Biochemistry Test 1 Biochemistry Test 1: Chapter 4

Question Answer
What is the difference between configuration and conformation? Configuration is a form where change would require breaking bonds (cis/trans) and conformation is a form where change can occur without breaking bonds (the shape)
What are the 4 levels of protein structure? Primary structure (string of amino acids), secondary structure (alpha helix or beta pleated sheets), Tertiary structure (polypeptide chain), and Quaternary structure (assembled subunits)
Polypeptides consist of _______________ linked by a peptide bond. amino acids
What is another name for peptide bonds? amide bonds
What does the term residue refer to? each amino acid in a protein is called a residue
Explain dehydration synthesis. synthesis with water as a byproduct
Explain hydrolysis. Breakdown of a molecule with the consumption of water
What is the directionality of protein primary structures? From amino-terminal residue to the carboxyl-terminal residue
What unit represents g/mol? dalton
What is the mean molecular weight for an amino acid? 110 g mol^-1
Give 3 facts about peptide bonds. Peptide bonds are essentially planar, have resonance, and are uncharged
Can peptide bonds rotate? NO
Why are most peptide bonds in the trans configuration? To minimize steric clashes between neighboring R groups
Can bonds connected to the alpha carbon rotate? YES
Know what phi (?) and psi (?) represent. Phi (?) = angle around the alpha carbon and the amide nitrogen bond. Psi (?) = angle around the alpha carbon and the carbonyl carbon bond
True or False: In a fully extended polypeptide, both phi (?) and psi (?) are 180 degrees True
How are alpha helixes stabilized? Stabilized by hydrogen bonds nearby residues
How are beta pleated sheets stabilized? Stabilized by hydrogen bonds between adjacent segments that may not be nearby
What is the term for irregular arrangement of the peptide chain? Random coil, remember random coils are not secondary structures.
How is the helical backbone held together? By the parallel hydrogen bonds between the backbone amides and carbonyl oxygens of every 4th aa on the amino terminal side
True or False: Side chains point out and are roughly perpendicular with helical axis. True
True or False: the alpha helix is a left handed helix. FALSE, it is a right handed helix with hydrogen bonds between in 3 and 4 aa apart
What determines the tertiary structure of a polypeptide chain? Hydrophilic and hydrophobic interactions
True or False: Small hydrophobic residues such as Ala and Leu are strong helix formers. True
What are the 2 possible chain orientations within a beta sheet? Parallel and antiparallel
Which beta sheet orientation is stronger? antiparallel
Why are antiparallel beta sheets stronger than the parallel orientation? Because the H bonds in the parallel orientation are bent making them weaker. In the antiparallel orientation the h-bonds are linear
What are the 2 major classes of tertiary protein structures ? fibrous and globular
Give one example of a globular protein. myoglobin
Define domain. part of a polypeptide chain that is independently stable

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