Final

Question 1

Which six elements account for the major weight of most organisms?

Answer 1

Hydrogen, carbon, nitrogen, oxygen, phosphorus and sulfur.

Question 2

What are the different types of AAs classified by R groups?

Answer 2

Aliphatic (hydrophobic), Aromatic (hydrophobic), Sulfur-containing, Alcohol-containing, Basic, Acidic

Question 3

Glycine is the only AA without…

Answer 3

a chiral carbon.

Question 4

Carboxylic acid terminus on an AA has a pKa of what? The terminal amine has a pKa of what?

Answer 4

~ 2; ~9

Question 5

Which AAs are basic?

Answer 5

Histidine (His/H), Lysine (Lys/K), and Arginine (Arg/R)

Question 6

Which AAs are acidic?

Answer 6

Aspartate (Asp/D), Glutamate (Glu/E), Asparagine (Asn/N), and Glutamine (Gln/Q)

Question 7

Which AAs are neutral?

Answer 7

Alcohol containing AAs: Serine (Ser/S), Threonine (Thr/T)
Sulfur containing AAs: Cysteine (Cys/C), Methionine (Met/M)
Aromatic AAs: Phenylalanine (Phe/F), Tyrosine (Tyr/Y), Tryptophan (Trp/W)
Aliphatic AAs: Alanine (Ala/A), Valine (Val/V), Leucine (Leu/L), Isoleucine (Ile/I), Glycine (Gly/G), Proline (Pro/P)

Question 8

Tertiary structure is stabilized by what interactions?

Answer 8

disulfide bonds, ionic bonding, H-bonding, hydrophobic interactions

Question 9

What are disulfide bonds?

Answer 9

Covalent bond between –SH group of two cysteine residues.

Question 10

Describe the primary structure of proteins.

Answer 10

The linear sequence of AAs in a polypeptide chain, linked by peptide bonds between the carboxyl group of one AA and the amino group of another. The peptide bonds are covalent and planar, providing a stable backbone for the protein.

Question 11

Describe AAs in protein structures. (Like water solubility)

Answer 11

The hydrophobic core consists of nonpolar AAs (e.g., Val, Leu, Phe), while the hydrophilic surface interacts with water through polar and charged residues (e.g., Ser, Asp, Lys). This distribution drives protein folding, with amphipathic structures like α-helices and β-sheets aiding solubility in globular proteins. Fibrous proteins are often insoluble and provide structural integrity.

Question 12

Describe a typical alpha helix structure.

Answer 12

It forms a rigid, R-handed spiral, with a tightly packed polypeptide backbone. The side chains of the AAs extend outward, preventing steric hindrance, and H bonds stabilize the structure. H bonds occur b/w the carbonyl group of one AA and the amide group of an AA that is 3 to 4 residues ahead, forming a characteristic n+4 H-bond pattern.

Question 13

Describe Alpha helix protein secondary structure in acidic and basic solutions.

Answer 13

In acidic solutions, side chains of basic residues can become protonated, leading to electrostatic repulsion and destabilization of the helix. In basic solutions, acidic side chains become negatively charged, causing similar destabilizing effects.

Question 14

What is a reducing sugar? Non-reducing sugar?

Answer 14

A reducing sugar is a carbohydrate that contains a free hemiacetal group, allowing it to reduce other substances, such as Cu2+. Non-reducing sugars lack a free hemiacetal because their anomeric carbons are involved in glycosidic bonds.

Question 15

Give examples of non-reducing and reducing sugars.

Answer 15

Non-reducing: Sucrose
Reducing: glucose, maltose, cellobiose, lactose

Question 16

Which kind of DNA fragment can be recognized by restriction enzyme?

Answer 16

EcoRI: A type II restriction enzyme that cuts DNA specifically at the 5’GAATTC-3’ sequence, forming sticky ends. It’s restriction site of EcoRI is a palindrome (sequence same backward as forward) and it cuts DNA after G forming sticky ends with AATT.

Question 17

What are the different types of enzyme inhibitors?

Answer 17

Competitive, non-competitive, and uncompetitive inhibitors.

Question 18

Competitive inhibitors bind to which type of enzymes?

Answer 18

Bind to the active site of the enzyme, competing with the substrate. They bind free enzymes and can be overcome by increasing substrate concentration.

Question 19

Non-competitive inhibitors bind to which type of enzymes?

Answer 19

Bind to an allosteric site on free enzyme or the enzyme-substrate complex, reducing the enzyme’s catalytic efficiency without affecting substrate binding.

Question 20

Uncompetitive inhibitors bind to which type of enzymes?

Answer 20

Bind only to the enzyme-substrate complex, preventing product formation. Effects cannot be reversed by increasing substrate concentration​.

Question 21

Describe the hemoglobin-oxygen binding curve.

Answer 21

The curve is sigmoidal, reflecting cooperative binding, where the binding of 1 oxygen molecule increases hemoglobin’s affinity for subsequent oxygen molecules. This allows efficient oxygen loading in high-oxygen environments (lungs) and unloading in low-oxygen environments (tissues). The curve is influenced by factors like pH, carbon dioxide , and 2,3-BPG, which shift it left (increased affinity) or right (decreased affinity).

Question 22

What are the stabilizing forces for DNA in solution?

Answer 22

H bonding (between complementary base pairs), base stacking interactions (between adjacent bases), and electrostatic interactions ((phosphate groups)

Question 23

Describe the enzyme binding affintiy.

Answer 23

Is indicated by the Michaelis constant (K𝑚), which represents the substrate concentration at which the reaction rate is half its maximum. A low K𝑚​ signifies high substrate affinity, while a high K 𝑚 m ​ indicates low affinity.

Question 24

Describe catalytical efficiency with the Michaelis constant.

Answer 24

Catalytic efficiency combines substrate binding and turnover, represented by kcat ​/K𝑚. Here, kcat ​ (turnover number) is the number of substrate molecules converted to product per enzyme molecule per second under saturation. High kcat​ and low K𝑚 ​ result in greater catalytic efficiency, essential for enzyme performance under physiological conditions.

Question 25

Write the linear burke plot equation.

Answer 25

1/v0 = km/vmax[S] + 1/vmax

Question 26

Give the MM equation. What does it describe?

Answer 26

v0 = vmax[S]/km + [S]
It describes how initial reaction velocity varies with substrate concentration.

Question 27

What does enzyme catalysis do?

Answer 27

Enzyme catalysis lowers the activation energy of a reaction by stabilizing the transition state, enabling substrates to convert to products more efficiently.

Question 28

Describe the enzyme catalysis mechanism in a few sentences.

Answer 28

A substrate binds to enzyme’s active site, forming an enzyme-substrate complex. Catalysis often involves acid-base interactions, covalent intermediates, or conformational changes in the enzyme, followed by product release and enzyme regeneration.

Question 29

Describe classification of lipids by functions and compare the structures.

Answer 29

Energy-storage lipids (triacylglycerols)
Membrane lipids (phospholipids, cholesterol)
Emulsification lipids (bile acids and cholic acid)
Chemical messenger lipids (steroid hormones and eicosanoids)
Protective-coating lipids (biological waxes)

Question 30

Describe the two general types of fatty acids.

Answer 30

Saturated fatty acids only have carbon-carbon single bonds while unsaturated fatty acids have one or more double bonded carbon-carbon in their structure. Monounstaturated and polyunsaturated.

Question 31

List cell membrane lipids.

Answer 31

Phospholipids, sphingoglycolipids,
cholesterol.

Question 32

List factors that influence membrane bilayer fluidity.

Answer 32

Increase temp increases fluidity, unsaturated fatty acyl groups do not pack as tightly, FA chain length, cholesterol helps regulate membrane fluidity by incorporating
between fatty acid chains in the lipid bilayer. (Too little = too fluid)

Question 33

List different membrane transports and the modes of transport.

Answer 33

Simple diffusion, channels and pores (passive transport), facilitated diffusion, active transport, primary, secondary transport
Uniport (1 mole.), symport (2 mole.s in same direction), antiport (2 mole.s in dif. directions)

Question 34

How does primary active transport and secondary transport work?

Answer 34

1: utilizes a direct source of energy (ATP or light)
2: Utilizes an ion concentration gradient to drive the
nonspontaneous process (a type of coupled reaction).

Question 35

Describe enzyme regulation based on ΔG° level.

Answer 35

Enzyme regulation based on ΔG° involves controlling the thermodynamic favorability of enzymatic reactions. Enzymes typically catalyze reactions with a negative ΔG° (exergonic reactions). Regulatory mechanisms include allosteric regulation, covalent modifications, and enzyme synthesis & degradation.