Download Unit 2 - Biochemistry and Cells Review (part I) - nh-chs

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
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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
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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 oxygenderived 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–)
cation
anion
Sodium ion (Na+)
Chloride ion (Cl–)
Sodium chloride (NaCl)
Copyright 2009, John Wiley & Sons, Inc.
Covalent Bonds

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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 + BAB) – Anabolism
 Atoms or molecules combine
 Energy is absorbed for bond formation

Decomposition reaction (ABA + 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
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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

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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
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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

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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

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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

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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

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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



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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
Copyright 2009, John Wiley & Sons, Inc.