Macromolecules Overview

Macromolecules, Page 1 of 36
Carbohydrates
Nucleic Acids
Macromolecules
Proteins
Table of Contents
Note to Students .......................................................................................................................................... 3
Objectives (all) and Video Links ................................................................................................................ 4-5
Section 1 (Carbohydrates)....................................................................................................................... 6-17
A. Monosaccharides................................................................................................................................ 7
1. Stereoisomers............................................................................................................................ 7
2. Anomers ................................................................................................................................. 7-9
3. Epimers ............................................................................................................................... 10-11
4. Reactions of monosaccharides ................................................................................................ 11
5. Activated monosaccharides .................................................................................................... 11
B. Disaccharides and Polysaccharides ............................................................................................ 11-13
C. Glycoproteins and Proteoglycans ............................................................................................... 13-14
D. Focus Questions .......................................................................................................................... 15-17
Section 2 (Nucleic Acids) ....................................................................................................................... 18-27
A. DNA Composition and Structure ................................................................................................. 18-19

B. Chromosomal Packaging ............................................................................................................. 19-23
C. RNA ............................................................................................................................................. 23-26

D. Focus Questions................................................................................................................................ 27
Section 3 (Proteins) .............................................................................................................................. 28-36

A. Amino Acids and Peptide Bonds .................................................................................................. 28-31
B. Protein Structure .......................................................................................................................... 32-35
C. Prosthetic Groups and Isoforms........................................................................................................ 36
D. Focus Questions ............................................................................................................................... 36
Note to Students:
This independent learning module describes the three major types of macromolecules
(carbohydrates, nucleic acids and proteins). It is meant to introduce you to the nomenclature and
general features of the macromolecules. There is no need to memorize any structures. The
learning objectives are designed to help guide you through the most important points.
Objectives and Video Links:

Carbohydrates:
1. define the term, carbohydrate
2. Compare and contrast glucose (blood sugar), fructose (fruit sugar) and galactose (milk sugar).
3. explain:
a. why glucose is defined as an aldohexose monosaccharide
b. the difference between D and L isomers, and note which is primarily found in the body
c. the difference between α and β isomers
d. why galactose and mannose are epimers of glucose
e. the terms anomeric carbon and reducing sugar
f. how a Clinitest differs from a glucose oxidase test
g. how glucuronic acid and sorbitol are derived from glucose
h. the difference between glucose and N-acetyl glucosamine
i. how glucose gets activated for metabolism
4. demonstrate knowledge of the structure of, composition of, and linkages in the disaccharides
lactose, sucrose, and maltose; know the general names of the enzymes that form and
hydrolyze these linkages
5. demonstrate knowledge of the structure of the homopolysaccharides glycogen, starch, and
cellulose with attention to the linkages between the monomeric units
6. compare and contrast N- and O-glycosylation of proteins
7. demonstrate knowledge of the characteristics, repeating unit, source and consequence of the
negative charges in glycosaminoglycans (GAGs)
8. state the cause of the mucopolysaccharidoses (MPS); compare and contrast Hurler and
Hunter syndromes (from the Independent Exploration in Biochemistry [IEB])
video link: https://1513041.mediaspace.kaltura.com/media/Carbohydrates/1_6emi4wks
Nucleic Acids:
1. the difference in the structural components of DNA and RNA
2. the monomeric units
3. the bonds that link the sugar and the base, and those that link the monomers
4. for DNA:
a. the double-helical structure of DNA including arrangement of the complementary
chains, the forces that hold them together, the designation of the ends, and the grooves
that form.
b. why GC pairs are harder to separate than AT pairs
c. the key differences between B, A and Z DNA
d. what is meant by denaturation (and the forces affected), how DNA can be denatured,
and why it can renature
e. what breaks phosphodiester bonds in DNA
f. chromatin including histone proteins and their charge, nucleosomes and their structure,
and hetero- and euchromatin
5. for RNA:
a. its structure and composition
b. the effect of alkali
c. the three main types and their functions
d. the post-transcriptional modifications to eukaryotic mRNA and to tRNA
e. the difference between coding and ncRNA
f. ribozymes
video link: https://1513041.mediaspace.kaltura.com/media/Macromolecules2/1_xfryx2pn
Proteins:
1. Define and discuss the following terms: peptide bond, peptide backbone, N-terminus, C-
terminus, disulfide bridge, α-helix, β-strand, β-sheet, β-turn, and prosthetic group.
2. Define the basic properties of the amino acid side chains (hydrophilic, hydrophobic, acidic,
basic, etc.)
3. Discuss how the inclusion of unusual amino acids (glycine, proline, and cysteine) affects the
structure of a protein.
4. Discriminate among primary, secondary, tertiary, and quaternary protein structures.
5. Define and discuss supersecondary structures (including zinc fingers, used for binding to
DNA)
6. Propose reasons why folded proteins have a finite number of conformations.
7. Define the function of a protein chaperone.
8. Define and discuss the role of noncovalent forces in stabilizing the structure of a protein
(hydrogen bonds, electrostatic interactions, salt bridges, and van der Waals forces).
9. Define protein isoforms.
video link: https://1513041.mediaspace.kaltura.com/media/Macromolecules3/1_wjsvcppl
SECTION 1 (CARBOHYDRATES)
Objectives for Carbohydrates

Students should be able to:
1. define the term, carbohydrate
2. Compare and contrast glucose (blood sugar), fructose (fruit sugar) and galactose (milk sugar).
3. explain:
a. why glucose is defined as an aldohexose monosaccharide
b. the difference between D and L isomers, and note which is primarily found in the body
c. the difference between α and β isomers
d. why galactose and mannose are epimers of glucose
e. the terms anomeric carbon and reducing sugar
f. how a Clinitest differs from a glucose oxidase test
g. how glucuronic acid and sorbitol are derived from glucose
h. the difference between glucose and N-acetyl glucosamine
i. how glucose gets activated for metabolism
4. demonstrate knowledge of the structure of, composition of, and linkages in the disaccharides
lactose, sucrose, and maltose; know the general names of the enzymes that form and
hydrolyze these linkages
5. demonstrate knowledge of the structure of the homopolysaccharides glycogen, starch, and
cellulose with attention to the linkages between the monomeric units
6. compare and contrast N- and O-glycosylation of proteins
7. demonstrate knowledge of the characteristics, repeating unit, source and consequence of the
negative charges in glycosaminoglycans (GAGs)
8. state the cause of the mucopolysaccharidoses (MPS); compare and contrast Hurler and
Hunter syndromes (from the Independent Exploration in Biochemistry [IEB])
Video: https://1513041.mediaspace.kaltura.com/media/Carbohydrates/1_6emi4wks
Carbohydrates are defined as polyhydroxy aldehydes or ketones (and their derivatives)
1. polyhydroxy: contains several hydroxyl (-OH) groups

aldehyde:
ketone:
2. simplest examples (shown as Fischer projection formulas)

Classification
A. Monosaccharides: simple sugars
1. Stereoisomers
Grouped by number of carbons and by carbonyl group; examples include
2. Anomers
Glucose (blood sugar): an aldohexose
a. the most abundant monosaccharide
1) form in which bulk of dietary carbohydrate is absorbed in

the intestine
2) major metabolic fuel of the body
3) precursor of many carbohydrates in the body
b. a typical monosaccharide
1) contains asymmetric (chiral) carbons (carbons attached to

four different atoms or groups), and so exists as
stereoisomers (same molecular formula but different
spatial configuration)
2) number of possible isomers is 2n, where n equals the

number of asymmetric carbons; for glucose, 24 or 16
possible isomers. Focus on D and L, α and β, and epimers.
(Note, however, that aldose/ketose isomerization, for
example glc 6-P ↔ frc 6-P, is important and will be
emphasized in glycolysis.)
3) D & L isomers are mirror images (enantiomers).
i) D if the OH on the asymmetric C farthest from the

carbonyl C projects to the right; L if left. Note: C #1
is at top as numbering begins at the end closest to
the carbonyl group.
ii) D form in the body; enzymes are specific for this
form; racemization, racemases.
iii) dextrose
4) α and β isomers are the result of ring formation in solution;

pyranose (6-membered) ring for glucose
i) aldehyde plus alcohol produces internal hemiacetal;

C #1 now is asymmetric; α and β isomers known as
anomers result.
ii) α if the OH on C # 1 projects to the same side as the
ring in a modified Fischer formula; β if the opposite
side. α and β isomers spontaneously (but slowly)
equilibrate through mutarotation.
iii) α if the OH and the CH2OH on the carbons linked by the O are
trans, with the OH pointing down in a Haworth formula; β if cis and
up.
5) Cyclization creates an anomeric carbon, i.e., the C of the original aldehyde

now bound to ring O, or a carbon simultaneously linked to two oxygens.
6) epimers: isomers that differ in the position of OH at only one carbon; not
mirror images so diasteriomers; epimerization, epimerases
Note: α and β forms of the same monosaccharide are a special type of epimer that differ only at
the anomeric C and so are called anomers; α and β - D glc. Epimers and isomers: glucose and
galactose as well as glucose and mannose are epimers because they differ in the stereochemistry
about a single chiral carbon. Galactose and mannose cannot be epimers because they differ at
two chiral carbons and are, therefore, isomers of one another.
3. Epimers
Oxidation-reduction reactions of monosaccharides
a. reducing sugar: anomeric C has OH available (i.e. not involved in bond
formation) to be oxidized as something else is reduced. A reducing sugar is
any sugar that can act as a reducing agent because it has a free aldehyde or
ketone group. All monosaccharides are reducing sugars. A ketose must
tautomerize to an aldose before it becomes a reducing sugar. Shown below is
fruit sugar or fructose.
b. Urine tests for glucose and reducing sugars
are available. Glucose oxidase is used to oxidize
glucose to a gluco-lactone plus H2O2. Peroxidase
is then used to visualize the H2O2. Clinitest, for
example, uses Benedict’s reagent (copper
reduction) to test for the presence of reducing
sugars in urine.
c. oxidation of terminal OH group
d. reduction of carbonyl C; yields new OH; creates a polyol

e. reduction of OH on
C #2; yields deoxy
sugar
4. Reactions of
monosaccharides
Monosaccharides can undergo replacement reactions
a. replace OH (usually at C #2) with NH2; yields an

amino sugar. The NH2 can be acetylated
producing N-acetylglucosamine
5. Activated monosaccharides
Monosaccharides get activated as a first step in their metabolism
a. b.
B. Disaccharides and Polysaccharides

Monosaccharides can be linked together; form glycosides
1. disaccharides . . . oligosaccharides . . . polysaccharides
2. glycosidic or glycosyl bond formed by glycosyltransferases via condensation of

OH on anomeric C with an OH of another sugar. [These bonds are cleaved by
glycosidases/glycosylases.]
3. important disaccharides (need to know)
1. lactose (milk sugar): galactose +

glucose. Is lactose a reducing sugar?
b. sucrose (table sugar): glucose +

fructose. Reducing sugar?
Note that in fructose, C2 is the

anomeric C.
c. maltose: glucose + glucose through

α 1,4 glycosidic bonds
4. important polysaccharides that

are homopolymers of glucose
a. glycogen: storage form

of glucose in animals.
1) branched polymer
of α–D-glucose
2) reducing versus
non-reducing ends
b. starch: storage form of glucose in plants

1) contains unbranched polymer of α-D-glucose, amylose
and a branched polymer, amylopectin (like glycogen but with fewer

branches)
c. cellulose: structural component of plant cell walls

1) unbranched polymer of β-D-glucose
5. Polymers of sugars differ from polymers of amino acids or nucleotides.
C. Glycoproteins and Proteoglycans

Complexes of carbohydrate and protein: glycoproteins vs proteoglycans
1. glycoPROTEINS: proteins with short, often branched chains of oligosaccharides
attached
2. proteoGLYCANS: large complexes of negatively charged heteropolysaccharides
associated with a small amount of protein (core protein); important components of
the extracellular matrix (ECM).
a. heteropolysaccharide chain = glycosaminoglycan (GAG)
mucopolysaccharide; long, unbranched, negatively charged
b. contains a repeating unit [acidic sugar-amino sugar]n usually
[glucuronate glucosamine] where the glucosamine frequently is acetylated
and often is sulfated; sulfate and carboxylate groups confer negative
charge.
1) Galactosamine may replace glucosamine.

2) Glucuronate may be converted to its C5 epimer, L-iduronate.
c. Large net negative charge favors extended conformation (bottle brush)

and extensive hydration; used as extracellular shock absorbers, lubricants,
molecular sieves.
d. Chondroitin sulfates, the most abundant proteoglycan GAGS in humans,

contain the repeating unit: [D-glucuronate — N-acetyl-D-galactosamine-
6(4)-sulfate]n
e. Chondroitin sulfates are one of six classes of proteoglycan GAGS (for

reference only)
1) chondroitin sulfates 5) hyaluronate (not attached to core
protein;
2) dermatan sulfate not sulfated)
3) heparan sulfate 6) keratan sulfate (has gal instead of
acidic
4) heparin (intracellular) sugar)
f. Deficiencies in the ability to degrade any one of the proteoglycan GAGS

(mucopolysaccharides), due to a deficiency in a lysosomal enzyme, lead
to pathology: mucopolysaccharidoses.
(Note: The mucopolysaccharidoses are the topic of the first Independent

Exploration Exercise)
D. Focus Questions
1. Which is the ketose sugar?
A. C. both
B. D. neither
2. Which is the D-isomer?
A. C. both
B. D. neither
3. Which is the α isomer?
A. C. both
B. D. neither
4. Which disaccharide is a reducing sugar? Which disaccharide has β-linkage? Which

disaccharide is lactose? Which disaccharide contains fructose?
A. C. both
B. D. neither
5. Which pair is epimers? Which is anomers?
A. α-D-glucose and β-D-glucose C. both

B. α-D-glucose and α-D-galactose D. neither
6. Define:
A. pyranose ring
B. racemization, mutarotation, epimerization
C. anomeric carbon
D. homopolymer
E. mucopolysaccharide and mucopolysaccharidoses
7. What are the two activated forms of glucose?
8. What monosaccharide(s) is/are found in glycogen? lactose? sucrose? maltose?
9. How does glycogen differ from cellulose in terms of structure?
10. In an O-glycosidic linkage in a glycoprotein, the OH of the sugar is linked to what? In an

N-linkage in a glycoprotein, the OH of the sugar is linked to what?
11. What is the general repeating disaccharide unit of a GAG (mucopolysaccharide)? What
is the net charge? How does this relate to structure? to function?
12. What is L-iduronate, and why is it unusual? (Hint: note the L.)
Answers to the 5 MCQ:

1. B
2. A
3. C (alpha; same side; trans)
4. A, A, A, B
5. C, A
SECTION 2 (NUCLEIC ACIDS)
Objectives for Macromolecules 2: Nucleic Acids

Students should be able to explain/describe:
1. the difference in the structural components of DNA and RNA
2. the monomeric units
3. the bonds that link the sugar and the base, and those that link the monomers
4. for DNA
a. the double-helical structure of DNA including arrangement of the complementary chains,
the forces that hold them together, the designation of the ends, and the grooves that form.
b. why GC pairs are harder to separate than AT pairs
c. the key differences between B, A and Z DNA
d. what is meant by denaturation (and the forces affected), how DNA can be denatured, and
why it can renature
e. what breaks phosphodiester bonds in DNA
f. chromatin including histone proteins and their charge, nucleosomes and their structure,
and hetero- and euchromatin
5. for RNA:
a. its structure and composition
b. the effect of alkali
c. the three main types and their functions
d. the post-transcriptional modifications to eukaryotic mRNA and to tRNA
e. the difference between coding and ncRNA
f. ribozymes
video: https://1513041.mediaspace.kaltura.com/media/Macromolecules2/1_xfryx2pn
A. DNA Composition and Structure
Sugar and phosphoryl group linked by ester bond. Nucleotide monophosphate (NMP) monomers are
linked by 3′-5′ phosphodiester bonds.
Pairing between the bases. The concept of "base-pairing" via H-bonding between the
hydrophilic edges of the bases is shown below:
1) adenine base-pairing with thymine is stabilized by 2

hydrogen bonds.
2) guanine base-pairing with cytosine is stabilized by 3

hydrogen bonds.
1o Structure: the sequence of the NMP monomers
B. Chromosomal Packaging
This specific base-pairing restriction results in:
1) the two strands of the double helix being complementary; only A,T pairing or C,G pairing occurs
between strands. In DNA the amount of dA equals dT, and dG = dC.
2) the two strands being antiparallel, that is they run in the opposite direction, forming a right-
handed helix.
2o Structure: the double helix

The two DNA strands form a twisted right-handed helix. The
base pairs that join the two strands are stacked like a spiral
staircase along the central axis of the helix. This “base stacking”
decreases the contact between water and the hydrophobic face
of a base (hydrophobic effect), and is a key stabilizing force of
the double helix. Electronic interactions (van der Waals forces)
between the stacked bases further stabilize the helix, as do the
H-bonds formed between complementary bases at their
hydrophilic edges.
The helix contains grooves of alternating size (major and minor)

that allow for the interaction of proteins and/or other molecules.
These ‘grooves’ allow for the binding of proteins that function as

transcription factors and are involved in RNA synthesis and gene
expression.
Disruption of the helical structure of DNA is referred to as denaturation or melting, and is essential
for replication and transcription. The reassembly of two separated strands in perfect register is
referred to as renaturation or annealing.
1) Denaturation of DNA:
a) Alkali treatment (pH > 11.3) causes the two strands of DNA to melt, i.e. H-bonds
are broken It does not destroy phosphodiester bonds of DNA.
b) Heat is also used to convert double-stranded DNA to single-stranded DNA.
The midpoint of heat denaturation (Tm) is precisely correlated with the average
base composition of the DNA; the higher the GC/AT ratio, the higher the Tm.
This is due to the three hydrogen bonds resulting from GC base-pairing and to
stacking interactions.
2) Renaturation of DNA:
a) Denatured DNA can realign and base-pair,

reforming a double helix essentially identical to
the original DNA. PCR (polymerase chain
reaction) takes advantage of multiple cycles of
heat denaturation/renaturation in order to
synthesize multiple copies of (amplify) DNA
templates of interest.
b) Denatured DNA can go through the process of hybridization and anneal with
complementary mRNA strands. Hybridization is extensively used in clinical
and research testing.
Structure of eukaryotic chromosomes:
A) 1,000 X more DNA than in prokaryotes (human nuclear DNA: ~3 X 109 bp per haploid cell,
1 METER; there are ~19,000 protein-coding genes).
B) ~30% consists of repetitive sequences.
Note: DNA is also found in mitochondria: mtDNA. mtDNA is double strandeds & circular, it codes
for just 13 proteins, and is found in multiple copies in the mitochondrial matrix.
The DNA in eukaryotic chromosomes exists in a highly compacted form known as nucleohistone
or chromatin. Nucleohistone consists primarily of DNA and proteins called histones. There are
five classes of histones: H1, H2A, H2B, H3, and H4.
Histones are proteins which:

i) are basic (+ charge since highly enriched for lys
and arg); recall DNA is acidic
ii) are highly conserved across species lines
iii) contain functional domains that are involved in
histone-histone and histone-DNA interactions
iv) have NH2-terminal “tails” on core histones that are
sites for covalent modifications such as acetylation
and phosphorylation that affect interactions with
DNA.
The interaction of DNA with histone proteins gives rise to nucleosome structures "Beads on a
String" in which DNA is wrapped around a core of histones. This wrapping generates supercoiled
DNA.
The histones H2A, H2B, H3, and H4 make up the nucleosome core forming an octamer, while
histone H1 is bound to the
linker DNA between each
nucleosome. Non-histone
proteins also are present in
nucleosomes.
Further compaction occurs

as the strings of
nucleosomes wind into
helical, tubular coils
(nucleofilaments or 30 nm
fiber or solenoid structures)
giving rise to higher order
DNA structures.
The solenoid structures can

further compact to ultimately form a chromosome.
Differential compaction:
i) euchromatin – less compacted, transcriptionally active
ii) heterochromatin – more compacted, transcriptionally inactive
C. RNA
General Features of RNA Structure
1) RNA is similar to DNA in that it is composed of nucleotides joined by 3' to 5'

phosphodiester bonds.
2) In RNA, the sugar is ribose that contains an hydroxyl group on the 2'-carbon.
Consequence is that alkaline hydrolysis will cleave phosphodiester links in RNA, in
contrast to DNA.
3) RNA contains the purine bases adenine
and guanine, and the pyrimidine bases
cytosine and uracil. It does not incorporate
thymine into its nucleotide chain.
4) RNA strands are single-stranded, rather than double-stranded as in DNA, and are
linear. Some RNAs, however, contain short regions of intramolecular base-pairing.
The three major types of RNA are mRNA, rRNA, and tRNA. All are required for protein synthesis.
mRNA
1) mRNA has considerable secondary and tertiary structure due to the formation of
loop-like structures within the RNA single strand.
a) When two regions of a ss RNA are complementary, they can base pair and
form a stem-loop or hairpin structure. The stem region is an A-form helix.
loop
G C
stem A U
A U
G C
G C
5′ 3′
2) mRNA is transcribed as a long primary transcript from regions of DNA that encode
for proteins; thus, these transcripts direct the biosynthesis of proteins. mRNA is
referred to as “coding RNA”.
3) The nascent mRNA is

further processed in
the nucleus then
transported into the
cytosol where it
ultimately directs
protein synthesis.
a) mRNAs contain
a 7-methylguanosine triphosphate attached at the 5′ hydroxyl group of the
ribose; known as the "methyl cap".
b) A poly(A) tail is attached to the 3′-end of eukaryotic mRNAs. This tail consists
of a series of adenosine monophosphates (AMP) joined by 3′-to-5′
phosphodiester bonds. As many as 200 adenine residues may be present in
a poly(A) tail.
c) The primary transcript (hnRNA or heterogeneous RNA) in eukaryotes is

processed in macromolecular complexes known as spliceosomes to form the
mRNA in the nucleus. Ribonucleoproteins associate with the hnRNA and are
involved in removing segments of the RNA that do not encode for amino acids
(introns) and joining the segments that do code for amino acids (exons).
tRNA
1) tRNAs are molecules which carry amino acids to ribosomes and ensure they are
incorporated into the appropriate positions in the growing polypeptide chain. They
are a type of ncRNA.
2) Cells contain at least 20 different tRNAs.
3) tRNA is characterized by a high percentage of modified bases. Most tRNAs contain

dihydrouridine (D), in which one of the double bonds of the base is reduced;
ribothymidine (T), in which a methyl group is added to uracil to form thymine; and
pseudouridine (ψ), in which uracil is attached to ribose by a carbon-carbon bond
rather than a nitrogen-carbon bond. (Structures shown are FYI).
a) T from U by methylation after U has been incorporated into RNA.
4) Most tRNA molecules

form 2ο structures that
resemble a cloverleaf; 3°
resembles inverted letter
“L”.
5) The loop closest to the 5'

end is known as the D-
loop because it contains
dihydrouridine (D). The second, or anticodon, loop contains the anticodon that base-
pairs with the codon on the mRNA, and the third loop (the TψC loop) contains both
ribothymidine (T) and pseudouridine (ψ). A fourth loop, known as the variable loop
because it varies in size, is frequently found between the anticodon and the Tψ
loops.
6) Base-pairing occurs in the stem regions, resulting in ds regions in ss RNA.

7) The CCA sequence at the 3′ end, added to all tRNAs as they are processed, is the
attachment site for the amino acid.
Ribozyme
1) RNA with catalytic activity
2) Example is rRNA of the large ribosomal subunit; it forms the peptide bond that links
amino acids in a protein.
D. Focus Questions
1. What are the three basic components of a nucleotide? What is the bond that binds
nucleotides in nucleic acids?
2. What forces are important in stabilizing the double helix? Why are GC pairs more stable
than AT pairs?
3. What base sequence is associated with formation of Z-DNA? What is a palindrome?
4. What types of treatment can denature DNA? How is RNA different?*
5. What are some differences between the genomes of E. coli and humans?
6. How does a mammalian cell consolidate its genetic material? What is euchromatin?
7. What are the components and what is the structure of a nucleosome? What charge do
histones carry, and why? What charge does DNA carry?
8. Is RNA double-stranded or single-stranded? What are the three main types of RNA in
eukaryotic cells? What is the function of each?
9. What are the modifications that occur to the primary transcript in the process of generating
mRNA molecules? (Details covered later.)
10. What constitutes a ribosome? How do prokaryotic and eukaryotic ribosomes differ?
11. What is the basic structure of a tRNA?
12. What are some of the modified bases found in a tRNA molecule?
13. What part of the tRNA structure is involved in amino acid binding?
14. What is meant by ncRNA? Is mRNA an example? rRNA? tRNA?
15. What is a ribozyme?
*FYI only
The 2′ OH on RNA can, under basic (alkaline) conditions, function as a nucleophile that cleaves
the phosphodiester linkage of the backbone, forming a 2′, 3′ cyclic phosphodiester on one
fragment and a free 5′ OH on the other.
SECTION 3 (PROTEINS)
Objectives for Macromolecules 3: Proteins

Students should be able to explain/describe:
1. Define and discuss the following terms: peptide bond, peptide backbone, N-terminus, C-
terminus, disulfide bridge, α-helix, β-strand, β-sheet, β-turn, and prosthetic group.
2. Define the basic properties of the amino acid side chains (hydrophilic, hydrophobic, acidic,
basic, etc.)
3. Discuss how the inclusion of unusual amino acids (glycine, proline, and cysteine) affects the
structure of a protein.
4. Discriminate among primary, secondary, tertiary, and quaternary protein structures.
5. Define and discuss supersecondary structures (including zinc fingers, used for binding to
DNA)
6. Propose reasons why folded proteins have a finite number of conformations.
7. Define the function of a protein chaperone.
8. Define and discuss the role of noncovalent forces in stabilizing the structure of a protein
(hydrogen bonds, electrostatic interactions, salt bridges, and van der Waals forces).
9. Define protein isoforms.
Videolink: https://1513041.mediaspace.kaltura.com/media/Macromolecules3/1_wjsvcppl
A. Amino Acids and Peptide Bonds
Amino acids:
Unusual amino acids:

The Peptide Bond:

The link between polymeric subunits in a carbohydrate is a
glycosidic bond. The link between the polymeric subunits in a
nucleic acid is the 3’-5’ phosphodiester bond. In proteins, it is
an amide bond (also known as a peptide bond). Because of the
resonance structure, the peptide bond behaves as a double
bond. In creating the bond, the lone pair of electrons from the
nitrogen attacks the backside of the carbonyl bond, splitting off
water and creating the new peptide bond.
The amide bond is planar, its dihedral

angle is either 0ο or 180ο and is known
as the omega (ω) angle. The torsion
angle formed between the nitrogen and
C-alpha carbon is the phi (φ) angle and
the torsion angle between the c-alpha
and carbonyl carbon is known as the psi
(ψ) angle. If the phi and psi angles for the whole protein are known, the
3-dimensional structure of the protein would also be known because
these angles determine protein structure.
There are several different descriptors to describe protein structure. A

protein’s primary structure is its sequence of amino acids. Stretches or
strands of proteins can have distinct local structural conformations or
secondary structure that depend on hydrogen bonding. The two main
types of secondary structure are the α-helix and the β-sheet. The
tertiary structure of a protein is the 3-dimensional shape of a single
chain that confers its biological activity. The quaternary protein
structure involves several protein chains that bind together to form a
biologically active complex.
Secondary Structure
There are four basic secondary structure motifs, three of which depend on internal hydrogen
bonding for stability.
• Beta Strand (extended chain)- This structure is an elongated straight chain that is
stabilized by hydrogen bonds that occur across the backbone, i.e. are perpendicular to the
backbone.
R1 O R3 O
H
HO N NH2
N N
H H
O R2 O R4
R5 O R7 O
H H
N N
H2N N OH
H
O R6 O R8
The arrows indicate the

Hydrogen bonding across direction of the main
the backbone chain (from amino-
toward carboxy-
terminus) and the “R”
groups represent the
amino acid side chains.
A parallel beta strand
occurs when both pairs
of the strand have the
same amino  carboxy
terminal orientation;
anti-parallel strands (as shown above) have opposite orientations. (shown below is a beta strand
as it appears in the context of the CD4 protein [protein database accession: 1cd4i]). Often this
elongated structure slightly zig-zags up and down forming pleats and is sometimes referred to as
a pleated sheet (β-sheet). The hydrogen bonding can be either intra-chain (as in the example
below) or can occur between adjacent chains (inter-chain).
• α-Helix (coiled chain)- One of the more common secondary structural motifs is the α-helix.
This structure resembles a coiled spring.
R1
N
H R3
R2
O
R5
R4
R7
R6
R7 R8
As is true for the β-sheet, the α-helix is stabilized by hydrogen bonding between the
nitrogen and oxygen on the backbone carbonyl. Unlike the β-sheet, the hydrogen bonding
of the α-helix can only occur in an intra-chain arrangement and parallel to the central axis.
As the amino acids spiral around a central axis, the backbone nitrogen (with a partial
positive charge) comes into hydrogen bonding distance [~2 Å] with the oxygen on the
backbone carbonyl that is 3.6 residues away (this is determined by the rise and pitch of
the helix). Because of the φ (phi) and ψ (psi) angles that need to be adopted by the amino
acid involved in a α-helix, it is difficult to incorporate a proline residue. The 5-membered
ring of proline causes a third bond to form with the backbone nitrogen, thus, this nitrogen
cannot participate in the required hydrogen bonding scheme of an α-helix.
• β-Turn- the turn motif is found in most proteins. The

β-turn is a small structured loop in the protein, stabilized
by a backbone hydrogen bond that causes the chain to
change directions. The ‘turn’ typically involves four amino
acids (usually including a pro and gly, in the loop.
• Random Coil- Essentially anything that cannot be

classified as helix, sheet or turn is a random coil. Random
coils are defined by their lack of “ordered” structure.
Supersecondary structure:
B. Protein Structure
Types of supersecondary structural motifs seen in DNA-binding proteins:
a) Helix-loop-Helix (dimer)
b) Zinc Finger
c) Leucine Zipper (dimer)
d) Homeodomain (contains helix-turn-helix)
Helix-loop-helix Zinc Finger

Helix
Helix-loop-helix
Loop Zinc Finger Cysteines
Histidines
Helix Cysteines
Histidines
Homeodomain
Leucine Zipper
Tertiary structure is the three dimensional structure of a single chain.
In the early 70’s, Chris Anfinsen did an interesting experiment. He

performed an experiment with a relatively small globular enzyme,
ribonuclease A. He took the catalytically active enzyme and complete
denatured it and reduced all of the disulfide bridges, rendering it
inactive. He dialyzed out all of the reagents, the protein refolded and
regained complete activity. Thus, he proved that the amino acid
sequence had all of the information necessary to refold the protein. He
got the Nobel Prize for this observation because until that point no one
believed that a protein could fold by itself without the help of an enzyme.
He was lucky to have used ribonuclease, a bigger protein might not have spontaneously refolded.
Protein Folding. As the amino terminus of a protein emerges from the ribosome, it immediately
starts the folding process. Secondary and
supersecondary structures form very quickly creating
a molten globule structure. With time, it folds into its
biologically active native structure. It turns out that
folding is largely dictated by the amino acid
sequence.
Chaperones were first discovered as heat shock proteins. When a cell is heated above its normal
physiologic temperature, A family of proteins is induced in the cell, known as heat shock proteins.
With more research, it was discovered that these proteins are actually chaperones that aid in the
re-folding of a protein. In the molten globule state of the protein, patches of hydrophobic residues
are often surface exposed. These are ‘sticky’ patches because of the hydrophobic effect. These
Sticky patches bind to one another and cause the protein to aggregate and possibly precipitate
before it can finish the folding process. Chaperones bind to the sticky patches preventing
aggregation so that the protein can find its final native state.
GroEL, a bacterial chaperone shown here is a great

example. The partially unfolded protein is allowed to
enter the ‘basket’, ATP is hydrolyzed and the energy
gained is used to change the conformation of the
chaperone to facilitate the folding process. ATP is
also hydrolyzed to facilitate the release of the folded
protein from the chaperone.
Quaternary Structure is the arrangement of multiple folded protein chains to create a multi
subunit complex. Hemoglobin is a good example. It is a functional complex comprised of two
alpha and two beta chains to form a tetramer.
β α
Hydrogen bonds
α
β
α2β 2 hemoglobin tetramer Triple Helix [Gly-Pro-Pro repeat]

Globular Protein Fibrous Protein
Subunits may associate to form oligomers (oligo = several or many & mer = body or subunits).
This association of subunits (which by themselves are usually devoid of activity) to form a
biologically active complex is known as the quaternary structure. The subunits can be identical
(homo) or different (hetero).
O HO O
HO
Some proteins are only biologically active
as a complex, consisting of the same or
different subunits. Hemoglobin, for
example, has a quaternary structure N N
consisting of two α-chains and two β- Fe
chains; and so is a heterotetrameric

N N
globular (compact) protein.
Subunits usually bind together via
noncovalent interactions, such as
hydrophobic interactions, hydrogen
binding and electrostatic interactions. Crystal structure of
Heme group used for
hemoglobin showing the carrying oxygen.
Outside of enzymatic functions, four prosthetic groups (the
quaternary structure is sometimes used heme groups)
to confer an appropriate mechanical
property. Collagen, for example, has three strands that come together to form a triple helix (not
a classical α-helix) using the motif Gly-X-Y (where X and Y can be most any amino acid but
frequently are proline and hydroxyproline, see below) to create a fibrous (elongated) protein.
C. Prosthetic Groups and Isoforms

Prosthetic Groups
As a final element of structure, it is important to note that some proteins require a prosthetic group
in order to be functionally active. Proteins sometimes incorporate non-amino acid groups (known
as prosthetic groups) to enable the functional attributes of the protein. The heme group for
hemoglobin aids in the oxygen transport function of the protein. The iron molecule in the center
of the heme prosthetic group binds molecular oxygen. Common prosthetic groups include
carbohydrate (glycoprotein), metal ions (metalloproteins), lipid (lipoproteins) and nucleic acid
(nucleoproteins).
Protein Isoforms
(iso meaning same & form meaning shape): A protein that has the same functions as another
protein, but which is encoded by the same or a different gene and may have small differences in
its sequence. For example, creatine kinase can be encoded by several different genes, giving rise
to different isoforms of the enzyme. One of the distinct isoforms is associated with the
myocardium and used as a marker for a myocardial infarct.
D. Focus Questions
1. Anfinsen showed that ribonuclease could refold without the aid of an enzyme. What
information did the protein use to refold?
2. Think of two different ways in which you could denature a protein.
3. Which of the two peptides shown below would be most readily water soluble:
G-L-V-Y or G-S-K-N?
4. Why might one of the two sequences below more readily participate in an alpha helix? G-
E-A-K-F or G-D-P-N-A
5. Why does the peptide bond carboxyl-nitrogen linkage exist either at 0° or 180°?
6. Why is the peptide bond more stable in the trans rather than the cis configuration?
7. What is the principle physical force that stabilizes secondary structures such as a beta
sheet or alpha helix?
8. What is the attractive force that allows that packing of atoms in the hydrophobic core of a
protein?
9. Distinguish between the effect of proline and of glycine on protein flexibility.
10. Protein phosphorylations are a major means of signaling inside a cell. Why does the
addition of a phosphate to a serine, threonine, or tyrosine make a major change to the
local environment of a protein?

Macromolecules Overview

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Macromolecules Overview

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Macromolecules, Page 1 of 36

Section 2 (Nucleic Acids) ....................................................................................................................... 18-27

A. DNA Composition and Structure ................................................................................................. 18-19

C. RNA ............................................................................................................................................. 23-26

Section 3 (Proteins) .............................................................................................................................. 28-36

Objectives and Video Links:

Objectives for Carbohydrates

Carbohydrates are defined as polyhydroxy aldehydes or ketones (and their derivatives)

1. polyhydroxy: contains several hydroxyl (-OH) groups

2. simplest examples (shown as Fischer projection formulas)

1) form in which bulk of dietary carbohydrate is absorbed in

2) major metabolic fuel of the body

3) precursor of many carbohydrates in the body

1) contains asymmetric (chiral) carbons (carbons attached to

2) number of possible isomers is 2n, where n equals the

3) D & L isomers are mirror images (enantiomers).

i) D if the OH on the asymmetric C farthest from the

4) α and β isomers are the result of ring formation in solution;

i) aldehyde plus alcohol produces internal hemiacetal;

5) Cyclization creates an anomeric carbon, i.e., the C of the original aldehyde

c. oxidation of terminal OH group

d. reduction of carbonyl C; yields new OH; creates a polyol

a. replace OH (usually at C #2) with NH2; yields an

B. Disaccharides and Polysaccharides

2. glycosidic or glycosyl bond formed by glycosyltransferases via condensation of

3. important disaccharides (need to know)

1. lactose (milk sugar): galactose +

b. sucrose (table sugar): glucose +

Note that in fructose, C2 is the

c. maltose: glucose + glucose through

4. important polysaccharides that

a. glycogen: storage form

b. starch: storage form of glucose in plants

and a branched polymer, amylopectin (like glycogen but with fewer

c. cellulose: structural component of plant cell walls

5. Polymers of sugars differ from polymers of amino acids or nucleotides.

C. Glycoproteins and Proteoglycans

1) Galactosamine may replace glucosamine.

c. Large net negative charge favors extended conformation (bottle brush)

d. Chondroitin sulfates, the most abundant proteoglycan GAGS in humans,

e. Chondroitin sulfates are one of six classes of proteoglycan GAGS (for

f. Deficiencies in the ability to degrade any one of the proteoglycan GAGS

(Note: The mucopolysaccharidoses are the topic of the first Independent

1. Which is the ketose sugar?

2. Which is the D-isomer?

3. Which is the α isomer?

4. Which disaccharide is a reducing sugar? Which disaccharide has β-linkage? Which

5. Which pair is epimers? Which is anomers?

A. α-D-glucose and β-D-glucose C. both

7. What are the two activated forms of glucose?

8. What monosaccharide(s) is/are found in glycogen? lactose? sucrose? maltose?

9. How does glycogen differ from cellulose in terms of structure?

10. In an O-glycosidic linkage in a glycoprotein, the OH of the sugar is linked to what? In an

Answers to the 5 MCQ:

SECTION 2 (NUCLEIC ACIDS)

Objectives for Macromolecules 2: Nucleic Acids

1) adenine base-pairing with thymine is stabilized by 2

2) guanine base-pairing with cytosine is stabilized by 3

1o Structure: the sequence of the NMP monomers

2o Structure: the double helix

The helix contains grooves of alternating size (major and minor)

These ‘grooves’ allow for the binding of proteins that function as