BIOLOGY II

Chapter 5 Notes

I. Most macromolecules are polymers

What is a macromolecule?

(1) There is a natural hierarchy of structural level in biological organization

(2) As one moves up the hierarchy, new properties emerge because of interactions among subunits at the lower levels

(3) Form fits function

Polymer- Large molecule consisting of many identical or similar subunits connected

together; complex sugars (disaccharides)

Monomer- Subunit or building block molecule of a polymer; simple sugar

(monosaccharide)

Macromolecule- Large organic polymer (carbohydrates)

There are four classes of macromolecules in living organisms:

1. Carbohydrates

2. Lipids

3. Proteins

4. Nucleic Acids

Most polymerization reactions in living organisms are condensation reactions.

Polymerization reactions- link two or more small with repeating structural units

Condensation reactions- monomers are covalently linked, net removal of water

molecule for each covalent linkage

-Requires energy

-Process requires biological catalysts or enzymes

Hydrolysis- breaks covalent bonds between monomers by the addition of water

molecules

-Digestive enzymes catalyze hydrolytic reactions which break apart large

food molecules into monomers that can be absorbed into the bloodstream

II. A limitless variety of polymers can be built from a small set of monomers

Structural variation of macromolecules is the basis for the enormous diversity of life

-Unity in life as there are only about 40-50 common monomers used to construct

macromolecules

-Diversity in life as new properties emerge when these universal monomers are arranged in different ways

III. Organisms use carbohydrates for fuel and building material

Carbohydrates- organic molecules made of sugars and their polymers

A. Monosaccharides- Simple sugar in which C,H, and O occur in the ration of (CH₂O)

Ø are major nutrients for cells

Ø Can be produced by photosynthetic organisms from CO₂, H₂O, and sunlight

Ø Store energy in their chemical bonds which is harvested by cellular respiration

Ø Their carbon skeletons are raw material for other organic molecules

Characteristics of a sugar:

1. An –OH group is attached to each carbon except one, which is double bonded

to an oxygen (carbonyl)

Aldehyde Ketone

Terminal carbon forms a Carbonyl group is within

double bonds with oxygen the carbon skeleton

2. Size of the carbon skeleton varies from 3 to 7 carbons. The most common monosaccharides are:

Classification	Number of Carbons	Example
Triose Pentose Hexose	3 5 6	Glyceraldenhyde Ribose Glucose

3. Special arrangements around asymmetric carbons may vary. For example.

glucose and galactose are enantiomers

The small difference between isomers affects molecular shape which gives these molecules distinctive biochemical properties.

4. In aqueous solutions, monosaccharides form rings. Chemical equilibrium favors the ring structure

B. Disaccharides

Disacaccharides- A double sugar that consists of two monosaccharides

joined by a glycosidic linkage.

Glycosidic linkage- Covalent bond formed by a condensation reaction between two sugar monomers. For example, maltose

Examples of disaccharides:

Disaccharide	Monomers	General Comments
Maltose Lactose Sucrose	Glucose + Glucose Glucose + Galactose Glucose + Fructose	Sugar important in brewing beer Sugar present in milk Table sugar; most prevalent disaccharide; transport form in plants

C. Polysaccharides

Polysaccharides- Macromolecules that are polymers of a few hundred or

thousand monosaccharides

Ø Are formed by linking monomers in enzyme-mediated condensation reactions

Ø Have two important biological functions:

1. Energy storage (Starch and glycogen)

2. Structural support (Cellulose and chitin)

1. Storage Polysaccharides

Cells hydrolyze storage polysaccharides into sugars needed. Two most common storage polysaccharides are starch and glycogen

Starch- Glucose polymer that is a storage polysaccharide in plants

Ø Helical glucose polymer with 1-4 linkages

Ø Stored as granules within plant organelles called plastids

Ø Amylopectin is branched polymer

Ø Most animals have digestive enzymes to hydrolyze starch

Ø Major sources in the human diet are potato tubers and grains (e.g. wheat, corn, rice and fruits of other grasses)

Glycogen- Glucose polymer that is a storage polysaccharide in animals

Ø Large glucose polymer that is more highly branched that amylopectin

Ø Stored in the muscle and liver of humans and other vertebrates

2. Structural Polysaccharides

Structural polysaccharides include cellulose and chitin

Cellulose- Linear unbranched polymer

Ø A major structural component of plant cell walls

Ø Differs from starch (also a glucose polymer) it is glycosidic linkages

Starch	Cellulose
Glucose monomers are in a configuration (-OH group on carbon one is below the ring’s plane). Monomers are connected with a 1-4 linkage.	Glucose monomers are in bconfiguration (-OH group on carbon one is above the ring’s plane). Monomers are connected with a b 1-4 linkage.

Ø Cellulose and starch have different 3D shapes and properties as a result of differences in glycosidic linkages.

Ø Cellulose reinforces plant cell walls. Hydrogen bonds hold together parallel cellulose molecules in bundles of microfibrils.

Ø Cellulose cannon be digested by most organisms, including humans, because they lack an enzyme that can hydrolyze the b 1-4 linkage. (Exceptions are some symbiotic bacteria, other microorganisms and some fungi.)

Chitin- A structural polysaccharide that is a polymer of an amino sugar.

Ø Forms exoskeletons of arthropods

Ø Found as a building material in the cell walls of some fungi

Ø Monomer is an amino sugar, which is similar to beta-glucose with a nitrogen- containing group replacing the hydroxyl on carbon 2.

IV. Lipids are mostly hydrophobic molecules with diverse functions

Lipids- Diverse group of organic compounds that are insoluble in water, but will dissolve in nonpolar solvents (e.g. ether, chloroform, benzene). Important groups are fats, phosopholipids and steroids.

A. Fats

Fats- Macromolecules constructed from:

1. Glycerol, a three-carbon alcohol

2. Fatty acid (carboxylic acid)

Ø Composed of a carboxyl group at one end and an attached hydrocarbon chain (“tail”)

Ø Carboxyl functional group (“head”) has properties of an acid

Ø Hydrocarbon chain has a long carbon skeleton usually with an even number of carbon atoms (most have 16-18 carbons)

Ø Nonpolar C-H bonds make that chain hydrophobic and not water soluble

Ester Linkage- Bond formed between a hydroxyl group and a carboxyl group

Triacylglycerol- A fat composed of three fatty acids bonded to one glycerol by

ester linkages

Some characteristics of fat include:

Ø Fats are insoluble in water. The long fatty acids chains are hydrophobic because of the many nonpolar C-H bonds

Ø The source of variation among fat molecules is the fatty acid composition

Ø Fatty acids in a fat may all be the same, or some (or all) may differ

Ø Fatty acids may vary in length

Ø Fatty acids may vary in the number and location of carbon-to-carbon double bonds:

SATURATED FAT	UNSATURATED FAT
No double bonds between carbons in fatty acid tail Carbon skeleton of fatty acid is bonded to maximum number of hydrogens (saturated with hydrogens) Usually a solid at room temperature Most animal fats e.g. bacon grease, lard, and butter	One or more double bonds between carbons in fatty acid tail Tail kinks at each C=C, so molecules do not pack closely enough to solidify at room temperature Usually a liquid at room temperature Most plant fats e.g. corn, peanut, and olive oil

Ø In many commercially prepared food products, unsaturated fats are artificially hydrogenated to prevent them from separating out as oil (e.g. peanut butter and margarine)

Fats serves many useful functions, such as:

Ø Energy storage. One gram of fat stores twice as much energy as a gram of polysaccharide.

Ø More compact fuel reservoir that carbohydrate. Animals store more energy with less weight than plants

Ø Cushions vital organs in mammals (e.g. kidney)

Ø Insulates against heat loss (e.g. mammals such as whales and seals)

B. Phosopholipids

Phosopholipids- Compounds with molecular building blocks of glycerol, two fatty

acids (Important because they make up membrane boundaries)

Ø Hydrocarbon tails are hydrophobic and the polar head (phosphate group with attachments) is hydrophilic

Ø Cluster in water; One such cluster, a micelle (bubble theory), assembles so the hydrophobic tails turn towers the water-free interior; and the hydrophilic phosphate heads arrange facing outward in contact with water

Ø Are major constituents of cell membranes. At the cell surface, phospholipids form a bilayer held together by hydrophobic interactions among the hydrocarbon tails. Phospholipids in water will spontaneously form such a bilayer

Aqueous Solution

Hydrophilic heads-

point towards exterior

of bilayer

Hydrophilic tails-

point toward interior

of bilayer

C. Steroids

Steroids- Lipids which have four fused carbon rings with various functional

groups attached

Cholesterol, an important steroid:

Ø Is the precursor to many other steroids including vertebrate sex hormones and bile acids

Ø Is a common component of animal cell membranes

Ø Can contribute to atherosclerosis

V. Proteins are the molecular tools for most cellular functions

Polypeptide chains- polymers of amino acids are arranged in a specific linear

sequence and are linked by peptide bonds

Protein- a macromolecule that consists of one or more polypeptide chains folded

and coiled into specific conformations

Ø Are abundant, making up 50% or more of cellular dry weight

Ø Have important and varied functions in the cell:

1. structural support

2. storage (of amino acids)

3. transport (e.g. hemoglobin)

4. signaling (chemical messengers)

5. cellular response to chemical stimuli (receptor proteins)

6. movement (contractile proteins)

7. defense against foreign substances and disease-causing organisms (antibodies)

8. catalysts of biochemical reactions (enzymes)

Ø Vary extensively in structure; each type has unique 3D shape (conformation)

Ø Though vary in structure and function, are commonly made of only 20 amino acids monomers

V. A polypeptide is a polymer of amino acids connected in a specific sequence

Amino acid = building block molecule of a protein; most consist of an

asymmetric carbon, termed the alpha carbon, which is covalently

bonded to:

1. hydrogen atom

2. carboxyl group

3. amino group

4. variable R group (side chain) specific to each amino acid. Physical and chemical properties of the side chain determine the uniqueness of each amino acid

Amino acids contain both carboxyl and amino functional groups. One group acts as a weak acid and the other group acts as a weak base; can exist in three ionic states; pH of the solution determines which ionic state predominates

1. Nonpolar side groups (hydrophobic). Amino acids with nonpolar groups are less soluble in water

2. Polar side groups (hydrophilic). Amino acids with polar side groups are soluble in water.

Polar amino acids can be grouped further into:

a. uncharged polar

b. charged polar

>acidic side groups: dissociated carboxyl group gives these side groups a negative charge

>basic side groups: an amino acid with an extra proton gives these side groups a net positive charge

Peptide bond: covalent bond formed by a condensation reaction that links the

carboxyl group of one amino acid to the amino group of another

(like amino acids)

v has polarity with an amino group on one end (N-terminus) & a carboxyl group on the other (C- terminus)

v has a backbone of the repeating sequence: -N-C-C-N-C-C-

VI. A protein’s function depends on its specific conformation

Protein conformation- 3D shape of a protein

Native conformation- functional conformation of a protein found under normal biological

ü enables a protein to recognize and bind specifically to another molecule (e.g. hormone/receptor, enzyme/substrate, and anitbody/antigen)

ü is a consequence of the specific linear sequence of amino acids in the polypeptide

ü is produced when a newly formed polypeptide chain coils and folds spontaneously, mostly in response to hydrophobic interactions

ü is stabilized by chemical bonds and weak interactions between neighboring regions of the folded protein (disulfide bridges)

A. Four levels of protein structure

1. primary structure

2. secondary structure

3. tertiary structure

4. quaternary structure

1. Primary Structure

primary structure: unique sequence of amino acids in a protein

· determined by genes

· slight change can affect a protein’s conformation and function

· Frederick Sanger determined the amino acid sequence in insulin

2. Secondary Structure

secondary structure: regular, repeated coiling and folding of a protein’s polypeptide backbone

q contributes to a protein’s overall conformation

q stabilized by hydrogen bonds between peptide linkages in the protein’s backbone (carbonyl and amino groups)

q The major types of secondary structure are alpha (a) helix and beta (b) pleated sheet

a. Alpha (a) Helix

Alpha (a) Helix- secondary structure of a polypeptide that is a helical coil stabilized by hydrogen bonding between every fourth peptide bond (3.6 amino acids per turn)

¨ described by Linus Pauling and Robert Corey in 1951

¨ found in fibrous proteins (e.g. alpha –keratin and collage) for most of their length and in some portions of globular proteins

b. Beta (b) Pleated Sheet

Beta (b) pleated sheet- secondary protein structure which is a sheet of antiparallel chains folded into according pleats

· parallel regions are held together by either intrachain on interchain hydrogen bonds (between adjacent polypeptides)

· make up the dense core of many globular proteins (e.g. lysozyme) and the major portion of some fibrous proteins (e.g. fibroin, the structural protein of silk)

3.Teritary Structure

Tertiary structure- irregular contortions of a protein due to bonding between side chains (R groups); 3^rd level of protein structure superimposed upon primary and secondary structure

a. weak interactions

ü Hydrogen bonding between polar side chains

ü ionic bonds between charged side chains

ü hydrophobic interactions between nonpolar side chains in protein’s interior

hydrophobic interactions- (Hydro=water; phobos=fear) The clustering of hydrophobic molecules as a result of their mutual exclusion from water

b. covalent linkage

Disulfide bridges form between two cysteine monomers brought together by folding of the protein. This is a strong bond that reinforces conformation

4 .Quaternary Structure

Quaternary structure- structure that results from the interaction among several polypeptides (subunits) in a single protein

ü For example: collagen, a fibrous protein with three helical polypeptides supercoiled into a triple helix; found in animal connective tissue, collagen’s supercoiled quaternary structure gives it strength

ü Some globular proteins have subunits that fit tightly together. For example: hemoglobin, a globular protein that has four subunits (2 a chains and 2 b chains

B. What determines Protein Conformation?

A protein’s 3D shape is a consequence of the interactions responsible for secondary and tertiary structure.

o This conformation is influenced by physical and chemical environmental conditions

o If a protein’s environment is altered, it may become denatured & lose its native conformation

Denaturation- A process that alters a protein’s native conformation and biological activity. Proteins can be denatured by:

• Transfer to an organic solvent. Hydrophobic side chains, normally inside the protein’s core, move towards the outside. Hydrophilic side chains turn away from the solvent towards the molecule’s interior
• Chemical agents that disrupt hydrogen bonds, ionic bonds, and disulfide bridges
• Excessive heat. Increased thermal agitation disrupts weak interactions

The fact that some denatured proteins return to their native conformation when environmental conditions return to normal is evidence that a protein’s amino acid sequence (primary structure) determines conformation. It influences where and which interactions will occur as the molecule arranges into secondary and tertiary structure.

C. The Protein- Folding Problem

Even though primary structure ultimately determines a protein’s conformation, 3D shape is difficult to predict solely on the basis of amino acid sequence. It is difficult to find the rules of protein folding because:

§ Most protein through several intermediate stages in the folding process; knowledge of the final conformation does not reveal the folding process required to create it

§ A protein’s native conformation may be dynamic, alternating between several shapes

Using recently developed techniques, researchers hope to gain new insights into protein folding:

§ Biochemists can now track a protein as it passes through its intermediate stages during the folding process

§ Chaperone protein have just been discovered that temporarily brace a folding protein

Rules of protein folding are important to molecular biologists and the biotechnology industry. This knowledge should allow the design of proteins for specific purposes

VIII. Nucleic acids store and transmit hereditary information

Protein conformation is determined by primary structure. Primary structure, in turn, is determined by genes- hereditary units that consist of DNA, a type of nucleic acid.

There are 2 types of nucleic acids:

1. Deoxyribonucleic Acid (DNA)

§ Contains coded information that programs all cell activity

§ Contains directions for its own replacement

§ Is copied and passed from one generation of cells to another

§ In eukaryotic cells, is found primarily in the nucleus

§ Make up genes that contain instructions for protein synthesis. Genes do not directly make up proteins, but direct the synthesis of mRNA

2. Ribonucleic Acid (RNA)

§ Functions in the actual synthesis of proteins coded by DNA

§ Sites of protein synthesis are on ribosomes in the cytoplasm

§ Messenger RNA (mRNA) carries genetic message from the nucleus to the cytoplasm

§ The flow of genetic information goes from DNA to RNA to protein

Nucleus Cytoplasm

Genetic message is mRNA Genetic message

transcribed from DNA translated into a

onto mRNA protein

A-T A-U mRNA

C-G (DNA) C-G (RNA) t-RNA

rRNA

IX. A DNA strand is a polymer with an information-rich sequence of nucleotides

Nucleic acid- Polymer of nucleotides linked together by condensation reactions

Nucleotide- Building block molecule of a nucleic acid; made of (1) a 5-carbon sugar covalently bonded to (2) a phosphate and (3) a nitrogenous base

1. Pentose (5-Carbons Sugar)

There are two pentoses found in nucleic acids: ribose and deoxyribose

2. Phosphate

The phosphate group is attached to the number 5 carbons of the sugar

3. Nitrogenous Base

There are 2 families of nitrogenous bases:

Pyrimidine= Nitrogenous base characterized by a 6-membered ring made up of carbon a nitrogen atoms. For example:

Cytosine (C)

Thymine (T) –found only in DNA

Uracil (U)- found only in RNA

Purine= Nitrogenous base characterized by a 5-membered ring fused to a 6-member ring. For example: (double ringed)

Adenine (A)

Guanine (G)

Nucleotides have various functions:

§ Are monomers for nucleic acids

§ Transfer chemical energy from one molecule to another (e.g. ATP)

§ Are electron acceptors in enzyme-controlled redox reactions of the cell (e.g. NAD)

DNA is a polymer of nucleotides joined by phosphodiester linkages between the phosphate of on nucleotide and the sugar of the next

§ Results in a backbone with a repeating pattern of sugar-phosphate-sugar-phosphate

§ Variable nitrogenous bases are attached to the sugar-phosphate backbone

§ Each gene contains a unique linear sequence of nitrogenous bases which codes for a unique linear sequence of amino acids in a protein

X. Inheritance is based on precise replication of DNA

In 1953, James Watson and Francis Crick proposed the double helix as the 3D structure of DNA

• Consists of 2 nucleotide chains wound in a double helix
• Sugar-phosphate backbones are on the outside of the helix
• Nitrogenous bases are paired in the interior of the helix and are held together by hydrogen bonds
• Base-pairing rules are that adenine (A) always pair with thymine (T); guanine (G) always pairs with cytosine (C)
• 2 strands of DNA are complimentary and thus can serve as templates to make new complementary strands. It is this mechanism of precise copying that makes inheritance possible
• Most DNA molecules are long- with thousands or millions of base pairs

XI. We can use DNA and proteins as tape measures of evolution

Closely related species have more similar sequences of DNA and amino acids, than more distantly related species. Using this type of molecular evidence, biologists can deduce evolutionary relationships among species