Download What are the major types of organic molecules?

What are the major types of organic molecules?
(All key terms are in bold writing)
I. many biological molecules are _________________
A. polymers are _____________ or branching chains based on repeating subunits
(monomers)
1. example: ________ (the polymer) are made from __________(the monomers)
2. example: nucleic acids (the _______) are made from nucleotides (the __________)
Polymer
Monomer
B. very large polymers (hundreds of subunits or more) are called __________________
C. polymers are ______________ into monomers by hydrolysis (“break with _________”)
1. typically requires an ___________ to occur at a decent rate
2. hydrogen from water is attached to one monomer, and a __________ from water is
attached to the other
D. monomers are covalently linked to form polymers by __________________
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1. also typically requires an enzyme to occur at a decent rate
2. typically the equivalent of a __________molecule is removed (dehydration synthesis)
II. The four major classes of biologically important organic molecules are:
A.
B.
C.
D.
(and related compounds)
(and related compounds)
Read pp.30-31; answer p.31 #1-2
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Carbohydrates
III. carbohydrates include ____________, ____________, and ____________
A. carbohydrates contain only the elements ____________, ____________, and
____________
B. the ratio works out so that ________________ are typically (CH2O)n
C. carbohydrates are the main ____________ in biological systems created for
____________ ____________ and consumed for ____________ ____________;
some are also used as ____________ materials
IV.
grouped into ____________, ____________, and ____________
1. monosaccharides are ____________ sugars (a single monomer)
 have 3, 4, 5, 6, or 7 carbons
 referred to as trioses, tetroses, ____________, hexoses, and ____________
 examples of pentoses include ____________ and deoxyribose (part of
____________ ____________)
 examples of hexoses include glucose, fructose, and galactose; glucose is most
abundant
 Examine the three different ways of representing glucose. All describe the same
formule of C6H12O6
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2. _______________ consist of two ___________________ units
 the two monomers are joined by a glycosidic linkage or ____________
____________
 formed when the equivalent of a ____________ molecule is removed from the two
___________________
 an oxygen atom is bound to a carbon from each ____________
 typically, the linkage is between carbon ____ of one and _____ of the other
 ____________, ____________, and ____________ are common disaccharides
 maltose (malt sugar): has ______ glucose subunits
 sucrose (table sugar): ___________ + fructose
 lactose (milk sugar): glucose + _____________
3. polysaccharides are __________________ made of repeating ___________________
units linked together by _______________ bonds
 number of subunits varies, typically _________________
 can be branched or ___________________
 some are easily broken down and are good for ___________ ___________
(examples: starch, glycogen)
 some are harder to break down and are good as ___________ ___________
(example: cellulose)
 starch is the main storage _______________ of ________________
 polymer made from α-glucose units linked primarily between carbons 1 and 4
 plants store starches in organelles called _______________, a type of plastid
 __________________ is the main storage carbohydrate of ______________
 similar to starch, but very highly branched and more _________-____________
 is _______ stored in an organelle; mostly found in ___________ and
___________ ___________
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 cellulose is the major structural component of most plant __________ __________
 polymer made from -glucose units linked primarily between carbons 1 and 4
(similar to starch, but note that the 1-4 linkage makes a huge difference)
 unlike starch, most organisms cannot ___________ cellulose (we lack the ability
to break the link between the units of glucose)
 cellulose is a major constituent of ___________, wood, and ___________
 cellulose contains ___________of the carbon in found in plants
 fibrous cellulose is the “fiber” in your ___________
 some fungi, bacteria, and protozoa make enzymes that can break down
___________
 animals that live on materials rich in cellulose, e.g. cattle, sheep and termites,
contain _____________________ in their gut that are able to break down
cellulose for use by the animal
4. carbohydrates can be modified from the basic (CH2O)n formula
 many modified carbohydrates have important ___________ roles
 example: ___________ – structural component in fungal cell walls and arthropod
exoskeletons
 example: ___________ in cartilage
 example: glycoproteins and glycolipids in ___________ ___________
Read pp.32-33; answer p.33 #1-2
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IV.
Lipids
lipids are fats and ________-_________ substances
A. lipids are a ____________________ group of compounds defined by ______________,
not structure
B. ___________ or ___________ compounds
C. lipids are principally __________________, and are relatively _______________ in water
(some do have polar and nonpolar regions
1. lipids consist mainly of ___________ and ___________
2. some ___________ and/or _________________, mainly in the polar regions of lipids
that have such regions
D. roles of ___________ include serving as _________________ structural components, as
________________ molecules, and as ___________ ___________ molecules
E. major classes of lipids that you need to know are __________________(fats),
_________________________, and _______________
F. triacylglycerols contain ___________ joined to three ___________ ___________
1. ___________ is a three carbon ___________ with 3 ___________groups
2. a fatty acid is a long, __________________ hydrocarbon chain ___________ group at
one end
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 ___________ fatty acids contain _____ carbon-carbon ___________ ___________
(usually solid at room temp)
 ___________ fatty acids contain ___________ or ___________ double bonds
(usually liquid at room temp)
 __________________________ – one double bond
 __________________________ – more than one double bond
 about ______ different fatty acids are commonly found in triacylglycerols; most
have an even number of carbons
3. ___________________ results in an _____________ _____________ between a fatty
acid and the glycerol
 one attached fatty acid = _________________________
 two = _________________________
 three = _________________________
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4. triacylglycerols (also called triglycerides) are the most abundant _______________,
and are important sources of ________________
G. phospholipids consist of a _________________ molecule, a ______________ group
esterified to the third ______ group of glycerol, and an organic molecule (usually
charged or polar) esterified to the phosphate
1. phospholipids are amphipathic; they have a _____________ end (the two fatty acids)
and a __________ end (the phosphate and organic molecule)
2. this is often drawn with a polar “head” and two nonpolar “tails”
3. the nonpolar (or __________________) portion of the molecule tends to stay away
from water, and the polar (or _________________) portion of the molecule tends to
interact with water
4. because of this character phospholipids are important constituents of biological
_____________________
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H. steroids have a backbone of four _____________ rings
1. ____________ ____________ extend from the rings; length and structure of the side
chains varies
2. one type of steroid, _____________________, is an important component of cell
membranes
3. other examples: many hormones such as ________________, _________________
p.35 #1+2
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Proteins
V. proteins are __________________________ that are _____________________ formed from
_____________ _____________ monomers
A. proteins have great _____________ _____________ and perform many _____________
B. roles include _____________ catalysis, _____________, transport, structure/support,
motion, _____________; protein _____________ determines protein _____________
C. _____________ are polymers made of amino acid _____________ linked together by
_____________ _____________
1. amino acids consist of a central or alpha _____________; bound to that carbon is a
_____________ atom, an _____________ group (-NH2), a _____________ group (COOH), and a variable _____________ group (R group)
 the R group determines the _____________ and much of the chemical properties of
the amino acid
 there are ________ amino acids that commonly occur in proteins; pay attention to
what makes an R group polar, nonpolar, or ionic (charged) and thus their
______________________ or ________________________nature
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 _____________ and _____________ can usually make their _____________
amino acids
 many _____________ must obtain some amino acids from their diet
(_____________amino acids)
 there are 9 essential amino acids that humans cannot produce and must therefore
eat.
2. the peptide bond joins the _____________ group of one amino acid to the
_____________ group of another; is formed by a __________________ reaction
3. two amino acids fastened together by a peptide bond is called a _____________,
several amino acids fastened together by peptide bonds are called a
____________________
D. the ____________________ of amino acids determine the ____________________ (and
thus the properties) of a protein
E. proteins have 4 levels of organization or structure
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1. primary structure (1) of a protein is the sequence of _____________
_____________ in the _____________ chain
2. secondary structure (2) of a protein results from _____________ bonds involving
the backbone, where the peptide chain is held in structures, either a coiled α-helix or
folded β-pleated sheet; proteins often have both types of secondary structure in
different regions of the chain
3. tertiary structure (3) of a protein is the overall _____________ shape of a
_____________ polypeptide chain, determined by _____________ structure
combined with _____________ between _____________ groups (NOTE: book
defines this in a confusing way, use my way)
4. quaternary structure (4) of a protein results from _____________ between
_____________ or more _____________ polypeptide chains
 the interactions are of the same type that produce 2 and 3 structure in a single
polypeptide chain
 when present, 4 structure is the final _____________-_____________ structure of
the protein (the protein ___________________)
 example: hemoglobin has _______ polypeptide chains
 not all proteins have _____ structure
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5. ultimately the secondary, tertiary, and quaternary structures of a protein derive from its
________________ structure, but molecular _________________ may aid the
folding process
6. protein conformation determines _____________
7. denaturation is __________________ of a protein, disrupting 2, 3, and 4 structure
 changes in _____________, _____________, or exposure to various
_____________ can cause denaturation
 denatured proteins typically _____________ perform their normal biological
function
 denaturation is generally _____________
F. enzymes are _________________ substances that regulate the _____________ of the
chemical ________________ in living organisms; most _____________ are
_____________ (covered in some detail later in this course)
G. “related compounds” –amino acids; modified amino acids; polypeptides too short to be
considered true proteins; and modified short polypeptides
p.39 #1-3
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Nucleic Acids
VI.
nucleic acids transmit ________________ information by determining what
________________ a cell makes
A. two classes of nucleic acids found in cells: ________________ acid (DNA) and ________________ acid (RNA)
1. DNA carries the ________________ ________________ cells use to make ________________
2. RNA functions in ________________ ________________ according to mechanisms
we will learn about in gr.12.
B. nucleic acids are ________________ made of ________________ monomers
1. a nucleotide consists of
 a five-carbon ________________ (ribose or deoxyribose)
 one or more ________________ groups, and
 a ________________ base, an organic ring compound that contains nitrogen
2. purines are ________________ -ringed nitrogenous bases
3. pyrimidines are ________________ -ringed nitrogenous base
C. DNA typically contains the purines ________________ (A) and ________________
(G), and the pyrimidines ________________ (C) and ________________ (T)
D. RNA typically contains the purines ________________ (A) and ________________ (G),
and the pyrimidines ________________ (C) and ________________ (U)
E. nucleotides are fastened together by ________________________ bonds
1. the ________________ group of one nucleotide is fastened to the ________________
of the adjacent nucleotide
2. the joining is yet another _________________________________ reaction
3. the way that they are joined creates a ___________________________ strand
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F. the sequence of the 4 ________________ fastened to the ________________ -phosphate
backbone is genetic information
G. DNA is typically a ________________ stranded molecule
1. the two ________________ twist into a double ________________
2. ________________ bonds between the ________________ bases of opposite strands
hold the strands together
3. DNA can easily replicate because of ________________________ base pairing. This
means that the sequence of one strand of DNA ________________ the sequence
for the __________________________ strand of DNA.
 A matches with ______
 G matches with ______
H. RNA is typically a ________________ stranded nucleic acid molecule, having only a
single _______________________ chain
I. “related compounds” – nucleotides, modified nucleotides, dinucleotides
J. some single and double nucleotides with important biological functions:
1. ________________ tri________________ (ATP) is an important ________________ carrying compound in ________________
2. cyclic adenosine ________phosphate (cAMP) is a ________________ intermediary
compound
3. ________________ adenine ________________ (NAD+) is an ________________
carrier which is oxidized or reduced (loses or gains electrons) in many
________________ reactions
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Review of Biological Molecules
1. Discuss hydrolysis and condensation/dehydration, and the connection
between them.
2. Carbohydrates: what are they, and what are they used for? What terms are
associated with them (including the monomers and the polymer bond
name)? Give some examples of molecules in this group.
3. Lipids: what are they, and what are they used for? What terms are
associated with them (including majors classes and bond names)? Give
some examples of molecules in this group.
4. Polypeptides/Proteins: what are they, and what are they used for? What
terms are associated with them (including the monomers and the polymer
bond name)? Give some examples of molecules in this group.
5. Discuss the four levels of protein structure.
6. Nucleic acids: what are they, and what are they used for? What terms are
associated with them (including the monomers and the polymer bond
name)? Give some examples of molecules in this group.
7. What are 5’ and 3’ ends? What does “antiparallel” mean in DNA?
8. What are ATP, cAMP, and NAD+?
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KEY
What are the major types of organic molecules?
1.
many biological molecules are polymers
A. polymers are long chains or branching chains based on repeating subunits (monomers)
 example: proteins (the polymer) are made from amino acids (the monomers)
 example: nucleic acids (the polymer) are made from nucleotides (the monomers)
B. very large polymers (hundreds of subunits or more) are called macromolecules
C. polymers are degraded into monomers by hydrolysis (“break with water”)
 typically requires an enzyme to occur at a decent rate
 hydrogen from water is attached to one monomer, and a hydroxyl from water is attached to the other
D. monomers are covalently linked to form polymers by condensation/dehydration
 also typically requires an enzyme to occur at a decent rate
 typically the equivalent of a water molecule is removed (dehydration synthesis)
2.
The four major classes of biologically important organic molecules are: carbohydrates, lipids, proteins or polypeptides (and
related compounds), and nucleic acids (and related compounds)
3.
carbohydrates include sugars, starches, and cellulose
A. carbohydrates contain only the elements carbon, hydrogen, and oxygen
B. the ratio works out so that carbohydrates are typically (CH2O)n
C. carbohydrates are the main molecules in biological systems created for energy storage and consumed for energy production;
some are also used as building materials
D. grouped into monosaccharides, disaccharides, and polysaccharides
 monosaccharides are simple sugars (a single monomer)
 have 3, 4, 5, 6, or 7 carbons
 referred to as trioses, tetroses, pentoses, hexoses, and heptoses
 examples of pentoses include ribose and deoxyribose (part of nucleic acids)
 examples of hexoses include glucose, fructose, and galactose; glucose is most abundant
 Examine the three different ways of representing glucose. All describe the same formula of C6H12O6
 disaccharides consist of two monosaccharide units
 the two monomers are joined by a glycosidic linkage or glycosidic bond
 formed when the equivalent of a water molecule is removed from the two monosaccharides
 an oxygen atom is bound to a carbon from each momomer
 typically, the linkage is between carbon 1 of one and 4 of the other
 maltose, sucrose, and lactose are common disaccharides
 maltose (malt sugar): has two glucose subunits
 sucrose (table sugar): glucose + fructose
 lactose (milk sugar): glucose + galactose
 polysaccharides are macromolecules made of repeating monosaccharides units linked together by glycosidic bonds
 number of subunits varies, typically thousands
 can be branched or unbranched
 some are easily broken down and are good for energy storage (examples: starch, glycogen)
 some are harder to break down and are good as structural components (example: cellulose)
 starch is the main storage carbohydrate of plants
 polymer made from α-glucose units linked primarily between carbons 1 and 4
 plants store starches in organelles called amyloplasts, a type of plastid
 glycogen is the main storage carbohydrate of animals
 similar to starch, but very highly branched and more water-soluble
 is NOT stored in an organelle; mostly found in liver and muscle cells
 cellulose is the major structural component of most plant cell walls
 polymer made from -glucose units linked primarily between carbons 1 and 4 (similar to starch, but note that the
1-4 linkage makes a huge difference)
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

unlike starch, most organisms cannot digest cellulose (we lack the ability to break the link between the units of
glucose)
 cellulose is a major constituent of cotton, wood, and paper
 cellulose contains ~50% of the carbon in found in plants
 fibrous cellulose is the “fiber” in your diet
 some fungi, bacteria, and protozoa make enzymes that can break down cellulose
 animals that live on materials rich in cellulose, e.g. cattle, sheep and termites, contain microorganisms in their
gut that are able to break down cellulose for use by the animal
carbohydrates can be modified from the basic (CH2O)n formula
 many modified carbohydrates have important biological roles
 example: chitin – structural component in fungal cell walls and arthropod exoskeletons
 example: galactosamine in cartilage
 example: glycoproteins and glycolipids in cellular membranes
4.
lipids are fats and fat-like substances
A. lipids are a heterogeneous group of compounds defined by solubility, not structure
B. oily or fatty compounds
C. lipids are principally hydrophobic, and are relatively insoluble in water (some do have polar and nonpolar regions)
 lipids consist mainly of carbon and hydrogen
 some oxygen and/or phosphorus, mainly in the polar regions of lipids that have such regions
D. roles of lipids include serving as membrane structural components, as signaling molecules, and as energy storage molecules
E. major classes of lipids that you need to know are triacylglycerols (fats), phospholipids, and steroids
F. triacylglycerols contain glycerol joined to three fatty acids
 glycerol is a three carbon alcohol with 3 -OH groups
 a fatty acid is a long, unbranched hydrocarbon chain carboxyl group at one end
 saturated fatty acids contain no carbon-carbon double bonds (usually solid at room temp)
 unsaturated fatty acids contain one or more double bonds (usually liquid at room temp)
 monounsaturated – one double bond
 polyunsaturated – more than one double bond
 about 30 different fatty acids are commonly found in triacylglycerols; most have an even number of carbons
 condensation results in an ester linkage between a fatty acid and the glycerol
 one attached fatty acid = monoacylglycerol
 two = diacylglycerol
 three = triacylglycerol
 triacylglycerols (also called triglycerides) are the most abundant lipids, and are important sources of energy
G. phospholipids consist of a diacylglycerol molecule, a phosphate group esterified to the third -OH group of glycerol, and an
organic molecule (usually charged or polar) esterified to the phosphate
 phospholipids are amphipathic; they have a nonpolar end (the two fatty acids) and a polar end (the phosphate and
organic molecule)
 this is often drawn with a polar “head” and two nonpolar “tails”
 the nonpolar (or hydrophobic) portion of the molecule tends to stay away from water, and the polar (or hydrophilic)
portion of the molecule tends to interact with water
 because of this character phospholipids are important constituents of biological membranes
H. steroids have a backbone of four carbon rings
 side chains extend from the rings; length and structure of the side chains varies
 one type of steroid, cholesterol, is an important component of cell membranes
 other examples: many hormones such as testosterone, estrogens
5.
proteins are macromolecules that are polymers formed from amino acids monomers
A. proteins have great structural diversity and perform many roles
B. roles include enzyme catalysis, defense, transport, structure/support, motion, regulation; protein structure determines protein
function
C. proteins are polymers made of amino acid monomers linked together by peptide bonds
 amino acids consist of a central or alpha carbon; bound to that carbon is a hydrogen atom, an amino group (-NH2), a
carboxyl group (-COOH), and a variable side group (R group)
 the R group determines the identity and much of the chemical properties of the amino acid
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
there are 20 amino acids that commonly occur in proteins; pay attention to what makes an R group polar, nonpolar,
or ionic (charged) and thus their hydrophobic or hydrophilic nature
 most amino acids have enantiomers; when this is so, the amino acids found in proteins are nearly always of the Lconfiguration
 plants and bacteria can usually make their own amino acids; many animals must obtain some amino acids from their
diet (essential amino acids)
 the peptide bond joins the carboxyl group of one amino acid to the amino group of another; is formed by a condensation
reaction
 two amino acids fastened together by a peptide bond is called a dipeptide, several amino acids fastened together by
peptide bonds are called a polypeptide
D. the sequence of amino acids determine the structure (and thus the properties) of a protein
E. proteins have 4 levels of organization or structure
 primary structure (1) of a protein is the sequence of amino acids in the peptide chain
 secondary structure (2) of a protein results from hydrogen bonds involving the backbone, where the peptide chain is
held in structures, either a coiled α-helix or folded β-pleated sheet; proteins often have both types of secondary
structure in different regions of the chain
 tertiary structure (3) of a protein is the overall folded shape of a single polypeptide chain, determined by secondary
structure combined with interactions between R groups (NOTE: book defines this in a confusing way, use my way)
 quaternary structure (4) of a protein results from interactions between two or more separate polypeptide chains
 the interactions are of the same type that produce 2 and 3 structure in a single polypeptide chain
 when present, 4 structure is the final three-dimensional structure of the protein (the protein conformation)
 example: hemoglobin has 4 polypeptide chains
 not all proteins have 4 structure
 ultimately the secondary, tertiary, and quaternary structures of a protein derive from its primary structure, but molecular
chaperones may aid the folding process
 protein conformation determines function
 denaturation is unfolding of a protein, disrupting 2, 3, and 4 structure
 changes in temperature, pH, or exposure to various chemicals can cause denaturation
 denatured proteins typically cannot perform their normal biological function
 denaturation is generally irreversible
F. enzymes are biological substances that regulate the rates of the chemical reactions in living organisms; most enzymes are
proteins (covered in some detail later in this course)
G. “related compounds” –amino acids; modified amino acids; polypeptides too short to be considered true proteins; and
modified short polypeptides
6.
nucleic acids transmit hereditary information by determining what proteins a cell makes
A. two classes of nucleic acids found in cells: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)
 DNA carries the genetic information cells use to make proteins
 RNA functions in protein synthesis according to mechanisms we will discuss later in the semester
B. nucleic acids are polymers made of nucleotide monomers
 a nucleotide consists of
 a five-carbon sugar (ribose or deoxyribose)
 one or more phosphate groups, and
 a nitrogenous base, an organic ring compound that contains nitrogen
 purines are double-ringed nitrogenous bases
 pyrimidines are single-ringed nitrogenous bases
C. DNA typically contains the purines adenine (A) and guanine (G), and the pyrimidines cytosine (C) and thymine (T)
D. RNA typically contains the purines adenine (A) and guanine (G), and the pyrimidines cytosine (C) and uracil (U)
E. nucleotides are fastened together by phosphodiester bonds
 the phosphate group of one nucleotide is fastened to the sugar of the adjacent nucleotide
 the joining is yet another condensation reaction
 the way that the are joined creates a polynucleotide strand with 5’ and 3’ ends
F. the sequence of the 4 bases fastened to the sugar-phosphate backbone is genetic information
G. DNA is typically a double stranded molecule
 the two strands twist into a double helix
 hydrogen bonds between the nitrogenous bases of opposite strands hold the strands together
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 the two strands are antiparallel
H. RNA is typically a single stranded nucleic acid molecule, having only a single polynucleotide chain
I. “related compounds” – nucleotides, modified nucleotides, dinucleotides
J. some single and double nucleotides with important biological functions:
 adenosine triphosphate (ATP) is an important energy carrying compound in metabolism
 cyclic adenosine monophosphate (cAMP) is a hormone intermediary compound
 nicotinamide adenine dinucleotide (NAD+) is an electron carrier which is oxidized or reduced in many metabolic
reactions
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