Protein Structure
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| 4 Molecular Organization Levels of Proteins | Primary
Secondary
Tertiary
Quaternary
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| Functions of Proteins | Signaling, Transport, Catalysis, Movement, Structure, Regulation
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| Primary Structure | Sequence of Amino Acids. Known primary structure may be used to diagnose or study disease.
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| Amino Acids are joined by _________ bonds. | Peptide
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| How are peptide bonds formed? | N terminus to C terminus
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| Limitations of DNA sequencing | -Can't predict the disulfide bonds
-Can't identify post-translational
modifications
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| AA sequence is determined by: | sequencing the coding region of DNA
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| Secondary Structures | alpha-helix, beta-sheets, beta-bends
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| alpha-helix | -spiral, tightly packed structure
-side chains extend outward
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| protein contents of alpha helices | -keratins are nearly entirely alpha-hilical
-myoglobin contains only 8% alpha-helices
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| alpha helix hydrogen bonding | occurs between the carbonyl oxygen and the amide hydrogen of the backbone
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| disrupts alpha helix formation | -proline
-large number of charged AA that form ionic bonds
-large numbers of AA with bulky side chains
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| beta sheets | -appear pleated
-hydrogen bonds are perpendicular to polypeptide backbone
-parallel or anti-parallel
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| interchain bonds (beta sheets) | separate polypeptide chains
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| intrachain bonde (beta sheets) | single polypeptide
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| beta bends | -reverse turns
-generally composed of 4 amino acids (often includes proline or glycine)
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| tertiary structure | -folding of domains and final arrangement of domains
-Primary structure of polypeptide chain determines tertiary structure
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| Domains | fundamental functional 3D structural units of polypeptide
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| core domain (tertiary) | is built from a combination of motifs
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| The Four types of interactions that cooperate to stabilize tertiary structure of proteins | -Disulfide bonds
-Hydrophobic interactions
-Hydrogen bonds
-Ionic interactions
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| Disulfide bond | formed by sulfhydryl groups (-SH) of two Cys residues
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| Hydrophobic interactions | -form between nonpolar side chains
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| process of folding | -process of folding in vivo often begins co-translationally from N-terminus
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| chaperones | -“heat shock proteins” - involved in various stages of folding
-Keep protein unfolded
-Increase the rate
-Protect from unproductive interactions
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| examples of chaperones | GroEL, GroES
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| Denaturation | -unfolding and disorganizing of protein’s secondary and tertiary structures
-done by heat, chemicals, and ions of heavy metals
-can be reversible or irreversible
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| Quality control | misfolded proteins are tagged and degraded in the cell
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| Amyloids | -Accumulation of spontaneously aggregating proteins caused by misfolding
-Associated with degenerative diseases like Alzheimer's disease.
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| Components of amyloid plaque in Alzheimer's | -amyloid precursor protein
-neurofibrillary tangles in the brain caused by abnormal form of tau protein
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| Prion protein (PrP) | -Infectious protein produced in brain, resistant to proteolysis
-causes transmissible spongiform encephalopathies (TSEs)
-Creutzfeldt-Jakob disease in humans
-Scrapie in sheep
-Bovine spongiform encephalopathy “mad cow disease” in cattle
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