Chapter 3

base

(1) A substance that can accept a hydrogen ion in solution. (Contrast with acid.) (2) The purine or pyrimidine attached to the sugar in a nucleoside. -The base is linked to the first carbon of the monosaccharide (termed the 1-prime or 1′ carbon), and the phosphate groups are linked to the 5′ carbon of the monosaccharide

substrates

(1) The molecule or molecules on which an enzyme exerts catalytic action. (2) The base material on which a sessile organism lives. -Substrate molecules bind to a particular site on the enzyme, called the active site, where catalysis takes place.

polynucleotides

-A nucleic acid strand consisting of more than 20 nucleotides. -which include the longest polymers in the living world. Some DNA molecules contain hundreds of millions of nucleotides.

An enzyme lowers the activation energy of a reaction in one of three ways:

-Inducing strain: Once a substrate has bound to its active site, an enzyme can cause bonds in the substrate to stretch, putting it in an unstable state. This causes the strained bonds to have higher potential energy (they are weaker), making them easier to break. -Substrate orientation: When free in solution, substrates are randomly moving from place to place, vibrating, rotating, and tumbling. They only rarely have the proper orientation to react when they collide. When bound to an enzyme, however, substrates are held in the correct orientation to bring the appropriate parts of the substrates together, facilitating bond breakage or formation. -Adding chemical groups: The side chains (R groups) of an enzyme's amino acids, or of its cofactor(s), may be directly involved in the reaction. For example, in acid-base catalysis, the acidic or basic side chains of the amino acids in the active site transfer H+ ions to or from the substrate, destabilizing a covalent bond in the substrate and permitting the bond to break.

The basic structures of DNA and RNA monomers differ in two respects:

-The monosaccharide in DNA is deoxyribose, whereas in RNA it is ribose. -DNA is composed of nucleotides with bases cytosine (C), thymine (T), adenine (A), and guanine (G). RNA has A, G, and C, but its fourth base is uracil (U not T).

These 20 amino acids can be grouped according to the properties conferred by their side chains:

-five amino acids have electrically charged side chains (+1 or −1), attract water (are hydrophilic), and attract oppositely charged ions. -Five amino acids have polar side chains (δ+, δ−) and tend to form hydrogen bonds with water and other polar or charged substances. These amino acids are also hydrophilic. -Seven amino acids have side chains that are nonpolar hydrocarbons or very slightly modified hydrocarbons. In the watery environment of the cell, these hydrophobic side chains may cluster together in the interior of the protein, or interact with lipids in membranes.

Important to realize three points here:

1.DNA replication and transcription depend on the base-pairing properties of the nucleotides. In both replication and transcription, complementary base pairing to a DNA template strand is used to synthesize the new nucleic acid molecule. The resulting new DNA or RNA strand is complementary to the existing DNA template strand. One implication of this is that the new strand will be in the opposite orientation as the template strand; if the template strand is 3′ to 5′ reading from left to right, then the new strand will be synthesized 5′ to 3′ going from left to right. 2.The entire DNA molecule is copied during DNA replication. Since DNA holds essential information, it must be replicated completely so that each new cell or new offspring receives a complete set of DNA from its parent (FIGURE 3.13A). 3.Gene expression is the transcription of specific DNA sequences into complementary RNA. Sequences of DNA that are transcribed into RNAs that are themselves functional, or that represent a template for protein synthesis, are called genes (FIGURE 3.13B). The complete set of DNA in a living organism is called its genome. However, not all DNA in the genome encodes genes, and not all genes are expressed to make protein. For example, in humans the gene that encodes the major protein in hair (keratin) is expressed only in skin cells. The genetic information in the keratin-encoding gene is transcribed into RNA and then translated into the protein keratin in these cells. In other tissues, such as the muscles, the keratin gene is not transcribed but other genes are—for example, the genes that encode proteins present in muscles but not in skin

kinases

A class of enzymes that catalyze the addition of phosphate groups to proteins.

Fatty Acid

A fatty acid consists of a long nonpolar hydrocarbon chain with a terminal polar carboxyl functional group (─COOH). RE: A molecule made up of a long nonpolar hydrocarbon chain and a polar carboxyl group. Found in many lipids.

Saturated Fatty Acid

A fatty acid in which all the bonds between carbon atoms in the hydrocarbon chain are single bonds(─C─C─C─C─)—that is, all the bonds are saturated with hydrogen atoms. (Contrast with unsaturated fatty acid.) Double bonds between carbon atoms (─C═C─) do not occur in a saturated fatty acid because all the available bonds to carbon are saturated with hydrogen atoms. Saturated fatty acid molecules are relatively straight molecules and thus are able to pack together tightly, like pencils in a box. As noted above, this allows molecular interactions and a relatively high melting point. Saturated fats are usually solid at human body temperature (37°C), for example.

Amphipathic

A fatty acid thus has two opposing chemical properties: a hydrophilic end and a long hydrophobic "tail." A molecule that is partly hydrophilic and partly hydrophobic is amphipathic.

Steroids

A four-ringed lipid molecule (examples include cholesterol in membranes and steroid hormones). They are an important class of lipids in plants and animals. Cholesterol is a steroid that is essential in animal membranes.

3.1 Macromolecules

A giant (molecular weight > 1,000) polymeric molecule. The macromolecules are the proteins, polysaccharides, nucleic acids, and lipids. Note that lipids are included here because they often occur as large aggregates of smaller molecules. These macromolecules are formed by exergonic reactions that form covalent bonds between smaller molecules.

polypeptides

A large molecule made up of many amino acids joined by peptide linkages. Large polypeptides are called proteins. A functional protein may be made up of one or more polypeptides.

peptides

A molecule containing two or more amino acids.

oligonucleotides

A nucleic acid made up of 20 or fewer monomers. -In living systems, oligonucleotides are primarily RNA molecules and act to regulate the synthesis of new DNA as well as help regulate the expression of information encoded in DNA

nucleoside

A nucleotide without the phosphate group; a nitrogenous base attached to a sugar. -a nucleotide is a nucleoside mono-, di-, or triphosphate

oligopeptides

A peptide made up of fewer than 20 amino acids

Receptor proteins

A protein that can bind to a specific molecule (ligand), or detect a specific stimulus, within the cell or in the cell's external environment.

regulatory proteins

A protein that controls the rate of a biological process.

Storage proteins

A protein that functions to store amino acids for protein synthesis or energy.

Structural proteins

A protein that is involved in physical stability or movement of a cell or organism.

Signal proteins

A protein that is used to communicate with other cells to elicit a response.

Defensive proteins

A protein that recognizes and responds to substances or particles that invade an organism from the environment.

metabolic pathway

A series of enzyme-catalyzed reactions so arranged that the product of one reaction is the substrate of the next.

Triglycerides

A simple lipid in which three fatty acids are combined with one molecule of glycerol. The lipids with which you are most familiar, fats and oils, are triglycerides. Triglycerides are excellent stores for chemical-bond energy.

Monosaccharides

A simple sugar. Oligosaccharides and polysaccharides are made up of monosaccharides. Monosacchrides consist of five or six carbon atoms, termed pentoses and hexoses respectively. Different monosaccharides often have the same chemical formula and represent structural or stereoisomers.

allosteric site

A site on a protein (often on a polypeptide that is distinct from the one containing the active site) that can bind a substance that alters the conformation of the protein, changing its functionality.

Lipids

A structurally and functionally diverse group of compounds defined by their insolubility in water. They are nonpolar, hydrophobic molecules (insoluble in water) that include fats, oils, waxes, steroids, and the phospholipids that make up biological membranes. Lipids contain mostly C─C and C─H nonpolar bonds, which have high chemical-bond energy compared with C─O and O─H bonds.

Bilayer

A structure that is two layers in thickness. In biology, most often refers to the phospholipid bilayer of membranes; a sheet two molecules thick, with water excluded from the core

Residues

A subunit of a macromolecule.

Glycerol

A three-carbon molecule with three hydroxyl functional groups (─OH); a component of phospholipids and triglycerides. These molecules are joined by condensations reactions.

irreversible inhibition

A type of inhibition in which an inhibitor permanently binds to the protein, rendering it nonfunctional. -This type of inhibition is rare in normal circumstances because it inactivates the enzyme.

genes

A unit of heredity. Used here as the unit of genetic function which carries the information for a polypeptide or RNA. -Gene expression is the transcription of specific DNA sequences into complementary RNA.

Phospholipid

Also contain fatty acids bound to glycerol; a lipid containing a phosphate group; an important constituent of cellular membranes. (See lipids.) However, in phospholipids a charged phosphate-containing molecule replaces one of the fatty acids, making phospholipids amphipathic. The charged phosphate-containing functional group (there are several different kinds in different phospholipids) attracts polar water molecules, while the two fatty acids are hydrophobic and aggregate together and with other hydrophobic substances.

phosphatases

An enzyme that removes phosphate groups from proteins. Protein kinases and phosphatases are common across species.

enzyme-substrate complex (ES)

An intermediate in an enzyme-catalyzed reaction; consists of the enzyme bound to its substrate(s). -The binding of substrate(s) (S) to the active site of an enzyme (E) produces an enzyme-substrate complex (ES) which is held together by one or more means, such as hydrogen bonding, ionic bonds, van der Waals interactions, or temporary covalent bonding. -The enzyme (E) is in the same chemical form at the end of the reaction as it was at the beginning. While bound to the substrate(s), it may change chemically, but by the end of the reaction it has been restored to its initial form and is ready to catalyze the same reaction again.

amino acids

An organic compound containing both NH2 and COOH groups, and one of 20 different side chains (in common amino acids). Peptides are polymers of amino acids. Thus amino acids have both acidic and basic properties -The central carbon atom of an amino acid—the α (alpha) carbon—has four available electrons for covalent bonding. In all amino acids, two of the electrons are occupied by the two functional groups noted above, and a third is occupied by a hydrogen atom. The fourth bonding electron is shared with the R group, or side chain, that differs in each amino acid.

ligand

Any molecule that binds to a receptor site of another (usually larger) molecule. Ligands are usually signals that bind to receptors.

Carotenoids

Are lipids that can absorb energy from particular wavelengths of light (e.g., β-carotene in plants and vitamin A in animals).

Glycosidic bond/linkage

Bond between carbohydrate (sugar) molecules through an intervening oxygen atom (—O—).(—O—).Also called glycosidic linkage. RE: Two hydroxyl (─OH) groups are involved in the reaction, which produces a molecule of water: A−OH+HO−B→A−O−B+H2O

Polymer

Carbohydrates, nucleic acids, and proteins are polymers, large molecules formed by covalent bonds between smaller molecules called monomers.

3.5 Enzymes

Catalytic molecules that increase the rate of biochemical reactions. -In almost all of the thousands of chemical reactions occurring in a cell at a particular time, activation energy is lowered by enzymes -An enzyme can change the rate of a reaction substantially by reducing the activation energy

conformational change

Change in the shape of a protein, which can affect the protein's function.

nucleotide

Consists of three components: a monosaccharide (the pentose ribose or deoxyribose), a nitrogen-containing base, and one to three phosphate groups.

Disulfide bridges

Disulfide bridges help stabilize the three-dimensional structure of proteins.

Brown Fat

Gets its color from iron-rich mitochondria and plays an important role in thermoregulation, particularly in infants. RE: In mammals, fat tissue that is specialized to produce heat. It has many mitochondria and capillaries, and a protein that uncouples oxidative phosphorylation.

Unsaturated Fatty Acid

In an unsaturated fatty acid, the hydrocarbon chain has one or more double bonds between carbon atoms (─C═C─). Linoleic acid, for example, has two double bonds near the middle of the hydrocarbon chain. This results in kinks to what otherwise is a linear, straight chain. Such kinks prevent the unsaturated molecules from packing together tightly, resulting in a lower melting temperature and the possibility of a fluid state at body temperature.

Tertiary structure

In reference to a protein, the relative locations in three-dimensional space of all the atoms in the molecule. The overall shape of a protein. (Contrast with primary, secondary, quaternary structures.) -Tertiary structure of a protein arises from bending and folding of the polypeptide chain, which results in a three-dimensional structure -it is the interactions between R groups—the amino acid side chains—that determine tertiary (and quaternary) structure. --Covalent disulfide bridges between cysteines. --Ionic interactions between charged side chains. These include ionic bonds between positive and negative charges on side chains. For example, arginine (which has a positively charged R group) and glutamic acid (which has a negatively charged R group) can stabilize a particular three-dimensional structure. Conversely, repulsion of like-charged side chains can prevent incorrect three-dimensional structures from forming. --Hydrogen bonds between side chains. --van der Waals interactions, which stabilize associations between hydrophobic side chains.

3.2 Carbohydrates

Large group of molecules with similar atomic compositions but that differ greatly in size, chemical properties, and biological functions; Organic compounds containing carbon, hydrogen, and oxygen in the ratio 1:2:11:2:1 (i.e., with the general formula Cm(H2O)nCm(H2O)n. Common examples are sugars, starch, and cellulose. Carbohydrates with 12 or fewer carbons are termed simple sugars

denatured

Loss of activity of an enzyme or a nucleic acid molecule as a result of structural changes induced by heat or other means. In many cases a denatured protein will return to its normal tertiary structure when it cools or when the denaturing chemicals are removed, demonstrating that all the information needed to specify the protein's unique shape is contained in its primary structure

Cofactors

Many proteins require an additional organic, nonprotein molecule or an inorganic ion, often a metal ion, in order to function. -These cofactors vary in how tightly they bind to the protein -Tightly bound cofactors include those that are covalently bound to the protein, in which case they are called prosthetic groups. -loosely bound cofactors often become chemically modified and leave the protein in order to be returned to their initial state. -Loosely bound cofactors that bind to enzymes are often termed coenzymes.

Mono- and Disaccharides

Mono- and disaccharides are the main carbohydrates in cells and can readily enter the pathways that break them down to release energy. Mono- and disaccharides can be covalently bonded to proteins or lipids, modifying their solubility and function. The monosaccharides ribose and deoxyribose (see Figure 3.5) are also a component of nucleotides that make up nucleic acid macromolecules (see Key Concept 3.3).

purine

One of the two types of double-ring nitrogenous bases in nucleic acids. Each of the purines—adenine and guanine—pairs with a specific pyrimidine.

pyrimidine

One of the two types of single-ring nitrogenous bases in nucleic acids. Each of the pyrimidines—cytosine, thymine, and uracil—pairs with a specific purine.

Lipoproteins

Phospholipids can form single-layer spherical structures called lipoproteins that have hydrophobic interiors and hydrophilic exteriors and which are used for transporting lipids in aqueous solutions. Lipids packaged inside a covering of protein so that they can be circulated in the blood.

3.3 Nucleic acids

Polymers that store, transmit, and express genetic (hereditary) information. RE: A polymer made up of nucleotides, specialized for the storage, transmission, and expression of genetic information. DNA and RNA are nucleic acids. -nucleic acids they contain just one phosphate group.

Transport proteins

Proteins that carry substances within an organism and across biological membranes.

catabolic

Referring to a synthetic reaction in which complex molecules are broken down into simpler ones and energy is released. (Contrast with anabolic.)

anabolic

Referring to a synthetic reaction in which simple molecules are linked to form more complex ones; requires an input of energy and captures it in the chemical bonds that are formed.

allosteric regulation

Regulation of the activity of a protein (usually an enzyme) by the binding of an effector molecule to a site other than the active site.

inhibitors

Regulatory molecules that bind to a protein (usually an enzyme) and prevent it from functioning (often by preventing binding of the substrate(s) of the enzyme).

White Fat

Serves to store energy and provide thermal insulation that helps regulate body temperature.

Proteolysis

Some proteins are nonfunctional because they are too long when first synthesized. To become functional, a part of the protein must be removed by breaking a particular peptide bond in a hydrolysis reaction—a process called proteolysis. -In some proteins, proteolysis does not result in activation but instead produces an inactive protein. Whether the result is activation or inactivation depends on the protein involved.

motor proteins

Specialized proteins that use energy to change shape and move cells or structures within cells.

complementary base pairing

The AT (or AU), TA (or UA), CG, and GC pairing of bases in double-stranded DNA, in transcription, and between tRNA and mRNA.

catalyze

The ability to increase the rate of a reaction without undergoing a chemical change. -It is important to note that like any catalyst, an enzyme does not cause a reaction to occur, but it increases the rate of the reaction. -The vast majority of enzymes are proteins, but a few important enzymes are RNA molecules called ribozymes.

Phospholipid Bilayer

The basic structural unit of biological membranes; a sheet of phospholipids two molecules thick in which the phospholipids are lined up with their hydrophobic "tails" packed tightly together and their hydrophilic, phosphate-containing "heads" facing outward. Also called lipid bilayer.

peptide bond

The bond between amino acids in a protein; formed between a carboxyl group and amino group (—CO—NH—)(—CO—NH—) with the loss of water molecules. Also called peptide linkage.

genome

The complete DNA (or in the case of some viruses, RNA) sequence for a particular organism or individual.

phosphodiester bond

The connection in a nucleic acid strand, formed by linking two nucleotides. Also called phosphodiester linkage.

DNA replication

The creation of a new strand of DNA in which DNA polymerase catalyzes the exact reproduction of an existing (template) strand of DNA. How the information in DNA is used to synthesize proteins involves two processes: transcription and translation.

R group

The distinguishing group of atoms of a particular amino acid. Also known as a side chain.

DNA (deoxyribonucleic acid)

The fundamental hereditary material of all living organisms. In eukaryotes, stored primarily in the cell nucleus. A nucleic acid using deoxyribose rather than ribose. -DNA stores information, and some of that information encodes instructions for building proteins. -DNA sequences also encode information for recognition by a variety of proteins that interact with DNA.

Monomers

The minimal repeating subunit of a macromolecule. (amino acids in proteins, nucleotides in nucleic acids, monosaccharides in polysaccharides). Which are often referred to as residues when in polymers.

active site

The region on the surface of an enzyme or ribozyme where the substrate binds, and where catalysis occurs.

primary structure

The specific sequence of amino acids in a protein. (Contrast with secondary, tertiary, quaternary structure.)

quaternary structure

The specific three-dimensional arrangement of polypeptide subunits in a protein composed of multiple polypeptides. (Contrast with primary, secondary, tertiary structure.)

binding affinity

The strength of the interaction between a ligand and the protein molecule to which it binds. -higher affinity values are associated with more specific binding

Side Chain Modification

The structure of a protein can be modified by the covalent bonding of a chemical group to the side chain of one or more of its amino acids. The chemical modification of just one amino acid can alter the shape and function of a protein -Side chain modification is important in enzyme regulation

Transcription

The synthesis of RNARNA using one strand of DNADNAas a template.

Translation

The synthesis of a protein (polypeptide). Takes place on ribosomes, using the information encoded in messenger RNA.

RNA (ribonucleic acid)

These macromolecules are long, unbranched polymers containing from just a few to hundreds of millions of nucleotide monomers

Disaccharides

They are composed of two monosaccharides joined in a condensation reaction. -Sucrose, common table sugar, is an important disaccharide formed in plants from a glucose molecule and a fructose molecule.

Oligosaccharides

They are constructed from three to ten monosaccharides joined by glycosidic bonds. -Modified and unmodified oligosaccharides are often covalently bonded to proteins or lipids, which alter their function and solubility. -Oligosaccharides bound to the proteins and lipids on the outer surfaces of cells function as recognition signals.

Polysaccharides

They are large polymers of hundreds to thousands of monosaccharides connected by glycosidic bonds. RE: A macromolecule composed of many monosaccharides (simple sugars). Common examples are cellulose and starch. -Polysaccharides can be linear chains of monomers, attached via 1,4 glycosidic bonds, or they can be branched from 1,6 glycosidic bonds. The specific monomers that make up a polymer are often referred to as residues in polysaccharides and other macromolecules. -Linear chains of polysaccharides can align in close proximity and form hydrogen bonds with neighboring chains. Parallel alignment of polysaccharide chains allows them to form dense sheets or strong fibers. -The most abundant biological macromolecule on the planet is the polysaccharide cellulose, the major structural component of plant cell walls.

Proteins

They are polymers made up of tens to tens of thousands of monomers called amino acids. A compound consisting of one, or more polypeptides. Occurs with its polypeptide chains extended in fibrous proteins, or coiled into a compact macromolecule in enzymes and other globular proteins.

Starches

They are the principal energy storage compounds of plants, and glycogen is the principal energy storage compound in animals, fungi, and bacteria.

secondary structure

consists of regular, repeated spatial patterns in different regions of a polypeptide chain. -In reference to a protein, localized regularities of structure, such as the αα helix and the ββ pleated sheet. (Contrast with primary, tertiary, quaternary structure.) -There are two common types of secondary structure, both determined by hydrogen bonding between the amino acids that make up the primary structure:α (alpha) helix and β (beta) pleated sheet

β (beta) pleated sheet

formed from two or more sequences of amino acids that are extended and aligned in the polypeptide. The sheet is stabilized by hydrogen bonds between the ─NH groups and the ─CO groups on the two chains, which may be in the same or opposite directions.

α (alpha) helix

right-handed like the threads on a screw. The R groups extend outward from the peptide backbone of the helix. The coiling results from hydrogen bonds that form between the ─NH group on one amino acid and the ─CO group on another within the same turn of the helix

3.4 Polypeptides

the fourth and final type of biological macromolecule we will discuss in this chapter. In terms of structural and functional diversity, they are at the top of the list. Compared with proteins, the lipids, carbohydrates, and nucleic acids are relatively inactive in cells.