Post on 01-Apr-2015
Copyright 2009, John Wiley & Sons, Inc.
Unit 2: Biochemistry and Cells Review
Copyright 2009, John Wiley & Sons, Inc.
Structure of Atoms Units of matter of all elements are called atoms.
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.
Atomic Number and Mass Number Atomic number = number of protons in the nucleus. Mass number = the sum of its protons and neutrons.
Copyright 2009, John Wiley & Sons, Inc.
Ions, Molecules, & Compounds
Ions an atom that gave up or gained an extra
electron written with its chemical symbol and (+) or (-)
Molecule two or more atoms held together by a chemical
bond written as molecular formula showing the
number of atoms of each element (H2O)
Copyright 2009, John Wiley & Sons, Inc.
Free Radicals
A free radical is 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.
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.
Copyright 2009, John Wiley & Sons, Inc.
Ionic Bonds When an atom loses or gains a valence electron,
ions are formed.
Positively and negatively charged ions are attracted to one another to form and ionic bond. 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.
Ionic Bonds
Sodium atom (Na)(11p+; 12n0; 11e–)
Chlorine atom (Cl)(17p+; 18n0; 17e–)
Sodium ion (Na+) Chloride ion (Cl–)
Sodium chloride (NaCl)
cation anion
Copyright 2009, John Wiley & Sons, Inc.
Covalent Bonds Covalent bonds are formed by the atoms of
molecules sharing one, two, or three pairs of their valence electrons. Covalent bonds are common and are the 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. In a nonpolar covalent bond, atoms share the
electrons equally; one atom does not attract the shared electrons more strongly than the other atom
Copyright 2009, John Wiley & Sons, Inc.
Copyright 2009, John Wiley & Sons, Inc.
Polarity
Covalently bonded molecules Some are non-polar
Electrically neutral as a molecule
Some are polar Have a positive
and negative side
Copyright 2009, John Wiley & Sons, Inc.
Hydrogen Bonds
are weak intermolecular bonds; they serve as links between polar molecules.
give water considerable cohesion which creates a very high surface tension
Copyright 2009, John Wiley & Sons, Inc.
Chemical Reactions
New bonds form and/or old bonds are broken.
Metabolism is “the sum of all the chemical reactions in the body.”
Law of conservation of energy The total mass of reactants equals the total
mass of the products.
Copyright 2009, John Wiley & Sons, Inc.
Energy Transfer in Chemical Reactions Energy is the capacity to do work.
An exergonic reaction is one in which the bond being broken has more energy than the one formed so that extra energy is released, usually as heat (occurs during catabolism of food molecules).
An endergonic reaction is just the opposite and thus requires that energy be added, usually from a molecule called ATP, to form a bond, as in bonding amino acid molecules together to form proteins.
Copyright 2009, John Wiley & Sons, Inc.
Activation Energy
Energy it takes to start a chemical reaction
Copyright 2009, John Wiley & Sons, Inc.
Catalysts and chemical reactions 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.
Types of Chemical Reactions Synthesis reaction (A + BAB) – Anabolism
Atoms or molecules combine Energy is absorbed for bond formation
Decomposition reaction (ABA + B) – Catabolism Molecule is broken down Chemical energy is released
Copyright 2009, John Wiley & Sons, Inc.
Inorganic vs. Organic Compounds Organic compounds
Contain at least one carbon to hydrogen bond Most are covalently bonded Example: C6H12O6 (glucose)
Inorganic compounds Lacks carbon Tend to be simpler compounds Example: H2O (water)
Copyright 2009, John Wiley & Sons, Inc.
Water
Is the most important and abundant inorganic compound in all living systems
65% of the human body is made of water
Water’s most important property is polarity, the uneven sharing of valence electrons
Enables reactants to collide to form products
Copyright 2009, John Wiley & Sons, Inc.
Properties of Water Water is a good solvent because the polarity of
water and its bent shape allow it to interact with several neighboring ions or molecules.
Water has a high heat capacity because it can absorb or release a relatively large amount of heat with only a modest change in its own temperature.
Heat of vaporization or the amount of heat needed to change from liquid to gas is also high evaporation of water from the skin removes large
amount of heat
Copyright 2009, John Wiley & Sons, Inc.
Acids, Bases, and Salts
Acids - are proton donors Release hydrogen ions (H+)
Bases - are proton acceptors Release hydroxyl ions (OH–)
Salts - dissociate into ions in the presence of water Vital to many body functions Include electrolytes which conduct electrical
currents
Copyright 2009, John Wiley & Sons, Inc.
Dissociation of Acids, Bases, and Salts
Copyright 2009, John Wiley & Sons, Inc.
pH
Measures relative concentration of H+ ions pH 7 = neutral pH below 7 = acidic pH above 7 = basic Buffer systems maintain
pH values of different parts of the body.
Copyright 2009, John Wiley & Sons, Inc.
Basic Chemistry - Review Topics using Textbook Structure of atoms Atomic mass and mass number Ions, molecules, compounds Free radicals Chemical bonds (covalent, ionic, hydrogen) Forms of energy and chemical reactions Types of reactions Inorganic compounds Water and it’s properties pH (acids and bases) Buffer systems
Copyright 2009, John Wiley & Sons, Inc.
Organic Compounds
organic compound - any compound that contains, at least one, carbon to hydrogen bond
functional groups (small clusters of atoms) can determine the characteristics of the organic molecule (p.43)
isomers have the same molecular formulas but different structures (glucose & fructose are both C6H12O6)
Copyright 2009, John Wiley & Sons, Inc.
Carbohydrates
Carbohydrates provide most of the energy needed for life when they are converted to ATP and include sugars, starches, glycogen, and cellulose.
Some carbohydrates function as food reserves. Carbohydrates are divided into three major groups
based on their size: monosaccharides, disaccharides, and polysaccharides
Copyright 2009, John Wiley & Sons, Inc.
Monosaccharides
Monosaccharides are one sugar molecule
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 Polysaccharides are the
largest carbohydrates and may contain hundreds of monosaccharides.
The principal polysaccharide in the human body is glycogen, which is stored in the liver or skeletal muscles.
When blood sugar level drops, the liver hydrolyzes glycogen to yield glucose which is released from the liver into the blood
Copyright 2009, John Wiley & Sons, Inc.
Lipids
Lipids, nonpolar molecules that store energy, structural support for cell membrane
Hydrophobic- mostly insoluble in polar solvents such as water
combines with proteins (lipoproteins) for transport in blood
Example: triglycerides, phospholipids, steroids, fats
Copyright 2009, John Wiley & Sons, Inc.
Triglycerides Triglycerides are the most plentiful lipids in the body
and provide protection, insulation, and energy (both immediate and stored). At room temperature, triglycerides may be either
solid (fats) or liquid (oils). Triglycerides provide more than twice as much
energy per gram as either carbohydrates or proteins.
Excess dietary carbohydrates, proteins, fats, and oils will be deposited and stored in adipose tissue as triglycerides.
Copyright 2009, John Wiley & Sons, Inc.
Phospholipids
Phospholipids are important cell membrane components.
They are amphipathic, with both polar and nonpolar regions a polar head
forms hydrogen bonds with water 2 nonpolar fatty acid tails
interact only with lipids
Copyright 2009, John Wiley & Sons, Inc.
Steroids Steroids have four rings of carbon atoms Steroids include
sex hormones bile salts some vitamins (ex. vitamin D) cholesterol, with cholesterol serving as an
important component of cell membranes and as starting material for synthesizing other steroids.
Copyright 2009, John Wiley & Sons, Inc.
Proteins
Account for over half of the body’s organic matter Provide for construction materials for body
tissues Play a vital role in cell function
Act as enzymes, hormones, and antibodies Examples: keratin and collagen
Copyright 2009, John Wiley & Sons, Inc.
Protein Structure Constructed from combinations of 20 amino acids.
dipeptides formed from 2 amino acids joined by a covalent bond called a peptide bond
polypeptides chains formed from 10 to 2000 amino acids. Dipeptides formed from 2 amino acids joined by a covalent
bond called a peptide bond dehydration synthesis
Copyright 2009, John Wiley & Sons, Inc.
Structural Organization of Proteins Levels of structural organization include
primary secondary tertiary quaternary
The resulting shape of the protein greatly influences its ability to recognize and bind to other molecules.
Denaturation of a protein by a hostile environment causes loss of its characteristic shape and function.
Copyright 2009, John Wiley & Sons, Inc.
Enzymes
Catalysts in living cells are called enzymes. Enzymes are highly specific in terms of the
“substrate” with which they react. Enzymes are subject to variety of cellular controls
(contained in DNA) Enzymes speed up chemical reactions by increasing
frequency of collisions, lowering the activation energy and properly orienting the colliding molecules.
Copyright 2009, John Wiley & Sons, Inc.
Nucleic Acids Made from chains of nucleotides
Deoxyribonucleic acid (DNA) forms the genetic code inside each cell and thereby regulates most of the activities that take place in our cells throughout a lifetime.
Ribonucleic acid (RNA) relays instructions from the genes in the cell’s nucleus to guide each cell’s assembly of amino acids into proteins by the ribosomes.
Copyright 2009, John Wiley & Sons, Inc.
RNA Structure
Differs from DNA single stranded ribose sugar not deoxyribose sugar uracil nitrogenous base replaces thymine
Types of RNA within the cell, each with a specific function messenger RNA ribosomal RNA transfer RNA
Copyright 2009, John Wiley & Sons, Inc.
Adenosine Triphosphate (ATP) ATP is the chemical energy used by all cells
Energy is released by breaking high energy phosphate bond (removal of terminal phosphate group by enzyme - ATPase)
leaves ADP (adenosine diphosphate) ATP is replenished by oxidation of food fuels
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