Chapter 3: Proteins

Amino acids & polypeptides

Properties of proteins
Protein structure and folding
Protein modifications: binding & covalent
Protein degradation

Polypeptides are linear strings of amino acids

Amino acid: central carbon (Ca) bonded to:
1. One ______ group (-NH2 => -NH3+)
2. One ____________ (-COOH => -COO-)
3. One hydrogen, and Polypeptide order:
4. One ________ (R-group) N (amino) to C (carboxyl)

_______ bond = covalent bond

between the carboxyl of one
amino acid and the amino of
the next one = “backbone”
= condensation reaction,
loss of H2O, loss of charge
Reverse reaction = hydrolysis, H2O
breaks peptide bond
 Amino Acids differ only by their sidechains:
Class 1 = nonpolar, hydrophobic
Types: ________ (CH2 & CH3 groups) & ________

Class 2 amino acids: polar but uncharged (at pH 7)

Types: hydroxyl, amide & sulfhydryl

Glycosylatio
n

Hydroxyl AA’s: serine, threonine & tyrosine can be

modified by ____________:

Cysteine can form _________: -CH2-S-S-CH2-

 Class 3 amino acids: charged (highly polar)
Positive (_______) & negative (_________)

Lysines in histones can be modified by

acetylation or methylation

Interactions between residues (amino acids) in a

polypeptide:
1. Ionic: pos & neg charges attract, strong
in a nonpolar environment
- _______ (or phosphorylated)
sidechains & N- and C- termini
2. Hydrogen “bonding”: all polar groups
- amino and carbonyl groups in
peptide bond
- polar and charged side chains
3. “Hydrophobic” interactions: all _______
sidechains
4. __________ between some cysteines
What makes a polypeptide a protein?
Random polypeptide: multiple 3D conformations, no single
stable one
Protein: a few stable
_____________

Proteins ___ to one

or more specific
targets: small
molecules, nucleic
acids, proteins, etc.
- changes 3D
conformation

Proteins perform a

Protein binding to other molecules

“Binding” = _____________ interactions: ionic,

H-bonding, hydrophobic combination
- binding is reversible, sometimes rapidly:
on- and off-rates => strength of binding
Binding sites on proteins are specific for one or more
molecules
- some proteins have multiple binding sites

Protein ____________when binding a target

molecule – may change its ______ for
other molecules
 Elements of protein structure: 1°, 2°, 3°, 4°
1° (primary) = ______ of amino acids, N => C

2° (secondary) = repeated local

conformation
Most common = ________ &
_______, H-bonding
between backbone
amine and carbonyl
Random coil = no regular pattern

3° (tertiary) = __________ of 2°structure

Red = a-helix, yellow=b-strand, white=random

4° (quaternary) = oligomeric arrangement:

multiple polypeptides

Folding a protein into its correct 3° structure

Some proteins achieve their native folds spontaneously

- can be denatured them and they will re-fold
Many proteins require help from
________________: folding
proteins (heat-shock proteins)
- chaperones bind many newly-
synthesized proteins to
prevent misfolding and
aggregation
- _________ bind some proteins
to help them fold in a protected
environment
 Protein folding & domains
Proteins adopt a stable 3° structure in
order to:
1. Keep their outer surface soluble:
bury most ________________
2. Maximize the internal bonding
interactions: ionic & H-bonds
Folding units of large proteins are
domains: independently-folding
parts of the polypeptide
- various 2° structure elements
in domains
__________ proteins are often
stabilized by disulfide bonds

Protein 3° organization
_______ proteins:
mostly polar surfaces
mainly nonpolar interiors Acti
n Spectrin
- nonpolar surface patches may
be used to form oligomers

__________ proteins:
expose most sidechains (a, b or
random structures)
often form ________ (insoluble)

Trans-membrane proteins:
___________to partition into
lipid bilayer core
- may have polar internal
 Protein representation
Structural methods (XRD, NMR, EM) identify positions of
all (non-H) atoms that are in stable
locations
Space-filling display shows __________
(except hydrogen) at correct size
- mostly see facing surface

Stick display can show all atoms, or just

polypeptide backbone at correct locations

Ribbon display shows 2° structure, not atoms,

and allows full 3D structure to be seen

Antibodies: extracellular proteins

IgG = hetero-________ of two different polypeptides
Heavy (H) chain = 4 domains (green & blue)
Light (L) chain = 2 domains - all domains mostly b sheets
Disulfide bonds:
- within each domain
- between ______
- between ______
Domains similar in
structure => gene
duplications
Variable domains
make specific
binding sites
Modification of protein structure & activity
Non-covalent changes:
Environmental changes (pH, ion concentrations, small
molecules) can cause changes in
proteins that affect their
function

Binding of ____________ (ions,

nucleotides) can change activity of
some proteins, usually briefly
- binding of an ____________ can
occur at a “second” site, changing the
shape of its primary site
= allostery

Allosteric activation: G-proteins

G-protein changes its structure & activity when it binds
GTP, usually caused by binding an ____________
G-proteins are enzymes: catalyze ________________
to GDP + Pi (slowly), returning the G-protein to its
original state (no GTP bound)

Most G-proteins in their

GTP-bound form activate
other proteins
by _______
them.
 Inactiv
G e
GT GT Enzym
P P e
G
GT
P
G GD Active
GD P Enzyme
P
GE
F
GA GA
P P G
GT
G P P
GE GD i Active
F P Enzyme

G = G-protein
GEF = GTP - Exchange Factor Inactiv
GAP = GTPase - Activating e
Protein Enzym
e

What is an enzyme? (a little biochemistry)

Proteins play many roles in cells: structure, motility,

regulation of other activities, some hormones, signal
receptors, membrane transport, binding other
molecules, but a key one is to perform ________
__________

All enzymes are proteins (catalytic RNA is a

ribozyme), but not all proteins are enzymes.

An enzyme must bind one or more substrates,

and catalyze a change in at least one
_______________
Modification of protein structure & activity
Covalent modifications: long-lasting, but _____
_________

May be used for _______

of activity, or for cellular
___________

Example of non-reversible
modification: hydrolysis
of polypeptide chain
– sometimes used for
activation of a protein

Reversible covalent modifications:

Phosphorylation: major mechanism of
regulating activity of many enzymes
- terminal phosphate of ATP
transferred to serine, threonine, or
tyrosine by action of a ______
- revered by action of a
_________
(Enzymes specific for certain AA
sequences

Methylation or acetylation of lysine by

methyl or acetyl transferase
- changes affinity for other proteins
or for DNA
Covalent modifications
Disulfide bond formation helps
preserve protein structure,
mainly ______________

Glycosylation adds ____________

to asparagine, serine or
threonine in external &
_______________ proteins for
identification and/or protection

Lipid (farnesyl group here) can be

attached to cysteine, usually to
localize a protein to a _______
- converts a cytoplasmic protein
to a _______________

Covalent modifications

Ubiquitination (ubiquitinylation) attaches

a small protein, ubiquitin, to ______
_________ using a complex family of
enzymes
- most common signal = destruction of
protein by ____________
- other signals using same method with
small ubiquitin-like modifiers (SUMO)
localize the modified protein to other
locations
- attachment is via an isopeptide bond,
only known “branching” of a
polypeptide
 Protein degradation by proteases

All cellular proteins have limited lifetimes – turnover

rates vary by protein

Several _________ are active in most cells, most very

specific for processing individual proteins
- low-specificity proteases that destroy any protein
must be sequestered from cell proteins
- some are stored in the __________, protected by a
membrane
- others are self-compartmentalized, preventing
cytoplasmic proteins from reaching the active sites:
___________ and others

Proteasomal digestion
Proteasome = large (> 1 Mda) protein complex with a core
particle that contains general protease sites
“Caps” recognize ____________ proteins, bind and unfold
them, and deliver them to core
Proteins hydrolyzed into small peptides, then other proteases
digest to AA’s
Ubiquitin: small
protein
Lysosomal digestion
Lysosomes are organelles containing a mixture of
_________ enzymes
- lysosomal membrane protects cell from these enzymes
- lysosome _________ various membranes: damaged
organelles, endocytic
vesicles (via endosomes),
- uptake of ________
proteins in aggregates

Complete digestion, and

release of amino acids
to cytoplasm

Extracellular digestion

Some cells secrete proteases into extracellular space to

digest _________________
- important for remodeling (e.g., wound healing) and
for ________ of some cells through tissue