Summary of protein structure/function

1. The 20 common aa’s have different R groups.

2. Amino acids are linked by peptide bonds to form
polypeptides & proteins.
3. Proteins are often large & have complex native
(d) structures, but patterns do exist: 1°, 2°, 3°, &
4° structures (also motifs, etc.)
4. Native protein structure is maintained by: peptide
bonds (1°), weak interactions (2°, 3°, & 4°), and
disulfide bonds ( 3° & 4°).
5. Protein function depends on native structure.
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Amino acids & Protein Structure
1. Most jobs (except information storage) in cells
are performed by proteins.

2. Proteins usually have only a few possible stable

conformations. How does a protein get from one
conformation to another? Mostly by rotation about
single bonds.

3. Specific protein conformation (structure) is

required to maintain function.

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I. Functions of Proteins See Biochemistry

II. The "-amino acids (aa)

A. Name comes from the structure: The "-C atom
is next to the C
O (carbonyl) C.
'
amino carboxyl
group group
1) carboxylic acid group H H
2) "-amino group
O

H N C C
3) side chain (a.k.a., R group)
4) Circle the "-carbon! side chain R O H

5) Is there a chiral (asymmetric) carbon atom?

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B. Except for glycine (where R = H), the 20
common aa all have at least one chiral C atom.
Refer to models.

1. L- and D- designations are based on reference

to glyceraldehyde. Biomolecules are linked
through biosynthetic pathways. Biochemists
usually go with this designation.

2. The R- & S- designations used in the modeling

lab are geometrically based.

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 Most "-amino acids have a chiral C atom. This
means you can have L- and D- isomers.

L-Alanine D-Alanine
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C. Amino acids (The “20 common”. What does
that mean?) can be grouped based on similarities
in the side chains (R group)

1. Non-polar
2. Polar but uncharged at normal pH
3. Negatively charged (Remember, we are
referring to the side chain.)
4. Positively charged

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 Six of the 20 common amino acids
Gly Ala Val
H O H O H O

H2N C C OH H2N C C OH H2N C C OH

H
H H C H H C C
H

H C H
H H

Cys Asp Lys

H O H O H O

H2N C C OH H2N C C OH H2N C C OH

H C H H C H (CH2)4

S C N
H H O O H H

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D. Why should we care about amino acid side
chains?

1. The side chains play a major role in

determining protein structure/function.

2. Example: Sickle-cell trait is caused by a valine

being substituted for glutamic acid at only one
position (out of ~146) in the $-chain of
hemoglobin.

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 Importance of amino acid side chain structure in
human health:
Wild type human Hb has glutamic acid (Glu) at
position 6 of its $-chain. Sickle-cell Hb has Val at
position 6. The remaining 145 amino acid residues
are identical! Val
Glu
H H O H H O

N C6 C N C6 C

CH2 CH CH3

CH2 CH3

C O

O-
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III. Peptide Bond (links monomers to form a polymer)
A. Comment on building big molecules (a.k.a.,
macromolecules)

1. Essentially all biological macromolecules are

polymers. Polymers are made by linking a
large number of monomers together: See CD.

n A ö A-A-A-A-A-.....-An-2-An-1-An

2. This is like building a wall out of bricks (as

opposed to from stucco).
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3. In proteins, aa are the monomers. They are
linked together by peptide bonds. Note -N-C-
C-N-C-C-N-C-C- repeating pattern (see
below). Which C is (are) the carbonyl-C,
which is the "-C?
Gly-Ala
CH3 O-
H

O C C

H C N O Atoms shown in red

are all in the same
H N+ C H plane. Comment re.
nature of peptide bond.
H H
H
peptide bond
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4. Nomenclature

a) Two linked aa form a dipeptide (above =

glycyl-alanine)
b) Three form a tripeptide
c) A moderate number (roughly < 30) form an
oligopeptide
d) A larger number form a polypeptide

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 A peptide containing 8 amino acid residues (an octomer)
Full name: Valyl-Histidyl-Leucyl-Threonyl-Prolyl-Glutamyl-Glutamyl-Lysine

In 3 letter abbrev: Val-His-Leu-Thr-Pro-Glu-Glu-Lys

In 1 letter abbrev: V-H-L-T-P-E-E-Y Atoms in the peptide backbone

are shown in blue.

O O O O O O O O

H H H H H H H
+H3N CH C N CH C N CH C N CH C N C C N CH C N CH C N CH C O-

CH CH3 CH2 CH2 CH OH CH2 CH2 CH2

CH3 CH CH3 CH3 CH2 CH2 CH2

N
CH3 C C CH2
-
NH -O O O O
CH2

Can you locate each residue's side chain and determine whether H N+ H
it is non-polar, polar but not charged, acidic, or basic?
H

Can you make predictions about the solubility in water of each residue's side chain?
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5. Peptides can be named by listing their aa
sequence, starting from the amino terminal
end. What is the amino terminal end?

6. The peptide bond exhibits resonance. What is

it? (Darth Vader’s voice.)
a) Resonance occurs when there is more than one
stable way to arrange the electrons in a molecule
or ion. See next page.
b) Structures with resonance often behave like
something in between the different resonance
forms.

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 c) Structures that exhibit resonance tend to be more
stable than you would otherwise think.

Ca H Ca H

C N C N+

O Ca -O Ca

Peptide bond resonance:

1. All six atoms shown are in the same plane.
2. Therefore both the central C and N atoms behave like they
are trigonal planar, sp2 hybridized. (right-hand structure).
3. Note that neither of the structures above provides a perfect
model for all aspects of peptide bond structure/function.

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IV. Primary (1°) Structure of Proteins: the
sequence of amino acids
A. Specific proteins in your body have specific
sequences. That is, every (? see below?) insulin
A-chain starts with Gly the amino terminus, then
Ile, etc.

B. This sequence is called the primary structure of

the protein. (Polymorphism? Heterozygosity?)

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V. Secondary (2°) Structure of Proteins
A. Secondary structure is regular, repetitive
structure held in place by intrachain Hydrogen
Bonding and comes in two main forms:

1. "-helix

2. $-sheet (two forms of this):

a) parallel [aligned NöC, NöC]
b) anti-parallel [aligned NöC, CöN]

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B. Some generalizations:

1. Most proteins have obvious 2° structure.

2. Many proteins have more than 50% of their aa

involved in 2° structure.

C. Specialized 2° structures exist. Example:

Collagen triple helix. (proline hydroxylation and
scurvy knaves.)

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Part of the A "-helix from human
Hb (beta chain)

Can you:
1) Trace the peptide backbone?
2) Find the amino terminal end?
3) Locate the Hydrogen Bonds that
maintain the "-helical structure?
4) Are these Hydrogen Bonds
perfectly aligned?

Would the "-helical structure be

maintained if the Hydrogen Bonds
were disrupted?
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Drawing of a $-sheet
H O R H O R H O

N C CH N C CH N C
CH N C CH N C CH

R H O R H O R

R O H R O H R

CH C N CH C N CH
C N CH C N CH C N

O H R O H R O H

indicates Hydrogen Bond

Can you:
1) Trace the peptide backbones?
2) Find the amino terminal ends of the backbones?
3) Is this a parallel or anti-parallel structure?
4) Are these Hydrogen Bonds perfectly aligned?
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VI. Tertiary (3°) Structure of Proteins
A. Tertiary (3°) describes the location of each of the
protein’s atoms in 3-D space. (Re. bends, twists,
etc. in secondary structure)

B. Usually, 100% of a given type of protein is in the

same 3° structure (Hb, BSE & prions?); this is a
very non-random, highly organized situation. If
something is unfavorable in entropy terms ()S),
there must be a significant amount of bonding
()H) holding it in place.
What forces maintain very non-random structures?
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Remember: )G = )H ! T)S ?

1. Peptide bonds (covalent) maintain 1° structure.

2. Hydrogen bonds maintain 2° structure.
3. 3° structure is maintained by different amounts
of a-e different proteins:
a) covalent bonds (!S!S! are a common type)
b) hydrogen bonds (??? re. H bonds to solvent)
c) ionic bonds (salt bridges)
d) hydrophobic interactions (keep the inside on the inside)
(actually, mostly a system )S term)
Comments re. Hydrophobic Collapse & protein folding
e) London Forces Essentially all proteins do b-e in
various amounts.

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VII. Quaternary (4°) Structure of Proteins
(requires multiple subunits)

A. This describes how the subunits fit together.

B. Examples of proteins with multiple subunits:

1. hemoglobin ("2$2)
2. insulin (A chain and B chain)
3. hCG ($-subunit clinical importance? )

What does hCG stand for?

When do (& which?) humans make hCG?
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 hCG structure (pdb: 1hrp) "-subunit: blue; $-subunit: pale green. Red
& bright green atoms are carbohydrate (sugar) molecules that are covalently attached to hCG.

Space-filling model Ribbon model (backbone)

2° structure is mostly $-sheet with a short "-helix in the alpha subunit.

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VIII. Protein Structure re. to Function
A. Protein structure has a massive effect on protein
function. Usually alteration in structure radically
alters (often destroys) protein function.

B. The key to the function of most proteins is the

creation of a unique environment (space) where
catalysis, transport, or binding can occur.

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IX. Myoglobin & Hemoglobin
A. Myoglobin re. O2 storage and diffusion.

1. Myoglobin meaning: myo globin

2. Diving mammals (cetaceans) & myoglobin.

See 1mbo Protein Data Bank structure.

Our myoglobin is not used for O2 storage, but

to increase the rate of O2 diffusion in our
muscles.

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B. Hemoglobin (Hb) and O2 & CO2 transport.
Maximize O2 binding & release efficiency!!!
1. Hb does have more than 1 stable conformation

a) High O2 affinity form: main form present in

lungs (higher pH).

b) Low affinity form: present mostly in

extremities (lower pH).

c) Hb shifts back & forth between these forms

as it moves through your circulatory system.

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 This graph shows that Hb has different forms that have different
affinity for O2. (From google images
[Link]
Cg/9A24hL_HUtA/s320/oxyhemoglobin%[Link]&imgrefurl=[Link]
[Link]&usg=__lI-yrXzq_9VwL97hPMCwaBwJG2A=&h=310&w=320&sz=45
&hl=en&start=135&zoom=1&tbnid=v8ZgJ_iEO2EdBM:&tbnh=142&tbnw=147&prev=/images%3Fq%3Doxyg
en%2Bhemoglobin%2Bdissociation%2Bcurve%26hl%3Den%26biw%3D1280%26bih%3D839%26gbv%3D2%2
6tbs%3Disch:10%2C4423&itbs=1&iact=hc&vpx=1012&vpy=212&dur=8193&hovh=221&hovw=228&tx=143
&ty=93&ei=2z_lTJTJEYP98Aaoj53DDQ&oei=kD_lTLarH4K8lQfx_Y22Cw&esq=8&page=7&ndsp=23&ved=
1t:429,r:11,s:135&biw=1280&bih=839

8 8
tissues lungs

Is all of the O2 is released as HbC(O2)4 goes from lungs to tissues ?

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2. Logic: high affinity form binds O2 in lungs
{Hb + 4O2 ö HbC(O2)4}, when HbC(O2)4
reaches tissues, there is a shift to the low
affinity form, and O2 is released {HbC(O2)4 ö
Hb + 4O2}.

3. Other modifiers: bisphophoglycerate (BPG)

and CO2 favor formation of low affinity form.
That is, they help Hb let go of its O2.
!
4. Hb also binds CO2 (as HCO ) and transports it
3
to the lungs for removal.

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pH Effects: from: [Link]
via gooogle images

Left hand curve has a higher or lower

fraction of the high-affinity Hb form
than the right hand curve?

Which part of your circulatory system

would be a good match for the central
curve?

Which part for the right hand curve?

8 8
tissues lungs

Can you explain why one part of your circulatory system would be more
acidic?
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Altitude, etc. effects on O2 release from Hb are mediated
by bisphosphoglycerate (BPG).

The best figure I have found is at Univ Arizona Biochem class:

[Link]
[Link]/classes/bioc462/462a/NOTES/hemoglobin/hemoglobin_function.htm&usg=__XX4Sa3WZ2fGhQdvbNonOAr4TY60=&h=348&w=
433&sz=6&hl=en&start=0&zoom=0&tbnid=Rf6x7RxmCOXhkM:&tbnh=101&tbnw=126&prev=/images%3Fq%3Dhemoglobin%2Bbpg%2Beffect%2Bdis
sociation%2Bcurve%26hl%3Den%26sa%3DG%26biw%3D1280%26bih%3D839%26gbv%3D2%26tbs%3Disch:1&itbs=1&iact=hc&vpx=1084&vpy=131
&dur=268&hovh=101&hovw=126&tx=93&ty=51&ei=ikflTKu5B4H7lwejlLm3Cw&oei=ikflTKu5B4H7lwejlLm3Cw&esq=1&page=1&ndsp=33&ved=1t:
429,r:6,s:0

Increasing [BPG] shifts Hb to which form, high-affinity for O2

or low-affinity?

So BPG functions to help Hb .

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Human hemoglobin Backbone: ribbons. One heme associated w/ each subunit: cylinders.

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C. O2 transport and the fetal-maternal unit.

1. One view: Human Hb is really good at

binding O2, but not very good at releasing it.

2. What consequences does this have re. fetus?

3. How do we deal with this problem?

a) You didn’t make much Hb $-chain when you were fetal.
b) You made a variant of the $-chain called (.
c) Therefore fetal Hb is "2(2.
d) Fetal Hb has higher affinity for O2 than does adult Hb, in
part because fetal Hb does not bind BPG. (So it stays in
higher affinity form.)
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 Look at the myoglobin, normal hemoglobin, foetal (fetal)
hemoglobin comparison figure at:
[Link]

8 8
tissues lungs

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D. Sickle Cell Anemia. (HbS = sickle cell
hemoglobin) Thoughts from the group?

1. Small structure change = big function change

2. View structure of wild type (wt) human Hb.

3. Compare sequences (1° structure) of the wt

(1a3n) & sickle-cell, HbS, (2hbs) hemoglobin
$-subunit. (Note: yellow-green and sea-foam
colours represent the $-chains in the RasMol
representation of [Link].)
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 See different pages titled: Comparison of HbA & HbS

Normal (wt) human $-hemoglobin subunit sequence:

1 6 10
Val-His-Leu-Thr-Pro-Glu-Glu-Lys-Ser-Ala-.......-His146

Sickle-cell human $-Hb subunit sequence:

1 6 10
146
Val-His-Leu-Thr-Pro-Val-Glu-Lys-Ser-Ala-.......-His

Only one difference out of 146 aa residues!!!

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 4. How does this change alter Hb and rbc function?
a) Glu side chain is charged. H2O “likes” to be by it.

b) Val side chain is non-polar. Does H2O like to be by it?

Recall that ordered H2O cages are unfavorable ()S).

c) During a Sickle Cell crisis (favored by low PO ), separate 2

HbS molecules stick together to minimize Val6 contact

with water. This minimizes cage formation by H2O, but
HbS forms insoluble polymers (all kinds of problems).

HbSA(O2)4(aq) W HbS(s) + 4 O2(aq)

What effect would decreasing [O2] have on above equilibrium?
(What percentage of Hb is normally in the deoxy form?)

Should sickle-cell patients run wind sprints in the mountains?

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5. Why has HbS trait persisted in some
populations?

6. How different are human & chimpanzee Hb?

7. How might this relate to human origins???

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X. Dietary Protein & Digestion (Atkins strikes again?)
We can (no longer) make all of the necessary amino acids
from scratch (from diet). These aa’s are called
(Should remind you of something?)
A. They are: isoleucine
leucine
lysine
methionine
phenylalanine
threonine
tryptophan
valine (In PKU patients?)
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 Comment on high lysine corn.

B. Example of an amino acid we can make: serine

3-phosphoglycerate ö 3-phosphohydroxypyruvate ö 3-phosphoserine ö serine

Where in our metabolic processes is 3-

phosphoglycerate produced?

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