Protein Function Flashcards
Learning Outcomes
After this lecture, students should be able to:
* explain that amino acid sequences show evolutionary relationships of proteins and determine, shape,
flexibility and function of proteins
* explain that all proteins bind other molecules named ligands via non-covalent interactions
* define different types of proteins and describe their features
* explain how enzymes work and how they are regulated
* explain how motor proteins move cargos in cells
Proteins come in a variety of shape and sizes
BUT the shapes can often change
Proteins are: “the agents of
biological
function and the expression
of genetic information”
All Proteins Bind Other Molecules
- Proteins almost always bind other molecules.
These molecules are referred to as ligands - Ligand may be:
➢ Ion (e.g. Mg2+)
➢ small molecules (e.g. ATP)
➢ Macromolecules (e.g. other proteins, DNA) - Binding to binding sites is specific due to
shape complementarity - Binding is via non-covalent interactions
The shape, flexibility and function of proteins is determined
by the amino acid sequence
All Proteins Bind Other Molecules
- Binding of a ligand causes the protein to fold to provide a close fit
- Non fitting ligands fall out of the binding site because the sum on non-covalent interactions is too
weak as they do not fit well ➔ unwanted associations are prevented - Correct ligand binds ➔ many non-covalent interactions due to tight fit into the binding site
Antibodies Bind Ligands Called Antigens
Antibodies: produced by immune system against foreign molecules or antigens = ligands
* Two heavy and two light chains, variable and constant domains
* bind antigens with antigen binding site, leading to antigen destruction
* Variable domains have variable loops ➔ to changing length & amino acid sequence ➔
specificity of antibody to antigen ➔ potentially billions produced by an immune system
Many Structural Proteins Are Fibrous Proteins – part I
- Keratin protein has alpha
helical regions - Keratin monomers
assemble into dimers - Dimers form staggered
tetramers - Eight tetramers form
intermediate filaments
Alberts et al. (6ed) Molecular Biology of the Cell, Figs 16-67 & 16-68
Keratin intermediate filaments (green) are part of the
cytoskeleton of epithelial cells that forms a scaffold
from the nucleus (black) to the edges of the cell (blue)
Many Structural Proteins Are Fibrous Proteins – part II
Several human genetic disorders are characterised by blistering of the skin - due to
mutations in keratin genes
Mouse model (above) - normal and mutant keratins co-assembled → clumping &
disruption of keratin network in basal cells → blistering of skin
Some features of enzymes photo
Many Proteins Belong to Large Families
- Relationships determined
by comparing similarities &
differences in amino acid
sequences → more similar
sequences cluster on same
branches of evolutionary
trees - Functionality also typically
reflected in clustering
Examples of Enzyme classes
Schematic of an enzyme catalysed reaction
- Enzyme (E) binds specific ligand (substrates, S) forming an enzyme
substrate complex (ES) - Enzyme catalyses a change (e.g. cleavage) of the substrate forming
an enzyme product complex (EP) - EP rapidly dissociates releasing the product (P) from the enzyme
(E) - Binding involves noncovalent interactions in the active site
- Organization of atoms in the active site is optimized for catalysis
- Enzymes speed up chemical reactions without being altered
Most enzymes are globular
proteins
Example: Lysozyme (blue) bound
to a substrate (red)
Enzymes are proteins that speed up reactions
- They are proteins. (some RNAs
may also catalyze reactions) - They speed up reactions by
reducing the activation energy
required for that reaction to occur. - Enzymes are not consumed
during a reaction. - They will be available to bind new
substrates and catalyze the same
reaction repeatedly.
Enzymes are proteins that speed up reactions photo
Schematic of an enzyme catalysed reaction photo
Enzymes can encourage a reaction in several ways
Regulation occurs
* at the level of gene expression
* by compartmentalising enzymes
* by regulating enzyme degradation
* *by binding other molecules
* *by phosphorylation
Enzymes can encourage a reaction in several ways
memorise the writing
make sure u remember this
Enzymes Are Regulated - Negative regulation
learn the possible speicifccs of this
Connected metabolic pathways are regulated
by feedback inhibition
- The products of one enzyme-catalysed reaction may be the
substrates for another → metabolic pathways - Regulation of pathways is at the level of individual enzymes
- Feedback inhibition at multiple points regulates connected metabolic
pathways - In the example, each amino acid controls the first enzyme specific to
its own pathway ➔ regulating its own synthesis
Connected metabolic pathways are regulated
by feedback inhibition photo
Enzymes Are Regulated – Allosteric regulation
Enzymes regulated by effector molecules are
Allosteric Proteins
* most proteins
* two or more different conformations
* activity regulated by switching conformations
Regulatory and active sites “communicate”
* Binding of an effector to the regulatory site
changes the shape of the enzyme
o Binding of a positive regulator = allosteric
activator changes the shape of the active
site so that the substrate can bind better
o Binding of a negative regulator = allosteric
inhibitor changes the shape of the active
site so that the substrate binds less well or
not at all
Enzymes Are Regulated – Allosteric regulation phpoto
Enzymes can be Regulated
by Phosphorylation
- Phosphorylation occurs on amino acids
- Catalysed by protein kinases
- Requires that the amino acid has a hydroxyl
group
o often on serine residues, can also be
threonine or tyrosine
Phosphate from ATP - Protein phosphatase remove phosphate groups
from the amino acid - Some proteins are activated, others inactivated
by phosphorylation - Protein kinases and protein phosphatases are
also enzymes
Enzymes can be Regulated
by Phosphorylation photo
Kinesin & Dynein Move Cytoplasmic Components Along Microtubules
- Kinesin & dynein are motor proteins moving along microtubules (part of cytoskeleton)
- They move cytoplasmic components – cargo – along microtubules in opposite directions
- ATP hydrolysis occurs at the head regions of the motor proteins
- Cargo is bound at the tail regions of the motor proteins
Motor Proteins move by conformational changes
Kinesin & Dynein Move Cytoplasmic Components Along Microtubules
Movie: Motorproteins move ‘things’ in cells
Can you …
- … give examples of what a protein ligand could be?
- … explain how a protein interacts with a ligand?
- … explain how the structure of antibodies and structural proteins relate to function?
- … recall how enzymes are named and relate enzyme classes to their function?
- … give a definition of protein families explain how they relate to the evolution of proteins?
- … explain how enzymes influence reactions by referring to energy and their substrate?
- … describe the steps of an enzyme catalysed reaction?
- … describe and compare positive and negative regulation of enzymes by effector molecules and how
this relates to allosteric regulation of an enzyme? - … explain the regulation of an enzyme by phosphorylation and dephosphorylation?
- … describe the role of cellular motor proteins and how they work?
