Proteins Flashcards
What is the definition of protein?
- polypeptides that range in length
- function as enzymes, hormones, membrane pores, and receptors
- elements of cell structure
What is the primary structure of an amino acid? What type of bonds stabilize this structure?
- linear arrangement of amino acids coded by DNA
- stabilized by the formation of covalent peptide bonds between adjacent amino acids
- encodes for all the information needed for folding at higher structural levels
What is the secondary structure of a protein? What type of bonds stabilize this structure?
- local structure determined by nearby amino acids
- stabilized by H bonding between different amino acid residues
- include two subtypes: alpha-helices and beta-pleated sheets
What are alpha-helices?
- part of secondary protein structure
- rodlike structures in which the peptide chain coils clockwise around a central axis
- stabilized be intramolecular H bonds between carbonyl oxygen and amide H atom 4 residues down the chain
- side chains of amino acids point away from the helix core
What are beta-pleated sheets?
- part of secondary structure of proteins
- either parallel or antiparallel
- peptide chains are alongside eachother
- stabilized by intramolecular bonds between carbonyl oxygen atoms on one chain and amide H atoms in an adjacent cahin
- side chains of amino acids point above and below the plane of the sheet
What role does proline play in secondary protein structure?
- proline has a rigid cyclic structure that creates a kink in the peptide chain when in the middle of an alpha-helix
- found between chains in beta-pleated sheets
What is the tertiary structure of a protein? What bonds stabilize this structure?
- 3D shape of a single polypeptide chain
- stabilized by hydrophobic interactions, acid-base interactions (salt bridges), H-bonding, and disulfide bonds
What is a disulfide bond?
-occur when 2 cysteine molecules are oxidized and create a covalent bond to form cystine
Explain hydrophobic interactions in proteins
- these interactions push hydrophobic R groups to the interior of a protein
- leads to an increase in entropy (S) of surrounding H2O molecules
- creates a negative Gibbs free energy
What is the quaternary structure of a protein? What bonds stabilize this structure?
- not all proteins have this structure
- exist for proteins that contain more than one polypeptide chain
- Ex. hemoglobin
- structure is an aggregate of smaller globular peptides (subunits) and represents the functional form of a protein
- stabilized by hydrophobic interactions btw nonpolar side chains, electrostatic interactions btw ionic groups of opposite charge, H bonds btw polar groups, disulfide bonds
What are the functions of the quaternary protein structure?
- stability
- reduce amount of DNA needed to encode the protein complex
- bring catalytic sites closer together
- induce cooperativity
What are conjugated proteins?
proteins with covalently attached molecules called prosthetic groups – can be a metal ion, vitamin, lipid, carbohydrate, nucleic acid
Lipoproteins
have a lipid prosthetic group
Glycoproteins
have a carbohydrate prosthetic group
Nucleoproteins
have a nucleic acid prosthetic group
What is protein denaturation?
- occurs when a protein loses its 3D structure and can no longer catalyze reactions (inactive)
- heat does this by increasing the average KE thus disrupting hydrophobic interactions
- solutes do this by disrupting elements of secondary, tertiary, and quaternary structure
Structural Proteins
- have highly repetitive secondary structure and supersecondary structure – repetitive organization of secondary structural elements called a motif
- fibrous nature
- intermolecular forces maintain tertiary structure that give each protein a character shape
- includes collagen, elastin, keratin
Collagen
- comprised of 3 alpha-helical motifs
- strong and flexible
- found in connective tissue, extracellular matrix, bone, muscle, skin
Elastin
- found in extracellular matrix of connective tissue
- stretches and recoils like a spring to restore original tissue shape
- highly coiled and cross-linked
Keratin
- found in intermediate filaments in epithelial cells
- contribute to integrity of cell and function as regulatory protein
- includes actin and tubulin
Actin
- protein that makes up microfilaments and thin filaments in myofibrils (rod of muscles)
- major muscle component
- have positive and negative side so motor proteins can travel unidirectionally along filament
What is the most abundant structural protein in eukaryotes?
actin
Tubulin
- protein that makes up microtubules
- has polarity – negative end located adjacent to the nucleus and positive end in periphery of cell
- aid in cell division and intercellular transport via motor proteins
Motor Proteins
- display enzymatic activity by acting as ATPase which can power conformational change necessary for motor function
- have transport interactions with actin and/or microtubules
- includes myosin, kinesins, dyneins
Myosin
- primary motor protein
- interacts with actin
- the thick filament in a myofibril
- movement of head creates power stroke of sarcomere contraction by hydrolyzing ATP to move along the actin myofibril which contracts the sarcomere
Kinesins
- motor protein associated with microtubules
- have two heads (one always attached to tubulin)
- align chromosomes during metaphase
- depolymerize microtubules during anaphase
- bring vesicles toward positive end of microtubule (towards outside of cell)
- “Karry-out”
Dyenin
- motor protein associated with microtubules
- have two heads with one always attached to tubulin
- involved in sliding movement of cilia and flagella
- bring vesicles towards negative end of microtubule – towards inside of cell
- “Dyne-In”
Binding Proteins
- bind a specific substrate either to isolate it in body or hold its concentration at a steady state
- includes: hemoglobin, Ca2+ binding proteins, DNA binding proteins
Cell Adhesion Molecules (CAM)
- proteins found on surface of most cells
- help bind cell to extracellular matrix of another cell
- includes all integral membrane proteins
- examples: cadherins, integrins, selectins
Cadherins
- glycoproteins that mediate Ca2+ dependent cell adhesion
- hold similar cell types together
- found in intercellular junctions (tight junctions)
Integrins
- proteins that have two membrane-spanning chains (alpha and beta) which bind to and communicate with extracellular matrix
- role in cellular signaling
- impact cellular function by promoting cell division or apoptosis
- regulate how neutrophils (found in blood) adhere to endothelial lining
Selectins
- bind carbohydrate molecules that project from other cell surfaces
- weakest formed CAM bonds
- role in host defense
- regulate how neutrophils (found in blood) adhere to endothelial lining
Immunoglobulins
- antibodies
- most prominent protein type in immune system
- produced by B-cells
- function to neutralize targets in the body and recruit other cells to eliminate the threat
Describe the structure of Immunoglobulins
- Y shaped proteins made of two identical heavy chains and two identical light chains that are held together by disulfide linkages and noncovalent interactions
- both chains have constant and variable domains
- tertiary structure
What is the antigen binding region of immunoglobulins?
- located on the Y tips of antibodies
- contain specific polypeptide sequences that bind a single specific antigenic sequence
What is the constant region of immunoglobulins?
part of antibody involved in the recruitment and binding of other cells in the immune system
What is an Epitope?
part of antigen that immunoglobulin attaches to
List the 3 outcomes that occur when an antibody binds to its antigen
- neutralization of pathogen or toxin
- marking of the antigen for destruction
- creation of insoluble antigen-antibody complexes that can be phagocytized and digested by macrophages
Functions of Enzyme-Linked Receptors
- participate in cell signaling through extracellular ligand binding
- initiate 2nd messenger cascades
What are the 3 protein domains of enzyme-linked receptors?
- membrane-spanning (anchor receptor in cell membrane)
- ligand binding (induces conformational change when ligand binds)
- catalytic domain
G-Protein Coupled Receptors
- integral membrane proteins involved in signal transduction
- have 7 membrane spanning alpha helices
- 3 main types: Gs, Gi, Gq
Gs Function
- stimulates adenylate cyclase
- leads to an increase in cAMP levels
Gi Function
- inhibits adenylate cyclase
- leads to decreased in cAMP levels
Gq Function
- activates phospholipase C which cleaves a phospholipid to form PIP2 which is cleaved into DAG and IP3
- IP3 opens Ca2+ channels in the endoplasmic reticulum
List the steps involved in initiation of 2nd messenger systems
(1) ligand binding engages G protein
(2) GDP is replaced with GTP, and the alpha subunit dissociates from the beta and gamma subunits
(3) activated alpha subunit alters the activity of adenylate cyclase or phospholipase C
(4) GTP is dephosphorylated to GDP, and the alpha subunit rebinds to the beta and gamma units
