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BIOLS 102
Dr. Tariq Alalwan
Biology, 10e
Biology
10e
Sylvia Mader
Lectures by Tariq Alalwan, Ph.D.
Learning Objectives
 List the features of carbon that result in the diversity of organic molecules.  Describe how macromolecules are assembled and disassembled.
 Distinguish among monosaccharides, disaccharides, and polysaccharides.
 Compare storage polysaccharides with structural polysaccharides.
 Distinguish among fats, phospholipids, and steroids, and describe the composition, characteristics, and biological functions of each.
Learning Objectives (cont.)
 Describe the structure and functions of proteins.
 Describe the features that are shared by all amino acids and explain how amino acids are grouped into classes based on the characteristics of their side chains.
based on the characteristics of their side chains
 Distinguish among the four levels of organization of protein molecules.
 Compare the structure and function of DNA and RNA in cells
 Relate the structure of ATP to its function in cells.
Chapter 3: Organic Chemistry
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Organic Molecules
 Inorganic – Chemistry of elements other than carbon
 Organic – Carbon‐based chemistry
Carbon Atom
 Carbon atoms:
 Contain a total of 6 electrons
 Only four electrons in the outer (valence) shell
 Very diverse as one atom can bond with up to four
other V di
b d i h f
h atoms
 Often bonds with other carbon atoms to make hydrocarbons – chains of carbon atoms bonded exclusively to hydrogen atoms
 Can exist as unbranched (e.g. octane) or branched chains, or as rings (e.g. cyclohexane)
Functional Groups
 Functional groups:
 Specific combinations of bonded atoms
 Attached as a group to other molecules

Always react in the same manner, regardless of where attached

Determine activity and polarity of large organic molecules
 Many functional groups, but only a few are of major biological importance
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Functional Groups (cont.)
 Six functional groups are of biological importance
 Hydroxyl group (–OH)
 Carbonyl group (C=O)
 Carboxyl group (HO–C=O)
 Amino group (–NH2)
 Sulfhydryl group (–SH)
 Phosphate group
Functional Groups ‐ Hydroxyl
 Composed of a hydrogen atom bonded to an oxygen atom: ‐OH
 Organic molecules containing a hydroxyl group are known as alcohols
k
l h l
 Polar, why?
 Forms hydrogen bonds; present in sugars and some amino acids
 Example: Methanol
Functional Groups ‐ Carbonyl
 Composed of a carbon atom double‐bonded to an oxygen atom: C=O
 Polar
 If carbonyl group at the end of the skeleton: aldehyde
If b
l h d f h k l
ld h d
 If carbonyl group within (internal) the skeleton: ketone
 Present in sugars
Formaldehyde
Chapter 3: Organic Chemistry
Acetone
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Functional Groups ‐ Carboxyl
 Composed of an oxygen double bonded to a carbon atom that is also bonded to a hydroxyl group (hydroxyl group + carbonyl group = carboxyl group)
 Organic molecules containing a carboxyl group are known as carboxylic acids
 Polar and acidic, why?
 Carboxyl groups are essential constituents of amino acids
 Example: acetic acid
Functional Groups ‐ Amino
 Composed of a nitrogen atom covalently bonded to two hydrogen atoms: ‐NH2
 Organic molecules containing an amino group are known as amines
 Polar
 Forms hydrogen bonds
 Present in amino acids and nucleic acids
 Example: Glycine
Functional Groups ‐ Sulfhydryl
 Composed of a sulfur atom covalently bonded to a hydrogen atom: ‐SH
 Organic molecules containing a sulfhydryl group are known as thiols
 Forms disulfide bonds
 Present in some amino acids (i.e. proteins)
 Example: Ethanethiol
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Functional Groups ‐ Phosphate
 An ion composed of a phosphate ion covalently attached by one of its oxygen atoms to the carbon skeleton
 Can release one or two hydrogen ions, producing C l
t h d
i
d i ionized forms with 1 or 2 units of negative charge
 Polar, acidic
 Present in nucleotides (i.e. nucleic acids) and phospholipids
Un-ionized form
Isomers
 Isomers ‐ organic molecules that have:
 Identical molecular formulas, but
 Differing internal arrangement of atoms (i.e. structures) and properties
Macromolecules
 Some molecules are called macromolecules because of their large size
 Usually consist of many repeating units
 Resulting molecule is a polymer (many parts)
 Repeating units are called monomers
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Making and Breaking Macromolecules
 Dehydration (synthesis)
 Macromolecule is assembled by removing an –OH group from one subunit and an H from other subunit
 Thus removing a water molecule (H2O) for every subunit that is added to a macromolecule
 Also called water‐losing or condensation reaction
 Energy is required to break the chemical bonds when water is extracted
 Cells must supply energy to assemble macromolecules
Making and Breaking Macromolecules (cont.)
 Hydrolysis (digestion)
 Macromolecules are disassembled into their constituent parts by adding an –OH group to form i
b ddi O f
one subunit and an H to form the other subunit
 Thus adding a water molecule for every macromolecule that is disassembled
 Energy is released when the energy storing bonds are broken
Synthesis and Degradation
of Polymers
 Polymers ‐ large molecules consisting of long chains of repeating subunits (monomers)
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1. Carbohydrates
 Loosely defined group of molecules that contain C, H, and O in molecular ratio of 1C:2H:1O, with an empirical formula of (CH2O)n
 Are named based on the number of sugar units they contain
 Monosaccharides
one sugar unit (mono‐)
 Disaccharides
two sugar units (di‐)
 Polysaccharides
many sugar units (poly‐)
Monosaccharides
 Single sugar molecules
 Quite soluble and sweet to taste
 Play central role in energy storage
 Examples
E
l
 Glucose, fructose and galactose

Hexoses ‐ Six carbon atoms

Isomers of C6H12O6
 Ribose and deoxyribose 
Pentoses – Five carbon atoms

C5H10O5 & C5H10O4
Disaccharides
 Contain two monosaccharides joined by a covalent bond
 Soluble and sweet to taste
 Play a role in the transport of sugars
 Common disaccharides:
 Sucrose (table sugar)

1 glucose + 1 fructose joined by dehydration
 Maltose (malt sugar)

Two glucose units joined by dehydration
 Lactose (milk sugar)

1 glucose + 1 galactose joined by dehydration
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Synthesis and Degradation
of Maltose, a Disaccharide
Polysaccharides  Polymers of monosaccharides (a single long chain or a branched chain) consisting of repeating units of simple sugars, usually glucose
 Low solubility; not sweet to taste
 Common polysaccharides:
 Starches: Energy storage in plants
 Glycogen: Energy storage in animals
 Cellulose: Structural polysaccharide in plants
Starch  Form of carbohydrate used for short‐term energy storage in plants
 Polymer consisting of glucose subunits
 Starch occurs in two forms
 Amylose (unbranched chain)
 Amylopectin (branched chain)
 Plant cells store starch as granules in amyloplasts
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Structure of Starch
Glycogen  Form in which glucose subunits are stored as an energy source in animal tissues
 Similar in structure to plant starch but more extensively branched and more water soluble
 Stored mainly in liver and muscle cells
Structure of Glycogen
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Cellulose
 Cellulose
 Long, coiled insoluble polymer of glucose
 Glucoses connected differently than in starch
 Structural component of plants (fibers)
 The most abundant carbohydrate
 Indigestible by most animals
Structure of Cellulose
Other Carbohydrates
 Chitin
 Polymer of glucose
 Each glucose with an amino group
 Very resistant to wear and digestion
 Forms the exoskeletons of arthropods and cell walls of fungi
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2. Lipids
 Compounds soluble in nonpolar solvents, and relatively insoluble in water (hydrophobic)
 Consist mainly of carbon and hydrogen, with few yg
g
g p
oxygen‐containing functional groups
Types of Lipids: Triglycerides
 Triglycerides (Fats)
 Structure = glycerol + 3 fatty acids

y
3
g
Glycerol: a 3‐carbon alcohol with each carbon bearing a hydroxyl group

Fatty acids: long hydrocarbon chains (ranging from 4 to 36 carbons) ending in a carboxyl group

The 3 fatty acids of a triglyceride are not necessarily the same
Dehydration Synthesis of Triglyceride
 Three fatty acids attached to each glycerol molecule
 Carboxylic acid at one end
 Carboxylic acid connects to –OH on glycerol in dehydration reaction
y
Chapter 3: Organic Chemistry
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Triglycerides (cont.)  Functions
 Long‐term energy storage

Efficient energy storage molecules because of their high concentrations of C H bonds
concentrations of C‐H bonds
 Insulation 
The fat (blubber) beneath the skin in marine animals
 Cushioning

Excellent shock absorber and provides natural ‘cushioning’ to vital organs Saturated and Unsaturated Fatty Acids
 Saturated fats
 All internal C atoms are bound to at least two H atoms, no double bonds between C atoms

Results in maximum number of hydrogen atoms therefore, Results in ma
imum number of h drogen atoms therefore said to be saturated
 Tend to be straight and fit close together
 Found in animal fat and solid vegetable shortening
 Solid at room temperature

Example: butter
Saturated and Unsaturated Fatty Acids
 Unsaturated fats
 Double bonds between at least one pair of C atoms

Results in less than maximum number of hydrogen atoms therefore said to be unsaturated
therefore, said to be unsaturated
 Have low melting points because the fatty acids chains cannot closely align

Double bonds cause “kinks” or bends in the chains
 Most are liquid at room temperature

Example: vegetable oil
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Types of Fatty Acids
Phospholipids
 Derived from triglycerides
 Modified fats with two fatty acid chains rather than three
 Two fatty acids attached instead of three
T f tt id tt h d i t d f th
 Third fatty acid is replaced by a phosphate group

The fatty acids are nonpolar and hydrophobic

The phosphate group is polar and hydrophilic
 Phospholipids are amphipathic lipids, with one hydrophilic end and one hydrophobic end
Phospholipids (cont.)
 Molecules self arrange when placed in water
 Polar phosphate “heads” next to water
 Nonpolar fatty acid “tails” overlap and exclude water
 Spontaneously form double layer and a sphere
 Phospholipids are basic components of cell membranes

Phospholipid bilayer
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Phospholipid Bilayer in Cell Membranes
Steroids
 Steroids – lipids composed of four attached C rings
 Side chains distinguish one steroid from another
 Steroids of biological importance include:
 Cholesterol
 Hormones (e.g. reproductive, cortisol, etc.)
 Bile salts (emulsify fats)
 Found in eukaryotic cell membrane
 Plant cell membranes contain molecules similar to cholesterol
 High levels of cholesterol in the blood may contribute to cardiovascular disease
Steroid Diversity
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Waxes
 Long‐chain fatty acid bonded to a long‐chain alcohol
 High melting point
 Waterproof coating on leaves, bird feathers, mammalian skin and arthropod exoskeleton
 Resistant to degradation
3. Proteins
 Classification of proteins according to biological function
 Support – collagen in ligaments and tendons & keratin in nails and hair
 Enzymes – biological catalysts that accelerate chemical reactions within cells
 Transport – hemoglobin that carry oxygen in RBCs; channel & carrier membrane proteins
 Defense – antibodies that prevent infections
 Hormones – regulatory hormones that influence metabolism in cells (e.g. insulin)
 Motion – contractile proteins; actin and myosin in muscles, microtubules
Amino Acids
 Proteins are made up of various combinations of 20 types of repeating subunits called amino acids
 are joined together by peptide bonds
 are organic molecules
 consist of

two characteristic end groups

a side group (or side chain)
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Structure of Amino Acids
 Each amino acid has a central alpha carbon atom  Two end groups
 an amino group (NH2)
 a carboxyl group (COOH)
 A side (R group)
 bonded to the α carbon between the two end groups
 varies from one amino acid to another
 determines the unique chemical properties of the amino acid
Amino Acids in Proteins
 Amino acids are grouped by properties of their side chains
p
 Nonpolar side chains are hydrophobic
 Polar side chains are hydrophilic
 A side chain with a carboxyl group is acidic
 A side chain that accepts a hydrogen ion is basic
The Polypeptide Backbone
 Amino acids joined together end‐to‐end
 COOH of one amino acid covalently bonds to the NH2 of the next amino acid
Special name for this bond Peptide Bond  Special name for this bond ‐

2 amino acids bonded together – Dipeptide

3 amino acids bonded together – Tripeptide

Many amino acids bonded together – Polypeptide
 Characteristics of a protein are determined by composition and sequence of amino acids
 Virtually unlimited number of proteins
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Synthesis and Degradation of a Peptide
Four Levels of Protein Organization
 There are four main levels of protein organization:  Primary – refers to the linear sequence of amino acids that make up the polypeptide chain  Secondary – refers to the formation of a regular pattern of twists or folds of the polypeptide chain
 Tertiary – refers to the 3‐D shape formed by bending and twisting of the polypeptide chain
 Quaternary – refers to the 3‐D structure of resulting from two or more polypeptide chains interactions
Levels of Protein Structure
 Primary level
 The specific amino acid sequence producing a long chain with a COOH group on one end and NH2 group on th th
the other
 Specified by instructions in a gene
 Slight change in primary structure can be detrimental

Example: Sickle‐cell anemia
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Primary Structure of a Protein Levels of Protein Structure (cont.)
 Secondary level
 Results from H‐bonding between individual amino acids of the polypeptide chain  Two common patterns:

α ‐helix (helical coil) was the first pattern discovered

β ‐pleated sheet was the second pattern discovered
 Both types may occur in the same polypeptide chain
 Fibrous proteins are either mostly alpha helices or beta pleated sheets Secondary Structure
 α Helix  Hydrogen bonds form between every 4th amino acid  Basic structural unit of fibrous, elastic proteins (e.g. hair ,
p
( g
and horn)  β Pleated Sheet  Chain folded back with regions of chain parallel to itself  Hydrogen bonds hold it in this conformation  Spider silk and silkworm silk are mostly β pleated sheets Chapter 3: Organic Chemistry
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Secondary Protein Structure
Levels of Protein Structure (cont.)
 Tertiary level
 Overall 3‐D shape of an individual polypeptide chain
 Determined by four main factors involving interactions among R groups of the same polypeptide chain
 Four factors in tertiary structure:
• 3 weak interactions (hydrogen bonds, ionic bonds, and hydrophobic interactions) • Strong covalent bonds (disulfide bonds between SH groups of two cysteines)
 Denaturation – process by which a protein changes its shape (tertiary and secondary) or even unfolds when its “tolerance range” for some factor is exceeded
Levels of Protein Structure (cont.)
 Quaternary level
 3‐D structure resulting from two or more polypeptide chains interacting in specific ways to form a biologically active molecule
ti l
l
 Examples:

Hemoglobin, a globular protein consisting of 4 polypeptide chains (2 alpha chains and 2 beta chains) with a central heme (iron) unit 
Collagen, a fibrous protein with 3 helical polypeptide chains
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Quaternary Structure of Proteins
© 2009 Cengage - Wadsworth
4. Nucleic acids
 Nucleic acids
 long polymers of repeating subunits called nucleotides
 transmit hereditary information and determine what proteins a cell manufactures
 Two types
 DNA

Deoxyribonucleic acid
 RNA

Ribonucleic acid
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Nucleic acids
 Deoxyribonucleic acid (DNA)
 Double‐stranded helical spiral (twisted ladder)
 Serves as genetic information center (blueprint) in genes or chromosomes
 Specifies the amino acid sequence of proteins through the sequences of nucleotides
 Ribonucleic acid (RNA)
 Part single‐stranded, part double‐stranded
 Serves primarily in assembly of proteins
 In nucleus and cytoplasm of cell
The Nucleotides of Nucleic Acids
 Nucleotides are made up of three parts:
 A phosphate group (makes the molecule acidic)
 A five‐carbon sugar, either deoxyribose (in DNA) or ribose
b
(
(in RNA)
)
 A nitrogenous base (4 kinds in DNA, 3 kinds in RNA, 3 common to both

Nucleotide subunits connected end‐to‐end to make nucleic acid

Sugar of one connected to the phosphate of the next

Sugar‐phosphate backbone
Nitrogenous Bases
 Nitrogenous base may be either a double‐ring purine or a single‐ring pyrimidine
 DNA contains four nitrogenous bases:
 Two purines: adenine (A) and guanine (G)
 Two pyrimidines: cytosine (C) and thymine (T)
 RNA contains the purines adenine and guanine, and the pyrimidines cytosine and uracil (U)
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Structure of DNA and RNA
 DNA is double stranded with complementary base pairing; RNA is single stranded
 Complementary base pairing occurs where two strands of DNA are held together by hydrogen bonds between purine and pyrimidine bases
 The number of purine bases always equals the number of pyrimidine bases
 In DNA, thymine is always paired with adenine; cytosine is always paired with guanine; A + G = C + T
 Two strands of DNA twist to form a double helix; RNA does not form helices
Nucleotide Structure
DNA
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RNA
Comparison of DNA and RNA
Other Nucleic Acids
 Adenosine triphosphate (ATP)  Composed of adenine, ribose, and three phosphates
 Primary energy molecule of all cells
 In cells, one phosphate bond is hydrolyzed –
I ll h
h t b d i h d l d yields:
i ld

The molecule adenosine diphosphate (ADP)

An inorganic phosphate molecule pi

Energy
 Other high energy molecules nicotinamide adenine dinucleotide (NAD+) and flavin adenine dinucleotide (FAD+)
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ATP
Chapter 3: Organic Chemistry
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