Biochemistry Exam 3: Chapter 11, 12, 13, 15 Review Guide

Enzyme complexes

Organized structures of enzymes that enhance metabolic efficiency by improving proximity, coordination, and regulation.

Proximity effect

The benefit wherein substrates are located close together, reducing diffusion time during enzymatic reactions.

Coordination in enzyme complexes

The simultaneous or sequential action of enzymes in a complex that minimizes side reactions.

Regulation of enzymes

Coordinated control of multiple enzymes in a metabolic pathway to optimize cellular function.

Catabolism

The biochemical process of breaking down complex molecules to release energy; it is exergonic.

Anabolism

The biochemical process of building complex molecules from simpler ones, requiring energy input; it is endergonic.

Coupling of reactions

Method of linking unfavorable reactions to favorable ones to enable biochemical processes.

ATP

Adenosine triphosphate; a nucleotide that serves as the primary energy carrier in cells.

Phosphoryl transfer

The transfer of a phosphate group, energetically favorable due to resonance stabilization and electrostatic repulsion.

ATP hydrolysis

The reaction that breaks down ATP to release energy, powering biological processes.

Energy sources in muscles

Initial reliance on stored ATP and creatine phosphate, shifting to glycolysis and aerobic respiration with continued exercise.

Proton gradients

Concentration differences of protons across a membrane that drive ATP synthesis during oxidative phosphorylation.

Stages of energy extraction

Process of extracting energy from food, consisting of digestion, activation/breakdown, and oxidative phosphorylation.

NAD+

Nicotinamide adenine dinucleotide; an electron carrier in metabolic reactions, especially in oxidation.

FAD

Flavin adenine dinucleotide; a crucial electron carrier involved in metabolic reactions and oxidative phosphorylation.

Coenzyme A

A cofactor that facilitates the transfer of acyl groups and is integral in metabolism.

Acetyl CoA

A key substrate in metabolism, contributing to the Krebs cycle and fatty acid synthesis.

Key metabolic reactions

Metabolic processes such as glycolysis, the citric acid cycle, and oxidative phosphorylation.

Regulation of metabolism

Control of metabolic pathways via enzyme amounts, substrate accessibility, and catalytic activities.

Membrane transporters

Proteins that facilitate the movement of substances across cellular membranes.

Active transport

Energy-requiring mechanism that moves substances against their concentration gradient.

Passive transport

Movement of substances down their concentration gradient without energy input.

Electrochemical potential

Combined forces of concentration and electrical potential affecting charged species across a membrane.

Na⁺–K⁺ ATPase

An enzyme that maintains sodium and potassium gradients across the plasma membrane, using ATP.

Multidrug resistance proteins

ATP-dependent transporters expelling toxins and drugs from cells, impacting chemotherapy effectiveness.

Secondary active transport

Process where the transport of one substrate is driven by the gradient of another ion, typically protons.

Ion channels

Membrane proteins facilitating the rapid movement of ions across membranes.

Nernst equation

Mathematical equation used to calculate the equilibrium potential for ions across a membrane.

Gap junctions

Channels that allow direct communication between adjacent cells by permitting the passage of small molecules.

Aquaporins

Specialized water channels that facilitate rapid water transport through cell membranes.

Fatty acid nomenclature

System of naming fatty acids according to carbon chain length and number/location of double bonds.

Functions of lipids

Roles in energy storage, signaling, and membrane structure.

Membrane structure

Lipid bilayers characterized by their asymmetric and fluid nature for dynamic interactions.

Phospholipid components

Consists of glycerol backbone, fatty acids, and phosphate group.

Glycerol vs Sphingosine backbone

Glycerol: three hydroxyl groups; Sphingosine: a long hydrocarbon chain with one hydroxyl and one amine group.

Glycolipid components

Carbohydrate moiety attached to a glycerol or sphingosine backbone with one or two fatty acid tails.

Cholesterol structure

Steroid composed of four fused hydrocarbon rings with a small hydroxyl group.

Micelles and liposomes

Structures formed by the amphipathic nature of phospholipids in aqueous environments.

Lipid bilayer permeability

Most polar substances cannot pass through without assistance due to the hydrophobic core of the bilayer.

Integral vs peripheral proteins

Integral proteins span the membrane; peripheral proteins are attached to the surface.

SNARE proteins

Mediators of vesicle fusion with target membranes for intracellular cargo transport.

Constitutional isomers

Isomers with the same molecular formula but different atomic connectivity.

Stereoisomers

Molecules with the same bonding sequence but different spatial arrangements.

Reducing sugars

Sugars capable of donating electrons, hence participating in oxidation/reduction reactions.

Advanced glycation end products (AGEs)

Compounds formed by the non-enzymatic reaction of sugars with proteins, implicated in diabetes.

Glycosidic linkage

Covalent bond between monosaccharides; can be O-glycosidic or N-glycosidic.

Fiber types

Insoluble fiber aids digestion; soluble fiber can influence cholesterol and glucose levels.

Glycoproteins

Proteins with carbohydrate components; involved in cell recognition and signaling.

N-linkage vs O-linkage

N-linkage attaches sugars to nitrogen on asparagine; O-linkage attaches sugars to oxygen on serine or threonine.

Post-translational modifications

Enzymatic modifications of proteins after synthesis that dictate their function.

I-Cell disease

Lysosomal storage disorder caused by defective glycosylation affecting enzyme targeting.

What is the importance of D-Glucose?

D-Glucose is essential for most organisms as it serves as a primary source of energy for cellular processes through cellular respiration and is a crucial building block for other carbohydrates.

What are reducing sugars?

Reducing sugars are those that can donate electrons to oxidizing agents, allowing them to reduce substances such as Fehling's or Benedict's solutions.

How is a test for reducing sugars conducted?

A test for reducing sugars involves heating a sugar solution with Fehling's solution, resulting in a brick-red precipitate if reducing sugars are present.

What is glycation?

Glycation refers to the non-enzymatic addition of sugars to proteins, resulting in the formation of advanced glycation end products (AGEs).

Why is glycation important in diabetes?

Increased levels of AGEs in the body are linked to diabetic complications, as they can contribute to insulin resistance and vascular damage.

What are SNAREs?

SNAREs are proteins that mediate the fusion of vesicles with target membranes, facilitating the transport of cargo within cells.

What is the empirical formula of a monosaccharide?

The empirical formula for monosaccharides is (CH{2}O){n}, where n is typically between 3 to 7.

What is the flat structure of glucose?

The flat structure of glucose, known as its Fischer projection, shows the carbon atoms arranged in a linear chain with the aldehyde group at one end.

What is the ring form of glucose?

Glucose can cyclize into a ring form, forming either α-D-glucopyranose or β-D-glucopyranose, depending on the orientation of the hydroxyl group on the anomeric carbon (C-1).

What are constitutional isomers?

Constitutional isomers have identical molecular formulas but differ in the connectivity of their atoms.

What are stereoisomers?

Stereoisomers have the same bonding sequence but differ in their spatial arrangement, such as D and L configurations.

What are enantiomers?

Enantiomers are a type of stereoisomer that are mirror images of each other.

What are diastereoisomers?

Diastereoisomers are stereoisomers that are not mirror images of each other.

What are integral membrane proteins?

Integral proteins span the lipid bilayer and are often involved in transport.

What are peripheral membrane proteins?

Peripheral proteins are attracted to membranes by weaker interactions and do not penetrate significant depths of the bilayer.

What typical motifs are seen in integral membrane proteins?

Integral membrane proteins often have specific structural motifs such as alpha-helices or beta-barrels that facilitate their integration into the lipid bilayer.

What is the function of Prostaglandin H2 Synthase in membrane dynamics?

Prostaglandin H2 Synthase is an example of an integral membrane protein that catalyzes reactions, showcasing its role in membrane dynamics.

What is lateral diffusion in membranes?

Lateral diffusion refers to the movement of lipids within the same layer of the bilayer.

What is transverse (flip-flop) diffusion?

Transverse diffusion is the movement of lipids from one layer to another, which occurs less frequently due to the energy barrier.

What is the FRAP technique?

Fluorescence Recovery After Photobleaching (FRAP) is a technique used to study the fluidity and dynamics of membranes by observing the recovery of fluorescence in a bleached region.

What factors influence the transition temperature (Tm) of fluid membranes?

The transition temperature (Tm) is influenced by fatty acid composition; shorter and more unsaturated fatty acids lower Tm, while longer and saturated chains increase Tm.

What are lipid rafts?

Lipid rafts are dynamic domains within the membrane that are enriched in cholesterol and specific lipids, playing important roles in signaling and protein sorting.

What is the difference between Gram Positive and Gram Negative bacteria?

Gram Positive bacteria have a thick peptidoglycan layer that retains the crystal violet stain, while Gram Negative bacteria have a thin peptidoglycan layer surrounded by an outer membrane and do not effectively retain the stain.

What is receptor-mediated endocytosis?

Receptor-mediated endocytosis is the specific uptake of molecules triggered by receptor binding, leading to internalization via vesicles.

What are membrane budding and fusion?

Membrane budding and fusion are critical processes in intracellular transport and signaling.

What are lipids' roles as energy sources?

Lipids serve as rich fuel sources and storage for energy.

How do lipids function in hormonal signaling?

Lipids act as signaling molecules that facilitate communication within and between cells.

What is the composition of cell membranes?

Membranes are made primarily of lipids, supporting their structural integrity and functionality.

What are the structural characteristics of membranes?

Membranes are composed of lipid bilayers that are sheet-like structures, two molecules thick, asymmetric, and fluidic, allowing dynamic interactions.

What are the basic components of a phospholipid?

A phospholipid is composed of a glycerol (or sphingosine) backbone, two fatty acids attached via ester bonds, and a phosphate group linked to an alcohol.

What is the difference between glycerol and sphingosine backbones?

Glycerol backbone is found in phosphoglycerides with three hydroxyl groups, while sphingosine backbone is found in sphingolipids with a long hydrocarbon chain, a single hydroxyl group, and an amine group.

What are the basic components of a glycolipid?

A glycolipid consists of a carbohydrate moiety attached to a backbone (glycerol or sphingosine) and one or two fatty acid tails.

What is the structure of cholesterol?

Cholesterol has a steroid structure consisting of four fused hydrocarbon rings, with a small hydroxyl group compared to its bulk.

How do micelles and liposomes form?

Micelles and liposomes form due to the amphipathic nature of phospholipids, where hydrophilic heads interact with water while hydrophobic tails avoid water, leading to spontaneous formation.

What is the permeability of lipid bilayers?

Lipid bilayers are impermeable to most polar and ionic substances due to their hydrophobic core, allowing small nonpolar molecules (e.g., O₂, CO₂) to diffuse freely, while large polar molecules and ions usually cannot pass without aid.

Define gap junctions.

Gap junctions are structures that enable communication between adjacent cells by allowing the passage of small molecules and ions. They are formed by proteins known as connexins.

What are aquaporins and their function?

Aquaporins are specialized water channels that facilitate the rapid transport of water across cell membranes while preventing the passage of protons and other charged ions, thus allowing selective permeability for water.

Explain the naming convention for fatty acids.

Fatty acids are named according to the number of carbon atoms in their chain and the position of any double bonds; the convention involves changing the final 'e' of the parent hydrocarbon name to 'oic'.

What do the two numbers in fatty acid nomenclature signify?

In fatty acid nomenclature, the first number indicates the total number of carbon atoms, while the second number represents the number of double bonds present (e.g., '18:1' means there are 18 carbons and 1 double bond).

What is the electrochemical potential?

The electrochemical potential is the sum of concentration and electric terms, representing the energy required to move a charged species across a membrane.

What is the formula for free energy change for moving a charged species?

The free energy change for moving a charged species is given by ΔG = RT ln(c2/c1) + ZFΔV where Z is the charge of the species, ΔV is the voltage across the membrane, and F is Faraday's constant (96.5 kJ V⁻¹ mol⁻¹).

What is the function of Na⁺–K⁺ ATPase?

The Na⁺–K⁺ ATPase maintains Na⁺ and K⁺ gradients across the plasma membrane by transporting 3 Na⁺ out and 2 K⁺ in per cycle through ATP hydrolysis, requiring magnesium (Mg²⁺).

What is the standard Gibbs energy change for the Na⁺–K⁺ ATPase?

The standard Gibbs energy change for the Na⁺–K⁺ ATPase is ΔG = 41.7 \text{ kJ mol}^{-1}.

What are Multidrug Resistance (MDR) proteins?

MDR proteins are ATP-dependent transporters that expel toxins and drugs, helping cancer cells remove toxic agents that enter the cell.

What are the structural features of MDR proteins?

MDR proteins contain multiple membrane-spanning regions and ATP-binding domains, enabling their function in pumping out drugs.

What is secondary active transport?

Secondary active transport is a coupled transport mechanism that uses the gradient of one ion (often protons) to drive the transport of another substrate across the membrane.

What are the types of secondary active transport?

Types of secondary active transport include:

• Symporters: Transport substrates in the same direction.
• Antiporters: Transport substrates in opposite directions.
• Uniporters: Transport a single substrate based on its concentration.

What is the function of ion channels?

Ion channels facilitate the rapid passive transport of ions across membranes, crucial for cellular functions such as action potentials.

What occurs during the action potential in terms of ion movement?

During an action potential, depolarization occurs when Na⁺ flows into the cell, and repolarization occurs as K⁺ flows out, facilitated by voltage-gated channels.