Biology Chapter 3: Macromolecules

All carbohydrates have the general structure

(C1H2O1)n or CnH2nOn

In most cells, ionization of amino acids causes the -COOH group to release a proton to become ____ and the NH2 group to gain a proton to become ____

-COO-; -NH3+

The base of a nucleotide is linked to the ____ carbon of the monosaccharide and the phosphate groups are linked to the ___ carbon of the monosaccharide

1'; 5'

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

1. The monosaccharide in DNA is deoxyribose, and in RNA it is ribose. 2. DNA has nucleotides with bases cytosine, thymine, adenine, and guanine. RNA has A, G, and C but Uracil replaces U.

An atom with _______ has an atomic number of 14.

14 protons

An atom has an atomic number of 12. Assuming neutrality, how many valence electrons does it have?

2

Proteins are composed of different combinations of _____ amino acids

20

Specificity of enzymes results from the exact _____ and ______ of the active site

3D shape; chemical properties

There are ____ different nucleotides in both RNA and DNA

4

the alpha carbon has ____ available electrons for covalent bonding

4

3'-A-T-G-A-A-C-T-G-5' which single-stranded DNA molecule will bind to this molecule in a complementary fashion?

5'-T-A-C-T-T-G-A-C-3'

Nucleic acids are said to be synthesized in the ____ to ____ direction.

5'; 3' because each incoming nucleotide is added to the 3' carbon atom of the last ribose/deoxyribose

saturated fatty acid

A fatty acid in which all the bonds between carbon atoms in the hydrocarbon chain are single bonds—that is, all the bonds are saturated with hydrogen atoms.

fatty acid

A molecule made up of a long nonpolar hydrocarbon chain and a polar carboxyl group. Found in many lipids.

Triglyceride

A simple lipid in which three fatty acids are combined with one molecule of glycerol.

Glycerol

A three-carbon alcohol with three hydroxyl groups; a component of phospholipids and triglycerides.

Complementary base pairing

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

enzyme-substrate complex (ES)

An intermediate in an enzyme-catalyzed reaction; consists of the enzyme bound to its substrate(s).

RNA (ribonucleic acid)

An often single-stranded nucleic acid whose nucleotides use ribose rather than deoxyribose and in which the base uracil replaces thymine found in DNA. Serves as genome from some viruses.

Lipids contain mostly _______ and _______ nonpolar bonds.

C-C and C-H

On which end of a growing polypeptide chain is the next amino acid added?

C-terminal

Numonic device for biomolecule composition

Carbs (CHO), Lipids (CHO), Proteins (CHON), Nucleic acids (CHONP)

_____ and _____ are both resistant to being broken down because it is difficult for chemicals or enzymes to access the bonds in these dense polysaccharides.

Cellulose; chitin

The entire DNA molecule is copied during

DNA replication

Which factor defines whether a reaction is endergonic?

Delta G

DNA with a higher G and C content is more stable at high temperatures than DNA with a high A and T content. Why?

Each G-C pair forms three hydrogen bonds between antiparallel strands, whereas each A-T pair forms just two.

Which bonds in triglycerides result from condensation reactions?

Ester

Oligopeptides are more common than polypeptides. True or false?

False

You hypothesize that increased light levels will enhance growth of your houseplants. You test this hypothesis, moving the plants to an area in your home with more light. Over several weeks, and you find that the plants begins to look fuller and healthier. This result proves your original hypothesis. True or false?

False

Where would the leucine side chain most likely be found in a protein dissolved in water?

In the interior of the protein in contact with nonpolar side chains

In a properly folded, active protein that is found in the aqueous environment of a cell, where would you expect to find isoleucine and valine residues?

In the interior of the protein with nonpolar side chains

Which of the following would be true of any given DNA molecule?

It would contain an equal number of purines and pyrimidines.

Which of the following is matched correctly with its building block?

Lipids -glycerol and fatty acids

In order to maintain an ideal membrane fluidity, cells of a fish can make chemical modifications to their membranes to deal with changes in temperature. How might you expect the lipids in a fish from warmer water to compare to those in a fish from colder water?

Lipids will have more saturated fatty acids in the warmer water fish.

main carbohydrates in cells that can enter the pathways that break them down to release energy

Mono/disaccharides

Lipids

Nonpolar, hydrophobic molecules that include fats, waxes, oils, steroids, and the phospholipids that make up biological membranes.

A fatty acid has two parts C-C and H-C bonds and ______ bonds which are polar. Making the mole cule _____.

O-C; amphipathic

Which of these molecules contains only nonpolar bonds?

O2

purine

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

pyrimidine

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

Why the did evolution of photosynthesis in the ancient ocean allow organisms to colonize land?

Oxygenation of the atmosphere formed protective ozone

_____ alignment of polysaccharide chains allows them to form dense _____ or strong _____

Parallel; sheets; fibers

A reaction between the -OH group on the 3' carbon atom of the ribose/deoxyribose in the last nucleotide of the existing chain and the triphosphate on the 5' carbon of the incoming nucleotide monomer releases a ________ molecule

Pyrophosphate

oligonucleotides are primarily _____ molecules

RNA

A single bacterium divides into two bacteria that are identical to, but smaller than, the original bacterium. Which characteristic of life does this best describe?

Replication and reproduction

polar, uncharged side chains

Serine, Threonine, Asparagine, Glutamine, tyrosine

Small molecules containing several hydroxyl groups are typically

Soluble in water

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.

Phosphodiester bond

The connection in a nucleic acid strand, formed by linking two nucleotides.

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.

What determines if a molecule is polar or nonpolar?

The differences in the electronegativities between the atoms

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.

Margarine is a butter substitute that is solid at room temperature. It is made from vegetable oils (often soybean or canola oil). The label on a container of margarine lists "hydrogenated vegetable oil" as the major ingredient. Which statement below best explains this?

The margarine stays solid at room temperature because the fatty acids in the triglycerides are saturated.

What determines the structure and function of a protein?

The sequence of amino acids making up its polypeptide chain

Cite a reason for the evolution of allosteric regulators in cells

They allow the cell to conserve energy by shutting down or activating reaction pathways only as needed.

Energy can be transformed during metabolic reactions.

True

Starch and cellulose may have the same chemical formula, but they have very different solubilities in water due to the different branching patterns in glucose. True or false?

True

Reaction to form a disaccharide

Two hydroxyl groups involved and produces a molecule of water (different disaccharides for different -OH groups and orientations

Disaccharides

a carbohydrate made up of monosaccharides joined in condensation reaction

proteins

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

unsaturated fatty acid

a fatty acid whose hydrocarbon chain contains one or more double bonds

steroids

a four-ringed lipid molecule (i.e. cholesterol in membranes and steroid hormones)

ligand

a molecule or ion that binds to another molecule (in this case protein)

Nucleotide components

a monosaccharide (the pentose ribose or deoxyribose), a nitrogen containing base, and one to three phosphate groups

oligopeptides (peptides)

a peptide made up of fewer than 20 amino acids

If you were given a diagram of a nucleotide, which of the following would expect to find as one of its components?

a phosphate

nucleic acids

a polymer made up of nucleotides, specialized for the storage, transmission, and expression of genetic information.

regulatory proteins

a protein that controls the rate or a biological process

signal proteins

a protein used to communicate with other cells to elicit a response

metabolic pathway

a series of reactions in which the product of one reaction is a substrate for the next

genes

a unit of heredity; used here as the unit of genetic function which carries the information for a polypeptide or RNA

Amino acids have both _____ and _____ properties

acidic; basic

nonpolar side chains

alanine, valine, leucine, isoleucine, phenylalanine, methionine, tryptophan

noncompetitive inhibition example of _____ regulation

allosteric

C6H12O6 is the chemical formula for

alpha glucose, fructose, and mannose

Proline is not found in

alpha helixes (because it has unusual ring stucture and relative inflexibility

The primary structure of proteins is the _______. The primary structure contains the information necessary for the formation of secondary structure, including the _______ and the _______. Secondary structure of proteins is stabilized by the formation of _______ bonds.

amino acid sequence; α helix; β pleated sheet; hydrogen

peptides are polymers of

amino acids

polymerization takes place in the _____ to _____ direction

amino; carboxyl (new parts added to carboxyl side (c-terminus))

Replication is the synthesis of _______, and transcription is the synthesis of _______.

an identical copy of DNA; an RNA copy of DNA

amino acid

an organic compound containing both NH2 and COOH groups and one of 20 different side chains.

The two strands of DNA are _____ with their 5' strands at opposite ends of the molecule

antiparallel

Phospholipids differ from triglycerides in that phospholipids

are amphipathic

When incorporated into a polypeptide chain not at the N or C terminus, _______ would make the charge of the polypeptide more positive.

arginine

tertiary structure

arises from bending and folding of the polypeptide chain, which results in a three dimensional structure

Maltose, or malt sugar, is composed of two glucose molecules bound by a glycosidic linkage. How can maltose be classified? Choose all that apply.

as a disaccharide

Many enzymes end in -_____

ase

nucleoside

base and either deoxyribose or ribose

Amino acids with bulky side chains like tryptophan are more likely to be in

beta pleated sheets

The basic structure of a biological membrane consists of a phospholipid _______, with a(n) _______ interior and _______ exterior.

bilayer; hydrophobic; hydrophilic

a protein's function is determined by its

binding characteristics

Allosteric regulators affect their target enzymes by

binding to a site other than the active site and causing a conformational change in the enzyme.

Glycosidic bond

bond between carbohydrate molecules through intervening oxygen atom

noncompetitive inhibitor

bonds at a site distinct from the active site, causing shape/function change

oligosaccharides

carbohydrates constructed from 3-10 monosaccharides joined by glycosidic bonds

Simple sugars

carbohydrates with 12 or fewer carbons

most carbon atoms in carbohydrates have a _____ functional group

carboxyl (-OH)

transport proteins

carry substances within the organism and across biological membranes

_____ are substances that speed up reactions without being permanently altered

catalysts

enzymes

catalytic proteins that speeds up a biochemical reaction

conformational change

change in the shape of a protein

environmental factors that can destabilize protein structure

changes in pH, altering ionic interactions, high concentrations of polar solutes, nonpolar substances in cases where van der waals interactions between hydrophobic groups are essential for maintaining the protein's structure

(tertiary structure) ionic interactions occur between

charged side chains. these include ionic bonds between positive and negative charges on side chains

kinases

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

brown fat

color from iron-rich mitochondria; in mammals, fat tissue that is specialized to produce heat. It has many mitochondria and capillaries, and a protein that uncouples oxidative phosphorylation

competitive inhibitor

competes with natural substrate for active site

The resulting RNA/DNA strand from replication/translation will to _____ to the existing DNA template strand

complementary

Which feature of DNA enables it to store genetic information and transfer the information to future generations?

complementary base pairing

The double-stranded regions of RNA are stabilized by

complementary base pairing between nucleotides in separate parts of the molecule; this affects shape and interaction

catabolic

complex molecules are broken down into simpler ones and energy is released

Glucose can bod to starch in a _____ reaction.

condensation

Glycerol and fatty acids are joined by _____ reactions.

condensation

DNA differs from RNA in that DNA

contains deoxyribose.

What type of bond forms between the carboxyl and amino groups in a growing polypeptide chain?

covalent

bilayers have no _____ bonds

covalent

Nucleotides in RNA are connected to one another in the polynucleotide chain by

covalent bonds between sugar and phosphate.

_ bonds are formed during anabolic reactions in the synthesis of macromolecules. In lipids there are ____________ bonds, whereas in carbohydrates there are ____________ bonds.

covalent; ester; glycosidic

The primary structure of a protein is established by ______ peptide bonds but higher levels of structure are determined largely by _____ bonds.

covalent; noncovalent

Special cases amino acid side chains

cysteine (forms disulfide bridges), glycine (allows for flexibility), proline (stabilizes ring structure in proteins)

(tertiary structure) covalent disulfide bridges occur between

cysteines

if a protein is heated slowly the thermal energy input will

disrupt the weaker interactions and break hydrogen bonds causing secondary, tertiary, and quaternary structure to break down

The base pairs of DNA and RNA are _____ to separate with input of energy

easy

Which physiological function would be least associated with proteins?

energy reserve

What is the biological role of carbohydrates?

energy storage

A high level of glucose causes water to

enter cells. Expend energy removing water

induced fit

enzyme changes shape when it binds the substrate, which alters the shape of the active site

phosphatases

enzymes that remove phosphate groups

Most biological catalysts are proteins (_____) a few are RNA molecules (_____)

enzymes; ribozymes

Which bonds in triglycerides result from condensation reactions?

ester

Macromolecules are formed by _____ reactions.

exergonic

Gibbs free energy is negative for _________________ reactions, which are typically associated with a ________________ change in enthalpy and a _______________ change in entropy.

exergonic; negative; positive

All carbohydrates are polymers.

false

Bonding between A-T is stronger than G-C in double stranded DNA.

false

For each reaction in a metabolic pathway, a small amount of energy disappears due to the increase in entropy.

false

Phospholipids are not amphipathic. True or False?

false

Olive oil melts at a lower temperature than beef fat because

fats contain more saturated fatty acids than oils do.

All lipids contain _____

fatty acids

Phospholipid Parts

fatty acids bound to glycerol but one fatty acid is replaced by charged phosphate-containing molecule

Triglycerides are synthesized from _____ and _____.

fatty acids; glycerol

Oligosaccharides can have special properties if modified by the addition of _______ _______

functional groups

In all amino acids two of the electrons are occupied by _____ a third is occupied by a ____ atom. The fourth bonding electron is shared with_____.

functional groups; hydrogen; r group

negatively charged side chains

glutamate and aspartate hydrophillic form hydrogen bonds with water and other polar or charged substances

Which linkages in cellulose result from condensation reactions?

glycosidic

Amphipathic

having both a hydrophilic region and a hydrophobic region

Saturated fatty acids have a _____ melting point and are _____ at room temperature. Unsaturated fatty acids have a _____ melting point and are _____ at room temperature.

high; solid lower; liquid

Some bases are able to "pair" with others through the formation of _____ bonds when two nucleic acids strands are physically close enough and in the appropriate orientation

hydrogen

linear chains of polysaccharides can align in close proximity and form _____ bonds with neighboring chains.

hydrogen

In an alpha helix, the coiling is stabilized by

hydrogen bonding of the N—H groups on one amino acid and the C=O groups on another.

(tertiary structure)van der waals interactions occur between

hydrophobic side chains and stabilize the associations between them

In a phospholipid, the "tail" is _____, the "head" is _____, making the molecule_____.

hydrophobic; hydrophilic, amphipathic

Carbohydrate isomers

important for function; binding to and interacting with other molecules

white fat

in mammals, fat tissue that stores energy and provides thermal insulation that helps regulate body temperature

Enzymes catalyze a reaction by doing what 3 things?

inducing strain, changing substrate orientation. or adding chemical groups

DNA is a purely ____ molecule

informational

polynucleotides

informational nucleic acids involved in heredity; longest polymers`

irreversible inhibition

inhibitor covalently bonds to side chains in the active site and permanently inactivates the enzyme (i.e. pesticides, drugs)

Starches and glycogen are water-_____

insoluble

The functional groups on the amino acids present on a protein's exposed outer surfaces are capable of

interacting with other molecules in the cell

Tertiary structure is determined by

interactions between the r groups

structural protein

involved in the physical stability or movement of a cell or organism

beta pleated sheet

is formed from 2 or more sequences of amino acids that are extended and aligned in a polypeptide. The sheet is stabilized by hydrogen bonds between the -NH groups and the -CO groups on the 2 chains

in many cases a denatured protein will return to its normal tertiary structure when

it cools or when the denaturing chemicals are removed

RNA is usually single stranded but

it often folds back on itself to form short double-stranded regions

polypeptides

large molecule made up of many amino acids joined by peptide linkages. Large polypeptides are called proteins

Polysaccharides

large polymers o hundreds to thousands of monosaccharides connected by glycosidic bonds

During a typical hydrolysis reaction in cells, the energy required to break bonds in the substrates is _______________ the energy released when bonds are formed in the products.

less than

Polysaccharides can be ______ chains of monomers attached by ___,___ glycosidic bonds, or they can be _____ from ___,___ glycosidic bonds.

linear; 1,4; branched; 1,6

Carotenoids

lipids that can absorb energy from particular wavelengths of light

secondary structure (protein)

localized regularities of structure, such as the alpha helix and the beta pleated sheet. determined by hydrogen bonding between amino. acids

coenzymes

loosely bound cofactors that bind to enzymes

denatured

loss of an activity of an enzyme or nucleic acid molecule as a result of structural changes induced by heat or other means

positively charged side chains

lysine, histidine, arginine hydrophillic attract oppositely charged ions

What is the biological role of lipids?

membrane formation and energy storage

Many enzymes require cofactors for carrying out reactions which include

metal ions, coenzymes, or prosthetic groups

Monosaccharides

monomers of carbohydrates; simplest carbohydrates usually in ring form, but sometimes linear

The "building blocks" of polysaccharides are _______, and these blocks are covalently linked together by _______.

monosaccharides; glycosidic linkages

Residues

name given to specific monomers that make up a polymer in polysaccharides and macromolecules

allosteric regulation

non-substrate molecule binds a site other than the active site; can activate or inactivate enzymes

Most nonbiological catalysts are

nonspecific

oligonucleotides

nucleic acids with a few to 20 monomers regulate synthesis of new DNA and regulate expression of information coded in DNA

proteolysis

occurs when protein is too long to be functional; part of the protein must be removed by breaking a particular peptide bond in a hydrolysis reaction

A functional protein may be made up of

one or more polypeptides

Carbohydrates

organic compounds containing carbon, hydrogen, and oxygen vary in size, chemical properties, and biological functions

Many sugars end in -____

ose

(nucleotides) Hydrogen bonds form between the partial negative charge on an _____ or _____ atom of one based, and the partial positive charge on a _____ atom of another base.

oxygen; nitrogen; hydrogen

What 3 components form the structure of a nucleotide?

pentose sugar, phosphate group, nitrogen-containing base

Monosaccharides consist of five or six carbon atoms termed

pentoses and hexoses

A triglyceride is primarily hydro_____.

phobic

Unlike other macromolecules, lipids are not _____ and are defined by their _____.

polymers; properties

A _______ allosteric regulator _______ the rate of an enzyme-catalyzed reaction by inducing the active site of the enzyme to become _______.

positive; increases; exposed

both secondary and tertiary structure derive from

primary structure

glycogen

principal energy storage compound in animals, fungi, and bacteria

Starches

principal energy storage compounds of plants

most complex of the macromolecules

proteins

(un)modified oligosaccharides are often covalently bonded to _____ or _____ which alter their function and solubility.

proteins; lipids

The bases of nucleic acids take one of two chemical forms _____ or _____

pyrimidine; purine

receptor protein

receive and respond to molecular signals from inside and outside the organism

Oligosaccharides bound to the proteins and lipids on the outer surfaces of cells function as _____ _____.

recognition signals

defensive proteins

recognize and respond to substances or particles that invade the organism from the environment

alpha helix

right handed (screw), r groups extend from peptide backbone, 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

different monosaccharides often have the _____ chemical formula and represent structural or stereoisomers.

same

Amino acids are identified by their

side chain (R group)

(tertiary structure) hydrogen bonds occur between

side chains

ligands are usually ______ that bind to _____.

signals; receptors

RNA is usually composed of a ______oligo/polynucleotide strand whereas DNA almost always contains _____ strands.

single; two

lipoproteins

spherical structure; lipids packaged inside a covering of protein so that they can be circulated in the blood

storage proteins

store amino acids and some other substances for later use

binding affinity

strength of the interaction between a ligand and the protein molecule to which it binds (higher values=more specific bonding)

In the DNA "ladder" the _______ groups form the sides of the ladder and the _____ with their hydrogen bonds form the rungs on the inside.

sugar-phosphate; bases

anabolic

synthesizing complex molecules from simpler ones with an input of energy

Complementary base pairing

takes place between purine and pyrimidine bases.

The central carbon atom of an amino acid is known as

the alpha carbon

peptide bond

the bond between amino acids in a protein; formed between a carboxyl group and amino group (-CO-NH-) with the loss of water molecules

genome

the complete set of DNA in a living organism

r group (side chain)

the distinguishing group of atoms of a particular amino acid

feedback inhibition

the final product acts as a noncompetitive inhibitor of the first enzyme, which shuts down the pathway

transcription

the process by which information encoded in DNA base sequences is used to synthesize RNA

Translation

the process by which information in RNA base sequences is used to synthesize proteins

Oligopeptides and polypeptides form via

the sequential addition of new amino acids to the ends of existing chains. The amino acid at the end of the peptide chain

quaternary structure

the specific 3-D arrangement of polypeptide chains in a protein composed of multiple polypeptides

primary structure

the specific sequence of amino acids in a protein

gene expression

the transcription of specific DNA sequences into complementary RNA

Why are lipids hydrophobic?

they consist mostly of hydrocarbons, which form nonpolar covalent bonds

oligopeptides have distinctive ______-______ structures

three dimensional

nucleotides usually contain _____ phosphates when they are monomers, but in nucleic acids they contain just _____ phosphate group.

three; one

prosthetic group

tightly bound cofactor that is covalently bonded to the protein

How the information in DNA is used to synthesize proteins involves two processes:

transcription and translation

Endergonic and exergonic reactions can both involve breaking of bonds.

true

Organization (e.g., building molecules, constructing tissues) in life requires energy inputs. True or False?

true

motor protein

use energy to change shape and move cells or structures within cells

Tertiary structure of proteins involves bonding between amino acid R groups. What kind of bond would form between the R groups of Leu, Phe, and Val?

van der Waals interaction