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Biochemistry CH 5 - Coggle Diagram
Biochemistry CH 5
characteristics of protein structures
the three classes of proteins are based on shape and solubility
fibrous
simple structure consisting of regular linear structure
play roles in cell structure
insoluble in water and dilute salt water
globular
spherically shaped
hydrophobic part is on the inside and the hydrophilic side is on the outside
very soluble in water
membrane
proteins in association with membranes
hydrophobic side chains are on the outside
insoluble in aqueous solutions
levels of organization in proteins
primary - sequence of amino acids
secondary - helical or pleated structure
tertiary - polypeptide chains bending and folding
quaternary - combining polypeptide chains
noncovalent forces drive higher orders of proteins
3D structures of proteins are called protein conformations
conformation ≠ configuration
conformation = 3D architecture, does not break covalent bonds when changed
configuration = geometric possibilities for a protein, must break covalent bonds to change
how proteins are purified and isolated from cells
two ways that proteins are categorized
size
electrical charge
ion exchange chromatography, electrophoresis, and solubility
proteins are the least soluble at their pI
affinity purification
typically more than one purification technique is used
size exclusion chromatography
electrophoresis
SDS-Polyacrylamide gel electrophoresis (SDS PAGE)
Isoelectric focusing
2D gel electrophoresis
Hydrophobic interaction chromatography
HPLC
affinity chromatography
ultracentrifugation
ion exchange chromatography
amino acid analysis
acid hydrolysis liberates amino acids from proteins
6N HCl at 110C
chromatography is used to separate amino acids
different proteins have different amino acids
primary protein structure
every protein has a unique amino acid sequence
sanger was the first person to sequence a protein
both chemicals and enzymes are used to sequence proteins
6 steps to Sanger sequencing
chains are separated and purified
disulfide bridges are cleaved
N and C terminals are identified
the chain is cleaved into even smaller fragments and sequence of each fragment is determined
Step 4 is repeated to generate overlap
sequence is determined using overlap
nature of amino acid sequences
homologous proteins have homologous amino acid sequences
orthologs
paralogs
related proteins have a common evolutionary origin
mutant protein = protein with slightly different amino acid sequence
other groups on proteins
covalent bonds after protein synthesis = post-translational modifications
prosthetic group = non-protein part that plays a role in protein function
functions of proteins
the do not store genetic information
they bind to target molecules using ligands
polypeptide synthesis in the lab
solid phase methods work best
solid phase synthesis