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SP MCAT Biochem > Proteins > Flashcards

Proteins Flashcards

1
Q

What is the definition of protein?

A
  • polypeptides that range in length
  • function as enzymes, hormones, membrane pores, and receptors
  • elements of cell structure
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2
Q

What is the primary structure of an amino acid? What type of bonds stabilize this structure?

A
  • 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
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3
Q

What is the secondary structure of a protein? What type of bonds stabilize this structure?

A
  • 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
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4
Q

What are alpha-helices?

A
  • 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
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5
Q

What are beta-pleated sheets?

A
  • 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
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6
Q

What role does proline play in secondary protein structure?

A
  • 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
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7
Q

What is the tertiary structure of a protein? What bonds stabilize this structure?

A
  • 3D shape of a single polypeptide chain

- stabilized by hydrophobic interactions, acid-base interactions (salt bridges), H-bonding, and disulfide bonds

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8
Q

What is a disulfide bond?

A

-occur when 2 cysteine molecules are oxidized and create a covalent bond to form cystine

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9
Q

Explain hydrophobic interactions in proteins

A
  • 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
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10
Q

What is the quaternary structure of a protein? What bonds stabilize this structure?

A
  • 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
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11
Q

What are the functions of the quaternary protein structure?

A
  • stability
  • reduce amount of DNA needed to encode the protein complex
  • bring catalytic sites closer together
  • induce cooperativity
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12
Q

What are conjugated proteins?

A

proteins with covalently attached molecules called prosthetic groups – can be a metal ion, vitamin, lipid, carbohydrate, nucleic acid

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13
Q

Lipoproteins

A

have a lipid prosthetic group

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14
Q

Glycoproteins

A

have a carbohydrate prosthetic group

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15
Q

Nucleoproteins

A

have a nucleic acid prosthetic group

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16
Q

What is protein denaturation?

A
  • 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
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17
Q

Structural Proteins

A
  • 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
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18
Q

Collagen

A
  • comprised of 3 alpha-helical motifs
  • strong and flexible
  • found in connective tissue, extracellular matrix, bone, muscle, skin
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19
Q

Elastin

A
  • found in extracellular matrix of connective tissue
  • stretches and recoils like a spring to restore original tissue shape
  • highly coiled and cross-linked
20
Q

Keratin

A
  • found in intermediate filaments in epithelial cells
  • contribute to integrity of cell and function as regulatory protein
  • includes actin and tubulin
21
Q

Actin

A
  • 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
22
Q

What is the most abundant structural protein in eukaryotes?

A

actin

23
Q

Tubulin

A
  • 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
24
Q

Motor Proteins

A
  • 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
25
Q

Myosin

A
  • 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
26
Q

Kinesins

A
  • 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”
27
Q

Dyenin

A
  • 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”
28
Q

Binding Proteins

A
  • 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
29
Q

Cell Adhesion Molecules (CAM)

A
  • 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
30
Q

Cadherins

A
  • glycoproteins that mediate Ca2+ dependent cell adhesion
  • hold similar cell types together
  • found in intercellular junctions (tight junctions)
31
Q

Integrins

A
  • 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
32
Q

Selectins

A
  • 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
33
Q

Immunoglobulins

A
  • 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
34
Q

Describe the structure of Immunoglobulins

A
  • 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
35
Q

What is the antigen binding region of immunoglobulins?

A
  • located on the Y tips of antibodies

- contain specific polypeptide sequences that bind a single specific antigenic sequence

36
Q

What is the constant region of immunoglobulins?

A

part of antibody involved in the recruitment and binding of other cells in the immune system

37
Q

What is an Epitope?

A

part of antigen that immunoglobulin attaches to

38
Q

List the 3 outcomes that occur when an antibody binds to its antigen

A
  • 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
39
Q

Functions of Enzyme-Linked Receptors

A
  • participate in cell signaling through extracellular ligand binding
  • initiate 2nd messenger cascades
40
Q

What are the 3 protein domains of enzyme-linked receptors?

A
  • membrane-spanning (anchor receptor in cell membrane)
  • ligand binding (induces conformational change when ligand binds)
  • catalytic domain
41
Q

G-Protein Coupled Receptors

A
  • integral membrane proteins involved in signal transduction
  • have 7 membrane spanning alpha helices
  • 3 main types: Gs, Gi, Gq
42
Q

Gs Function

A
  • stimulates adenylate cyclase

- leads to an increase in cAMP levels

43
Q

Gi Function

A
  • inhibits adenylate cyclase

- leads to decreased in cAMP levels

44
Q

Gq Function

A
  • 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
45
Q

List the steps involved in initiation of 2nd messenger systems

A

(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

SP MCAT Biochem (16 decks)

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