Protein Structure and Function Flashcards
Roles played by proteins:
Biochemical, cellular, physiological, phenotypic
Classes of Proteins
Enzymes Structural proteins Motility proteins Regulatory proteins Transport proteins Hormonal proteins Receptor proteins Defensive proteins Storage proteins
Enzymes
Catalysts; increase rates of chemical reactions
Structural proteins
Provide physical support and shape
Motility proteins
Involved in contraction and movement
Regulatory proteins
Control and coordinate cell function
Transport proteins
Move substances across membranes
Hormonal proteins
Communication between cells
Receptor proteins
Enable cells to respond to stimuli
Defensive proteins
Protect against disease
Storage proteins
Reservoirs of amino acids
Amino Acids
Monomers of proteins; 20 different amino acids; modified amino acids also exist; amino acid sequence unique for each particular protein; same basic structure; all amino acids (except glycine) contain a chiral/asymmetric alpha carbon; each amino acid has a unique R group which have different properties (basic, acidic, hydrophilic, hydrophobic)
Polymerization of Amino Acids
Amino acids are linked together into a linear polymer by dehydration/condensation reactions which form a peptide bond
Directionality of polypeptides
N-terminus (amino group) and C-terminus (carboxyl group)
Protein Synthesis
The process of elongating a chain of amino acids; immediate product is a polypeptide
Difference between polypeptides and proteins:
A polypeptide is the linear sequence of amino acids (primary structure); a protein is the association of secondary and tertiary structures to provide a functioning product
Monomeric protein
Contains a single polypeptide subunit
Multimeric protein
Contains two or more polypeptide subunits; dimers, trimers, tetramers, etc
Bonds and interactions important in protein folding and stability:
Hydrogen bonds Ionic bonds Disulfide bonds Van der Waals Forces Hydrophobic interactions
Levels of Organization in Protein Structure:
Primary - sequence of amino acids
Secondary - local folding of polypeptide
Tertiary - three dimensional conformation
Quaternary - interactions between monomeric proteins to form a multimeric unit
Secondary Structure
Describes local regions of structure that result from hydrogen bonding between NH and NO groups along polypeptide backbone
Two major patterns: alpha helix and beta sheets
Alpha Helix
Spiral in shape; 3.6 amino acids per turn; hydrogen bonds between NH and CO of every 4th amino acid; R groups outwardly facing; can have hydrophobic or hydrophilic faces
Beta Sheets
Beta strands; formed by hydrogen bonds between different polypetides or different regions of a single polypeptide; parallel or antiparallel conformation
Motifs
Certain units of secondary structure that consist of short stretches of alpha helices and beta sheets; found in many proteins; ie - hairpin loop, helix-turn-helix
Tertiary Structure
Reflects the unique aspect of the amino acid sequence because it depends on interactions of the R group; difficult to predict; results from the sum of the hydrophobic interactions and electrostatic interactions; provides function of protein
Native Conformation
The most stable three-dimensional structure of a particular polypeptide
Broad Categories of Proteins
Fibrous and globular
Fibrous Proteins
Extensive regions of secondary structure; highly ordered, repetitive structure; ie- fibroin (silk), keratin (hair), collagen (skin and tendons), elastin (ligaments and blood vessels)
Globular Proteins
Folded into compact structures; most common; more diverse; many have domains
Domains
A discrete locally folded unit of tertiary structure; usually has a specific function; typically 50-350 amino acids; proteins with similar functions will often share a common domain; proteins with multiple functions usually have a separate domain for each function
Prediction of Tertiary Structure
Primary structure determines the final folded shape of a protein; however, we are not able to predict how a given protein will fold due to the infinite possibilities and specific function
Quaternary Structure
The level of organization with the subunit interactions and assembly; specifically applies to multimeric proteins; some proteins consist of multiple identical subunits, or a variety of subunits
Formation of Tertiary Structure
Usually spontaneous, however, chaperones are sometimes required to aid in overcoming energy requirements and avoidance of thermodynamic pits
Beyond Quaternary Structure
Higher levels of assembly are possible for multiprotein complexes; often formed for multistep processes
Misfolding of Protein
Cause of several diseases:
Alzheimers, Huntingtons, Cystic fibrosis, BSA (Mad Cow), certain cancers
Modes of Protein Function Regulation
Proteolysis, phosphorylation/dephosphorylation; ligand binding; zymogens; GTPase switches; redox state; recruitment; localization
Experimental Determination of Protein Structure
X-ray diffration- crystallized samples; highest resolution
Cryoelectron microscopy- allows structure determination of non-crystalline specimens; useful with multiprotein complexes
