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