Copyright 2009, John Wiley & Sons, Inc. Unit 2: Biochemistry and Cells Review.

Copyright 2009, John Wiley & Sons, Inc.

Unit 2: Biochemistry and Cells Review


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)


Atomic Number and Mass Number Atomic number = number of protons in the nucleus. Mass number = the sum of its protons and neutrons.


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)


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


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.


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).


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


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


Polarity

Covalently bonded molecules Some are non-polar

Electrically neutral as a molecule

Some are polar Have a positive

and negative side


Hydrogen Bonds

are weak intermolecular bonds; they serve as links between polar molecules.

give water considerable cohesion which creates a very high surface tension


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.


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.


Activation Energy

Energy it takes to start a chemical reaction


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.


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


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)


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


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


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


Dissociation of Acids, Bases, and Salts


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.


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


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)


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


Monosaccharides

Monosaccharides are one sugar molecule


Disaccharides Combining 2 monosaccharides by dehydration

synthesis releases a water molecule. sucrose = glucose & fructose maltose = glucose & glucose lactose = glucose & galactose (lactose intolerance)


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


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


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.


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


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.


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


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


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.


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.


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.


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


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

Copyright 2009, John Wiley & Sons, Inc. Unit 2: Biochemistry and Cells Review.

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Transcript of Copyright 2009, John Wiley & Sons, Inc. Unit 2: Biochemistry and Cells Review.