capvt iii

Question 1

Four molecules characteristic of living things:

___, ____, ____, and ____.

With the exception of the ___, these biological molecules are ___ constructed by the ___ of smaller molecules called ____.

Answer 1

proteins
carbohydrates
lipids
nucleic acids

lipids

polymers

covalent bonding

monomers

Question 2

polymer: a ____made up of similar or identical subunits called ____.

monomer: a small molecule, two or more of which can be combined to form ____ (consisting of a few ____) or ___ (consisting of many monomers).

Answer 2

large molecule

monomers

oligomers

monomers

polymers

Question 3

Carbohydrates can form giant molecules by linking together chemically similar ___ (___) to form __.

Nucleic acids are formed from four kinds of __ linked together in long chains.

Lipids also form large structures from a limited set of smaller molecules, but in this case ____ maintain the ___ between the ___ that are held together by ___.

Answer 3

sugar monomers

(monosaccharides)

polysaccharides

nucleotide monomers

noncovalent forces

interactions

lipid monomers

covalent bonds

Question 4

macromolecule A giant (molecular weight > 1,000) ___.

The macromolecules:
____;
____; and
____.

Macomolecules: polymers of thousands or more atoms are.

Convenient to regard large lipid structures as macromolecules though, strictly speaking, they are not polymers.

Answer 4

polymeric molecule

proteins,
polysaccharides
nucleic acids

Question 5

Isomers: molecules with ___ but ___.

Polymers form from chemical linkage (__).

Answer 5

same composition
different structures
condensation reactions

Question 6

The ___ chemical behavior of ___ helps us understand the ___ of the ___ that contain them.

functional group: characteristic combination of atoms that contribute ___ (such as ___ or ___) when attached to larger molecules (e.g., carboxyl group, amino group).

Answer 6

consistent

functional groups

properties

molecules

specific properties

charge

polarity

Question 7

Isomers: molecules consisting of the ___ and ____, but differing in the ____by which the atoms are held together.

Answer 7

same numbers
kinds of atoms
bonding atoms

Question 8

Structural isomers: molecules made up of the ___ and ___, in which the atoms are _____.

Structural isomers differ in how their ___ are ___.

Consider two simple molecules composed of four carbon and ten hydrogen atoms bonded covalently, both with the formula C4H10.

These atoms can be linked in two different ways, resulting in different molecules.

Answer 8

same kinds

numbers of atoms

bonded differently

atoms

joined together

Question 9

cis-trans isomers In molecules with a ___ (typically between two carbon atoms), cis or trans depends on ______.

If on ___, the molecule is a ___; trans if ___ are on ___of the double bond.

Cis-trans isomers typically involve a double bond between two ___ sharing two pairs of electrons.

Answer 9

double bond

which side of the double bond similar atoms or functional groups are found

the same side

cis isomer

similar atoms

opposite side

double bond

carbon atoms

two pairs of electrons

Question 10

Optical isomers occur when a carbon atom has ____. This pattern allows for ___ different ways of making the attachments, each the mirror image of the other.

Such a carbon atom is called an ___, and the two resulting molecules are ___ of one another.

You can envision your right and left hands as optical isomers. Just as a glove is specific for a particular hand, some biochemical molecules that can interact with one optical isomer of a carbon compound are unable to “fit” the other.
optical isomers.

Answer 10

four different atoms or groups of atoms attached to it

two

asymmetric carbon

optical isomers

Question 11

A macromolecule’s structure reflects ___

Ex: A protein having a certain structure and function in an apple tree probably has a similar structure and function in a human being, because the protein’s chemistry is the same wherever it is found.

An important advantage of ____is that some organisms can acquire needed raw materials by eating other organisms.

The __ and __ of the chain of monomers in a macromolecule determine its ___ and ___.

The specific structure of a macromolecule determines its function in a given environment, regardless of its origin.

Answer 11

function

chemistry is the same wherever it is found

biochemical unity

sequence

chemical properties

three-dimensional shape

function

Question 12

Most macromolecules are formed by _____ reactions and broken down by
___ reactions.

Polymers are formed from monomers by a series of condensation reactions.

Condensation reactions result in the formation of ______.

A water molecule is released with each covalent bond formed.

The condensation reactions that produce the different kinds of polymers differ in detail, but in all cases ____ form only if water molecules are removed and ____ to the system.

Answer 12

condensation

hydrolysis

condensation reaction

covalent bonds between monomers

polymers

energy is added

Question 13

condensation reaction: chemical reaction in which two molecules become connected by a ___ and a ___. (AH + BOH → AB + H2O.)

The reverse, a hydrolysis reaction which results in the ___ into ____.

Water reacts with the covalent bonds that link the polymer together. For each covalent bond that is broken, a water molecule splits into __, each
becomes part of one of the ___ .

hydrolysis reaction: a chemical reaction that breaks a bond by ___ (AB + H2O ’ AH + BOH).

Answer 13

covalent bond

water molecule is released

breakdown of polymers

their components monomers

two ions (H+ and OH-)

products

inserting the components of water

Question 14

Proteins are ___ made up of ___ in different proportions and sequences.

Answer 14

polymers

20 amino acids

Question 15

Proteins consist of one or more polypeptide chains—_____ (linear) polymers of ____.

Variation in the sequences of amino acids in the ___ allows for the vast diversity in protein structure and function. Each chain folds into a particular three-dimensional shape that is specified by the ____ present in the chain.

Answer 15

unbranched

covalently linked amino acids

polypeptide chains

sequence of amino acids

Question 16

Enzymes: __ biochemical reactions

Structural proteins: Provide physical __ and __

Defensive proteins: Recognize and respond to __ substances (e.g., antibodies)

Signaling proteins: Control ___ processes (e.g., hormones)

Receptor proteins: Receive and respond to ___

Membrane transporters: ____ of substances across cellular membranes

Storage proteins: Store ___ for later use

Transport proteins: ___ and ___ substances within the organism

Gene regulatory proteins:
Determine the ___ of expression of a gene

Motor proteins: Cause ___ of structures in the cell

Answer 16

catalyze

speed up

stability

movement

nonself

physiological

chemical signals

regulate passage

amino acids

bind

carry

rate

movement

Question 17

A protein’s tertiary structure describes its ___ shape and is stabilized by ___, ___, ____ attractions, and in some proteins, ___ bonds.

Answer 17

three-dimensional shape

hydrogen bonds

hydrophobic interactions

ionic

disulfide

Question 18

Monomers of proteins link to make a ____.

Each amino acid has both a ___ and an ___ attached to the same carbon atom, called the α (__) carbon. Also attached to the α carbon atom, ___ and a ___, or ___.

Amino acid: organic compound containing both __ and __ groups.

Proteins are polymers of amino acids.

side chain See R group.

R group The ___ of atoms of a particular amino acid; also known as a ___.

Answer 18

macromolecule

carboxyl function group

amino functional group

alpha

hydrogen atom

side chain

R group

NH2

COOH

distinguishing group

side chain

Question 19

Features of Amino Acids and Their Side Chains

(A) Amino acids with __, charged ___, side chains;

(B) Amino acids with __ but uncharged side chains (___)

(C) Special cases

(D) Amino acids with __, __ side chains

Answer 19

electrically

hydrophilic

polar

hydrophilic

nonpolar

hydrophobic

Question 20

Disulfide bridge The __ between two __ (–S—S–) linking __ molecules or __ of the same molecule.

Answer 20

covalent bond

sulfur (-S–S-)

two

remote parts

Question 21

___ form the backbone of a protein

Linking amino acids involves a reaction between __ and __ attached to the __. The __ group of one amino acid reacts with the amino group of another, undergoing a ___ that forms a ___.

Just as a sentence begins with a capital letter and ends with a period, polypeptide chains have a beginning and an end. The “capital letter” marking 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. The “period” is the carboxyl group of the last amino acid added; this is the C terminus.

Two characteristics important to the three-dimensional structures of proteins:

1. In the C—N linkage, the adjacent α carbons ___ are not free to rotate fully, which limits the __ of the polypeptide chain.
2. The oxygen bound to the carbon (C=O) in the carboxyl group carries a slight ___, whereas the hydrogen bound to the nitrogen (N—H) in the amino group is___.

This asymmetry of charge favors ___ within the protein molecule itself and between molecules. These bonds contribute to the structures and functions of many proteins.

Answer 21

Peptide linkages

carboxyl

amino groups

α carbon

carboxyl

condensation reaction

peptide linkage, peptide bond

N-terminus

carboxyl

C-terminus

(α C—C—N—α C)

folding

negative charge (δ–)

slightly positive (δ+).

hydrogen bonding

Question 22

peptide linkage The bond between amino acids in a protein; formed between a ___ and ___(—CO—NH—) with the loss of ___.

Answer 22

carboxyl group

amino group

water molecules

Question 23

The primary structure of a protein is its ____. The precise sequence of amino acids in a ___ held together by ___ bonds constitutes the primary structure of a protein.

The single-letter abbreviations for amino acids are used to record the ___ of a protein.

Answer 23

amino acid sequence

polypeptide chain

peptide

amino acid sequence

Question 25

The secondary structure of a protein requires ___.

A protein’s secondary structure consists of ___, ___ spatial patterns in ____ of a polypeptide chain.

Two basic types of secondary structure; determined by hydrogen bonding between the amino acids:

1. _____; a right-handed coil that turns in the same direction as a standard wood screw; ___ extend outward from the ___ backbone of the helix. The coiling results from hydrogen bonds that form between the δ+ hydrogen of the ___ of one amino acid and the δ– oxygen of the __ of another. When this pattern of hydrogen bonding is established repeatedly over a segment of the protein, it ___ the coil.

Answer 25

hydrogen bonding

regular

repeated

different regions

The α (alpha) helix

R groups

peptide

hyogren bonds

N–H

C=O

repeatedly

stabilizes

Question 26

Two basic types of secondary structure; determined by hydrogen bonding between the amino acids:

The α (alpha) helix and

A ___ is formed from two or more polypeptide chains that are almost completely extended and aligned. The sheet is stabilized by hydrogen bonds between the __groups on one chain and the __ groups on the other.

A ß pleated sheet may form between separate polypeptide chains or between different regions of a single polypeptide chain that is bent back on itself.

β (beta) pleated sheet A type of protein secondary structure; results from hydrogen bonding between polypeptide regions running antiparallel to each other.

Answer 26

β (beta) pleated sheet

polypeptide chains

extended

aligned

hydrogen bonds

N-H

C=O

Question 27

The tertiary structure of a protein is formed by bending and folding

In many proteins, the polypeptide chain is __ at specific sites and then ___, resulting in the __ structure of the protein.

Although α helices and ß pleated sheets contribute to the tertiary structure, usually only portions of the macromolecule have these secondary structures, and large regions consist of tertiary structure unique to a particular protein.

The protein’s exposed outer surfaces present ___ capable of interacting with other molecules in the cell.

Answer 27

bent

folded back and forth

tertiary

functional groups

Question 28

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.

Question 29

Native proteins are __; denatured proteins have a ___.

Native proteins exist in one, preferred shape; denatured proteins can take many shapes.

Native proteins have hydrogen bonds that stabilize the structure __; denatured proteins have hydrogen bonds on the __, to water.

Answer 29

compact

larger volume

internally

exterior

Question 30

Many functional proteins contain two or more ___, called ___, each of them folded into its own unique ___.

The protein’s quaternary structure results from the ways in which ___ bind together and interact.

Quaternary structure The specific three-dimensional arrangement of ___.

Answer 30

polypeptide chains

subunits

tertiary structure

subunits

protein subunit

Question 31

Shape and ___ contribute to protein function

The shapes of proteins allow specific sites on their exposed surfaces to___ to other molecules, which may be large or small.

The specificity of protein binding depends on two general properties of the protein: its shape, and the chemistry of its exposed surface groups.

Shape. When a small molecule collides with and binds to a much larger protein, it is like a baseball being caught by a catcher’s mitt: the mitt has a shape that binds to the ball and fits around it.

Chemistry. The exposed R groups on the surface of a protein permit chemical interactions with other substances (Figure 3.12). Three types of interactions may be involved: ionic, hydrophobic, or hydrogen bonding. Many important functions of proteins involve interactions between surface R groups and other molecules.

Answer 31

surface chemistry

bind noncovalently

Question 32

Environmental conditions affect protein structure

Conditions that would not break covalent bonds can disrupt the weaker, noncovalent interactions that determine secondary, tertiary, and quaternary structure. Such alterations may affect a protein’s shape and thus its function.

___ cause more rapid molecular movements and thus can break hydrogen bonds and hydrophobic interactions.

___ 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 ___ such as urea can disrupt the hydrogen bonding that is crucial to protein structure. Urea was used in the experiment on reversible protein denaturation shown in

___ may also disrupt normal protein structure in cases where hydrophobic interactions are essential to maintain the structure.

Answer 32

Increases in temperature

Changes in pH

polar substances

Nonpolar substances

Question 33

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 ___ of one or more of its __. The chemical modification of just one amino acid can alter the shape and function of a protein.

Answer 33

side chain

amino acids

Question 34

Molecular chaperones help shape proteins

Within a living cell, a polypeptide chain is sometimes in danger of binding the wrong substance.

When a protein has not yet folded completely, it can present a surface that binds the wrong molecule.

Following denaturation. Certain conditions, such as moderate heat, can cause some proteins in a living cell to denature without killing the organism. Before the protein can refold, it may present a surface that binds the wrong molecule. In these cases, the inappropriate binding may be irreversible.

Many cells have a special class of proteins, called chaperones, that protect the ___ of other proteins. They bind to their partner proteins just as they are being made and also when they become denatured.

chaperone A protein that guards other proteins by counteracting ___ that threaten their three-dimensional structure.

Answer 34

chaperones

three- dimensional structures

molecular interactions

Question 35

___ Are the Basic Structural Unit of Carbohydrates

Carbohydrates usually have the general formula ___, which makes them appear as “hydrates of carbon” (a hydrate refers to water), hence their name.

However, carbohydrates are not really “hydrates” because the water molecules are not __. Rather, the linked carbon atoms are bonded with __ and __, the components of water.

Answer 35

Simple Sugars

(C1H2O1)n

intact

hydrogen atoms (–H)

hydroxyl groups (–OH)

Question 36

Carbohydrates have 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.

Question 37

Carbohydrates function primarily in storing and transporting chemical energy and as sources of carbon for building new macromolecules.

Polysaccharides of glucose all provide energy storage and structural functions but vary in ___ and type of ___ between glucose units.

Answer 37

branching patterns

glycosidic linkages

Question 38

1. Monosaccharides, such as glucose, are simple sugars. They are the ___ from which the larger carbohydrates are constructed.
2. Disaccharides (di, “two”) consist of two ___ linked together by __. The most familiar is sucrose.
3. Oligosaccharides (oligo, “several”) are made up of several (__) monosaccharides.
4. Polysaccharides such as starch, glycogen, and cellulose, are ___ made up of hundreds or thousands of monosaccharides.

Answer 38

simple sugars

monomers

covalent bonds

monosaccharides

covalent bonds

3-20

polymers

Question 39

Monosaccharides are simple sugars

All living cells contain the monosaccharide glucose; it is the “blood sugar” used to store and transport energy in humans. Cells use glucose as an energy source, breaking it down through a series of reactions that converts stored energy to more usable ___ energy and produce ___;

Glucose exists in straight chains and in ___. The ___ predominate in virtually all biological circumstances because they are more stable in water.

Answer 39

chemical

carbon dioxide

straight chains

ring forms

ring forms

Question 40

Pentoses are ____.

Two important pentoses: the backbones of the nucleic acids RNA and DNA contain ribose and deoxyribose. These two pentoses are not __ of each other; rather, one __ is missing from __ in deoxyribose (de-, “absent”). The absence of this oxygen atom is an important distinction between RNA and DNA

Answer 40

five carbon sugars

isomers

oxygen atom

carbon 2

Question 41

Common hexoses are glucose, fructose (so named because it was first found in fruits), mannose, and galactose.

hexose [Gk. hex: six] A sugar containing six carbon atoms.

Question 42

Glycosidic linkages bond monosaccharides
The disaccharides, oligosaccharides, and polysaccharides are all constructed from monosaccharides that are covalently bonded together by condensation reactions that form glycosidic linkages (Figure 3.17). A single glycosidic linkage between two monosaccharides forms a disaccharide.

glycosidic linkage Bond between carbohydrate (sugar) molecules through an intervening oxygen atom (–O–).

Disaccharides Form by Glycosidic The particular disaccharide formed depends on which monosaccharides are linked, on the site of linkage (i.e., which carbon atoms are involved), and on the form (α or β) of the linkage.

Question 43

Polysaccharides store energy and provide structural materials

n contrast to polypeptides, polysaccharides are not

glycosidic linkage Bond between carbohydrate (sugar) molecules through an intervening oxygen atom (–O–).

necessarily linear chains of monomers. Each monomer unit has several sites that are capable of forming glycosidic linkages, and thus branched molecules are possible.

Question 44

all starches are polysaccharides of glucose with α-glycosidic linkages (α–1,4 and α–1,6 glycosidic bonds; see Figure 3.18A), the different starches can be distinguished by the amount of branching that occurs at carbons 1 and 6 (see Figure 3.18B). Starch is the principal energy storage compound of plants. Some plant starches, such as amylose, are unbranched; others are moderately branched (for example, amylopectin). Starch readily binds water; if you’re a cook you know this. However, when water is removed, hydrogen bonds form between the unbranched polysaccharide chains, which then aggregate.

starch [O.E. stearc: stiff] A polymer of glucose; used by plants to store energy.

Question 45

GLYCOGEN
Glycogen is a 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.

But if it is glucose that is needed for fuel, why store it in the form of glycogen? The reason is that 1,000 glucose molecules would exert 1,000 times the osmotic pressure of a single glycogen molecule, causing water to enter cells where glucose is stored (see Key Concept 6.3). If it were not for polysaccharides, many organisms would expend a lot of energy expelling excess water from their cells.

Question 46

Like starch and glycogen, cellulose is a polysaccharide of glucose, but its individual monosaccharides are connected by ß- rather than by α-glycosidic linkages. Starch is easily degraded by the actions of chemicals or enzymes. Cellulose, however, is chemically more stable because of its ß-glycosidic linkages.

whereas starch is easily broken down to supply glucose for energy-producing reactions, cellulose is an excellent structural material that can withstand harsh environmental conditions without substantial change.