i. matter and energy a. matter matter is anything that takes up space and has mass three states...

CHEMISTRY OF LIFE

Biological Chemistry

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)

Isotopes of Hydrogen

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.

O2 O=O

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)

H2 H-H

CH4methane

Hydrochloric acid HCl

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.

Human Anatomy and Physiology, 7eby Elaine Marieb & Katja Hoehn

Copyright © 2007 Pearson Education, Inc.,publishing as Benjamin Cummings.

Figure 2.5: Formation of an ionic bond, p. 33.

+

Sodium atom (Na)(11p+; 12n0; 11e–)

Chlorine atom (Cl)(17p+; 18n0; 17e–)

Sodium ion (Na+)Chloride ion (Cl–)

Sodium chloride (NaCl)

CI–

Na+

(a)

(b)

ClNaClNa

–



Figure 2.12: Dissociation of a salt in water, p. 40.

Watermolecule

Saltcrystal

Ions insolution

H

HO

Na+

Cl–

Na+

Cl–

– +

+

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)

Water H2O

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

0.0-14.0) Neutralization - reacting acids with bases

yielding a water and a salt.



Figure 2.12: Dissociation of a salt in water, p. 40.

Watermolecule

Saltcrystal

Ions insolution

H

HO

Na+

Cl–

Na+

Cl–

– +

+



Figure 2.13: The pH scale and pH values of representative substances, p. 42.

Concentration in moles/liter

[OH–]

10–14

10–13

10–12

10–11

10–10

10–9

10–8

10–7

10–6

10–5

10–4

10–3

10–2

10–1

100

10–5

10–6

10–7

10–8

10–9

10–10

10–11

10–12

10–13

10–14

10–4

10–3

10–2

10–1

100

5

6

7

8

9

10

11

12

13

14

4

3

2

1

0

[H+] pH Examples

Lemon juice; gastricjuice (pH 2)Grapefruit juice (pH 3)Sauerkraut (pH 3.5)Tomato juice (pH 4.2)

Coffee (pH 5.0)

Urine (pH 5–8)Saliva; milk (pH 6.5)

Distilled water (pH 7)Human blood; semen (pH 7.4)

Egg white (pH 8)Seawater (pH 8.4)

Milk of magnesia (pH 10.5)

Household ammonia (pH 11.5–11.9)

Household bleach (pH 12)

Oven cleaner (pH 13.5)

Incre

asin

g a

lkalin

ity (

basic

ity)

Incre

asin

g a

cid

ity

Neutral[H+] = [OH–]

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).



Figure 2.14a-b: Carbohydrate molecules, p. 45.

Glucose Fructose Galactose Deoxyribose Ribose

Glucose Fructose

Dehydrationsynthesis

Hydrolysis

Glucose Glucose

Maltose

Sucrose

Galactose Glucose

Lactose

(a) Monosaccharides

CH2OH

H OH H

CH2OH

H OH H OH OHOH OH

O

HOHOH

H

HO

HH

O

HOHCH2OH

H

HO

HOCH2 O

HOHH

OH

H

HOH

OHOCH2

HHH

OH

H

OHOCH2

HHH

OH

H

+O

CH2OH

H

H

OH

OH

H

HO

HH

OH

O

OH

HO

H

HCH2OH

H

HO

H2O

H2O

HOCH2

O

HOCH2

H

H

OH

OH

H

HO

HH

O

HOCH2

H

HH

OH

OH

OHHH

(b) Disaccharides

CH2OH

H

O

O

HOCH2

HOCH2

H OH

HOCH2

H OH

O

HOHHH

HOH

O

HHOH

OHHH

O

O

H

H

OH

OHHO

HH

O

OH

HO

H

HCH2OH

H

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



Figure 2.17: Amino acids are linked together by dehydration synthesis, p. 49.

Amino acid Amino acid

Dehydrationsynthesis

HydrolysisDipeptide

Peptide bond

+N

H

H

C

R

H

O

N

H

H

C

R

CC

H

O H2O

H2O

N

H

H

C

R

C

H

O

N

H

C

R

C

H

O

OH OH OH

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



Figure 2.18a,c: Levels of protein structure, p. 51.

O

O

(c) Secondary structure (b-pleated sheet)

(a) Primary structure (polypeptide strand)

C

C

R H

N

N

C

H

C RH

H

C RH

O

O

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.



Figure 2.18b,d,e: Levels of protein structure, p. 51.

Heme group

(b) Secondary structure (-helix)

(d) Tertiary structure (e) Quaternary structure (hemoglobin molecule)

-helix



Energy

Activationenergy

Energyreleasedby reaction

Energy

Activationenergy

Energyreleasedby reaction

(a) Noncatalyzed reaction (b) Enzyme-catalyzed reaction

Enzymes lower a reactions activation energy which is the energy required by compounds in order to react.

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)



Figure 2.22a-b: Structure of DNA, p. 56.

Thymine (T)

Adenine (A)

Cytosine (C)

Guanine (G)

Deoxyribosesugar

Phosphate

Hydrogen bond

Key:

Sugar-phosphatebackbone

Adenine nucleotide Thymine nucleotide

PhosphateSugar PhosphateSugarThymine (T)Adenine (A)

H

N H HO

O

HN

N HN

N

HOOO

CH2

CH3

OH

H

H

HHH

O–

O–

O OO

H2C

OH

H

H

HH

H

A

A

G

A

T

T

T

C

G C

G C

A

A

G

G

N N

P

P

O–

A

O–

i. matter and energy a. matter matter is anything that takes up space and has mass three states...

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