur bonds
 Quaternary = many tertiary proteins bonded together

Peptide bond
H
H
R
O
N
C
C
+
H R
O
N
C
C
Dehydration H2O
synthesis
OH H
OH
H
H
H
Hydrolysis
H2O
Amino acid
Amino acid
Human Anatomy and Physiology, 7e
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H
R
O
H
R
O
N
C
C
N
C
C
H
H
Dipeptide
OH
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
Biological structures: Fibrous and Globular


Fibrous - strand-like appearance, mostly secondary
structure, and referred to as structural proteins
 Structural/mechanical - collagen, keratin, and
elastin
 Movement - actin and myosin in muscle
Globular - compact spherical tertiary proteins
referred to as functional proteins
 Functional proteins may denature
 Example of globular proteins are:





catalysts - enzymes
transport - hemoglobin
pH regulation - plasma proteins
metabolism regulation - peptide and protein hormones
body defense - antibodies
H
C
R
C
H
N
R
O
H
O
C
H
N
H
C
C
(c) Secondary structure (b-pleated sheet)
R
(a) Primary structure
(polypeptide strand)
Human Anatomy and Physiology, 7e
by Elaine Marieb & Katja Hoehn
Copyright © 2007 Pearson Education, Inc.,
publishing as Benjamin Cummings.

Enzymes - globular proteins that act as
biological catalysts of reactions and are made
up of protein and a cofactor/coenzyme (helpers
of enzymes).

Mechanism of enzyme action:
 Enzyme-substrate complex formation --> enzyme
binds substance (substrate) on which it acts to a
special site (active site) on the enzyme.
 Enzyme-substrate complex undergoes an internal
rearrangement that forms a product.
 Enzyme releases the product of the reaction and
now can catalyze another reaction.
Heme group
-helix
(d) Tertiary structure
(e) Quaternary structure
(hemoglobin molecule)
(b) Secondary structure
(-helix)
Human Anatomy and Physiology, 7e
by Elaine Marieb & Katja Hoehn
Copyright © 2007 Pearson Education, Inc.,
publishing as Benjamin Cummings.

Enzymes lower a reactions activation energy which is
the energy required by compounds in order to react.
Activation
energy
Energy
Energy
released
by reaction
Energy
(a) Noncatalyzed reaction
Human Anatomy and Physiology, 7e
by Elaine Marieb & Katja Hoehn
Activation
energy
Energy
released
by reaction
(b) Enzyme-catalyzed reaction
Copyright © 2007 Pearson Education, Inc.,
publishing as Benjamin Cummings.
D. Nucleic Acids
 Nucleic Acids (DNA and RNA) are composed
of nucleotides
 Nucleotide are the basic building blocks of our
genetic information (chromosomes)
 Each nucleotide contains three components:



Pentose sugar (ribose)
Phosphate group
Nitrogenous base (adenine, guanine, cytosine,
thymine, uracil)
Phosphate Sugar
O–
O P O
O–
Adenine (A)
H N
CH2
O
N
H H
H
H
N
Thymine (T)
H
N H O
N
CH3
H N
O
H
OH H
N
Adenine nucleotide
H
Sugar
Phosphate
H OH
H
H H
O–
H O
H2C O P O
O–
Thymine nucleotide
A
T
C
G
A
Sugar-phosphate
backbone
A
Key:
G
Thymine (T)
Adenine (A)
G
T
A
Cytosine (C)
Guanine (G)
Deoxyribose
sugar
Phosphate
Hydrogen bond
Human Anatomy and Physiology, 7e
by Elaine Marieb & Katja Hoehn
A
G
C
G
C
T
A
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publishing as Benjamin Cummings.