20.10.

20
Proteins 1 Lecture 1

hearniIdentify
ngoutcomes.tt
.
amino acid families based on chemical structure .

2. Give examples of protein

primary secondary tertiary and/or quaternary structures
,
,
.

3. Infer how alterations to

protein structure may affect protein function and lead to disease .

AMINO ACIDS
The monomers that bond
together to form proteins Amino acids are
asymmetric molecules
-

.
.

amine
group Amino acids in solution at neutral pH form zwithen.ms .

1 it

coo-ogndoiponhfcnimarge@IRO.si
④ acid
cargbgonxyplic
it
- -

-
c- ←

de Chai ,

The central carbon has 4 different substituents so two forms of the molecule are possible ( optical
-

isomers ) Proteins contain the L form isomer

only 1 where the amine
group is on the left )
-

PRIMARY STRUCTURE
→
chains of amino acids joined by peptide bonds that form between the CO0 of one amino acid

the NH5 of the next .

They are joined in a condensation reaction .

Protein chains are directional .

H H H

Hsi
1 I 1
Coo
-

⑤①④⑨⑤⑤
f G N
f
- -
- - -

R O R
"
peptide bond .

SECONDARY STRUCTURE
determined and maintained by hydrogen bonds between peptide groups The polypeptide folded into
→

.
chain is

B pleated sheet and held in place the and

an a- helix or -

by hydrogen bonds between hydrogen Oxygen

atoms .

In an d- helix the the

hydrogen bonds form between
every 4th amino acid
-

There are two forms of P pleated sheet

-

-
:

°
parallel sequences in
→
same direction
°
anti parallel-

sequences →
in opposite direction
-

B -

pleated sheets can be different peptide chains or one folded chain which
,
has B- turns .

TERTIARY STRUCTURE

far apart
→
the arrangement in space of amino acids that can be in

the linear sequence .

It involves several different interactions

determined by amino acid

sequence .
QUATERNARY STRUCTURE
→
different chains 1 subunits ) associated together by side chain interactions .

PROTEIN FUNCTION
Diff .int protein structures have different functions
-

: :

°
Globular proteins →
fold into compact structures , usually soluble

eg enzymes antibodies hormones

.

, ,

Fibrous proteins multiple strands held together by strong bonding usually

° →
,
insoluble structural proteins .

eg .

collagen keratin fibrin

, ,

°
Membrane proteins →

hydrophobic regions sit in cell membranes transmit

,
molecules and signals in and out of cells .

channels and receptors

eg .

alterations to the
Any protein structure changes how that protein functions which can mean that some processes
-

in the
body may not occur or some will occur at a faster rate than normal this can lead to
.
diseases .

eg Changes
.
in the structure of an enzyme changes the active site and then means it cannot bind to the substrate

prion diseases proteins ( prions) Infection

caused by infectious causes the host 's normal prions to switch
-

are .

to a conformation that aggregates This .

aggregation into the fibres in the brain causes neuronal cell death .
 20.10.20
Proteins 2 Lecture 2

hearningoutcomes.i
.
t
Describe how
enzymes increase the rate of reactions by acting as biological catalysts .

2. Sketch and explain mechanisms of isostatic and allosteric enzyme regulation and enzyme inhibition
3. Identity factors regulating enzyme activity .

4.
Classify proteinases from the active site .

5 .
Recall the properties of multi subunit enzymes and
-

multi -

enzyme complexes .

Enzymes are catalysts , they increase the rate of a chemical reaction without
being changed themselves They decrease
-

the energy of the

activation reaction
by :

bringing substrates together

°

excluding water
°

stabilising the transition state

°

transferring chemical groups

°

Enzymes catalyse reactions in both anabolic and catatonic processes .

ACTIVE SITE
the part of the
enzyme that performs
→
the catalytic reaction .

-
It binds the substrate and converts it into a product usually by making
,
or breaking chemical bonds Substrates bind
.

to
specific amino acid side chains -

by multiple weak forces ,

eg .
electrostatic interactions ,
van der Waals and hydrophobic
interactions .

Enzymes are very specific so

only specific substrates can fit in the active site .
This means that the function of the

usually very specific and is determined sequence of amino active site

enzyme is
by the shape and acids in the .

The induced fit model

-

suggests that the enzyme and substrate do not fit properly

together but when
they interact it induces a conformational change in the structure

Of the enzyme When the substrate binds enzyme substrate complex is formed The
an -

.
.

amino acid side chains in the active site

-

transform substrate molecules into the

transition state and then the product ,
when it gets released The enzyme .
can now bind
with another molecule of substrate .

I steric enzyme
reaction increases with substrate concentration until the enzyme is saturated
→
rate
of .

Allosteric enzyme
→
substrate and/or effectors induce conformational change in the enzyme that increases
activity .

ALLOSTERIC REGULATION
→
when
something binds to the
enzyme which increases or decreases the reaction rate , by causing an interchange
between catalytically active and inactive conformational states This .

happens often with multi sub unit enzymes The

-

allosteric sites are often located wher the sub units -

are joined .
 Cooperating -

regulation by substrate

when a substrate increases the capacity for to bind more substrate which increases the rate of
→
an
enzyme reaction .

Regulation by effectors
→
when other molecules than substrate bind to the allosteric site and either activate inactive the
or
enzyme by
:

1. Activators

2. Inhibitors

ACTIVATORS
→

binding of an activator stabilizes the conformation that has a

functional active site .
A conformational change in one

Subunit is transmitted to all others .

INHIBITORS

building of inhibitor stabilizes the inactive form of

→
an
an
enzyme .

Feedback regulation
Metabolic processes involve a series of catalyzed by lots of different enzymes The end product often
-

reactions .

feedback inhibits
-

the first
enzyme to prevent the build up of intermediates and the unnecessary use of metabolites

and
energy .

Competitive inhibitors
→
bind to active site instead of substrate binding
Non -

competitive inhibitors
→
binds to allosteric site of enzyme to change the shape of the active site so no more substrate can bind

Uncompetitive inhibitors

binds allosteric site but when enzyme substrate complex has formed prevents the products from being
→
so
to
only an -

released .

Most allosterically regulated enzymes constructed from two or more subunits Common features that they
-

are .
are :

are multi subunit

° -

enzymes
°
bind other ligands at sites other than the active sites
°
can be either activated or inhibited by allosteric ligands
°
exist in two major conformational states -

RI relaxed ) and then se)

often control key regulated
°
reactions in
major pathways ,
which must be

FACTORS AFFECTING ENZYME ACTIVITY

1 Concentration

Increasing substrate concentration increases enzyme activity up the point at which the
enzyme becomes
-

to

saturated long is substrate available

.

Increasing enzyme concentration will increase reaction rate as as there

to blind to .
2. Temperature
increasing temperature increases the thermal energy of substrate molecules so
they have sufficient energy to
-

of At higher temperatures
overcome the activation
energy Therefore
.
increases the rate reaction .
,
weak interactions

holding the 3D structure start to break which leads to denaturation of the

enzyme .

3. pH
all have an optimum pH Any deviation from the optimum leads decreased activity due to
enzymes to
-

changes in ionisation of at the active site

Larger deviations denaturation
groups .
can cause .

4. Post translational modification

-

A. Phosphorylation
causes changes in the
secondary and of enzyme altering it 's catalytic ability Specific
tertiary structure
-

hydroxy amino acid side chains (serine threonine or

tyrosine) may be phosphorylated The phosphorylated enzyme
-

,
.

may be more or less active than the de

phosphorylated form It acts as a rapid reversible switch to turn a metabolic
.

off according needs of the cell

pathway on or to the .

B.
Proteolytic activation

proteolysis is the action of an

enzyme that can break peptide bonds A larger inactive protein is split by
-

.
,

another
enzyme produce to the active form of the enzyme .
This is irreversible An .
example of this is enzymes
in digestion they are inactive
:
when made in pancreas and are transported to the small intestine where they are

activated to
enzymes that are essential in digestion . If proteolytic activation goes wrong it can ,
cause problems .

Canine pancreatitis caused auto digestion of the pancreas

is
by premature activation which causes .

5. Co
enzymes and cofactors
enzymes need the presence of cofactors ( small protein units) in order to function These be inorganic ions
non
may
-

(eg Mg
"
Zn
"
Fe
"
) complex organic molecules called Some co are bound at the active site and
.

, ,
or co enzymes .

enzymes
oxidised or reduced by the enzyme during its catalytic reaction .
Some examples are NADYNADH and NADPYNADPH
which are
really important in the
currency of energy and biosynthesis .

PROTEIN AS ES
→

enzymes which cleave ( split ) proteins .

This
may activate other enzymes
-

proteolytic activation .

They are classed by

what their active site looks like .

°
serine protein ases -

serine at active site

°
at active site
cysteine protein as es cysteine
-

°
at active site
as
party 1 protein ases aspartate
-

metal to protein as es metal ion I often zinc ) at active site

°
-
a

threonine
°
threonine protein ases -

at active site

Iso
enzymes
different forms of catalyse the same reaction They usually derived
→
an enzyme which -

active site is similar .

are

from different genes and often occur in different tissues .

EXAMPLE :
Lactate
dehydrogenase ILDH )
-

LDH has 4 subunits Itetramer) These.

are either subunit It or subunit M .
There are 5 different combinations that
are present in different tissues .
Under normal circumstances there is little LDH in the blood
,
.
Problems in tissues cause

Cell death which releases cell contents into the blood -

including LDH .
Blood tests can be carried out and the specific
subunits can be identified to indicate which tissue has a problem .

Multi enzyme
-

complex
→
several unit
an
aggregation of enzymes or co
enzymes into a single functional .

They perform a multi -

step transformation Numerous steps need

.
to be carried out in close proximity This
.
increases the

overall reaction rate minimizes side

,
reactions and means that intermediates are
immediately available for the next reaction .

fatty acid synthase

involved in lipid
-

biosynthesis .