BCH210 MIDTERM EXAM 2025/2026
QUESTIONS AND ANSWERS 100% PASS
WEEK 1 -
Covalent bond vs. non-covalent bonds in terms of structure - ANS Covalent: hold together
amino acids
Non-covalent: allow chains to fold into final structure
Protein cofactors - ANS non-protein molecules and metal ions that assist in structure and/or
function
Metal ion cofactors - ANS may interact with the protein or be involved in enzyme catalysis
(Ca2+, Co+, Mg2+, Zn2+)
Prosthetic groups - ANS typically larger structures; tightly bound molecules by covalent or
non-covalent forces
Transporters: covalently or non-covalently? - ANS Non-covalently (ex: O2 binding to heme)
Cofactors: covalently or non-covalently? - ANS Both
Coenzymes - ANS serve as "shuttles" for commonly used functional groups in chemical
reactions, so the reaction can occur properly
1 @COPYRIGHT 2025/2026 ALLRIGHTS RESERVED
,Chainbow image of protein - ANS can visualize in 3D, backwards from blue to red (blue is N-
terminus, red is C-terminus)
Different types of interactions (5) - ANS 1. Covalent forces
2. Ionic/electrostatic/salt bridges
3. Hydrogen bonding
4. Hydrophobic interactions/effect
5. VDW
Covalent forces - ANS - strongest
- depends on electron sharing
- nuclei closes together
Ionic/electrostatic interactions - ANS - 2nd strongest
- strength depends on polarity of charged species
- aka salt bridge: full charges
Hydrogen bonds - ANS - 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 - ANS - depends on entropy of water being released, causing
hydrophobic regions to come together
- hydrophobic effect
VDW - ANS - weakest
- non-covalent
2 @COPYRIGHT 2025/2026 ALLRIGHTS RESERVED
,- depends son size of atoms, distance between them
Why is water an important molecule? - ANS - 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 - ANS - 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 - ANS 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 - ANS
structure of amino acid - ANS amino group + carboxyl group +hydrogen group + R group
what is an essential amino acid - ANS body cannot make it, must be obtained from our diet -
depends on # steps it takes to mak
chiral amino acids - ANS most are chiral, with exception of glycine
which chirality isomer is more physiologically relevant? - ANS L isomer
how does chirality arise? - ANS when all functional groups on alpha carbon are different
3 @COPYRIGHT 2025/2026 ALLRIGHTS RESERVED
, zwitterion - ANS 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? - ANS BJOUXZ
amino acids can be metabolized to form what other important molecules? - ANS - hormones
- neurotransmitters
- DNA/RNA
- energy-producing intermediates
Disulfides bonds - ANS - covalent interactions
- can be intrachain or interchain
- stabilize structures
- PDI enzymes help catalyze this oxidation reaction
secreted vs cytosolic proteins: disulfide bonds - ANS - 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? - ANS reducing agents in cytosol
post-translational modifications (5 groups) - ANS 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 - ANS dehydration and oxidation leads to formation of green
fluorophore (after cyclization of ser65-tyr66-gly67)
4 @COPYRIGHT 2025/2026 ALLRIGHTS RESERVED
QUESTIONS AND ANSWERS 100% PASS
WEEK 1 -
Covalent bond vs. non-covalent bonds in terms of structure - ANS Covalent: hold together
amino acids
Non-covalent: allow chains to fold into final structure
Protein cofactors - ANS non-protein molecules and metal ions that assist in structure and/or
function
Metal ion cofactors - ANS may interact with the protein or be involved in enzyme catalysis
(Ca2+, Co+, Mg2+, Zn2+)
Prosthetic groups - ANS typically larger structures; tightly bound molecules by covalent or
non-covalent forces
Transporters: covalently or non-covalently? - ANS Non-covalently (ex: O2 binding to heme)
Cofactors: covalently or non-covalently? - ANS Both
Coenzymes - ANS serve as "shuttles" for commonly used functional groups in chemical
reactions, so the reaction can occur properly
1 @COPYRIGHT 2025/2026 ALLRIGHTS RESERVED
,Chainbow image of protein - ANS can visualize in 3D, backwards from blue to red (blue is N-
terminus, red is C-terminus)
Different types of interactions (5) - ANS 1. Covalent forces
2. Ionic/electrostatic/salt bridges
3. Hydrogen bonding
4. Hydrophobic interactions/effect
5. VDW
Covalent forces - ANS - strongest
- depends on electron sharing
- nuclei closes together
Ionic/electrostatic interactions - ANS - 2nd strongest
- strength depends on polarity of charged species
- aka salt bridge: full charges
Hydrogen bonds - ANS - 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 - ANS - depends on entropy of water being released, causing
hydrophobic regions to come together
- hydrophobic effect
VDW - ANS - weakest
- non-covalent
2 @COPYRIGHT 2025/2026 ALLRIGHTS RESERVED
,- depends son size of atoms, distance between them
Why is water an important molecule? - ANS - 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 - ANS - 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 - ANS 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 - ANS
structure of amino acid - ANS amino group + carboxyl group +hydrogen group + R group
what is an essential amino acid - ANS body cannot make it, must be obtained from our diet -
depends on # steps it takes to mak
chiral amino acids - ANS most are chiral, with exception of glycine
which chirality isomer is more physiologically relevant? - ANS L isomer
how does chirality arise? - ANS when all functional groups on alpha carbon are different
3 @COPYRIGHT 2025/2026 ALLRIGHTS RESERVED
, zwitterion - ANS 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? - ANS BJOUXZ
amino acids can be metabolized to form what other important molecules? - ANS - hormones
- neurotransmitters
- DNA/RNA
- energy-producing intermediates
Disulfides bonds - ANS - covalent interactions
- can be intrachain or interchain
- stabilize structures
- PDI enzymes help catalyze this oxidation reaction
secreted vs cytosolic proteins: disulfide bonds - ANS - 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? - ANS reducing agents in cytosol
post-translational modifications (5 groups) - ANS 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 - ANS dehydration and oxidation leads to formation of green
fluorophore (after cyclization of ser65-tyr66-gly67)
4 @COPYRIGHT 2025/2026 ALLRIGHTS RESERVED
