What is primary structure
Sequence of amino acids in a polypeptide chain
What is secondary structure
Hydrogen bonds are the hallmark in this type of structure
What is tertiary structure
Stabilized by non covalent interactions and disulfide bonds
What is quaternary structure
Subunits represent basic component
What is a peptide bond
Linkage between the amino group of one amino acid and the carboxyl group of another amino acid
What is alpha helix
Stabilized by H bonds between nearby amino acids (n+4) in a polypeptide chain
What is motif
Super secondary structures in proteins
Examples of helix breakers
Proline and glycine
What are strong helix formers
Alanine and leucine
What are some examples of beta turn formers
Proline and glycine
What is a native fold
3D fold to fulfill specific biological function
What are favorable interactions in proteins
Hydrophobic effect, h bonds, London dispersion, and electrostatic interactions
What linkages are in primary structure
Covalent
What linkages in secondary structure
H bonds
What linkages in tertiary structure
Covalent, h bonds, ionic, van der waals, hydrophobic
Linkages in quarternary structures
Same as tertiary
What causes the peptide bond
Resonance
What type of degradation uses phenyl isothiocyanate which labels N terminal amino acid
Edman degradation
What reagent is used in edman degradation
Phenyl isothiocyanate
Structure of globular proteins
Tertiary and quarternary
Solubility of globular proteins
Fully soluble
Functions of globular proteins
Dynamic
Examples of globular protein
Hgb, myoglobin, enzymes
Structure of fibrous proteins
Primary and secondary
Solubility of fibrous proteins
Insoluble
How to make fibrous proteins soluble
Break disulfide bonds
Function of fibrous proteins
Structural, support
Examples of fibrous proteins
Collagen, keratin and elastin
Collagen contains what type of tripeptide sequence
Glycine x proline or glycine x 4Hyp
Left or right handed collagen chain
Left
Three alpha collagen chain, right or left handed
Right
Making a triple helix in collagen helps what
Increase strength
Prolyl hydroxylase and Lysyl hydroxylase requires what
O2, Fe and vitamin c
What enzyme is needed for glycosylation of selected OH-Lys residues
Glucose or glucosyl-galactose
What enzyme is needed for hydroxylation of selected pro and lys residues
Prolyl hydroxylase and lysyl hydroxylase
The triple helix formation of pro collagen is what type of process
Spontaneous
Cleavage of extension peptides requires what enzyme
Peptidases
Assembly into microfibril is what type of process
Spontaneous
Cross link formation to assemble collagen fibril contains what enzyme and other factor
Lysyl oxidase and copper
Assembly into collagen fiber and aggregation of collagen fibers is what type of process
Spontaneous
Type one of collagen genetic disease
Osteogenesis imperfecta which is weak bones. Mutation in type one collagen by replacing glycine with bulky side chain
Type two collagen genetic disease
Chondriodysplasias which is abnormal cartilage, bone and joint deformities. Dwarfism
Type three of collagen genetic diseases
Ehlers danlos syndrome. LETHAL, aorta rupture due to fragile skin and blood vessels
Type 5 collagen genetic disorders
Ehlers danlos syndrome, hyper mobile joints, skin extensibility
How does cross link formation occur in elastin
Lysyl side chains become delaminates by lysyl oxidase
What is a desmosine and why important
Allysyl (3) and Lysyl side chain (1). This helps make elastin more stretchable
Intrinsically disordered proteins purposes and score
Allows for conformation to bind to many different partner proteins and PONDR score shows probablity of interaction mostly and N and C terminus
Proteins can be denatured by
Heat or cold, pH extremes, detergents, reducing agents and chaotropic agents
What are chaotropic agents
Disrupt H bonds and denatures secondary structure
What are examples of chaotropic agents
Urea and guanidinium hydrochloride
Example of reducing agent
Beta mercaptoethanol
What are examples of protein misfolding diseases
Alzheimers diseases, Parkinson’s disease, and Huntington’s disease, transmissible spongiform encephalopathies
Common feature of amyloidosis
Missfolded proteins due to aggregation of B sheets
How do prions spread
Prion protein attaches to healthy prion causing the alpha helices to turn into beta sheets
What are Lewy bodies
Insoluble aggregates caused by a disorderly protein in the brain in Parkinson’s disease
What activates pepsinogen
Hydrogen protons and pepsin
Where is pepsinogen found
Stomach
Pepsinogen targets what
Phenylalanine
What activates trypsinogen
Enteropeptidase and trypsin
Where is trypsinogen found
Pancreas
What does trypsinogen target
Lysine and arginine
What activates chymotrypsinogen
Trypsin and chymotrypsin
What is the source for chymotrypsinogen
Pancreas
What does chymotrypsinogen target
Aromatic and bulky amino acids