Basis Chemical of Life
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Introduction
Why study chemistry in an Anatomy and Physiology class?
- Body functions depend on cellular functions - Cellular functions result from chemical changes - Biochemistry helps to explain physiological processes
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Structure of Matter
Matter anything that takes up space and has mass (weight).
It is composed of elements.
Elements composed of chemically identical atoms:
Bulk elements required by the body in large amounts Trace elements - required by the body in small amounts Ultratrace elements required by the body in very minute amounts
Atoms smallest particle of an element
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Some Particles of Matter
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Elements and Atoms
Atoms are the smallest complete units of elements Protons, neutrons and electrons All matter is composed of elements Oxygen, nitrogen, hydrogen Elements are the parts of compounds Water, CO2, methane etc.
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Atomic Structure
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Atoms - composed of subatomic particles:
Proton carries a single positive charge
-
Neutron (n0) Proton (p+)
Neutron carries no
electrical charge Electron carries a single negative charge
Nucleus
Central part of atom Composed of protons and neutrons Electrons move around the nucleus
+ 0 0 0 +
+
0
-
Electron (e)
Lithium (Li)
Nucleus
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Atomic Number and
Atomic Number
Number of protons in the nucleus of one atom Each element has a unique atomic number Equals the number of electrons in the atom
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Isotopes
Isotopes
Atoms with the same atomic numbers but with different atomic weights Atoms with the same number of protons and electrons but a different number of neutrons Oxygen often forms isotopes (O16, O17, and O18) Unstable isotopes are radioactive; they emit energy or atomic fragments
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Molecules and Compounds
Molecule particle formed when two or more atoms
chemically combine
Compound particle formed when two or more atoms of
different elements chemically combine
Molecular formulas depict the elements present and
the number of each atom present in the molecule H2 C6H12O6 H2O
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Bonding of Atoms
Bonds form when atoms combine with other atoms Electrons of an atom occupy regions of space called electron shells which circle the nucleus For atoms with atomic numbers of 18 or less, the following rules apply: The first shell can hold up to 2 electrons The second shell can hold up to 8 electrons The third shell can hold up to 8 electrons
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Bonding of Atoms
Lower shells are filled first
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If the outermost shell is full, the atom is stable
+ + Hydrogen (H) Helium (He)
+0 + 0 0 0 + -
+
0
0
-
Lithium (Li)
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Bonding of Atoms: Ions
Ion
An atom that gains or loses electrons to become stable An electrically charged atom
Cation
A positively charged ion Formed when an atom loses electrons
11p+ 12n0 17p+ 18n0
Anion
A negatively charged ion Formed when an atom gains electrons
Sodium atom (Na)
Chlorine atom (Cl)
(a) Separate atoms If a sodium atom loses an electron to a chlorine atom, the sodium atom becomes a sodium ion (Na+), and the chlorine atom becomes a chloride ion (Cl).
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Ionic Bonds
Ionic Bonds
An attraction between a cation and an anion Formed when electrons are transferred from one atom to another atom
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Na+
+
11p+ 12n0
17p+ 18n0
Cl
Sodium ion (Na+)
Chloride ion (Cl)
(c) Salt crystal Ionically bonded substances form arrays such as a crystal of NaCl.
Sodium chloride (b) Bonded ions These oppositely charged particles attract electrically and join by an ionic bond.
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Covalent Bonds
Formed when atoms share electrons
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H -
H -
H2 -
+
+
+ -
+
Hydrogen atom
+
Hydrogen atom
Hydrogen molecule
Hydrogen atoms form single bonds Oxygen atoms form two bonds Nitrogen atoms form three bonds Carbon atoms form four bonds
HH O=O NN O=C=O
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Bonding of Atoms: Polar Molecules
Polar Molecules
Molecule with a slightly negative end and a slightly positive end
Results when electrons are not shared equally in covalent bonds Water is an important polar molecule
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Slightly negative end
(a)
15 Slightly positive ends
Hydrogen Bonds
Hydrogen Bonds
A weak attraction between the positive end of one polar molecule and the negative end of another polar molecule Formed between water molecules Important for protein and nucleic acid structure
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H O
H
H H H H O (b) H O H
Hydrogen bonds
O
O H
H
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Chemical Reactions
Chemical reactions occur when chemical bonds form or break among atoms, ions, or molecules Reactants are the starting materials of the reaction - the atoms, ions, or molecules Products are substances formed at the end of the chemical reaction NaCl Na+ + ClReactant Products
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Types of Chemical Reactions
Synthesis Reaction more complex chemical structure is formed A + B AB Decomposition Reaction chemical bonds are broken to form a simpler chemical structure AB A + B Exchange Reaction chemical bonds are broken and new bonds are formed AB + CD AD + CB Reversible Reaction the products can change back to the reactants 18 A + B n AB
Acids, Bases, and Salts
Electrolytes substances that release ions in water NaCl Na+ + ClAcids electrolytes that dissociate to release hydrogen ions in water
HCl H+ + Cl-
Bases substances that release ions that can combine with hydrogen ions
NaOH Na+ + OH-
Salts electrolytes formed by the reaction between an acid and a base
HCl + NaOH H2O + NaCl
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Acid and Base Concentration
pH scale - indicates the
concentration of hydrogen ions in solution Neutral pH 7; indicates equal concentrations of H+ and OHAcidic pH less than 7; indicates a greater concentration of H+
pH 0 1 Acidic
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Acidic Relative H+ Amounts of H+ (red) 3.0 and OH 2.0 apple (blue) gastric juice juice
5.3 4.2 cabbage tomato juice
8.4 7.4 6.6 Sodium Human cows biocarbonate blood milk 8.0 7.0 Egg Distilled white water 7 Neutral 8 10.5 milk of magnesia
11.5 Household ammonia Basic OH
6.0 corn 6
2 3 4 5 H+ concentration increases
9 10 11 12 13 14 OH concentration increases Basic (alkaline)
Basic or alkaline pH greater than 7;
indicates a greater concentration of OH20
Chemical Constituents of Cells
Organic v. Inorganic Molecules Organic molecules Contain C and H Dissolve in water and organic liquids Carbohydrates, proteins, lipids, and nucleic acids Inorganic molecules Generally do not contain C Usually dissociate in water, forming ions Water, oxygen, carbon dioxide, and inorganic salts
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Inorganic Substances
Water Most abundant compound in living material of Two-thirds the weight of an adult human Major component of all body fluids Medium for most metabolic reactions Important role in transporting chemicals in the body Absorbs and transports heat Oxygen (O2) Used by organelles to release energy from nutrients in order to drive cells metabolic activities Necessary for survival
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Inorganic Substances
Carbon dioxide (CO2) Waste product released during metabolic reactions Must be removed from the body Inorganic salts Abundant in body fluids Sources of necessary ions (Na+, Cl-, K+, Ca2+, etc.) Play important roles in metabolism
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Organic Substances Carbohydrates
Provide energy to cells Supply materials to build cell structures Water-soluble Contain C, H, and O Ratio of H to O close to 2:1 (C6H12O6) Monosaccharides glucose, fructose Disaccharides sucrose, lactose Polysaccharides glycogen, cellulose
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Organic Substances Carbohydrates
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O
O O
O
(a) Monosaccharide
(b) Disaccharide
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O
O O
(c) Polysaccharide
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Organic Substances Lipids
Soluble in organic solvents; insoluble in water Fats (triglycerides)
Used primarily for energy; most common lipid in the body Contain C, H, and O but less O than carbohydrates (C57H110O6) Building blocks are 1 glycerol and 3 fatty acids per molecule Saturated and unsaturated
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H H C O
O C
H C H
H C H H C H H C H
H C H H C H H C H
H C H H C H H C H
H C H H C H H C H
H C H H C H H
C
H C H H C H
H C
H C H H C H
H C H
H C H H C H
H C H
H C H H C H
H C H H C H
H C H H C H
H C H H C H
H C H H C H
H C H H C H H C H H C H H H
O H C O C
H C H
O H C H O C
H C H
H C H
H C H
H C H
H C H H
Glycerol portion
Fatty acid portions
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Organic Substances Lipids
Phospholipids
Building blocks are 1 glycerol, 2 fatty acids, and 1 phosphate per molecule Hydrophilic and hydrophobic Major component of cell membranes
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H H C C O O Fatty acid Fatty acid O H C H O P O O H C H H C H N H H
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H H H H C C C H Glycerol portion (a) A fat molecule O O O Fatty acid Fatty acid Fatty acid
H
Water-insoluble (hydrophobic) tail Water-soluble (hydrophilic) head
Phosphate portion (b) A phospholipid molecule (the unshaded portion may vary) (c) Schematic representation of a phospholipid molecule
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Organic Substances Lipids
Steroids
Four connected rings of carbon Widely distributed in the body, various functions Component of cell membrane Used to synthesize hormones Cholesterol
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H2 C HO C H
H2 C
H2 C CH3 C C HC
H2 CH3 H C C C CH
CH3 CH CH2 CH2 CH2 CH2 CH2 CH
CH3 CH3
CH CH2
C H2
C H
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(a) General structure of a steroid (b) Cholesterol
Organic Substances Proteins
Structural material Energy source Hormones Receptors Enzymes Antibodies
R H N H C H C O OH H
Protein building blocks are amino acids
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H C C C H C C H C C C H C O OH H H
H S H N H C C H H C O OH
H H
H
N H
(a) General structure of an amino acid. The portion common to all amino acids is within the oval. It includes the amino group (NH2) and the carboxyl group (COOH). The "R" group, or the "rest of the molecule, is what makes each amino acid unique.
(b) Cysteine. Cysteine has an R group that contains sulfur.
Phenylalanine. Phenylalanine has a complex R group. Improper metabolism of phenylalanine occurs in the disease phenylketonuria.
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Organic Substances Proteins
Four Levels of Protein Structure
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Amino acids
H
H
(a) Primary structureEach oblong shape in this polypeptide chain represents an amino acid molecule. The whole chain represents a portion of a protein molecule.
(c) Tertiary structure The pleated and coiled polypeptide chain of a protein molecule folds into a unique threedimensional structure.
C
(b) Secondary structureThe polypeptide chain of a protein molecule is often either pleated or twisted to form a coil. Dotted lines represent hydrogen bonds. R groups (see fig. 2.17) are indicated in bold.
H
N C R N
H O C H H
H H H O R H O H
C C N C C N C C N C H R C N C C N C O H R H C O N C N C HO C H O H R R H C O C H N R C HO N C H R O
R C H C
H N C C O H C N C N H C O H C O N H R H R
Three-dimensional folding
HO N H
C R
O
C C
R H C
H
N
R N O C C H N
C
HH H O R H O H H
H
O
C R
(d) Quaternary structureTwo or more polypeptide chains may be connected to form a single protein molecule.
R H C C
Pleated structure
H
Coiled structure
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Organic Substances Nucleic Acids
Base Sugar and Phosphate Encode amino acid sequences of proteins Building blocks are nucleotides
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P S
B
DNA (deoxyribonucleic acid) double polynucleotide RNA (ribonucleic acid) single polynucleotide 31
Enzymes Increase the rate of reactions Do not alter the reaction Are themselves not altered by the reaction Without enzymes, biochemical reactions proceed so slowly that life cannot be sustained. Recognized by the suffix "ase"; kinase, lipase, etc. Active sites - portion of enzyme that binds the substrate Substrate is the substance on which the enzyme acts. Enzyme binds substrate forming a complex, reaction occurs, products are released and enzyme is free to catalyze another reaction. Some reactions require the presence of "cofactors" like Ca++ or Mg++ or coenzymes like NAD and FAD (derived from vitamins, especially B vitamins) Slight increases in temperature speed up reactions, but if temperature is raised too much, protein will denature and enzyme is unable to act. There is also a pH optimum for each enzyme. Pepsin pH of 2, trypsin pH of 9.5 I. Metabolic Pathway - multiple enzymes involved in factory line assembly.
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Adenosine Triphosphate (ATP) 1. ATP is the bodies energy currency All living cells require energy to grow and function; contract muscle, build proteins, etc One form of energy can be converted to another, in our bodies food energy is converted to ATP ATP is adenosine with three attached phosphate molecules. Cleavage of the terminal phosphate releases energy to be used by the cell of the body. Breakdown of other molecules (food) provides energy necessary to reattach a phosphate and recycle: ADP + P to yield ATP.
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