The three important structural features of proteins:
a. Primary (1o) – The amino acid sequence (coded by genes)
b. Secondary (2o) – The interaction of amino acids
that are close together or far apart in the sequence
c. Tertiary (3o) – The interaction of amino acids
that are far apart in sequence
In 2o and 3o the primary interaction is noncovalent
Some proteins have quaternary structure (4o): noncovalent interaction
of multiple polypeptide chains (subunits)
Native structure (conformation)  biological function
Peptide bonds link amino acids in proteins
Figure 4.1
Residue or side chain
Amino-terminus
Carboxylterminus
Peptide bonds link amino acids in proteins
Primary sequence
Alanine Ala (A)
Serine Ser (S)
Dipeptide
Ala-Ser or AS
Peptide bonds link amino acids in proteins
Primary sequence has directionality
Figure 4.2
Important: the sequence Tyr-Gly-Gly-Phe-Leu is not the same as Leu-Phe-Gly-Gly-Tyr
Figure 4.3-the polypeptide backbone is rich
With hydrogen bond donors and acceptors
How many amino acids are typically found in polypeptide chains?
1 amino acid molecular weight is ~110 g/mol or 110 Da (Daltons)
Proteins can be very large, hundreds of amino acids long
The enzyme HMG-CoA reductase
MLSRLFRMHGLFVASHPWEVIVGTVTLTICMMSMNMFTGNNKICGWNYECPK
FEEDVLSSDIIILTITRCIAILYIYFQFQNLRQLGSKYILGIAGLFTIFSSFVFSTVVIH
FLDKELTGLNEALPFFLLLIDLSRASTLAKFALSSNSQDEVRENIARGMAILGPTF
TLDALVECLVIGVGTMSGVRQLEIMCCFGCMSVLANYFVFMTFFPACVSLVLEL
SRESREGRPIWQLSHFARVLEEEENKPNPVTQRVKMIMSLGLVLVHAHSRWIAD
PSPQNSTADTSKVSLGLDENVSKRIEPSVSLWQFYLSKMISMDIEQVITLSLALL
LAVKYIFFEQTETESTLSLKNPITSPVVTQKKVPDNCCRREPMLVRNNQKCDSV
EEETGINRERKVEVIKPLVAETDTPNRATFVVGNSSLLDTSSVLVTQEPEIELPRE
PRPNEECLQILGNAEKGAKFLSDAEIIQLVNAKHIPAYKLETLMETHERGVSIRR
QLLSKKLSEPSSLQYLPYRDYNYSLVMGACCENVIGYMPIPVGVAGPLCLDEKE
FQVPMATTEGCLVASTNRGCRAIGLGGGASSRVLADGMTRGPVVRLPRACDSA
EVKAWLETSEGFAVIKEAFDSTSRFARLQKLHTSIAGRNLYIRFQSRSGDAMGM
NMISKGTEKALSKLHEYFPEMQILAVSGNYCTDKKPAAINWIEGRGKSVVCEA
VIPAKVVREVLKTTTEAMIEVNINKNLVGSAMAGSIGGYNAHAANIVTAIYIAC
GQDAAQNVGSSNCITLMEASGPTNEDLYISCTMPSIEIGTVGGGTNLLPQQACL
QMLGVQGACKDNPGENARQLARIVCGTVMAGELSLMAALAAGHLVKSHMIH
NRSKINLQDLQGACTKKTA
Practice Problem
Draw the chemical structure of the tripeptide Glu – Ser – Cys at pH 7.
Answer the following with regard to this tripeptide:
1. Indicate the charge present on any ionizable group(s).
2. Indicate, using an arrow, which covalent bond is the peptide bond.
3. What is the net, overall charge of this tripeptide at pH 7? __________
4. What is this peptide called using the one-letter code system for amino acids? ______
Double bond character of the peptide bond
Bond lengths reveal
C-N is between a
single and a double
bond. (Figure 4.7)
Trans and Cis conformations of a peptide group
Figure 4.8
Nearly all peptide groups in proteins are in the trans conformation
The N-Ca and Ca-CO bonds are not rigid and rotation is possible
Figure 4.9
Phi angle
Psi angle
Ca
Are all angles “allowed”?
Ramachandran Plot
Figure 4.10
The amino acid cysteine also stabilizes proteins through the
formation of a disulfide bond.
Figure 4.4
Figure 4.5
Insulin
Secondary structure
of proteins
Alpha helix
Pitch is ~5.4 Å or
3.6 AAs
The coil in the alpha helix allows for Hydrogen bonding
Figure 4.12
The stability of the alpha
helix is dependent upon
the residues attached.
Gly and Pro are not
prevalent in most a-helix
The alpha helix can
sometimes be amphipathic.
Amphipathic a-helices are often
Found on the surface of proteins
hydrophilic
hydrophobic
A dehydrogenase globular protein
Secondary Structure – the Beta (b) sheet or Beta strand
Figure 4.15- the peptide chain is more elongated than
In the alpha helix.
Secondary Structure – the Beta (b) sheet or Beta strand
Antiparallel
N
C
Secondary Structure – the Beta (b) sheet or Beta strand
Parallel
C
C
Figure 4.17- both types of b-sheets are possible in one protein.
C
C
N
Figure 4.18 b-sheets can be found with a twist
The beta sheet.
Side chains alternate
from one side to another
The ability for polypeptides
to reverse direction requires
reverse turns and/or loops
Figure 4.19
A protein involved in
Fatty acid metabolism
Reverse Turns and loops
Figure 4.20
Type I b turn
Hydrogen bonding
Tertiary Structure of Proteins
Supersecondary
structures often
called “motifs”
Figure 4.27
Tertiary Structure of Proteins
Domains are
a combination
of motifs
Figure 4.28
Protein found on surface of some
Immune system cells
Tertiary structure
of proteins
Domains in Pyruvate kinase
this protein has 3 domains
a-Keratin: A fibrous protein with extensive secondary structure
Figure 4.21-A coiled coil protein
Collagen
-25% to 35% total protein in mammals
-Fibrous protein found in vertebrate
connective tissue (skin, bone, teeth)
- Triple helix structure
Strength is greater than steel
of equal cross section
-only 3 amino acids per turn
Figure 4.24. A super
helical structure
Collagen is
35% Glycine
21% Proline + Hydroxyproline
The repeating unit is
Gly – X – Y
X is usually Pro
Y is usually Hyp
triple helix is packed
with Glycines (red)
Read Clinical Insight (pg 55)– Osteogenesis
Imperfecta and Scurvy
4-hydroxyproline
For every Gly-X-Y, there is one interchain
Hydrogen bond (between chains).
Globular Proteins- very compact and water soluble
WHY?
Figure 4.25 - Myoglobin (153 amino acids)
Figure 4.26 - Distribution of amino acids in myoglobin
Interior
Surface
Charged amino acids
(blue)
Hydrophobic
amino acids
(yellow)
Quaternary Structure-multiple polypeptide strands
Intermingle though noncovalent interactions.
Figure 4.29
A dimer of two subunits (polypeptides)
Figure 4.30 Hemoglobin: a tetramer protein
This protein has primary, secondary
tertiary and quaternary structures
How do proteins
fold and unfold?
The information for proteins to fold is
contained in the amino acid sequence.
Can proteins fold by themselves
or do they need help?
Is there a way in which we can predict from
the primary sequence how a protein will fold??
First, we must denature a protein and see if it
will spontaneously refold to the native structure
How can we denature proteins?
a. Reducing agents
2-mercaptoethanol break disulfide bonds
b. heat
c. acids or bases
d. heavy metals (good Lewis acidsbind to cysteine)
e. chaotropic agent-Urea (help weaken hydrogen bonding and
eventually disrupt hydrophobic core.)
Figure 4.31 – 4 cystine residues in bovine ribonuclease A
Anfinsen’s protein folding Experiment.
Figure 4-32
Denature Protein with b-mercaptoethanol and Urea.
Anfinsen result after removal of urea and
most of the b-mercaptoethanol
Enzyme slowly regains activity!!
Native conformation is re-established
Conclusion: primary sequence specifies conformation
Figure 4.35 Energy well of
cooperative folding
Protein folding is very fast! ~ large
Proteins may take ~ hrs, but smaller
Proteins may fold in one step.
Read Clinical Insight
Amyloid fibrils and prion
diseases (pg 61)
Assignment
Read Chapter 4
Read Chapter 6
Topics not covered:
Chapter 5