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Protein Structure & Function

Proteins have a variety of functions in cells including enzymatic, structural, transport, and signaling roles. A protein's structure and function are determined by its amino acid sequence and how it folds into its tertiary and quaternary conformations through interactions between R groups and formation of alpha helices and beta sheets. Protein shape and interactions allow them to bind ligands specifically and carry out their functions, with some proteins assembling into larger machines to perform complex tasks in cells.

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231 views

Protein Structure & Function

Proteins have a variety of functions in cells including enzymatic, structural, transport, and signaling roles. A protein's structure and function are determined by its amino acid sequence and how it folds into its tertiary and quaternary conformations through interactions between R groups and formation of alpha helices and beta sheets. Protein shape and interactions allow them to bind ligands specifically and carry out their functions, with some proteins assembling into larger machines to perform complex tasks in cells.

Uploaded by

Dhruv Khurana
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PDF, TXT or read online on Scribd
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Chapter 4

Protein Structure
and Function
Proteins
● Make up about 15% of the cell
● Have many functions in the cell
● Enzymes
● Structural
● Transport
● Motor
● Storage
● Signaling
● Receptors
● Gene regulation
● Special functions
Shape = Amino Acid Sequence
● Proteins are made of 20 amino acids
linked by peptide bonds
● Polypeptide backbone is the repeating
sequence of the N-C-C-N-C-C… in the
peptide bond
● The side chain or R group is not part of
the backbone or the peptide bond
Polypeptide
Backbone
Amino Acids
NOTE: You need to know this table

Hydrophili Hydrophobic
Protein Folding
● The peptide bond allows for rotation
around it and therefore the protein can fold
and orient the R groups in favorable
positions
● Weak non-covalent interactions will hold
the protein in its functional shape – these
are weak and will take many to hold the
shape
Non-covalent Bonds in Proteins
Globular Proteins

● The side chains will help determine the


conformation in an aqueous solution
Hydrogen Bonds in Proteins

● H-bonds form between 1) atoms involved in the


peptide bond; 2) peptide bond atoms and R
groups; 3) R groups
Protein Folding
● Proteins shape is determined by the
sequence of the amino acids
● The final shape is called the
conformation and has the lowest free
energy possible
● Denaturation is the process of unfolding
the protein
● Can be down with heat, pH or chemical
compounds
● In the chemical compound, can remove
and have the protein renature or refold
Refolding

● Molecular chaperones are small proteins that


help guide the folding and can help keep the
new protein from associating with the wrong
partner
Protein Folding
● 2 regular folding patterns
have been identified –
formed between the
bonds of the peptide
backbone
● -helix – protein turns like
a spiral – fibrous proteins
(hair, nails, horns)
● -sheet – protein folds
back on itself as in a
ribbon –globular protein
● Core of many proteins is
Sheets the sheet
● Form rigid structures
with the H-bond
● Can be of 2 types
● Anti-parallel – run in an
opposite direction of its
neighbor (A)
● Parallel – run in the same
direction with longer
looping sections between
them (B)
● Formed by a H-bond
Helix between every 4th
peptide bond – C=O to N-
H
● Usually in proteins that
span a membrane
● The helix can either coil
to the right or the left
● Can also coil around
each other – coiled-coil
shape – a framework for
structural proteins such
as nails and skin
Levels of Organization
● Primary structure
● Amino acid sequence of the protein
● Secondary structure
● H bonds in the peptide chain backbone
● -helix and -sheets
● Tertiary structure
● Non-covalent interactions between the R
groups within the protein
● Quanternary structure
● Interaction between 2 polypeptide chains
Protein Structure
Domains
● A domain is a basic structural unit of a
protein structure – distinct from those
that make up the conformations
● Part of protein that can fold into a stable
structure independently
● Different domains can impart different
functions to proteins
● Proteins can have one to many
domains depending on protein size
Domains
Useful Proteins
● There are thousands and thousands of
different combinations of amino acids that can
make up proteins and that would increase if
each one had multiple shapes
● Proteins usually have only one useful
conformation because otherwise it would not
be efficient use of the energy available to the
system
● Natural selection has eliminated proteins that
do not perform a specific function in the cell
Protein
Families

● Have similarities in amino acid sequence and


3-D structure
● Have similar functions such as breakdown
proteins but do it differently
Proteins – Multiple Peptides
● Non-covalent bonds can form interactions
between individual polypeptide chains
● Binding site – where proteins interact with one
another
● Subunit – each polypeptide chain of large
protein
● Dimer – protein made of 2 subunits
● Can be same subunit or different subunits
Single Subunit Proteins
Different Subunit Proteins

● Hemoglobin
● 2 globin
subunits
● 2 globin
subunits
Protein Assemblies
● Proteins can form very
large assemblies
● Can form long chains if
the protein has 2
binding sites – link
together as a helix or a
ring
● Actin fibers in muscles
and cytoskeleton – is
made from thousands
of actin molecules as a
helical fiber
Types of Proteins
● Globular Proteins – most of what we
have dealt with so far
● Compact shape like a ball with irregular
surfaces
● Enzymes are globular
● Fibrous Proteins – usually span a long
distance in the cell
● 3-D structure is usually long and rod
shaped
Important Fibrous Proteins
● Intermediate filaments of the
cytoskeleton
● Structural scaffold inside the cell
● Keratin in hair, horns and nails
● Extracellular matrix
● Bind cells together to make tissues
● Secreted from cells and assemble in long
fibers
● Collagen – fiber with a glycine every third amino
acid in the protein
● Elastin – unstructured fibers that gives tissue an
elastic characteristic
Collagen and Elastin
Stabilizing Cross-Links

● Cross linkages can be between 2 parts of a


protein or between 2 subunits
● Disulfide bonds (S-S) form between adjacent -SH
groups on the amino acid cysteine
Proteins at Work
● The conformation of a protein gives it a
unique function
● To work proteins must interact with other
molecules, usually 1 or a few molecules from
the thousands to 1 protein
● Ligand – the molecule that a protein can bind
● Binding site – part of the protein that interacts
with the ligand
● Consists of a cavity formed by a specific
arrangement of amino acids
Ligand Binding
Formation of Binding Site

● The binding site forms when amino acids from


within the protein come together in the folding
● The remaining sequences may play a role in
regulating the protein’s activity
Antibody Family
● A family of proteins that can be created
to bind to almost any molecule
● Antibodies (immunoglobulins) are made
in response to a foreign molecule ie.
bacteria, virus, pollen… called the
antigen
● Bind together tightly and therefore
inactivates the antigen or marks it for
destruction
Antibodies
● Y-shaped molecules with 2 binding sites at
the upper ends of the Y
● The loops of polypeptides on the end of
the binding site are what imparts the
recognition of the antigen
● Changes in the sequence of the loops
make the antibody recognize different
antigens - specificity
Antibodies
Protein Machines

● Complexes of 10 or
more proteins that work
together such as DNA
replication, RNA or
protein synthesis, trans-
membrane signaling
etc.
● Usually driven by ATP
or GTP hydrolysis

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