Biology Test 1

If a protein is heated slowly and moderately, the heat energy will disrupt only the weak interactions, causing the secondary and tertiary structure to break down. The protein is then said to be

denatured

structural isomers

differ in how their atoms are joined together

Structural proteins

(provide physical stability and movement)

A comparison of native (untreated) and denatured proteins

- Native proteins are compact; denatured proteins have a larger volume - Native proteins exist in one, preferred shape; denatured proteins can take many shapes - Native proteins have hydrogen bonds that stabilize the structure internally; denatured proteins have hydrogen bonds on the exterior, to water

two characteristics of the peptide bond are especially important in the three-dimensional structures of proteins

1. in the C-N linkage, the adjacent alpha carbons are not free to rotate fully, which limits the folding of the polypeptide chain 2. The oxygen bound to the carbon in the carboxyl group carries a slight negative charge, whereas the hydrogen bound to the nitrogen (N-H) in the amino group is slightly positive. This asymmetry of charge favors hydrogen bonding within the protein molecule itself and between molecules. These bonds contribute to the structures and functions of many proteins.

Transport proteins

Bind and carry substances within the organism

Motor proteins

Cause movement of structures in the cell

Signaling proteins

Control physiological processes

Seven amino acids have side chains that are nonpolar and thus hydrophobic

In the watery environment of the cell, these hydrophobic groups may cluster together in the interior of the protein

the beginning of a polypeptide is the amino group of the first amino acid added to the chain and is known as the

N terminus

Receptor proteins

Receive and respond to chemical signals

Defensive proteins

Recognize and respond to nonself substances

Membrane transporters

Regulate passage of substances across cellular membranes

Storage proteins

Store amino acids for later use

Hexoses

a group of structural isomers with the formula C6H12O6. Common hexoses are glucose, fructose, mannose, and galactose

glycerol

a small molecule with three hydroxyl (-OH) groups

The reverse of a condensation reaction is a

hydrolysis reaction. They result in the breakdown of polymers into their component monomers. Water reacts with the covalent bonds that link the polymer together. For each covalent bond that is broken, a water molecule splits into two ions (H+ and OH-) which become the products

Waxes

on plants can help them retain water and exclude pathogens. honeycombs are made of wax. waxes are substances that are hydrophobic and plastic, or malleable, at room temperature. Each wax molecule consists of a saturated, long-chain fatty acid and a saturated, long-chain alcohol joined by an ester linkage. The result is a very long molecule with 40-60 CH2 groups.

most abundant protein

rubisco

beta pleated sheet

A beta pleated sheet is formed from two or more polypeptide chains that are almost completely extended and aligned. The sheet is stabilized by hydrogen bonds between the N-H groups on one chain and the C=O groups on the other. A beta pleated sheet may from between separate polypeptide chains or between different regions of a single polypeptide chain that is bent back on itself. Many proteins contain regions of both alpha helix and beta pleated sheet in the same polypeptide chain.

linking amino acids involves a reaction between

carboxyl and amino groups attached to the alpha carbon. the carboxyl group of one amino acid reacts with the amino group of another undergoing a condensation reaction that forms a peptide linkage.

Phospholipids form

biological membranes. Fatty acids have a hydrophilic end and a hydrophobic tail. It is part hydrophobic and parthydrophilic making it amphipathic. Phospholipids contain fatty acids bount to glycerol by ester linkages. Any one of several phosphate-containing compounds replaces the first or third fatty acids, giving phospholipids amphipathic properties. The phosphate group has a negative electric charge so this portion is hydrophilic. The two fatty acids are hydrophobic. The phospholipids can form a bilayer: a sheet two molecules thick, with water excluded from the core.

Each amino acid has both a

carboxyl functional group and an amino functional group attached to the same carbon atom, called the alpha carbon. Also attached to the alpha carbon atom are a hydrogen atom and a side chain, or R group

the end of a polypeptide chain is the

carboxyl group of the last amino acid added; this is the C terminus

Enzymes

catalyze (speed up) biochemical reactions

most abundant carbohydrate

cellulose

functional group

has specific chemical properties and when it is attached to a larger molecule, it confers those properties on the larger molecule. One of these properties is polarity

Lipids

hydrocarbons that are insoluble in water because of their many nonpolar covalent bonds. roles: - fats and oils store energy - phospholipids play important strcutural roles in cell membranes - carotenoids and chlorophylls help plants capture light energy -steroids and modified fatty acids play regulatory roles as hormones and vitamins -fat in animal bodies serve as thermal insulation - a lipid coating around nerves provides electrical insulation - oil or wax on the surfaces of skin, fur, feathers, and leaves repels water and prevents excessive evaporation of water from terrestrial animals and plants

The condensation reactions that produce the different kinds of polymers differe in detail, but

in all cases polymers form only if water molecules are removed and energy is added to the system

the specificity of protein depends on two general properties of the protein:

its shape, and the chemistry of its exposed surface groups

polymers containing thousands or more atoms are called

macromolecules

fatty acid

made up of a long nonpolar hydrocarbon chain and an acidic polar carboxyl group (COOH). These chains are very hydrophobic because of their abundant C-H and C-C bonds, which have similar electronegativity values making them nonpolar

Galactosamine

major component of cartilage, the material that forms caps on the ends of bones and stiffens the ears and nose

each kind of biological molecule is made up of monomers with similar chemical structures:

- proteins are formed from different combinations of 20 amino acids, all of which share chemical similarities - carbohydrates can form giant molecules by linking together chemically similar sugar monomers (monosaccharides to form polysaccharides) -nucleic acids are formed from four kinds of nucleotide monomers linked together in long chains -lipids also form large structures from a limited set of smaller molecules, but in this case noncovalent forces maintain the interactions between the lipid monomers that are held together by covalent bonds

Four categories of biologically important carbohydrates defined by the number of monomers

1. Monosaccharides - such as glucose, are simple sugars. They are the monomers from which the larger carbohydrates are constructred 2. Disaccharides - consist of two monosaccharides linked together by covalent bonds. The most familiar is sucrose, which is made up of covalently bonded glucose and fructose molecules 3. Oligosaccharides are made up of several (3-20) monosaccharides 4. Polysaccharides such as starch, glycogen, and cellulose, are polymers made up of hundreds or thousands of monosaccharides

two major situations when a polypeptide chain can bind to the wrong substance

1. just after the protein is made it might present a surface that binds the wrong molecule because it has not folded completely 2. following denaturation. before a protein refolds it may present a surface that binds the wrong molecule

Four levels of protein structure

1. primary - amino acids monomers are joined, forming polypeptide chains. Stabilized by peptide bonds 2. secondary - polypeptide chains may form alpha helices or beta pleated sheets. Stabilized by hydrogen bonds 3. tertiary - polypeptides fold, forming specific shapes. Stabilized by hydrogen bonds; disulfide bridges hydrophobic interactions 4. quaternary - two or more polypeptides assemble to form larger protein molecules. Stabilized by hydrogen bonds, disulfide bridges, hydrophobic interactions; ionic interactions

FIve amino acids have polar side chains

They are also hydrophilic and attract other polar or charged molecules

Amino acids can exist as optical isomers called

D-amino acids and L-amino acids. Only L-amino acids are commonly found in the proteins of most organisms and their presence is an important chemical signature of life

Gene regulatory proteins

Determine the rate of expression of a gene

Five amino acids have electrically charged (ionized side chains at pH levels typical of living cells

These side chains attract water (are hydrophilic) and attract oppositely charged ions of all sorts

Catotenoids

a family of light-absorbing pigments found in plants and animals. Beta-carotene is one of the pigments that traps light energy in leaves during photosynthesis. In humans a beta carotene can be broken down into two vitamin A molecules. Vitamin A is used to make the pigment cis-retinal which is required for vision. Carotenoids are responsible for the colors of carrots, tomatoes, punpkins, etc.

Steroids

a family of organic compounds whose multiple rings are linked through shared carbons. The steroid cholesterol is an important constituent of membranes, helping maintain membrane integrity. Other steroids function as hormones: chemical signals that carry messages from one part of the body to another. Cholesterol is synthesized in the liver and is the starting material for making steroid hormones such as testosterone and estrogen

alpha helix

a right-handed coil that turns in the same direction as a standard wood screw. The R groups extend outward from the peptide backbone of the helix. The coiling results from hydrogen bonds that form between the sigma+ hydrogen of the N-H of one amino acid and the sigma- oxygen of the C=O of another. When this pattern of hydrogen bonding is established repeatedly over a segment of the protein, it stabilizes the coil

Amino acids are simultaneously

acids and bases

Proteins undergo covalent modifications

after it is made, 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.

In saturated fatty acids

all the bonds between the carbon atoms in the hydrocarbon chain are single bonds. All the bonds are saturated with hydrogen atoms. These fatty acid molecules are relatively straight and pack together tightly

Starches

comprise a family of large molecules with similar structures. While all starches are polysaccharides of glucose with alpha-glycosidic linkages, the different starches can be distinguished by the amount of branching that occurs at carbons 1 and 6. Starch is the prinipal energy storage compound of plants. Starch readily binds water. However, when water is removed, hydrogen bonds form between the unbranched polysaccharide chains, which then aggregate. These aggregates are broken up when starch is heated, breaking the hydrogen bonds. The starch becomes less solid and crystalline and water is absorbed, making the starch even more amorphous.

Polymers are formed from monomers by a series of

condensation reactions (dehydration reactions)

secondary structure

consists of regular, repeated spacial patterns in different regions of a polypeptide chain. There are two basic types of secondary structure, both determined by hydrogen bonding between the amino acids that make up the primary structure. the alpha helix and the beta pleated sheet.

quaternary structure

consists of subunits. The quaternary structure results from the ways in which these subunits bind together and interact

polymers

constructed by the covalent bonding of smaller moleucles called monomers

Chemically modified carbohydrates

contain additional functional groups.

Three amino acids - cysteine, glycine, and proline are special cases

cysteine side chain - has a terminal SH group, can react with another cystein side chain in an oxidation reaction to form a covalent bond. Such a bond, called a disulfide bridge or disulfide bond, helps determine how a polypeptide chain folds glyceine side chain - consists of a single hydrogen atom. It is small enough to fit into tight corners in the interiors of protein molecules where larger side chains could not fit proline side chain - possesses a modified amino group that lacks a hydrogen atom and instead forms a covalent bond with the hydrocarbon side chain, resulting in a ring structure. This limits both its hydrogen-bonding ability and its ability to rotate around the alpha carbon, So proline is often found where a protein bends or loops

Some lipids have roles in

energy conversion, regulation, and protection

Pentoses

five-carbon sugars. Two pentoses are of particular biological importance: the backbones of the nucleic acids RNA and DNA contain ribose and deoxyribose, respectively. These two pentoses are not isomers of each other; one oxygen atom is missing from carbon 2 in deoxyribose.

tertiary structure

formed by bending and folding. Tertiary structure is a macromolecule's definitive three-dimensional shape, often including a buried interior as well as a surface that is exposed to the environment. The exposed outer surfaces present functional groups capable of interacting with other molecules in the cell. For tertiary structure, the interactions between R groups and the environment are key. A protein folds into its final shape in a way that maximizes all the interactions noted and minimizes inappropriate interactions, such as two positively charged residues (a term identifying monomers in a polymer) being near one another, or a hydrophobic residue being near water.

The side chains (r groups) of amino acids contain

functional groups that are important in determining the three-dimensional structure and thus the function of the protein

all living cells contain the monosaccharide

glucose; it is the blood sugar used to store and transport energy in humans. It is used as an energy source, breaking it down through a series of reactions that converts stored energy to more usable chemical energy and produce carbon dioxide. It exists in straight chains and in ring forms. The ring form predominate in virtually all biological circumstances because they are more stable in water. There are two versions of the glucose ring, called alpha and beta glucose, which differ only in the orientation of the -H and -OH groups attached to carbon 1. The alpha and beta forms interconvert and exist in equilibrium when dissolved in water.

The disaccharides, oligosaccharides, and polysaccharides are all constructed from monosaccharides that are covalently bonded together by condensation reactions that form

glycosidic linkages. A single glycopsidic linkage between two monosaccharides forms a disaccharide. The disaccharides maltose and cellobiose are made from two glucose molecules. Maltose and cellobiose are structural isomers but have different enzymes in biological tissues. Oligosaccharides contain several monosaccharides bound by glycosidic linkages at various sites. Many oligosaccharides have additional functional groups, which give them special properties. Oligosaccharides are often covalently bonded to proteins and lipids on the outer cell surface, where they serve as recognition signals. The different human blood groups get their specificities from oligosaccharide chains.

carbohydrates

make up a large group of molecules that all have similar atomic compositions but differ greatly in size, chemical properties, and biological functions. Usually have the general formula (C1H2O1)n four major biochemical roles 1. They are a source of stored energy that can be released in a form usable by organisms 2. They are used to transport stored energy within complex organisms 3. They serve as carbon skeletons that can be rearranged to form new molecules 4. They form extracellular assemblies such as cell walls that provide structure to organisms

Isomers

molecules that have the same chemical formula but with the atoms arranged differently

most abundant lipid

monogalactosyl diglyceride in leaves

optical isomers

occur when a carbon atom has four different atoms or groups of atoms attached to it. This pattern allows for two different ways of making the attachments, each the mirror image of the other

Proteins

polymers made up of 20 amino acids in different proportions and sequences. They consist of one or more polypeptide chains - unbranched (linear) polymers of covalently linked amino acids. Variation in the sequences of amino acids in the polypeptide chains allows for the vast diversity in protein structure and function. Each chain folds into a particular three-dimensional shape that is specified by the sequence of amino acids present in the chain

Cellulose

predominant component of plant cell walls. It is a polysaccharide of glucose with its individual monosaccharides connected by Beta rather than by alpha glycosidic linkages. It is chemically more stable than starch because of its Beta glycosidic linkages. This makes cellulose an excellent structural material that can withstand harsh environmental conditions without substantial change.

Chitin

principal structural polysaccharide in the external skeletons of insects and many crustaceans, and a component of the cell walls of fungi

chaperones

protect the three-dimensional structures of other proteins

Four kinds of molecules are characteristics of living things

proteins, carbohydrates, lipids, and nucleic acids

triglycerides

simple lipids. triglycerides that are solid at room temperature are called fats. liquid at room temperature are called oils. they are composed of two types of building blocks: three fatty acid molecules and one molecule of glycerol. making a triglyceride involves three condensation reactions. In each reaction, the carboxyl group of a fatty acid bonds with a hydroxyl group of glycerol, resulting in a covalent bond called an ester linkage and the release of a water molecule. The three fatty acids need not all have the same hydrocarbon chain length or structure

Vitamins

small molecules that are not synthesized by the human body or in some cases are synthesized in inadequate amounts and so much be acquired from the diet.

Polysaccharides

store energy and provide structural materials. In contrast to polypeptides, polysaccharides are not necessarily linear chains of monomers. Each monomer unit has several sites that are capable of forming glycosidic linkages, and thus branched molecules are possible.

Chemistry

the exposed R groups on the surface of a protein permit chemical interactions with other substances. Three types of interactions may be involved: ionic, hydrophobic, or hydrogen bonding

Condensation reactions result in

the formation of covalent bonds between monomers. A molecule of water is released with each covalent bond formed

In unsaturated fatty acids

the hydrocarbon chain contains one or more double bonds. The double bonds create kinks which prevent the unsaturated fat molecules from packing together tightly. The kinks are important in determining the fluidity and melting points of lipids. Animal fat has long chain saturated fatty acids packed tightly together and are usually solid and have high melting points. Plants have short or unsaturated fatty acids and pack together poorly and have low melting points and are usually liquids at room temperature. Fatty acids are excellent storehouses for chemical energy.

primary structure

the precise sequence of amino acids in a polypeptide chain held together by peptide bonds. The backbone of the polypeptide chain consists of the repeating sequence -N-C-C- made up of the N atom from the amino group, the alpha C atom, and the C atom from the carboxyl group in each amino acid.

Because they are determined by weak forces,

the three dimensional structures of proteins are influenced by environmental conditions. Increases in temperature cause more rapid molecular movements and thus can break hydrogen bonds and hydrophobic interactions Changes in pH can change the pattern of ionization of exposed carboxyl and amino groups in the R groups of amino acids, thus disrupting the pattern of ionic attractions and repulsions High concentrations of polar substances such as urea can disrupt the hydrogen bonding that is crucial to protein structure. Nonpolar substances may also disrupt normal protein structure in cases where hydrophobic interactions are essential to maintain the structure.

cis-trans isomers

typically involve a double bond between two carbon atoms, where the carbons share two pairs of electrons. When the remaining two bonds of each of these carbons are to two different atoms or groups of atoms, these can be oriented on the same side or different sides of the double-bonded molecule. If the different atoms or groups of atoms are on the same side, the double bond is called cis; if they are on opposite sides, the bond is trans. These molecules can have very different properties

Glycogen

water-insoluble, highly branched polymer of glucose. It is used to store glucose in the liver and muscles and is thus an energy storage compound for animals, as starch is for plants. Both glycogen and starch are readily hydrolyzed into glucose monomers, which in turn can be broken down to liberate their stored energy. 1000 glucose molecules exert 1000 times the osmotic pressure of 1 glycogen causing water to enter the cells where glucose is stored so that is why we use glycogen. So our cells won't have to expel water.

Shape

when a small molecule collides with and binds to a much larger protein, it is like a perfect fit. A given molecule will not bind to a protein unless there is a general fit between their three-dimensional shapes