Biology Chapter on Lipids

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Questions and Answers

What is the main function of cation exchange in resin?

To filter large molecules from a solution

To remove anions from a solution

To exchange cations for other cations in the resin (correct)

To enhance the stability of proteins

Which method is primarily used for peptide sequencing?

Edman Degradation (correct)

X-ray diffraction

Gel-filtration chromatography

SDS treatment

How does size exclusion chromatography separate molecules?

According to the size of the molecules and their ability to enter pores (correct)

Based on their charge

By their interaction with surface ions

Using temperature variations in the solution

What role does SDS play in the electrophoresis of proteins?

It denatures proteins making them smaller and negative Signup and view all the answers

What technique is best for determining the tertiary and quaternary structure of proteins?

X-ray crystallography and NMR Signup and view all the answers

What is the primary structure of nucleic acids?

The order of bases on the polynucleotide sequence Signup and view all the answers

Which of the following correctly describes phosphoacylglycerols?

They are glycerol esters with phosphate groups. Signup and view all the answers

What distinguishes active transport from passive transport mechanisms?

Active transport requires input of energy against a concentration gradient. Signup and view all the answers

Which of the following types of membrane proteins is directly associated with the lipid bilayer?

Membrane integral proteins Signup and view all the answers

Which molecules are primarily involved in the secondary structure of nucleic acids?

The specific base pairing interactions in double helices Signup and view all the answers

Which fatty acid is classified as saturated?

Palmitic acid Signup and view all the answers

What is true about facilitated diffusion?

It occurs with the aid of carrier/channel proteins. Signup and view all the answers

Which component is NOT a part of a nucleotide?

An ester bond Signup and view all the answers

What is the role of the Na+/K+ ATPase pump?

Moves sodium and potassium ions against their concentration gradients Signup and view all the answers

Which of the following is a characteristic of the fluid mosaic model?

Lipids and proteins exist as separate entities that can move laterally. Signup and view all the answers

What is the primary characteristic of lipids in relation to water?

They are insoluble in water but soluble in aprotic organic solvents. Signup and view all the answers

Which enzyme is specifically inactivated by DIPF through interaction with serine-195?

Chymotrypsin Signup and view all the answers

In the context of enzyme activity, what does phosphorylation specifically affect?

The tertiary structures of proteins. Signup and view all the answers

Which model describes the formation of an enzyme-substrate complex where both structures are complementary?

Lock and key model Signup and view all the answers

What defines an irreversible inhibitor in enzymatic reactions?

It binds covalently and permanently inactivates the enzyme. Signup and view all the answers

What is one role of coenzymes in enzymatic reactions?

They participate and are regenerated for further reactions. Signup and view all the answers

Which of the following statements correctly describes the induced-fit model?

The enzyme undergoes a conformational change upon substrate binding. Signup and view all the answers

Which amino acids are primarily involved in general acid-base catalysis as acidic groups?

Aspartic and Glutamic Acid Signup and view all the answers

What characterizes the V system in allosteric enzymes?

It alters Vmax without affecting K0.5. Signup and view all the answers

What is a common feature of passive transport mechanisms?

They involve the movement of molecules from high to low concentration. Signup and view all the answers

Study Notes

Lipids

A group of organic compounds insoluble in water, but soluble in organic solvents.
Lipids can be amphipathic in nature, containing both hydrophilic and hydrophobic regions.
Contain fatty acids, triacylglycerols, phosphoacylglycerols, and steroids.

Fatty Acids

Unbranched-chain carboxylic acids containing a hydrocarbon chain.
Saturated fatty acids lack C=C bonds and include palmitic acid and stearic acid.
Unsaturated fatty acids contain C=C bonds and include oleic acid, linoleic acid, and arachidonic acid.

Triacylglycerol (Triglyceride)

Esters of glycerol with three fatty acids.

Phosphoacylglycerols (Phospholipids)

Glycerol's alcohol group is esterified by phosphoric acid.

Lipids Bilayers

Composed of fatty acids with a polar surface containing charged groups.
Hydrophobic tails are located within the interior of the bilayer.

Detergent

Long tail and fewer double bonds.
Short tails and a high abundance of double bonds result in a more flexible phospholipid.

Fluid Mosaic Model

Describes membrane structure as fluid, allowing lateral motion of components in the membrane.
Components exist as separate entities, including lipid bilayer, proteins, glycolipids, and steroids like cholesterol.
There are no complexes; however, lipid-protein complexes can be formed.

Membrane Proteins

Functions include transport of substances across the membrane, receptor sites, and enzyme catalysis.
Held together by noncovalent interactions: ion-dipole, dipole-dipole, and loosely bonded.
Membrane integral proteins (Group A) have nonpolar amino acids (methionine, phenylalanine, isoleucine, tryptophan, leucine, alanine).
Anchored to the membrane by covalent bonding.

Concept of Gradient

Membranes are selective barriers, acting as solvents and being osmotic.
Molecules or ions move from a higher concentration gradient to a lower concentration gradient.
Movement of water is called osmotic pressure.

Passive Transport

Passive diffusion: a molecule or ion moves through an opening.
Facilitated diffusion: a molecule or ion is carried across a membrane by a carrier/channel protein.

Active Transport

Active transport: a substance is moved against a concentration gradient.
Primary active transport: Transport linked to the hydrolysis of ATP or other high-energy molecules; for example, the Na+/K+ ion pump.
Secondary active transport: Driven by an H+ gradient.

Nucleic Acids

Biopolymers made of monomer units called nucleotides.
Nucleotides contain a base derived from purine or pyrimidine, a monosaccharide (D-ribose or 2-deoxy-D-ribose), and phosphoric acid.

Pyrimidine/Purine Bases

Pyrimidine: Cytosine (in DNA and RNA), Thymine (in DNA and some RNA), Uracil (only in RNA)
Purine: Adenine (DNA and RNA), Guanine (DNA and RNA)

Nucleosides

Compounds consisting of D-ribose or 2-deoxy-D-ribose covalently bonded to a nucleobase by a N-glycosidic bond.
Examples include Cytidine (a ribonucleoside in RNA) and Deoxyguanosine (a deoxyribonucleoside in DNA).

1° Structure

The order of bases on the polynucleotide sequence.

2° Structure

The three-dimensional conformation of the polynucleotide backbone (double helix in DNA).

3° Structure

Supercoiling (in prokaryotes).

4° Structure

Interaction between DNA and proteins (histones in eukaryotes).

Ion Exchange Chromatography

Resin has a negative charge and attracts and hold cations from the solution.
Cations can be exchanged for other cations already bonded to the resin.
Anion Exchange: Exchange between anions and cations.

Size Exclusion/Gel-filtration Chromatography

Smaller molecules can enter pores of a stationary phase while larger molecules cannot.
Larger molecules come out first, followed by smaller molecules.

Electrophoresis

Charged molecules migrate in an electric field towards the opposite charge.
The more negative the charge, the faster the molecule migrates.
Proteins have different mobility based on charge and size (SDS treatment makes proteins smaller and negatively charged).

Primary Structure Determination

Peptide Sequencing: Edman Degradation

Protein Cleavage

Enzymes: Trypsin cleaves at the C-terminal of positively charged side chains; Chymotrypsin cleaves at the C-terminal of aromatic amino acids.
Chemical reagents: Cyanogen bromide

Determination of Tertiary and Quaternary Structure

X-ray and NMR data can determine the 3D structures of proteins.
X-ray diffraction pattern is produced by electrons scattering X-rays.

Predicting Protein Folding

Bioinformatics is used, and the first step is sequence homology (series of amino acids).

Enzyme Catalysis

Enzymes are protein catalysts that lower the activation energy of a reaction.
Examples include platinum surfaces and inorganic catalysts.

Catalytic Mechanism

Found at the level of protein chain:
- General acid-base catalysis: donation and acceptance of protons
  - Group C (acidic): Aspartic acid (Asp, D) and Glutamic acid (Glu, E)
  - Group D (polar basic): Histidine (His, H), Arginine (Arg, R), and Lysine (Lys, K)
- Nucleophilic Substitution Catalysts: Nucleophilic electron-rich atom attacks electron-deficient atom.
  - Group B (neutral polar): Serine (Ser, S), Cysteine (Cys, C), and tyrosine (Thr, T)
- Electrophilic Substitution Catalyst: Electrophilic electron-poor atom bonds an electron-deficient atom (metal ions).

Chymotrypsin

Enzyme that acts as a catalyst for hydrolysis, breaking peptide bonds and increasing the rate of reaction.
Targets peptide bonds at the C-terminal of aromatic side chains.
Effect of DIPF: Inactivates chymotrypsin by reacting with serine-195C.
Effect of TPCK: Reactive group that targets histidine 57.

Coenzymes

Small molecules, coreactants, and non-protein substances that participate in an enzymatic reaction and are regenerated for further reaction.
Metal ions can be used as coordination compounds (Zn2+, Fe2+).
Vitamins can also serve as coenzymes (NADH or NADPH).

E-S Complex Formation

Lock and key model: Complementary structures like a key fitting a lock.
Induced-fit model: Less stable, undergoes a conformational change upon substrate binding to become complementary.

Michaelis-Menten Kinetics

Describes the rate of enzymatic reactions as a function of substrate concentration.

Enzyme Inhibition

Reversible Inhibitor: Binds to an enzyme to inhibit it, but the inhibition can be reversed.
Irreversible Inhibitor: Causes inhibition that cannot be reversed.

Homotropic Effects

Allosteric interactions that occur when direct substrates or products bind to the protein (e.g., Aspartate to ATCase).

Heterotropic Effects

Allosteric interactions that occur when different substances bind to the protein (e.g., inhibitor of ATCase by CTP and activation by ATP).

Two Types of Allosteric Enzymes

K System: An enzyme where an inhibitor or activator alters the K_0.5 value.
V System: An enzyme where an inhibitor or activator alters the V_max value.

Control of Enzyme Activity via Phosphorylation

Covalent phosphorylation of specific side chains at the primary structure level (ion-ion, ion-dipole, dipole-dipole interactions).

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Description

This quiz explores the complex world of lipids, covering their structure, types, and functions. You'll learn about fatty acids, triacylglycerols, phospholipids, and lipid bilayers while understanding their roles in biological systems. Test your knowledge of their properties, including saturation levels and amphipathicity.