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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)

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biological chemistry
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.
slide3

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)
slide5

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
slide8

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
slide9

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)
slide12

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
slide13

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 valenceelectrons (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.
slide15

As a result of incomplete valence levels, atoms fill those levels by interacting with each other forming chemicalbonds (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)
slide17
CH4

methane

slide19

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.
figure 2 5 formation of an ionic bond p 33

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

+

Na

Cl

Na

Cl

Sodium ion (Na+)

Chloride ion (Cl–)

Sodium atom (Na)

(11p+; 12n0; 11e–)

Chlorine atom (Cl)

(17p+; 18n0; 17e–)

Sodium chloride (NaCl)

(a)

CI–

Na+

(b)

figure 2 12 dissociation of a salt in water p 40

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

Ions in

solution

Salt

crystal

Na+

Na+

Cl–

Cl–

+

H

Water

molecule

O

+

–

H

slide23

Hydrogen bonds– weak bonds formed between a slightly positive hydrogen and a slightly negative atom.

slide24

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...
slide26

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)
slide28

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 401

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

Ions in

solution

Salt

crystal

Na+

Na+

Cl–

Cl–

+

H

Water

molecule

O

+

–

H

figure 2 13 the ph scale and ph values of representative substances p 42

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

Concentration in moles/liter

[OH–]

[H+]

pH

Examples

0

100

10–14

1

10–1

10–13

2

Lemon juice; gastric

juice (pH 2)

10–2

10–12

3

Grapefruit juice (pH 3)

Sauerkraut (pH 3.5)

10–11

10–3

Increasing acidity

10–10

4

Tomato juice (pH 4.2)

10–4

5

Coffee (pH 5.0)

10–9

10–5

6

Urine (pH 5–8)

Saliva; milk (pH 6.5)

10–8

10–6

7

Distilled water (pH 7)

Human blood; semen (pH 7.4)

10–7

10–7

Neutral

[H+] = [OH–]

8

Egg white (pH 8)

Seawater (pH 8.4)

10–6

10–8

9

10–5

10–9

10

10–4

10–10

Milk of magnesia (pH 10.5)

Increasing alkalinity (basicity)

11

10–3

10–11

Household ammonia

(pH 11.5–11.9)

12

Household bleach (pH 12)

10–2

10–12

13

10–1

10–13

Oven cleaner (pH 13.5)

14

100

10–14

slide31

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
slide32

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.
slide34

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

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

CH2OH

CH2OH

HOCH2

HOCH2

HOCH2

O

O

O

O

O

H

HO

OH

OH

OH

H

H

H

H

H

HO

H

H

H

H

H

OH

H

OH

OH

HO

CH2OH

H

H

H

H

H

H

HO

OH

H

H

OH

OH

H

OH

OH

H

OH

Glucose

Fructose

Galactose

Deoxyribose

Ribose

(a) Monosaccharides

CH2OH

CH2OH

Dehydration

synthesis

HOCH2

HOCH2

H2O

O

O

O

O

H

H

H

H

H

H

H

H

+

H

HO

H

H

HO

OH

H

OH

O

OH

HO

HO

CH2OH

HO

CH2OH

Hydrolysis

H2O

OH

OH

H

H

OH

H

H

OH

Glucose

Fructose

Sucrose

HOCH2

HOCH2

HOCH2

HOCH2

H

H

O

O

H

O

O

H

OH

HO

OH

H

H

H

H

O

OH

H

OH

H

OH

H

OH

H

O

H

HO

H

H

H

H

OH

H

OH

H

OH

OH

H

Glucose

Glucose

Galactose

Glucose

Maltose

Lactose

(b) Disaccharides

slide36

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.
slide37

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

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

Peptide bond

Dehydration

synthesis

H

R

O

H

R

O

H

R

O

H

R

O

H2O

N

C

C

+

N

C

C

N

C

C

N

C

C

OH

H

OH

H

OH

H

H

H

H

H

Hydrolysis

H2O

Amino acid

Amino acid

Dipeptide

slide39

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

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

H

C

R

C

O

O

H

N

C

H

R

C

O

O

H

N

(c) Secondary structure (b-pleated sheet)

C

H

R

(a) Primary structure

(polypeptide strand)

slide41

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

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

Heme group

-helix

(d) Tertiary structure

(e) Quaternary structure

(hemoglobin molecule)

(b) Secondary structure

(-helix)

slide43

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

Activation

energy

Activation

energy

Energy

released

by reaction

Energy

released

by reaction

Energy

Energy

(b) Enzyme-catalyzed reaction

(a) Noncatalyzed reaction

slide44

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

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

Phosphate

Sugar

Adenine (A)

Thymine (T)

Sugar

Phosphate

O–

H

CH3

H

OH

N

N

H

H

O

H

P

O

CH2

O

O

H

O–

N

H

H

H

H

N

H

N

N

O–

H

H

O

H

N

P

H2C

O

O

O

H

OH

H

O–

Adenine nucleotide

Thymine nucleotide

A

T

C

G

A

Sugar-phosphate

backbone

A

Key:

G

Thymine (T)

G

Adenine (A)

T

A

Cytosine (C)

Guanine (G)

A

Deoxyribose

sugar

G

C

G

C

Phosphate

T

A

Hydrogen bond