BIOL 190 Exam #2

Define prosthetic group

non protein, organic substance; FIRMLY attached (opposite of coenzyme) e.g. heme group of hemoglobin

What are 6 functions of membrane proteins?

-Attachment to cytoskeleton and extracellular matrix. Maintains cell shape and stabilizes cytoskeleton. -Intercellular joining. Proteins on adjacent cells hook together, briefly, for cell interaction/sharing. -Signal transduction -Enzymatic activity -Cell-cell recognition -Transport

Define induced fit

-when a substrate binds to the enzyme's active site and the enzyme experiences a subtle change in shape -applies a bit of stress to the substance(s)- making the reaction easier to get started (=lower activation energy) -following the reaction the now products (they were substrates but are now products bc of reaction) are released and the enzyme returns to its original shape

How is it used to power co-transport?

An electrogenic pump creates an electrochemical gradient which includes an ion's concentration gradient plus the membrane potential created by having a net difference in charge across a membrane. ******

Define glycolipid

A complex lipid that contains carbohydrates and ceramides

What are coupled reactions? How are endergonic & exergonic reactions typically coupled in cells?

A coupling reaction in organic chemistry is a general term for a variety of reactions where two fragments are joined together with the aid of a metal catalyst. The energy released from the hydrolysis of ATP into ADP is used to perform cellular work, usually by coupling the exergonic reaction of ATP hydrolysis with endergonic reactions.

Define bilayer

A film two molecules thick (formed, e.g., by lipids), in which each molecule is arranged with its hydrophobic end directed inward toward the opposite side of the film and its hydrophilic end directed outward.

What characterizes a metabolic pathway in a living cell?

A linked series of chemical reactions occurring within a cell. In most cases of a metabolic pathway, the product of one enzyme acts as the substrate for the next. However, side products are considered waste and removed from the cell.

What is meant by substrate-level phosphorylation of ADP to form ATP? Which stages do this process? Does it capture the majority of free energy in the glucose molecule?

A metabolic reaction that results in the formation of ATP or GTP by the direct transfer of a phosphoryl (PO3) group to ADP or GDP from another phosphorylated compound

What is meant by osmosis?

A process by which molecules of a solvent tend to pass through a semipermeable membrane from a less concentrated solution into a more concentrated one, thus equalizing the concentrations on each side of the membrane.

Define active site

A region on an enzyme which binds to the substrate during a reaction

What is an electrogenic pump (this includes a proton pump)?

An electrogenic pump creates an electrochemical gradient which includes an ion's concentration gradient plus the membrane potential created by having a net difference in charge across a membrane.

Define & distinguish exergonic vs. endergonic

An exergonic reaction is the opposite of endergonic reaction. An exergonic reaction is a spontaneous reaction. The main difference between endergonic and exergonic is that endergonic reaction requires energy from the outside whereas exergonic reactions release energy to the outside.

What is meant by a closed vs. an open system? Is the Earth an open system? Is a living being an open system? Explain

An open system is defined as a "system in exchange of matter with its environment, presenting import and export, building-up and breaking-down of its material components." Closed systems, on the other hand, are held to be isolated from their environment. The Earth is essentially a closed system; it obtains lots of energy from the Sun but the exchange of matter with the outside is almost zero. Isolated systems can exchange neither energy nor matter with an outside system. Yes, the human is an open system, because it exchanges energy and matter with the environment.

Define coenzyme

An organic molecule required for the functioning of an enzyme

Define catabolism vs. anabolism

Anabolism builds complex molecules from simpler ones, while catabolism breaks large molecules into smaller ones.

Define allosteric site

Another binding region of the enzyme

What is the basic difference between active and passive transport?

Both use ion channels to move ions across the cell membrane, in or out of the cell. Differences: Passive Transport (or Diffusion) moves ions from high concentration to low, using no metabolic energy. Active Transport moves ions from low concentration to high, using metabolic energy in the form of ATP.

What role do carbohydrates play in membranes? How do they relate to cell-cell recognition?

Carbohydrates covalently linked to proteins (glycoproteins) or lipids (glycolipids) are also a part of cell membranes, and function as adhesion and address loci for cells. Complex carbohydrates coat the surfaces of cells and have the potential to carry the information necessary for cell-cell recognition. Sugar-specific receptors (lectins) are also present on cells, and can interact with sugars on apposing cells.

Define competitive inhibitor

Competitive inhibition is interruption of a chemical pathway owing to one chemical substance inhibiting the effect of another by competing with it for binding or bonding

Define & distinguish energy-releasing vs. requiring

Define energy-releasing: release heat Define energy-requiring: take in heat

Define thylakoid

Each of a number of flattened sacs inside a chloroplast, bounded by pigmented membranes on which the light reactions of photosynthesis take place, and arranged in stacks or grana

Distinguish exocytosis from endocytosis Within endocytosis, distinguish phagocytosis, pinocytosis, and receptor-mediated endocytosis. Note that receptor-mediated endocytosis allows the import of specific substances even if they are at low concentrations, because they bind to receptors, resulting in vesicle formation & ingestion

Endocytosis is the process of capturing a substance or particle from outside the cell by engulfing it with the cell membrane, and bringing it into the cell. Exocytosis describes the process of vesicles fusing with the plasma membrane and releasing their contents to the outside of the cell. Phagocytosis is the taking in of large food particles, while pinocytosis takes in liquid particles. Receptor-mediated endocytosis uses special receptor proteins to help carry large particles across the cell membrane.

Describe and distinguish the 1st and 2nd laws of thermodynamics. Does the 2nd law rule out the evolution of life on Earth? Why or why not?

First: states that energy cannot be created or destroyed in an isolated system Second: states that the entropy of any isolated system always increases. No, "only applies to a closed system"

Define oxidation

Gain of oxygen, loss of electrons

What is meant by ΔG? Why do we measure change in G rather than total energy?********

Gibbs free energy is a measure of the potential for reversible or maximum work that may be done by a system at constant temperature and pressure

What holds the membrane together? How does this relate to the amphipathic nature of phospholipids?

Hydrophobic interactions between the alkyl chains of neighboring lipids are a major component of membrane stability. Hydrogen bonds between lipids and between membrane proteins and lipids also hold a membrane together.

If the solution outside the cell is hypertonic to that inside, this means?

If concentrations of dissolved solutes are greater outside the cell, the concentration of water outside is correspondingly lower. As a result, water inside the cell will flow outwards to attain equilibrium, causing the cell to shrink.

How is membrane fluidity regulated? [describe both of the following]--saturation of FA tails--cholesterol

If unsaturated fatty acids are compressed, the "kinks" in their tails push adjacent phospholipid molecules away, which helps maintain fluidity in the membrane. The ratio of saturated and unsaturated fatty acids determines the fluidity in the membrane at cold temperatures.

kinetic vs. potential energy of location or structure includes thermal(includes heat)includes chemical

Kinetic: energy of relative motion of objects Potential: energy of location or structure includes thermal(includes heat)includes chemical

What determines the net direction of osmosis?

Osmosis is the net movement of water across a selectively permeable membrane driven by a difference in solute concentrations on the two sides of the membrane

What is acetyl CoA? How many carbons does it have? Does it store ample free energy? What part is re-used?

Molecule in cellular respiration. It is produced in the second step of aerobic respiration after glycolysis and carries the carbon atoms of the acetyl group to the TCA cycle to be oxidized for energy production. 2

Why do membranes have "sidedness" or "polarity"?

Molecules may be sorted and modified as they move from one side of the membrane to the other

Define substrate

Molecules on which an enzyme acts

What is NAD+? What is its corresponding reduced form? Remember, electrons stored on NADH have lost little of their potential energy. Hence, temporary storage of electrons with these "electron taxis" allows stepwise releaseof the free energy in glucose. This is preferable within a tiny cell, to the explosive release of the energy in glucose.

Nicotinamide adenine dinucleotide is a cofactor found in all living cells. The compound is called a dinucleotide because it consists of two nucleotides joined through their phosphate groups. One nucleotide contains an adenine nucleobase and the other nicotinamide. Nicotinamide adenine dinucleotide exists in two forms: an oxidized and reduced form, abbreviated as NAD+ and NADH respectively. ... The cofactor is, therefore, found in two forms in cells: NAD+ is an oxidizing agent - it accepts electrons from other molecules and becomes reduced.

Does osmosis require energy?

No

Define active transport. What does it require?

The movement of molecules across a membrane from a region of their lower concentration to a region of their higher concentration—against the concentration gradient Requires cellular energy to achieve this movement

Distinguish peripheral vs. integral proteins. How do they differ in the orientation of their amino acids with different properties?******

Peripheral protein is only located in the inner or outer surface of the phospholipid bilayer like floating iceberg whereas integral protein is embedded in the whole bilayer. Integral proteins have hydrophobic and hydrophilic areas where as peripheral do not.

What is the basic role of each component?

Phospholipids make up the basic fabric of the plasma membrane. They are amphipathic, meaning that they have both hydrophilic and hydrophobic regions. Integral membrane proteins are, as their name suggests, integrated into the membrane: they have at least one hydrophobic region that anchors them to the hydrophobic core of the phospholipid bilayer. Along with membrane proteins, these carbohydrates form distinctive cellular markers, sort of like molecular ID badges, that allow cells to recognize each other. These markers are very important in the immune system, allowing immune cells to differentiate between body cells, which they shouldn't attack, and foreign cells or tissues, which they should.

What are the 4 components of membranes?

Phospholipids, cholesterol, proteins, and carbohydrates.

Which component is primarily responsible for giving specific membranes their unique function?

Phospholipids?

Define plasmolysis

Plant cells exposed to low water potention. water moves out causing it to shrink

Distinguish primary active transport from cotransport (secondary active transport)

Primary active transport, which is directly dependent on ATP, moves ions across a membrane and creates a difference in charge across that membrane. Secondary active transport , created by primary active transport, is the transport of a solute in the direction of its electrochemical gradient and does not directly require ATP. Carrier proteins such as uniporters, symporters, and antiporters perform primary active transport and facilitate the movement of solutes across the cell's membrane.

What are oxidation-reduction reactions?

Reactions that involve the partial or complete transfer of one or more electron from one reactant to another.

Describe the 3 processes common to all cell signaling: reception, transduction, & response

Reception: In this stage the signal molecule is detected by the receptor protein of target cell. The signal molecule generally comes from outside and is new to the target cell, where as the receptor molecules/proteins are located outside/ inside to the target cell. In other terms reception can be defined as the target cell detection of signal molecule that is coming from outside of the cell. Transduction: This is second stage of cell signaling where the binding of signal molecule triggers the receptor protein of the target cell initiating the process of transduction. Response: It is the third stage of cell signaling where the transduced signal finally triggers a specific cellular response. This response may be in the form of cellular activity-such as catalysis by an enzyme (Eg: Glycogen phosphorylase), rearrangement of the cytoskeleton, or activation of specific genes in the nucleus.

Define and distinguish simple & facilitated diffusion.

Simple Diffusion: Here the diffusion occurs without the aid of an intermediary molecule such as channel proteins or carrier molecules. Facilitated Diffusion: Facilitated diffusion is the process of spontaneous transport of molecules or ions across a cell's membrane via specific trans-membrane proteins.

What properties of a molecule will affect whether or not it can cross the lipid bilayer via simple diffusion?

Three primary factors determine whether a molecule will diffuse across a cell membrane: concentration, charge and size.

What is meant by the "fluid mosaic model" of membrane structure?

The fluid mosaic model describes the structure of the plasma membrane as a mosaic of components —including phospholipids, cholesterol, proteins, and carbohydrates—that gives the membrane a fluid character. Plasma membranes range from 5 to 10 nm in thickness.

Define transmembrane, integral, & peripheral proteins

The integral membrane proteins are further classified as transmembrane proteins that span across the membrane, or integral monotopic proteins, which are to attached to only one side of the membrane.

Distinguish positive vs. negative feedback. Describe their possible benefits in the short and long term for cellular processes. Give an example of each as discussed in chapter 6. *****

The key difference between positive and negative feedback is their response to change: positive feedback amplifies change while negative feedback reduces change. This means that positive feedback will result in more of a product: more apples, more contractions, or more clotting platelets.

What is bulk transport? Does it require energy?

The movement of macromolecules such as proteins or polysaccharides into or out of the cell Yes

Define enzyme saturation

The point at which, the rate of reaction reaches maximum with no further increase at a particular substrate concentration

Define chemical equilibrium. Can a reaction at equilibrium do work? Can a reaction moving towards equilibrium do work? At equilibrium, are products & reactants at equal concentrations?

The state in which both reactants and products are present in concentrations which have no further tendency to change with time, so that there is no observable change in the properties of the system. The cell would die because there would be no free energy left to perform the work needed to keep it alive Cells stay out of equilibrium by manipulating concentrations of reactants and products to keep their metabolic reactions running in the right direction Reactions do not necessarily—and most often do not—end up with equal concentrations. Equilibrium is the state of equal, opposite rates, not equal concentrations

What is the main source of energy for the Earth?

The sun!

If the solution outside the cell is hypotonic to that inside, the net direction of osmosis will be?

The water outside the cell will flow inwards to attain equilibrium, causing the cell to swell and burst.

Describe ATP. What are its components? How does it store energy (i.e., in what part)? Is the hydrolysis of ATP endergonic or exergonic? Can it be coupled to endergonic or exergonic processes? What are 3 mechanisms by which ATP does work?

There are three sections of the ATP molecule. In the center is a sugar molecule called ribose. Attached to one end of the ribose are rings of carbon and nitrogen that form a base known as adenine. At the other end of the ribose is a group of three phosphates. Stores energy in phosphate bond Exergonic Yes Glycolysis, citric acid cycle, phosphorylation

Define thylakoid membrane

Thylakoid membranes of a chloroplast is an internal system of interconnected membranes, that carry out the light reactions of photosynthesis. They are arranged into stacked and unstacked regions called grana and stroma thylakoids, respectively, that are differentially enriched in photosystem I and II complexes.

Distinguish gated channel and carrier proteins.

Unlike channel proteins which only transport substances through membranes passively, carrier proteins can transport ions and molecules either passively through facilitated diffusion, or via secondary active transport. These carrier proteins have receptors that bind to a specific molecule (substrate) needing transport.

Define non-competitive inhibition

When an inhibitor binds to an allosteric site instead of an active so it does not compete with a substrate. The inhibitor's binding to the active site distorts the shape of the active site. Therefore, the substrate cannot bind to the active site anymore.

Define electronegativity (from Ch 2)

a measure of the tendency of an atom to attract a bonding pair of electrons

Define isotonic

a medium and cell are said to be isotonic when the solute concentrations of the medium and the cell are equal

What is an enzyme?

a substance produced by a living organism that acts as a catalyst to bring about a specific biochemical reaction.

Cell signaling can be classified in several ways (only summarized in class notes)

a) by distance: i) Local (signaling to adjacent cells):•paracrine: by one cell to numerous adjacent cells, includes growth factors stimulating division•synaptic: electric signal triggers neurotransmitter release which travels to adjacent target cell ii) Long-distance endocrine (hormone)signaling in animals: travel through circulatory system in plants: travel through xylem/phloem or in some cases through the air b) by receptor mechanism:•G-protein coupled receptor on plasma membrane:Signal molecule activates receptor protein which changes shape & activates G-protein which moves laterally on inner-membrane surface & activates another proteins, transmitting signal.--> Most common receptor mechanism•ligand-gated ion channel on plasma membrane Signal molecule opens protein channel which allows ion influx via diffusion--> common mechanism in the nervous system• intracellular receptor protein: common for steroids (hydrophobic) & hydrophobic gasses Signal molecule is hydrophobic and can cross into cytoplasm where binds with receptor. This receptor-complex acts as a transcription factorturning on certain genes, resulting in the production of certain proteins

Define cofactor

an ion or molecule that binds to an enzyme before substrates can bind

For each of the 3 stages of aerobic cellular respiration (summarized in class notes) know the following:

cellular compartment or boundary between compartments where the process occurs inputs: compounds going in (including # carbons of original glucose)outputs: compounds coming out (# carbons of original glucose)which compounds have high potential (free) energy which compounds have low potential energyATP generated & how total enzyme-catalyzed reactions

Define selective permeability

characteristic of a membrane that allows some substances to cross while preventing the crossing of others

Define stroma

fluid portion of the chloroplast; outside of the thylakoids

Define amphipathic

having both hydrophilic and hydrophobic parts

Define hypertonic

higher concentration of solutes (more salt)

Define reduction

loss of oxygen, gain of electrons

Define hypotonic

lower concentration of solutes (more water)

Define allosteric regulation Includes activation, inhibition, and cooperativity

may either inhibit or stimulate an enzyme's activity

Define glycoprotein

protein attached to a carb, involved in immune response

Define oxidizing agent

something that removes electrons from something else and itself is reduced

What is a catalyst?

substance that speeds up the rate of a chemical reaction

Define energy

the ability to do work

Define metabolism

the chemical processes that occur within a living organism in order to maintain life.

Describe a phosphorylation cascade (Fig. 5.24; discussed briefly in class, but not in notes).

•Benefit: allows for amplificationof the signal --> at each step, numerous molecules activated •A cascade, because phosphate groups are added in series to proteins:protein kinase: enzyme that adds a phosphate to a protein (effectively energizing it)keeps signal pathway on-->boosts signal transduction protein phosphatases: enzyme that removes a phosphate (effectively deactivating it)turns signal pathway off(then protein kinases can be re-used) •second messengers: non-protein molecules involved in signal transductioncAMP: cyclic AMP (adenosine monophosphate): involved in fightor flightresponseCa2+: calcium ion

Define reducing agent

•Readily donates electrons •Substance that is oxidized