biochemistry exam 2

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pKa has 4 meanings
- is equal to -logKa
- found in Henderson/hasselbach
- related to ionization of an acid
- smaller the pKa the stronger the acid
2 ionizable groups AA have
- NH3+
- COOH
some R groups have ionizable groups as well as the two on the AA
if pH 7 is greater than the pKa for the C terminal it will be

deprotonated
if the pKa is greater than pH7 on the N terminal then the

proton will not dissociate
the charge of the AA depends on the pH of the solution and the pKa of the ionizable groups
isoelectric point

is the pH at which the overall charge of the protein is 0
what statement best describes the primary structure of protein

N>C sequence of amino acids dictated by the mature mRNA
low pH will cause r groups with an amine such as His, Arg, and Lys to deprotonate
secondary structure refers to the

conformation generated by interaction of amino acids that are close in sequence
how are secondary structures stabilized

hydrogen bonding
2 types of structures of secondary structures
- regular
- irregular
2 types of regular secondary structures
- alpha
- beta
2 types of irregular structures of secondary structures
- hairpin turns
- irregular loops
proline is too floppy and glycine is to rigid to form the alpha helix structures
alpha helix description

carbonyl oxygen in each AA H bonds with the NH groups of an AA 4 residues ahead
myoglobin is consisted of a great deal of helical structures
amphipathic helices contain these 2

polar and non polar amino acids
what sheet has greater bonds compared to the other in the secondary structures

beta has greater bonds
the alpha helix involves the helical inside of the sheet while beta involved the back bone of the sheet
2 ways secondary beta sheets can be constructed
- anti-parallel chains run in different directions
- parallele chains running in the same direction
in fatty acid binding protein the direction of arrows shows the directionality which is antiparallel
the fatty acid binding protein is stabilized by what and contains these residues
- hydrogen bonds
- proline residues
the fatty acid binding protein contains a hair pin loop on the ends of the strands that are running parallel
what forces drive and stabilize secondary structures and what is involved?

hydrogen bonds involving the NH and the carbonyl oxygen in the back bone
tertiary structure

arrangement of secondary structures
tertiary structures are governed by

hydrophobic interactions
myoglobin contains hydrophobic and hydrophilic residues
how can the tert structure be stabilized

by covalent cross links
which AA can form these types of covalent cross links

disulfide linkages
4 forces that can stabilize tert structures
*google*
- ionic bond
- polypeptide backbone
- hydrogen bond
- disulfide linkage
- hydrophobic interactions
quaternary structure

arrangement of secondary and tert structures in one peptide relative to the arrangement of these structures in another
hemoglobin has 2 alpha and 2 beta chains
the quat structure is stabilized by these 4
- ionic interactions
- hydrophobic interactions
- disulfide bonds
- hydrogen bonding
4 jobs of proteins
- molecular
- cell components
- transporters
- enzymes involved in biological processes
how do proteins function molecularly

regulators of transcription/ translation activity
how to proteins function in cell components

they are involved in cytoskeletal proteins
how are proteins involved in transporters

transporters of fatty acids, O2, Ca, NO
how are proteins involved in enzymes that partake in biological proesses

they act as carbo, lipids, and nitrogen utilization

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biochemistry exam 2

Description

sfsu biochem

Updated

2014-03-11T23:39:37Z