Final Flashcards
Which six elements account for the major weight of most organisms?
Hydrogen, carbon, nitrogen, oxygen, phosphorus and sulfur.
What are the different types of AAs classified by R groups?
Aliphatic (hydrophobic), Aromatic (hydrophobic), Sulfur-containing, Alcohol-containing, Basic, Acidic
Glycine is the only AA without…
a chiral carbon.
Carboxylic acid terminus on an AA has a pKa of what? The terminal amine has a pKa of what?
~ 2; ~9
Which AAs are basic?
Histidine (His/H), Lysine (Lys/K), and Arginine (Arg/R)
Which AAs are acidic?
Aspartate (Asp/D), Glutamate (Glu/E), Asparagine (Asn/N), and Glutamine (Gln/Q)
Which AAs are neutral?
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)
Tertiary structure is stabilized by what interactions?
disulfide bonds, ionic bonding, H-bonding, hydrophobic interactions
What are disulfide bonds?
Covalent bond between –SH group of two cysteine residues.
Describe the primary structure of proteins.
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.
Describe AAs in protein structures. (Like water solubility)
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.
Describe a typical alpha helix structure.
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.
Describe Alpha helix protein secondary structure in acidic and basic solutions.
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.
What is a reducing sugar? Non-reducing sugar?
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.
Give examples of non-reducing and reducing sugars.
Non-reducing: Sucrose
Reducing: glucose, maltose, cellobiose, lactose
Which kind of DNA fragment can be recognized by restriction enzyme?
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.
What are the different types of enzyme inhibitors?
Competitive, non-competitive, and uncompetitive inhibitors.
Competitive inhibitors bind to which type of enzymes?
Bind to the active site of the enzyme, competing with the substrate. They bind free enzymes and can be overcome by increasing substrate concentration.
Non-competitive inhibitors bind to which type of enzymes?
Bind to an allosteric site on free enzyme or the enzyme-substrate complex, reducing the enzyme’s catalytic efficiency without affecting substrate binding.
Uncompetitive inhibitors bind to which type of enzymes?
Bind only to the enzyme-substrate complex, preventing product formation. Effects cannot be reversed by increasing substrate concentration.
Describe the hemoglobin-oxygen binding curve.
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).
What are the stabilizing forces for DNA in solution?
H bonding (between complementary base pairs), base stacking interactions (between adjacent bases), and electrostatic interactions ((phosphate groups)
Describe the enzyme binding affintiy.
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.
Describe catalytical efficiency with the Michaelis constant.
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.
Write the linear burke plot equation.
1/v0 = km/vmax[S] + 1/vmax
Give the MM equation. What does it describe?
v0 = vmax[S]/km + [S]
It describes how initial reaction velocity varies with substrate concentration.
What does enzyme catalysis do?
Enzyme catalysis lowers the activation energy of a reaction by stabilizing the transition state, enabling substrates to convert to products more efficiently.
Describe the enzyme catalysis mechanism in a few sentences.
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.
Describe classification of lipids by functions and compare the structures.
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)
Describe the two general types of fatty acids.
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.
List cell membrane lipids.
Phospholipids, sphingoglycolipids,
cholesterol.
List factors that influence membrane bilayer fluidity.
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)
List different membrane transports and the modes of transport.
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)
How does primary active transport and secondary transport work?
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).
Describe enzyme regulation based on ΔG° level.
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.
