Self Study-Protein Structure, Composition, Folding Flashcards
Structural proteins
Dynamic proteins
Classes of dynamic proteins
- Structure provide matrix for bone/connective tissue, giving structure and form
- Dynamic provide transport, metabolic control, contraction, chemical transformation. Include:
1. Enzymes- catalyze chem reactions (i.e. DNA Polymerase)
2. Transport proteins (i.e. Hb, ion channels)
3. Protective proteins (i.e. antibodies)
4. Movement (i.e. myosin, actin)
5. Regulatory proteins in metabolism (i.e. hormones and GPCR)
6. Gene regulatory proteins (control transcription/translation)
Amino acids
How many?
What is attached to C-alpha? Are they optically active?
Which isomers are found in humans?
How do amino acids act as buffers?
- 20
- COOH, NH2, H, R group (side chain)
- They are optically active due to asymmetry at C-alpha (Except glycine)
- Only L (amino group to left)
- donate and accept protons (COOH and NH2)
Amino Acid Characteristics
How does peptide reaction occur?
Peptide bond characteristics?
Peptide vs protein?
Disulfide bridge formation
Glutathione (what does it do, what is it made of, how does it react?)
Where are ionizable groups? What do they do?
Where do hydrophobic side chains normally go? What do they help with?
- Amino group reacts with Carboxyl group, eliminating H2O and forming peptide bond
- Like a double bond, cannot rotate around C-N bond, planar, C-alpha bonds do rotate (important for folding)
- Peptide <50 AA, protein >50 AA
- From oxidation of Cys in 2 thiols, involved in stabilizing protein structure
- Fights ROS, repairs oxidative damage to cell membrane, made of Glu-Cys-Gly, disulfide bridge forms between 2 glutathiones
- Free N/C termini and side chains of some AA, ionic interactions play a role in protein stability/structure and therefore function
- Go to interior of protein to help with protein folding, can also create a binding site for other proteins/ligands when clustered
Amino acid classification
Nonpolar
Uncharged Polar
Acidic (negatively charged at physiological pH)
Basic (positively charged at physiological pH)
- Ala, Gly, Ile, Leu, Met, Phe, Pro, Trp, Val
- Asn, Cys, Gln, Ser, Thr, Tyr
- Asp, Glu
- Arg, His, Lys
Buffers
Henderson-Hasselbalch equation
Pulmonary obstruction causes…
Why is pH important for drug absorption?
- pH= pKa + log([A-]/[HA]), increase A-, pH rises
- Incr CO2, Decr pH, respiratory acidosis
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Levels of protein organization
Primary structure
Secondary structure
Tertiary structure
Quaternary structure
Globular vs Fibrillar proteins
Homomultimer vs heteromultimer
- AA sequence (determines higher structures, a mutation can change an AA in sequence and either activate or diminish protein activity, or does nothing)
- local 3D folding (alpha helix, beta sheet, beta turn, random coil)
- 3D structure of protein (hydrophobic normally inside, hydrophilic/ionized normally outside to interact w/ H2O), stabilized by noncovalent 1)electrostatic, 2)hydrophobic, 3)H-bonds, 4)disulfide bonds. May have different domains with different functions
- non-covalent assoc. of polypeptide subunits into multi-subunit protein (not in all proteins)
- Globular proteins resemble globes, normally soluble in H2O (i.e. Hb)
- Fibrillar proteins resemble rods (i.e. Collagen), generally insoluble in H2O
- Homomultimer is same subunits come together
- Heteromultimer is different subunits come together (Hb is a Alpha2Beta2)
Types of secondary structure
Alpha helix
Beta pleated sheet
Beta turn
Random coil (where are they normally found)
- right handed helix kept together by H-bonds from C=) to N-H every 4th peptide, side chains point outside (Photo on left)
- 2 chains aligned parallel or antiparallel, H-bonds between C=O and N-H of adjacent chains, side chains point up and down (Photo on right)
- Reverse direction of polypeptide chain, allowing compact globular proteins
- Any other less ordered structure, many found at binding site or active centers of proteins (i.e. immunoglobulin antigen-binding sites)
What are quaternary structure advantages?
- Stability- can shield more hydrophobic residues from H2O located inside the protein
- Genetically economical- homomultimers need only 1 gene for a complex protein
- Efficiency- heteromultimers have active sites brought close together, allow substrate to be channeled between subunits, homomultimers allow multiple substrates to be processed at once
- Cooperativity- Subunit interactions can facilitate a reaction (i.e. in Hb, one subunit becoming active helps others convert to active conformation)
Steps in protein folding
Native structure
- Short range interactions form secondary structures
- Fold on each other to form domains (larger folded segments)
- Once folded, disulfide bonds can stabilize and quaternary structure can form
- Final conformation, which is the most stable
Chaperones
What are they and what do they do?
What are they required for?
What family do they belong to? When does synthesis of these increase?
- Assisit in protein folding process (including quaternary structure formation)
- Bind protein surfaces so they don’t form insoluble aggregates (which occur when protein conc. is high)
- Required for: Refolding proteins as they cross membranes (including transport into mitochondria and into and out of ER), proteins must be unfolded to pass through membranes
- Heat shock proteins (HSP), their synthesis increases when cells are cultured at higher temperatures since that’s when proteins denature and need help re-folding so cell doesn’t die
Denaturation
What happens?
Causes?
- Loss of function always occurs, due to disrupted 2/3/4º structure, weakening hydrophobic/ionic interactions and leading to no or improper folding
- Caused by change in pH, ionic strength, temperature
Diseases of Defective Protein Folding
Alzheimer’s
Creutzfeldt-Jakob disease
- Amyloid protein precursor doesn’t fold properly, leads to spontaneous aggregation into long, fibrillar protein assemblies (amyloids)
- nervous system dysfunction including ataxia, dementia, paralysis (normally fatal). Caused by misfolding of prion protein (goes from normal soluble to insoluble amyloid fiber conformation due to 2 alpha helices becoming beta strands)
