Chapter 3 Biological Molecules

Carbohydrates, Lipids, and Nucleic Acids + Proteins

hydrocarbons

Consist of carbon and hydrogen.

Covalent bonds store considerable energy.

These are nonpolar → when functional groups ARE ADDED, THEY CONFER chemical properties to the molecule

Functional groups

Small, reactive groups of atoms which give larger molecules specific chemical properties

(Ex. hydroxyl, carbonyl, carboxyl, amino, phosphate, sulfhydryl)

Hydroxyl

(—OH) (Ex. Alcohols)

Polar

Hydrogen bonds with water, facilitating dissolving of organic molecules

Carbonyl

(C = O) (Ex. Aldehydes and Ketones)

Building blocks of carbohydrates + supply energy for cell activities

Carboxyl

(Ex. Carboxylic acids)

Give organic molecules acid properties (-OH group releases H+)

Amino

Acts as an organic base by accepting a proton (H+)

→ Converts from non-ionized to ionized

(Ex. Amines)

Ethyl alcohol

A type of alcohol

Acetaldehyde

A type of aldehyde

Phosphate

(Ex. Organic Phosphates)

Molecules that contain these act as weak acids

Sulfhydryl

(Ex. Thiols)

Easily converted into covalent bond → loses its hydrogen atom as it binds

In many reactions, two of these groups form a disulfide linkage

Isomers

Molecules with the same molecular or empirical formula but different molecular structures

Structural Isomers

Same chemical formula but arrangement of atoms are different

Example: glucose – aldehyde and fructose - Ketone

Stereoisomers

Differ in how groups attached

Examples are D-sugars and L-sugars

Enantiomers → mirror image molecules, chiral carbon

Polymer

built by linking monomers

Monomer

small, similar chemical subunits

Dehydration synthesis

Formation of large molecules by the removal of water

Monomers are joined to form polymers

Hydrolysis

Breakdown of large molecules by the addition of water

Polymers are broken down to monomers

Carbohydrates

Molecules with a 1:2:1 ratio of carbon, hydrogen, oxygen

C—H covalent bonds hold much energy

Monosaccharides

Simplest carbohydrate

(Ex. Glucose)

All occur in linear form

If they have 5+ carbons they can fold back and form a ring

α-glucose (Alpha glucose)

—OH group pointing below the plane of the ring

β-glucose (Beta glucose)

—OH group pointing above the plane

Disaccharides

Assembled from two monosaccharides covalently joined by a dehydration synthesis reaction

Ex. Maltose formed by a glycosidic bond that links two α-glucose molecules with oxygen

Maltose

Assembled from two α-glucose molecules (1 → 4 carbon linkage)

Sucrose

Formed from an α-glucose and fructose (1 → 2 linkage)

Lactose

Assembled from galactose and β-glucose (1 → 4 linkage)

Polysaccharides

Long chains (10+) of monosaccharides → linked through dehydration synthesis

May be linear, unbranched molecules or may contain branches which side chains of sugar units are attached

Ex. Amylose and Glycogen

Amylose

A plant starch

Formed from α-glucose units joined end to end in alpha (1 → 4) linkages

Glycogen

Found in animal tissues

Formed from glucose units joined in chains by α( 1 → 4 ) linkages

Side branches are linked to the chains by α(1 → 6) linkages (boxed in blue).

Cellulose

Primary fiber in plant cell walls

Formed from glucose units joined end to end by beta (1 → 4) linkages

Chitin

A reinforcing fiber in the external skeleton of arthropods and the cell walls of some fungi

Beta (1 → 4 linkage)

Lipids

Water-insoluble, primary nonpolar biological molecules composed of mostly hydrocarbons

Three common types: neutral, phospho-, and steroids

Neutral Lipids

Found in cells as energy-storage molecules and have no charged groups (nonpolar)

Two types:

Oils → liquid at biological temps

Fats → semisolid

Fatty Acid

A type of lipid that contains a single hydrocarbon chain with a carboxyl group (—COOH) at one end

Triglycerides

Form by dehydration synthesis between three-carbon glycerol (an alcohol) and three fatty acid side chains

→ ester linkage forms between -COOH group of the fatty acid and the -OH group of the glycerol

→ Polar groups of glycerol eliminated which forms a nonpolar molecule

Serve as energy reserves in animals

Saturated fatty acid

A fatty acid that binds the maximum number of hydrogen atoms

→ only single bonds exist between carbon atoms

Monounsaturated

Fatty acids with one double bond

Polyunsaturated

Fatty acids with more than one double bond

Unsaturated Fatty Acids

Fatty acids (such as vegetable oils) bend at a double bond and are more fluid at biological temperatures

Phospholipids

Composed of → Glycerol + 2 fatty acids (nonpolar “tails”) + a phosphate group (polar “head”)

Form all biological membranes

Four types → – Serine, ethanolamine, Choline, and Inositol

Micelles

Lipid molecules orient with polar (hydrophilic) head toward water and nonpolar (hydrophobic) tails away from water

Phospholipid bilayer

More complicated lipid structure where 2 layers form

→ Hydrophilic heads point outward

→ Hydrophobic tails point inward toward each other

The structural basis of membranes

Waxes

Formed when fatty acids combine with long-chain alcohols/hydrocarbon structures

Harder and less greasy than fats

Steroids

Lipids with structures based on a framework of four carbon rings

Sterols

The most common steroids

Have a single polar OH group linked to one end of the ring framework and a complex, nonpolar hydrocarbon chain at the other end

Ex. Cholesterol (picture shown)

Steroid hormones

Control development, behavior, and many internal biochemical processes

Examples: Sex hormones

→ Estradiol (an estrogen) → has an —OH

→ Testosterone → has an =O where the —OH was + an extra estradiol

Nucleic Acids

A polymer (ex. DNA and RNA)

Monomers → nucleotides that are connected by phosphodiester bonds

Nucleotide

Monomers that are sugar + phosphate + nitrogenous base

Connected by phosphodiester bonds

Nucleosides

A structure containing only a nitrogenous base and a five-carbon sugar

Nitrogenous base

Link covalently to a five-carbon sugar

Ex. Deoxyribose in DNA deoxyribonucleotides + Ribose in RNA ribonucleotides

Pyrimidines

Nitrogenous bases with one carbon-nitrogen ring

Ex. Uracil (U), thymine (T), and cytosine (C)

Purines

Nitrogenous bases with two carbon–nitrogen rings

Adenine (A) and guanine (G)

Deoxyribonucleic acid (DNA)

Encodes information for amino acid sequence of proteins

Double helix → 2 polynucleotide strands connected by hydrogen bonds

Base-pairing rules → A with T → G with C

Consist of polynucleotide chains, with one nucleotide linked to the next by a phosphodiester bond

DNA base pairs

Ribonucleic acid (RNA)

Exist mainly as single polynucleotide chains (singlestranded) → however, these molecules can fold back on themselves to form double-helical regions

The uracil (U) base takes the place of thymine (T), forming A–U base pairs

adenosine triphosphate (ATP)

Primary energy currency of the cell

A type of nucleotide

NAD+ and FAD+

Electron carriers for many cellular reactions

A type of nucleotide

Proteins

Polymers of amino acid monomers → contain an animo and a carboxyl group

Amino Acids

TWENTY common ones that get grouped into five classes based on side groups

→ nonpolar, polar, charged (positive or negative charge)

Many chemical groups contain reactive functional groups, such as —NH2, —OH, —COOH, or —SH, which interact with other atoms in the same protein or outside the protein

All of them can act as acids or bases

Peptide Bonds

Link amino acids into polypeptide chains (the subunits of proteins)

Formed by a dehydration synthesis reaction between the —NH2 group of one amino acid and the —COOH group of another amino acid

Polypeptide Chain

Has an N-terminal end and a C-terminal end

→ New amino acids are linked only to the C-terminal end

Nonpolar Amino Acids

Uncharged Polar Amino Acids

Negatively Charged Amino Acids

Positively Charged Amino Acids

Primary structure

The precise sequence in which amino acids are linked

Changing even a single amino acid alters secondary, tertiary, and quaternary structures – which can alter or destroy the biological function of a protein

Secondary structure

The amino acid chain (primary structure) is folded into arrangements that form the protein’s structure

alpha (α) helix → twisted into a regular right-hand spiral

beta (β) strand → zigzags in a flat plane, forming a sheet

→ Most proteins have segments of both arrangements

Tertiary structure

Gives a protein its overall three-dimensional shape (conformation)

Determines a protein’s function and chemical activity and solubility

Quaternary structure

The presence and arrangement of two or more polypeptide chains

Hydrogen bonds, polar and nonpolar attractions, and disulfide linkages hold the multiple polypeptide chains together

The Random Coil

Has an irregularly folded arrangement

Segments of this provide flexible sites that allow α-helical or β-strand segments to bend or fold back on themselves

→ also act as “hinges” that allow major parts of proteins to move with respect to one another

Denaturation

Unfolding a protein from its active conformation so that it loses its structure and function

Caused by chemicals, changes in pH, or high temperatures

For some proteins it’s permanent and for others it’s reversible

Chaperonins

“Guide proteins” that bind temporarily with newly synthesized proteins, directing their conformation toward the correct tertiary structure and inhibiting incorrect arrangements

Domains

The large subdivision caused by folding of the amino acid chain(s)

In proteins with multiple functions, individual functions are often located in different ____.

Protein Combinations

• Proteins link with lipids to form lipoproteins, which form parts of cell membranes

• Proteins link with carbohydrates to form glycoproteins, which function as enzymes, antibodies, recognition and receptor molecules, and parts of extracellular supports

• Proteins link with nucleic acids to form nucleoproteins, which form structures such as chromosomes

Uracil

(It is a Pyrimidine)

Thymine

(It is a Pyrimidine)

Cytosine

(It is a Pyrimidine)

Adenine

(It is a Purine)

Guanine

(It is a Purine)

Alanine

A Nonpolar Amino Acid

Glycine

A Nonpolar Amino Acid

Isoleucine

A Nonpolar Amino Acid

Phenylalanine

A Nonpolar Amino Acid

Methionine

A Nonpolar Amino Acid

Cysteine

A charged polar amino acid

Tyrosine

A charged polar amino acid

Aspartic Acid

A negatively charged amino acid

Histidine

A positively charged amino acid