Protein Structure and Function

Flashcards for review

DNA Mutations Leading to Disease

Mutations in DNA can produce defective proteins that result in disease such as cancer, cystic fibrosis, and sickle cell anemia.

Weak Bonds and Macromolecule Shape

Weak bonds determine the shape of macromolecules, like the double-stranded helix of DNA, through hydrogen bonds between complementary base pairs.

Weak Bonds and Self-Assembly

Weak bonds facilitate reversible self-assembly of pre-synthesized subunits into specific structures, such as membrane lipid bilayers and protein polymers.

Weak Bonds and Molecular Specificity

Weak bonds determine the specificity of most molecular interactions, like enzyme-substrate specificity and catalysis.

Environmental Effects on Weak Bonds

Molecules denature upon environmental changes (pH, temperature, ionic strength) that affect the strengths of weak bonds.

Binding Specificity

Tight binding requires multiple complementary weak interactions and complementary surfaces.

Four Major Types of Noncovalent Interactions

Ionic bonds, hydrogen bonds, van der Waals interactions, and hydrophobic interactions.

Hydrophobic Interactions

Water forces non-polar (uncharged) surfaces out of solution to maximize hydrogen bonding.

Ionic Bonds

Electrons are donated/accepted by atoms rather than shared.

van der Waals Interactions

Weak force produced by fluctuations in electron clouds of atoms that are brought in close proximity.

Learning Objectives (Proteins)

Codes and properties of amino acids, types of interactions that help stabilize protein structure, formation of 1°, 2°, 3°, & 4° structure, modular nature of proteins and evolutionary results, how proteins are classified & compared by sequence &/or by structure.

Additional Protein Concepts

Proteins have built-in instructions for assembly, and their function is defined by their 3-dimensional landscape. Proteins can be regulated (turned on & off), they often function in networks or multi-molecular complexes, and allosteric effects lead to conformational changes and changes in activity.

Protein Shape Specification

Amino acid sequence.

Protein Folding

Proteins fold into a conformation of lowest energy.

Common Folding Patterns

Alpha helix and beta sheets are common folding patterns, with helices forming readily and beta sheets forming rigid structures at the core.

Protein Classification

Proteins can be classified into families.

Stabilization of Extracellular Proteins

Extracellular Proteins Are Often Stabilized by Covalent Cross-Linkages.

Amino Acid Properties

L isomer is found in proteins and the alpha carbon is chiral center in an amino acid.

Genetic code degeneracy

small change in codons creates big change in amino acid.

Condensation Reaction

Joining amino acids.

Primary Protein structure

Linear arrangement of amino acids.

Sequence and Structure

Sequence of amino acids provides the key to 3D shape/structure.

Peptide bond

Peptide bond has partial double bond character.

Protein Sequence Direction

Protein sequences are always written from N-terminus (on left) to the C-terminus (on right).

Ramachandran Plot

Describes allowed angles in protein backbones.

Factors Involved in Protein Folding

Bonding, Hydrophobic Effect, Protein Folding, Amino Acid propensities.

Alpha helix

Helices almost always right handed in proteins.

Secondary Structures

Secondary structures are the core elements of protein architecture.

Beta Sheets

Beta sheets form rigid structures that are often found in the core of proteins.

Noncovalent bond role in protein folding

All 3 types of noncovalent bonds help a protein fold properly, and multiple weak bonds cooperate to produce a strong bonding arrangement.

Polypeptide folding

The polypeptide chain folds in 3-D to maximize weak interactions. Hydrogen bonds play a major role in holding different regions together.

Protein Denaturation

Proteins can be denatured by chaotropic agents like urea.

Things to remember about proteins

levels of structure are 1°,2°,3°,4°, codes - 3 Letter & 1 Letter, Functions – binding, catalysis, switching, structural.

Protein Structure

Structure is determined by sequence.

Protein Domain

Protein Domains consist of independently folding stretches of amino acids A single polypeptide chain can fold into one or more domains.

Tertiary Structure

Overall folding of a polypeptide chain yields its tertiary structure.

Membrane Spanning Helices

Linear stretches of amino acids indicate membrane spanning helices. ~20 Amino acids are required to span the membrane, quick way to identify integral membrane proteins.

Coiled Coils

i.e. hydrophobic effect.

Quaternary Structure

Interactions between multiple polypeptide chains produces quaternary structure.

Protein Domains

Modular units from which larger proteins are built.

Src Protein

Src Protein (ATP shown in red) Modularity – Protein made from several domains.

Sequence variance

Different Sequences lead to Different Architecture cytochrome C lactic dehydrogenase immunoglobulin fold.

Homeodomains separated by more than a billions years of evolution

Yeast & Drosophila have only been around for a few hundred million years, yet are separated by more than a billion years of evolution.

Evolutionary Trace of an SH2 Domain

Amino acids colored by proximity to ligand Important residues are conserved.

Modular nature of proteins

Protein domains are often swapped or shuffled.

Fibronectin

Many proteins have domain combinations.

Structure Function Paradigm

Collagen (tough, inelastic)Elastin (Stretchy) Paradigm:Structure reflects Function.

Disulfide Bonds

Covalent Disulfide Bonds in extracellular proteins.

Antibodies

Antibodies have repeated framework domains and special binding domains Protein interactions typically require many weak bonds.

Km in enzyme kinetics

A bigger Km means weaker binding Km is the substrate concentration @ half the maximal rate, Vmax.

Km significance

Km is an approximate measure of substrate affinity for the enzyme: it is numerically equal to the concentration of [S] at V = 0.5 Vmax.

kcat Significance

kcat is the turnover number for the enzyme.

Allosteric Regulation

Allosteric regulators bind to enzymes and alter their activity by changing the enzyme’s 3D structure, regulatory binding sites are located separately from substrate binding site (i.e. active site) Positive Regulation.

Cooperative Binding

Cooperative Binding by multi-subunit enzymes allows enzymes to respond more quickly to changes in concentration ATC carbamoyl phos + D è carbamoyl aspartate.

ATC carbamoyl phos + D è carbamoyl aspartate

synthesis of pyrimidines allosterically regulated (i.e. like Hemoglobin) activated by ATP (a purine) inhibited by pyrimidines (feedback inhibition).

Controlling Proteins

Allosteric Enzymes Have Binding Sites That Influence One Another Phosphorylation Can Control Protein Activity by Triggering a Conformational Change GTP-Binding Proteins Are Also Regulated by the Cyclic Gain and Loss of a Phosphate Group.

GTPase

Hydrolysis of GTP leads to conformational changes that can pass along a signal like a SWITCH.

Protein Activity Regulation

Protein activity may be regulated by multiple mechanisms 1. Phosphorylation 2. Binding to GTP or ATP 3. Allosteric regulation 4. Feedback inhibition.

Directional Movement

Motors take advantage of leverage.

Assembly by proximity

kinase move to apical surface in fly embryo Assembly by proximity greatly speeds up the assembly line.

Ubiquitination

Degradation by ubiquitination.

DnaJ and DnaK binding

DnaJ binds to the unfolded or partially folded protein and then to DnaK.

Protein Folding Intermediates

Discrete folding intermediates are formed.

Diffraction

Reflection of x-ray beam