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Protein Structure and Function

Proteins are made up of amino acids and take on specific 3D shapes that determine their function. The shape of a protein is determined by its amino acid sequence and weak interactions between residues that allow folding into regular structures like alpha helices and beta sheets. Proteins can interact with other molecules through domains and binding sites on their surfaces to carry out important roles in the cell.

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Priyanshu Kumar
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16 views

Protein Structure and Function

Proteins are made up of amino acids and take on specific 3D shapes that determine their function. The shape of a protein is determined by its amino acid sequence and weak interactions between residues that allow folding into regular structures like alpha helices and beta sheets. Proteins can interact with other molecules through domains and binding sites on their surfaces to carry out important roles in the cell.

Uploaded by

Priyanshu Kumar
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© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as DOC, PDF, TXT or read online on Scribd
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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

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

 Sheets
• Core of many proteins is 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)

 Helix
• Formed by a H-bond 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
• Quaternary 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

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

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