Biology 112

Spring 2002

Campos

Chemistry of life

I.  Introduction

-  living things are composed of the same chemical elements as the nonliving world and obey the same physical and chemical laws

-  living things have unique characteristics, properties -- life

-  structural hierarchy to biological systems:  atomic level to biosphere

-  to understand life:

• understand properties of molecules that make up living systems and reactions in which they participate
• understand basic concepts regarding building blocks of such molecules -- atoms

II.  Atoms

A.  General characteristics

1. All matter is composed of atoms

• consist of a positively charged nucleus containing one or more protons

• may contain one or more neutrons

• negatively charged electrons move around nucleus

2. Atoms and constituents have mass

• proton and neutron have mass of about 1 dalton (1.7 x10^-24 grams)

  • mass of proton serves as standard unit of molecular mass measurement (atomic mass unit)

• mass of electron is very small -- not factored into calculation of mass of an atom

3. Atomic constituents are charged and neutral

• proton has charge of +1

• neutron is neutral

• electron has charge of -1

-  charge of atom depends on number of protons and electrons

4. Atoms are mostly empty space

• if you expand atom proportionately to the size of the largest dome in the world:

  • the nucleus would be the size of a grain of salt, electrons would be too small to see

  • remainder of this enormous atom would be empty space

B.  Elements

1.  Elements are pure substances that contain only one type of atom -- for example, hydrogen consists solely of hydrogen atoms

-  more than 100 different elements are found in the universe

• elements arranged in a periodic table
• periodic table groups the elements according to their physical and chemical properties
  • arranges elements left to right based on number of protons
  • arranges elements in columns based on similarities in their properties

2. Characteristics of an element

• atomic number -- number of protons in each of its atoms
• atomic weight (mass) -- total number of protons and neutrons in nucleus of each of its atoms, mass of atom in daltons

3.  About 98% of the mass of living organisms is made of carbon, hydrogen, nitrogen, oxygen, and sulfur.

III.  Chemical reactions between elements

A.  Electron behavior

1.  Chemical reactions are changes in atomic composition of substances

• depend on the number and arrangement of electrons in elements
• involve changes in relationship of electrons with one another

2.  Electrons arranged in electron shells (energy levels) around nucleus

• first electron shell can hold two electrons
• second electron shell can hold eight electrons
• third electron shell can hold eight electrons
• usually outermost shells hold only eight electrons

4.  The outermost electron shell determines how an atom combines with other atoms

• outermost shell with eight electrons -- no unpaired electrons -- atom is stable
• atoms of chemically reactive elements have unpaired electrons in outer shell
• seek to attain stability by:
  • sharing electrons with other atoms
  • gaining or losing electrons from outer shell

B.  Chemical bonds

- a chemical bond is an attractive force that links two atoms to form a molecule

-  types of chemical bonds:

• covalent bonds
• hydrogen bonds
• ionic interactions

1.  Covalent bonds consist of shared pairs of electrons

• hydrogen molecule
• behavior of carbon -- methane molecule example
• covalent bonding capabilities of biologically important elements
• multiple covalent bonds
• covalent bonds are very strong

2.  Polar vs. nonpolar covalent bonds -- equal vs. unequal sharing of electrons

- sometimes when atoms share electrons, nucleus of one atom exerts a great attraction on the electron pair than the other nucleus -- pair tends to be closer to that atom

- electronegativity -- attractive force that atom exerts on electrons; ability of an atom to attract electrons

• nonpolar covalent bonds form when electronegativities between two atoms about equal -- ethane
• polar covalent bonds form when atoms with strong electronegativity (oxygen) bond to atoms of weak electronegativity (hydrogen)
  • no net charge, but charge distributed unevenly between

- example of water (H₂O)

• d-
• d+

3.  Hydrogen bonds

- form between an electronegative atom and a hydrogen bonded to an electronegative atom

• example of hydrogen bonds between molecules:  water
• example of hydrogen bonds within a molecule -- stabilization of protein and DNA structure

- hydrogen bonds only 1/10 the strength of covalent bond -- however, when many H-bonds form they have considerable strength

4.  Ionic bonds

-  ionic bonds are formed by electrical interactions between ions bearing opposite charges

-  ions form when an atom gains or loses one or more electrons

- when one interacting atom is much more electronegative than the other a complete transfer of one or more electrons occurs

-  example of NaCl

- ions can interact with other ions or with polar molecules -- basis of solubility of ions in aqueous systems

5.  Hydrophilic and hydrophobic molecules

- hydrophilic molecules are polar molecules that interact with water 

- hydrophobic molecules -  nonpolar molecules that interact with one another -- can't form hydrogen bonds, nonpolar molecules aggregate

V.  Acids, bases and the pH scale

- acids are substances that dissolve in water and release hydrogen ions (H⁺)

- bases are substances that dissolve in water and accept hydrogen ions (H⁺)

- acids donate H⁺; bases accept H⁺

1.  Strong acids completely dissociate in solution:

• HCl -->H⁺ + Cl^-       

• H₂SO₄ --> 2H⁺ + SO₄^2-

2.  Weak acids partly dissociate in solution

• H₂CO₃ <--> H⁺ + HCO₃^-

3.  Strong bases completely dissociate in water, tie up H⁺

NaOH --> Na⁺ + OH^-

4.  Weak bases do not completely dissociate in solution and as such are slower to accept H⁺

• H₂CO₃ <--> H⁺ + HCO₃^-

• NH₂ + H⁺ <-->  NH₃⁺

5.  The pH scale

- the pH scale indicates the strength of a solution of an acid or base

• the scale is arrayed as a set of values 1 through 14

• these values may be measured by electronic instruments

- the pH value is defined as the negative logarithm of the hydrogen ion concentration in moles per liter (molar concentration):

• pH = - log₁₀ [H⁺]  

VI.  Biological molecules -- large molecules (macromolecules) that are basis of all living things

- there are four major types of biological macromolecules: 

• proteins

• carbohydrates

• lipids

• nucleic acids

- these macromolecules are made the same way in all living things, and they are present in all organisms in roughly the same proportions

- macromolecules are giant polymers

-  macromolecules are formed by covalent bonds between monomers

• macromolecules are formed when monomers are joined by condensation reactions (dehydration synthesis)
• hydrolysis reaction breaks polymers into monomers

A.  Carbohydrates

- contain C, H, O; H:O ratio = 2:1

- classified according to size/solubility as a monosaccharides, disaccharides, or polysaccharides

1. Monosaccharides: simple sugars

- single chain or ring structures containing 3-7 C

- C:H:O ratio = 1:2:1

- examples are glucose (C₆H₁₂O₆), and ribose (C₅H₁₀O₅)

- named according to the number of C they contain; most important in body are hexoses and pentoses

a. Hexoses (6C)

i. glucose: most important CH₂O in body; all ingested CH₂Os are broken down into glucose

ii. & iii. fructose and galactose: isomers of glucose, same number of C, arranged differently

b. Pentoses: (5C)

i. deoxyribose - DNA component

ii. ribose - RNA component

2. Disaccharides: double sugars

- formed when 2 monosaccharides are joined by dehydration synthesis (loss H₂0)

• sucrose
• maltose
• lactose

- disaccharides are too large to pass through cell membranes, must be digested to monosaccharide subunits prior to absorption

3. Polysaccharides: long chains of simple sugars linked together by dehydration synthesis

- due to size, they are water insoluble

- great storage products; also have structural roles

- polysaccharides of importance to body: starch & glycogen, both glucose polymers

• starch: storage CH₂O formed by plants
• glycogen: storage carbohydrate in animal tissue, found primarily in skeletal muscle & liver cells

B.  Lipids

- organic compounds insoluble in water but readily soluble in other lipids a

- contain C, H, O; however oxygen proportions in lipids are much lower than in CH₂O.

• phosphorous found in some more complex lipids

- lipids are diverse:

• triglycerides (neutral fats)
• phospholipids
• steroids

1. Triglycerides (TGs): neutral fats

a. Structure

i. glycerol: modified simple sugar

ii. three fatty acids: long chains of C and H with organic acid groups at one end

b. Synthesis

- fatty acids attached to glycerol backbone by dehydration synthesis; glycerol backbone is identical in all TGs, fatty acid chains vary in length and saturation

- concept of saturation: 

• fatty acid chains with only single covalent bonds between carbons are saturated hydrocarbon chains
• fatty acid chains with one or more double covalent bonds between carbons are unsaturated hydrocarbon chains
• saturation and length of fatty acid hydrocarbon chains determines how solid a TG is at a given temperature
  • TGs with short and/or unsaturated fatty acid are liquid at the right temperature (plant lipids such as vegetable oils)
  • TG with longer and/or saturated fatty acids are solid at room temperature (animal lipids such as lard, butter)

c. Functions:

- major source of stored energy in body; insulation and protection (in fat deposits)

2. Phospholipids

a. Structure

• modified TGs with phosphorous containing group and two fatty acid chains
• phosphate group gives phospholipids characteristic properties
  • polar head
  • TGs form two non polar tails

b. Functions:

- chief component of biological membranes

3. Steroids:

- flat molecules formed by 4 interlocking hydrocarbon rings

- in body, most important steroid is cholesterol

• structure is the basis for all other body steroids
  • bile salts
  • vitamin D
  • sex hormones
  • adrenal cortical hormones

D.  Proteins

- basic structural material of body

- also play vital roles in cell function

• enzymes
• hemoglobin
• contractile proteins
• some hormones

- most varied function of any molecule in the body

- may contain C, O, H, N, S, P

1. Amino acids and peptide bonds

- building block of proteins are amino acids (aa), linked together by peptide bonds

2. Levels of protein structure

a. Primary structure: linear sequence of aa, the polypeptide chain; determines all other levels of structure

b. Secondary structure

• conformation of the polypeptide chain
• stabilized by hydrogen bonding

c. Tertiary structure: specific regions of polypeptide secondary structure fold onto one another to form compact ball-like molecule

• the 3-D shape assumed by various areas of secondary structure

d. Quaternary structure: tertiary structures of two or more polypeptide chains aggregate to form a complex protein (hemoglobin)

3.  Examples of structural and functional roles for proteins

• keratin -- fibrous protein
• enzymes -- globular proteins

E.  Nucleic acids

- linear polymers specialized for storage, transmission and usage of information

-  two types:

• DNA
• RNA

-  DNA molecules encode hereditary information and pass it from generation to generation

- RNA molecules copy information in segments of DNA to specify the sequence of amino acids found in proteins

1.  General structure of nucleic acids

- building blocks are nucleotides

• composed of pentose sugar -- ribose or deoxyribose
• phosphate group 
• nitrogenous base
  • purines -- adenine, guanine -- 2 ringed structures (DNA and RNA)
  • pyrimidines -- cytosine and thymine in DNA; cytosine and uracil in RNA -- single ringed structures

2.  DNA structure

-  a polymer of nucleotides -- two strands of nucleotides twisted around each other in a double helix, held together by hydrogen bonds

• analogy of a ladder twisted about itself
  • each side of ladder formed by alternating sugar-phosphate units 
  • rungs of ladder formed by nitrogenous bases hydrogen bonding with each other -- hold two nucleotide strands together

- principle of complementary base pairing:

• adenine always hydrogen bonds thymine
• cytosine and guanine always hydrogen bond

-  reason for such pairing:

• available hydrogen bonding sites
• one ring base pairs with two ring base

- consequences of complementary of bases:

• molecule easily replicated
• molecule translated to RNA sequence

3.  RNA structure

- single strand of nucleotides

- phosphate/ribose/nitrogenous base

• bases are A, U, G, C

- produced from a DNA template

- three types

• mRNA
• rRNA
• tRNA

F. Adenosine triphosphate (ATP)

-  the energy currency of cells