BCH210 midterm || with complete solution.
Covalent bond vs. non-covalent bonds in terms of structure correct answers Covalent: hold
together amino acids
Non-covalent: allow chains to fold into final structure
Protein cofactors correct answers non-protein molecules and metal ions that assist in structure
and/or function
Metal ion cofactors correct answers may interact with the protein or be involved in enzyme
catalysis (Ca2+, Co+, Mg2+, Zn2+)
Prosthetic groups correct answers typically larger structures; tightly bound molecules by covalent
or non-covalent forces
Transporters: covalently or non-covalently? correct answers Non-covalently (ex: O2 binding to
heme)
Cofactors: covalently or non-covalently? correct answers Both
Coenzymes correct answers serve as "shuttles" for commonly used functional groups in chemical
reactions, so the reaction can occur properly
Chainbow image of protein correct answers can visualize in 3D, backwards from blue to red
(blue is N-terminus, red is C-terminus)
Different types of interactions (5) correct answers 1. Covalent forces
2. Ionic/electrostatic/salt bridges
,3. Hydrogen bonding
4. Hydrophobic interactions/effect
5. VDW
Covalent forces correct answers - strongest
- depends on electron sharing
- nuclei closes together
Ionic/electrostatic interactions correct answers - 2nd strongest
- strength depends on polarity of charged species
- aka salt bridge: full charges
Hydrogen bonds correct answers - type of electrostatic interaction -- non-covalent
- strength is proportional to polarity of H and other molecule
- N, O, F, Cl, Br
- can occur between molecules or within parts of single molecule
Hydrophobic interactions correct answers - depends on entropy of water being released, causing
hydrophobic regions to come together
- hydrophobic effect
VDW correct answers - weakest
- non-covalent
- depends son size of atoms, distance between them
Why is water an important molecule? correct answers - can form up to 4 transient HB (unequal
sharing of electrons)
- important for molecule stabilization
,- important for formation of complex structures (can bring distant parts of molecule together)
Water and biochemical molecules correct answers - water can participate in hydrolysis reactions
(h20 breaks amide and carbonyl bond)
- macromolecules may fold to exclude water -- preventing reactions from occurring
- maximizing number of interactions of hydrophilic functional groups with water for solubility
Biochemistry and drug design correct answers Binding interactions are IMF are important for
drug design -- presence or absence of functional groups can assist with solubility and binding to
specific targets
WEEK 2 correct answers
structure of amino acid correct answers amino group + carboxyl group +hydrogen group + R
group
what is an essential amino acid correct answers body cannot make it, must be obtained from our
diet - depends on # steps it takes to mak
chiral amino acids correct answers most are chiral, with exception of glycine
which chirality isomer is more physiologically relevant? correct answers L isomer
how does chirality arise? correct answers when all functional groups on alpha carbon are
different
zwitterion correct answers molecule or ion that has separate positive and negative charges, but an
overall net charge of 0
, what one letter amino acids don't exist in alphabet? correct answers BJOUXZ
amino acids can be metabolized to form what other important molecules? correct answers -
hormones
- neurotransmitters
- DNA/RNA
- energy-producing intermediates
Disulfides bonds correct answers - covalent interactions
- can be intrachain or interchain
- stabilize structures
- PDI enzymes help catalyze this oxidation reaction
secreted vs cytosolic proteins: disulfide bonds correct answers - disulfide bond formation is post-
translational modification that occurs in some secreted proteins as they pass through ER
- cytosolic proteins usually contained cystEINES due to reducing nature of cytosol
how are disulfide bonds can be broken? correct answers reducing agents in cytosol
post-translational modifications (5 groups) correct answers 1. disulfide bond formation
(stabilization)
2. phosphorylation (stabilization, increase solubility)
3. ubiquitination (degradation)
4. glycosylation (signaling)
5. methyl, acetyl, hydroxyl, carboxyl additions
GFP: aa modification correct answers dehydration and oxidation leads to formation of green
fluorophore (after cyclization of ser65-tyr66-gly67)
Covalent bond vs. non-covalent bonds in terms of structure correct answers Covalent: hold
together amino acids
Non-covalent: allow chains to fold into final structure
Protein cofactors correct answers non-protein molecules and metal ions that assist in structure
and/or function
Metal ion cofactors correct answers may interact with the protein or be involved in enzyme
catalysis (Ca2+, Co+, Mg2+, Zn2+)
Prosthetic groups correct answers typically larger structures; tightly bound molecules by covalent
or non-covalent forces
Transporters: covalently or non-covalently? correct answers Non-covalently (ex: O2 binding to
heme)
Cofactors: covalently or non-covalently? correct answers Both
Coenzymes correct answers serve as "shuttles" for commonly used functional groups in chemical
reactions, so the reaction can occur properly
Chainbow image of protein correct answers can visualize in 3D, backwards from blue to red
(blue is N-terminus, red is C-terminus)
Different types of interactions (5) correct answers 1. Covalent forces
2. Ionic/electrostatic/salt bridges
,3. Hydrogen bonding
4. Hydrophobic interactions/effect
5. VDW
Covalent forces correct answers - strongest
- depends on electron sharing
- nuclei closes together
Ionic/electrostatic interactions correct answers - 2nd strongest
- strength depends on polarity of charged species
- aka salt bridge: full charges
Hydrogen bonds correct answers - type of electrostatic interaction -- non-covalent
- strength is proportional to polarity of H and other molecule
- N, O, F, Cl, Br
- can occur between molecules or within parts of single molecule
Hydrophobic interactions correct answers - depends on entropy of water being released, causing
hydrophobic regions to come together
- hydrophobic effect
VDW correct answers - weakest
- non-covalent
- depends son size of atoms, distance between them
Why is water an important molecule? correct answers - can form up to 4 transient HB (unequal
sharing of electrons)
- important for molecule stabilization
,- important for formation of complex structures (can bring distant parts of molecule together)
Water and biochemical molecules correct answers - water can participate in hydrolysis reactions
(h20 breaks amide and carbonyl bond)
- macromolecules may fold to exclude water -- preventing reactions from occurring
- maximizing number of interactions of hydrophilic functional groups with water for solubility
Biochemistry and drug design correct answers Binding interactions are IMF are important for
drug design -- presence or absence of functional groups can assist with solubility and binding to
specific targets
WEEK 2 correct answers
structure of amino acid correct answers amino group + carboxyl group +hydrogen group + R
group
what is an essential amino acid correct answers body cannot make it, must be obtained from our
diet - depends on # steps it takes to mak
chiral amino acids correct answers most are chiral, with exception of glycine
which chirality isomer is more physiologically relevant? correct answers L isomer
how does chirality arise? correct answers when all functional groups on alpha carbon are
different
zwitterion correct answers molecule or ion that has separate positive and negative charges, but an
overall net charge of 0
, what one letter amino acids don't exist in alphabet? correct answers BJOUXZ
amino acids can be metabolized to form what other important molecules? correct answers -
hormones
- neurotransmitters
- DNA/RNA
- energy-producing intermediates
Disulfides bonds correct answers - covalent interactions
- can be intrachain or interchain
- stabilize structures
- PDI enzymes help catalyze this oxidation reaction
secreted vs cytosolic proteins: disulfide bonds correct answers - disulfide bond formation is post-
translational modification that occurs in some secreted proteins as they pass through ER
- cytosolic proteins usually contained cystEINES due to reducing nature of cytosol
how are disulfide bonds can be broken? correct answers reducing agents in cytosol
post-translational modifications (5 groups) correct answers 1. disulfide bond formation
(stabilization)
2. phosphorylation (stabilization, increase solubility)
3. ubiquitination (degradation)
4. glycosylation (signaling)
5. methyl, acetyl, hydroxyl, carboxyl additions
GFP: aa modification correct answers dehydration and oxidation leads to formation of green
fluorophore (after cyclization of ser65-tyr66-gly67)
