Proteins (Serwer 1) Flashcards
Proteins of bone and dentin
- Collagen (type 1)
- Fibronectin
- Osteocalcin
- Osteopontin
- Bone sialoptotein
Major structural protein, 90% of total protein in bone and dentin
Collagen (type 1)
Helps direct formation of and needed to maintain collagen matrix in bone and dentin
Fibronectin
Minor in amount, but important in bone and dentin
- Osteocalcin
- Osteopontin
Glycoprotein of bone and dentin
Bone sialoprotein
Non-collagenous proteins constitute ____% of bone protein, ___% of them coming from serum, and ___% from bone cells. Functions are not well characterized.
- 10-15
- 25
- 75
Typical Composition of Bone and Percent by dry weight
- Hydroxyapatite (50-70%)
- Collagen (20-40%, mostly type 1)
- Non-collagen proteins (1-2%)
- Lipids (3%)
- Water (5-10%)
Polymers with 3D structures that promote functions including enzymatic activity and formation of essential structures
Proteins
Molecules that consist of repeating subunits
Polymers
The repeating subunit of a protein
Amino acid
The linkage between amino acids in a protein is _______.
An amide linkage
The primary structure of a protein is ________.
The sequence of amino acids
Rotation around the peptide bond is restricted by _____.
Resonance (partial double bond)
Describe secondary structure
3-dimensional, local
The rotation angles of the other two bonds are ________.
Sterically restricted
Spiral staircases with amino acid steps
Alpha helices
Alpha helices: ___ steps/turn, or interact ___ steps away
3.6
4
Alpha helices: ___ nm/residue
0.15
Alpha helices: Sidechains project _______
Up and out
Alpha helices: _____ handed
Right (rotates clockwise)
Alpha helices: ____ and ____ amino acids uncommon
- Pro
- Gly
Alpha helices: The donor-backbone _____ and acceptor-backbone _____ form a ______ bond
- Amide nitrogen
- Carbonyl oxygen
- Hydrogen
Fully extended conformations
Beta strands
Beta strands: The distance between neighboring resides is ____ vs 0.15 nm in alpha helix.
0.35
Beta strands: Strands pair via donor-acceptor backbone _____ bond like those that stabilize alpha helices.
Hydrogen
Beta strands: ______ often connects adjacent anti-parallel strands
Sharp, four-residue turn (B-turn)
Beta strands can align both ____ and ____ to form beta sheets.
Parallel and Antiparallel
Beta strands: side chains project above and below the sheet in an ______ fashion.
Alternating
Beta strands: Amino acid resides with _____, _____ chains are most common
Bulky, branched
_____ B-sheet can wrap as a helix forming a _____
Parallel
B-helix
Beta strands: variations in proteins
B-hairpin
Greek key
Collagen Triple Helix is rich in ______ which point to _____ of helix
Glycine (smallest amino acid; makes up about 1/3)
Inside
The collagen trip helix is a _________ with ____ residue per turn.
Stretched, left handed alpha helix
~3
The collagen trip helix lacks ____-strand H-bonds
Intra
NMR spectroscopy requires a ______ of the purified protein (~___mL at high concentration), while X-ray crystallography requires _______ (~__mm in each dimension).
- Soluble solution (0.25)
- Well-ordered crystal (0.1)
NMR spectroscopy uses a sample placed in ______, while X-ray crystallography _______.
- Strong magnetic field
- Irradiates the crystal with high intensity x-rays
NMR spectroscopy can be applied to proteins of ____, while X-ray crystallography can be applied to proteins of _____.
- Up to 50 kDa
- Any size
______ is emerging and done with a frozen sample which has many pictures taken and makes final image.
Cryo-electron microscopy
Refers to the three-dimensional structure of the entire polypeptide chain
Tertiary structure
Tertiary structure: The 3D structure is stabilized by ____ bonds, _____ and _____ interactions, and _____ linkages between _____ residues.
- Hydrogen
- Electrostatic (+ and -)
- Hydrophobic
- Disulfide
- Cysteine (forms cystine)
_____ states that tertiary structure is determined by primary structure.
Anfinsen Hypothesis
____ or ____ unfolds protein and ____ breaks S-S bonds
Urea or Guanidine hydrochloride
B-mercaptoethanol
Proteins are renatured by removing denaturants by _____.
Dialysis
Stabilization of tertiary structure is dependent on ____ and ____ interactions
- Hydrophobic
- Electrostatic
The arrangement of protein subunits in a multimeric complex
Quaternary structure
Quaternary structure: the individual polypeptide chains are ____ of the multimeric complex
Subunits
Quaternary structure: subunits associate into a quaternary structure though the _____ bonds that stabilize tertiary structures of proteins.
Same
Quaternary structure: the _________ is one of the most well-known and highly characterized multi-protein complexes
Hemoglobin heterotetromer
Describe the method(s) that could be used to determine the three-dimensional structure of a 35 kDa protein.
- NMR spectroscopy
- X-ray crystallography
- Cryo-electron microscopy
The partial double bond character of the peptide bond restricts neighboring groups to a single _______ .
Plane
If an atom-sized gremlin climbed an α-helix as though the α-helix were a staircase and then looked straight up, how far above the gremlin would the next stair be?
1.5 nm
By how many degrees must you rotate when going from one amino acid to the next in an α-helix?
360 degrees/ 3.6 = 100 degrees
How does beta-sheet structure differ from that of α-helix? What is meant by parallel and anti-parallel chains?
- Beta is stretched so that the distance between amino acids is greater
- Parallel chains have the N to C terminus running in the same direction
Define tertiary structure.
The way in which secondary structures are configured
Define denaturation and renaturation as applied to proteins.
- Denaturation is breaking secondary and tertiary structure
- Renaturation is bringing it back
What was the fundamental principle tested in the studies conducted by C.B. Anfinsen on protein renaturation?
Whether tertiary structure is determined by primary structure
In general, what are three roles that a protein can play in a cell?
Scaffold, enzyme, structure
