*OBJ - Protein: Structure-Function Relationship Flashcards
Define supersecondary structures or motifs, and explain their functional significance
- Motifs/supersecondary structure: small region of tertiary structure that have a combo of secondary elements in a specific geometrical pattern associated with a specific functional/structural role - between 2ndary & 3ary
- part of a bigger structure to get its original conformation
Describe domains with special reference to globin fold. Explain how domains are associated with a specific functions and contribute to the architecture of multifunctional proteins
Domains: large functional modules that can fold independently
- units of function; can have 1 or many
Alpha domains: alpha helices & loops
designed to bind to oxygen through Heme group (Myoglobin & Hb)
Globin Fold
Beta Domains: predominantly antiparallel B strands with hydrophobic core -> barrel like structure (B-barrel)
Alpha/Beta Domains: “Rossman Fold” NAD+ binding domain; alpha/beta barrels
Summarize the types of modified amino acid residues found in protein, their functional significnace, the respective chemical group associated with the modifications, and the amino acid residues modified in each case
1) Glycosylation
2) Lipid Attachment
3) Phosphorylation
4) Acetylation
5) Carboxylation
6) Hydroxylation
How posttranslational modification play a critical role in collagen structure
requires proline be hydroxylated, otherwise can’t Covalently cross-link
List the metal ions that are commonly found to be part of protein tertiary structure enhancing functional capability, with special reference to globin fold and zinc finger structures
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Zinc, Iron
Identify the amino acid residues that are good metal ligands
Cysteines & Histidines -> Zn
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Describe the architectural plan of the coiled-coil structure of a leucine zipper, and its function
Helix-loop-helix = Ca++ binding site (Trop C)
Helix-turn-helix = DNA binding; turn = small loop so 1 helix can interact with MAJOR groove of DNA; turns on/off transcription regulation
Coiled-coil/Leucine Zipper motif = every 7th residue is a Leucine & where the 2 helices interact/cross; they do not BIND directly to DNA, but dimerize the process/brings it together
- left handed supercoil
- think of an old telephone cord
- i.e. Fibrinogen
Zinc Finger Motif: mediate/directly involved in DNA binding; present in transcription factors
- alpha helix with 2 beta strands held together by a Zinc atom/ 2 cysteines & 2 histidines as metal coordinators
Demonstrate how the information for protein folding is encoded within the primary structure of a protein (ribonuclease A)
- folding encoded in primary structure (AA order)
- secondary structures quickly form -> Molten Globule State and then slowly fold into tertiary “Folded Native State” with biological activity
- Ribonuclease A can be reversibly denatured/forced into an unfolded/inactive state and will spontaneously reform folded configuration
Describe how different physical and chemical factors may affectprotein stability, and define protein denaturation
Irreversible denaturation
- Extremes pH (ionizing AA side chains/change electrostatic interactions)
- Chemical Denaturants (breaks H bonds)
- Temperature (H bonds)
Chaperones - prevent protein misfolding/guide protein by preventing the wrong interactions
Draw the different types of membrane insertions of membrane proteins, and describe the method used to predict membrane-spanning regions of a protein from its primary amino acid sequence (use of hydropathy plot)
Integral - through the membrane wiht nonpolar residues in the membrane regions
alpha helices: channels; transporters; hormone receptors, signal transduction
beta sheets: bacterial outer membrane porins, mitochondrial outer membrane proteins
Extracellular - responsibe for ligand bonding/ion gates for ion gated chanels; site of glycosylation; initiate transmembrane signalling
Intracellular: binding site for signaling proteins (G protein); site of phosphorylation; transmits transmembrane signaling to intracellular components
Hydropathy index: scale of a residue’s hydrophobic tendencies (negative = polar/H-philic)
PIC
Describe the consequence of protein misfolding with special emphasis to prion disease
alpha helix vs beta sheets & hydrogen bonding
ex: Cystic Fibrosis - thick music is from misfolded Cl channel protein
Define Isoelectric point (pI), and describe its significance in diagnostic proteomics
Isoelectric point = zwitteron predominates - net charge = 0
pI determines its electrophoretic mobility on a pH gradient (will move to where the net charge is 0 -> pH = pI)
Iso electric focusing: separating proteins based on their pI; then can be separated by size
Globule Protein tertiary structure
Hydrophobic residues tend to be clumps together in the interior
- if on the surface: form protein-protein interaction sites
Hydrophillic residues tend to be on the surface
- if on the inside: for catalytic sites
**Cystine disulfides prefer the interior of the protein
Glycosylation
AA modification/Posttranslational Modifications
- Protein folding
- Protein targeting for membrane proteins/secratory proteins
Lipid Attachment
AA modification/Posttranslational Modifications
- allows membrane anchoring of proteins both integral & peripheral
