Cell Biology and Biochemistry: Terminology and Concepts, Quizzes of Biology

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Metabolism

the totality of an organism's chemical reactions; it is an emergent property of life that arises from interactions between molecules within the cell; never at equilibrium. TERM 2

Metabolic Pathway

DEFINITION 2 begins with a specific molecule and ends with a product; each step is catalyzed by a specific enzyme. TERM 3

Catabolic Pathway

DEFINITION 3 releases energy by breaking down complex molecules into simpler compounds. TERM 4

*Example of Catabolism

DEFINITION 4 Cellular Respiration, which is the breakdown of glucose in the presence of oxygen. TERM 5

*Example of Anabolism

DEFINITION 5 the synthesis of protein from amino acids.

Anabolic Pathway

consumes energy to build complex molecules from simpler ones. TERM 7

Bioenergetics

DEFINITION 7 the study of how organisms manage their energy resources. TERM 8

Energy

DEFINITION 8 the capacity to cause change; the ability to do work; exists in various forms, some of which can perform work. TERM 9

Potential Energy

DEFINITION 9 energy that matter possesses because of its location or structure; example: starch. TERM 10

*Chemical Energy

DEFINITION 10 is Potential Energy available for release in a chemical reaction.

Kinetic Energy

energy associated with motion TERM 12

*Open System

DEFINITION 12 energy and matter can be transfered between the system and its surroundings. *(organisms are open systems.); constant flow of materials. TERM 13

First Law of Thermodynamics

DEFINITION 13 the energy of the universe is constant; also called the Principle of Conservation of Energy; ** Energy can be transferred and transformed but it cannot be created or destroyed. TERM 14

Closed System

DEFINITION 14 isolated from its surroundings. (liquid in the thermos); eventually reach equilibrium and then do no work. TERM 15

Second Law of Themodynamics

DEFINITION 15 every energy transfer or transformation increases the entropy (disorder) or the universe; the evolution of more complex organisms does not violate this law.

Free Energy

Energy that can do work when temperature and pressure are in uniform (living cell); (G) organized energy; change is Free Energy is DELTA G; *DeltaG is equal to Gfinal-Ginitial; SLIDE 24- TERM 17

Spontaneous

Processes

DEFINITION 17 occur without energy input. they can happen *quickly (explosion) or slowly (rusting car). TERM 18

Products are less organized

if:

DEFINITION 18 Gf is less than Gi (negative value); the reaction is spontaneous and exergonic. Breaking molecules apart by hydrolysis. TERM 19

Endergonic Reaction

DEFINITION 19 absorbs free energy from its surroundings and its non spontaneous. energy required. TERM 20

Bioluminescence

DEFINITION 20 Organisms convert energy to light.

A cell does 3 main kinds of work:

1. Chemical 3. Transport 3. Mechanical ; each are powered by the hydrolysis of ATP. TERM 22

Energy

Coupling

DEFINITION 22 the use of an exergonic process to drive an endergonic process. TERM 23

ATP (adenosine triphosphate)

DEFINITION 23 cell's energy shuttle; composed of ribose(a sugar), adenine (a nitrogenous base), and three phosphate groups. TERM 24

Metabolic Pathway

DEFINITION 24 begins with a specific molecule and ends with a product; each step is catalyzed by a specific enzyme; The speed of the reaction is increased by enzymes. TERM 25

Catalyst

DEFINITION 25 a chemical agent that speeds up a reaction without being consumed by the reaction.

Enzyme

a catalyst protein; Hydrolysis of sucrose by the enzyme sucrase is an example of an enzyme-catalyzed reaction. TERM 27

Free Energy of Activation (Activation Energy)

DEFINITION 27 the initial energy needed to start a chemical reaction. TERM 28

Substrate

DEFINITION 28 the reactant that an enzyme acts on. TERM 29

Enzyme-substrate complex

DEFINITION 29 enzyme binds to its substrate. (**R groups of amino acids in active site binds specific substrates) TERM 30

Induced Fit

DEFINITION 30 of a substrate brings chemical groups of the active site into positions that enhance their ability to catalyze the reaction.

Speed of enzyme activity influenced by:

substrate concentration and concentration of enzyme. TERM 32

An enzymes activity can be affected by:

DEFINITION 32

1. General environmental factors (temperature and pH) 2. Chemicals that specifically influence the enzyme (cofactors). TERM 33

pH and temperature

DEFINITION 33 affects the 3D shape of the enzyme proteins. TERM 34

Cofactors

DEFINITION 34 are nonprotein enzyme helpers, required for proper active site function. TERM 35

Inorganic Cofactor

DEFINITION 35 (a metal in ionic form): zinc, copper, iron, etc.

Organic Cofactor

(coenzyme): vitamins, vitamin derivatives TERM 37

Competitive inhibitors

DEFINITION 37 bind to the active site of an enzyme, competing with the substrate. Example: Sarin Nerve Gas and Methanol. TERM 38

*Treatment of someone ingests Methanol:

DEFINITION 38 intravenous infusion of ethanol. TERM 39

Noncompetitive Inhibitors

DEFINITION 39 bind to another part of an enzyme (NOT the active site), causing the enzyme to change shape and making the active site less effective. Examples: toxins, heavy metal poisoning, poisons, pesticides, and antibiotics. TERM 40

Allosteric Regulation

DEFINITION 40 may either inhibit or simulate an enzyme's activity; occurs when a regulatory molecule binds to a protein at one site and affects the protein's function at another site; most are made from polypeptide subunits.

Cooperativity

a form of allosteric regulation that can amplify enzyme activity; binding by a substrate to one active site stabilizes favorable conformational changes at all other subunits. Example: Oxygen Binding to Hemoglobin. TERM 42

Feedback Inhibition

DEFINITION 42 the end product of a metabolic pathway shuts down the pathway; prevents a cell from wasting chemical resources by synthesizing more product than is needed. TERM 43

*Example of Feedback Inhibition

DEFINITION 43 Isoleucine production regulated by feedback inhibition (negative feedback) to allosteric enzyme threonine deaminase. TERM 44

Plasma Membrane

DEFINITION 44 the boundary that separates the living cell from its surroundings; selective barrier that allows sufficient passage of oxygen, nutrients and waste to service the volume of every cell. TERM 45

Selective

Permeability

DEFINITION 45 the plasma membrane exhibits this; allows some substances to cross it more easily than others.

Hydrophobic Molecules

(nonpolar), such as hydrocarbons. Can dissolve in the lipid bilayer and pass through the membrane rapidly. - * O2, CO (non polar molecules) can cross easily. TERM 47

Transport Proteins

DEFINITION 47 allow passage of hydrophilic substances across the membrane; Some, called Channel Proteins, have a hydrophilic channel that certain molecules or ions can use as a tunnel. - *bypasses hydrophobic region of bilayer; Specific for the substance that it moves. (Channel or Carrier) TERM 48

Aquaporins

DEFINITION 48 Channel proteins which facilitate the passage of water. (*Water is a polar molecule) TERM 49

Carrier Proteins

DEFINITION 49 Transport proteins that bind to molecules and change shape to shuttle them across the membrane. TERM 50

Concentration Gradient

DEFINITION 50 the difference in concentration of a substance from one area to another. Movement from [higher] to [lower]; unaffected by the concentration of other substances. no work done.

Passive Transport

The diffusion of a substance across a biological membrane. Requires no energy from the cell to make it happen. TERM 52

Simple Diffusion

DEFINITION 52 the movement of gases (O2, CO2) and lipids through the phospholipid bilayer. TERM 53

Facilitated Diffusion

DEFINITION 53 larger and more polar molecules and ions cannot pass through the bilayer - requires help from membrane proteins through this process. TERM 54

Diffusion

DEFINITION 54 the tendency for molecules to spread out evenly into the available space. TERM 55

Dynamic Equilibrium

DEFINITION 55 as many molecules cross one way as cross in the other direction.

Osmosis

the diffusion of water across a selectively permeable membrane; water diffuses across a membrane from the region of lower solute concentration to the region of higher solute concentration. TERM 57

Tonicity

DEFINITION 57 the ability of a solution to cause a cell to gain or lose water. TERM 58

Isotonic Solution

DEFINITION 58 solute concentration is the same as that inside the cell; no net water movement across the plasma membrane. TERM 59

Hypertonic Solution

DEFINITION 59 solute concentration is greater than that inside the cell; cell LOSES water. TERM 60

Hypotonic Solution

DEFINITION 60 solute concentration is less than that inside the cell; cel GAINS water.

Osmoregulation

the control of water balance; is a necessary adaptation for life in such environments TERM 62

Turgid

DEFINITION 62 (firm); a plant cell in a hypotonic solution swells until the wall opposes uptake. TERM 63

Flaccid

DEFINITION 63 (limp); a plant cell and its surroundings are isotonic, there is no net movement of water into the cell; the plant may wilt. TERM 64

Plasmolysis

DEFINITION 64 a usually lethal effect; In a hypertonic environment, plant cells lose water; eventually, the membrane pulls away from the wall. TERM 65

In Facilitated

Diffusion:

DEFINITION 65 transport proteins speed the passive movement of molecules across the plasma membrane.

Channel Proteins

provide corridors that allow a specific molecule or ion to cross the membrane. Include: Aquaporins and Ion Channels. TERM 67

Ion Channels

DEFINITION 67 open or close in response to a stimulus; (gated channels); Example: voltage or electric shock TERM 68

Cystinuria

DEFINITION 68 a kidney disease that is an example of a disease caused by malfunctions in specific transport systems. - Cysteine not transported back into cell (lacks carrier protein); remains in urine, crystallizes (may form stones). TERM 69

Active Transport

DEFINITION 69 moves substances against their concentration gradient; requires energy, usually in the form of ATP; not spontaneous; performed by specific proteins embedded in the membrane. **(ALL carrier proteins and NOT channel proteins); allows cells to maintain concentration gradients that differ from their surroundings. TERM 70

Sodium-Potassium Pump

DEFINITION 70 One type of active transport system; terminal phosphate group from ATP is transferred to carrier protein to provide energy for the pump.

Membrane Potential

is the voltage difference across a membrane. TERM 72

Voltage

DEFINITION 72 is created by differences in the distribution of positive and negative ions. TERM 73

Electrochemical Gradient

DEFINITION 73 two combined forces drive the diffusion of ions across a membrane; consists of: 1. a chemical force and 2. a electrical force. TERM 74

Chemical Force

DEFINITION 74 the ion's concentration gradient. TERM 75

Electrical Force

DEFINITION 75 the effect of the membrane potential on the ion's movement.

Cotransport

occurs when active transport of a solute indirectly drives transport of another solute. TERM 77

Endocytosis

DEFINITION 77 the cell takes in macromolecules by forming vesicles from the plasma membrane; a reversal of exocytosis and involves different proteins. TERM 78

3 types of Endocytosis:

DEFINITION 78

1. Phagocytosis: "cellular eating" 2. Pinocytosis: "cellular drinking" 3. Receptor-mediated endocytosis TERM 79

Phagocytosis

DEFINITION 79 cell engulfs a particle/bacterium in a vacuole; The vacuole fuses with a lysosome to digest the particle. (Lysosome filled with digestive enzymes to destroy the particle/bacterium); forms a food vacuole TERM 80

Pinocytosis

DEFINITION 80 molecules are taken up when extracellular fluid is gulped into tiny vesicles; Usually performed to take in H2O; A lot of water at one time.

Receptor-Mediated endocytosis

binding of ligands to receptors triggers vesicle formation; Brings in large numbers of specific molecules; Human cells use this to take in cholesterol TERM 82

*Hypercholesterolemia

DEFINITION 82 inherited disease where LDL receptors are defective; cholesterol not taken into cells; leads to atherosclerosis. TERM 83

Ligand

DEFINITION 83 any molecule that binds specifically to a receptor site of another molecule. TERM 84

Phospholipid

DEFINITION 84 composed of two fatty acids attached to glycerol and a phosphate group; major component of all cell membranes; (* In cell membranes, a double layer of phospholipid is formed); most abundant lipid in the plasma membrane. TERM 85

Amphipathic Molecules

DEFINITION 85 (phospholipids) containing both hydrophobic and and hydrophilic regions.

Fluid Mosaic Model

states that a membrane is a fluid structure with a "mosaic" of various proteins embedded in it. TERM 87

Freeze-Fracture Studies

DEFINITION 87 a specialized preparation technique that splits a membrane along the middle of the phospholipid bilayer; supports the fluid mosaic model TERM 88

Two Major Populations of Membrane Proteins:

DEFINITION 88

1. Peripheral Proteins 2. Integral Proteins TERM 89

Peripheral Proteins

DEFINITION 89 bound to the surface of the membrane. TERM 90

Integral proteins

DEFINITION 90 penetrate the hydrophobic core. (The hydrophobic regions of an integral protein consist of one or more stretches of non polar amino acids, often coiled into alpha helices).

Transmembrane Proteins

Integral proteins that span the membrane. TERM 92

Six Major Functions of Membrane Proteins:

DEFINITION 92

1. Transport 2. Enzymatic Activity 3. Signal Transduction 4. Cell-Cell Recognition 4. Intercellular Joining 5. Attachment to the cytoskeleton and extracellular matrix (ECM) TERM 93

Transport

DEFINITION 93 protein provides a channel across the membrane, selective for a particular solute passage. Some move substances across the membrane by altering its shape. TERM 94

Enzymatic Activity

DEFINITION 94 protein on membrane is an enzyme to catalyst reactions in the aqueous environment. TERM 95

Signal Transduction

DEFINITION 95 protein (receptor) has a binding site for an external chemical messenger. Binding causes change in protein structure inside membrane to relay the signal.

Cell-Cell Recognition

some glycoproteins serve as ID tags recognized by membrane proteins of other cells. TERM 97

Intercellular Joining

DEFINITION 97 proteins that join adjacent cells together (Example: Gap junctions, tight junctions) TERM 98

Attachment to the cytoskeleton and

extracellular matrix (ECM)

DEFINITION 98 membrane proteins connect to microfilament/cytoskeletal components to maintain cell shape, stabilize membrane protein location. TERM 99

Glycolipids

DEFINITION 99 membrane carbohydrates may be covalently bonded to lipids TERM 100

Glycoproteins

DEFINITION 100 membrane carbohydrates may be covalently bonded more commonly to proteins.

Example of Cell-Cell Recognition

Blood type caused by RBC glycoproteins. TERM 102

Asymmetrical Distribution

DEFINITION 102 of proteins, lipids and associated carbohydrates in the plasma membrane is determined when the membrane is built by the ER and Golgi Apparatus. TERM 103

Light Microscope (LM)

DEFINITION 103 visible light passes through a specimen and then through glass lenses, which magnify the image; about 1000 times the size; most sub cellular structures, including organelles and too small to be resolved by an LM. TERM 104

Electron Microscopes (EMs)

DEFINITION 104 two basic types; used to study sub cellular structures. TERM 105

Scanning Electron Microscopes (SEMs)

DEFINITION 105 focus a beam of electrons onto the surface of a specimen, providing images that look 3-D; scans the top of the image.

Transmission Electron Microscopes

(TEMs)

focus a beam of electrons through a specimen; used mainly to study the internal structure of cells; penetrates the image and shows inside. TERM 107

The quality of an image depends on:

DEFINITION 107 Magnification, Resolution, Contrast TERM 108

Magnification

DEFINITION 108 the ratio of object's image size to its real size. TERM 109

Resolution

DEFINITION 109 the measure of the clarity of the image, or the minimum distance of two distinguishable points TERM 110

Contrast

DEFINITION 110 visible differences in parts of the sample

Cell

Fractionation

takes cells apart and separates the major organelles from one another; enables scientists to determine the functions of organelles TERM 112

Prokaryotic

DEFINITION 112 Only organisms of the domains Bacteria and Archaea; no nucleus; no membrane bound organelles; cytoplasm bound by plasma membrane; do not have a nuclear envelope. TERM 113

Eukaryotic

DEFINITION 113 Protists, fungi, animals, and plants; SLIDE 16 Lesson 14; much larger than prokaryotic; internal membranes that partition the cell into organelles. TERM 114

Basic Features of all cells:

DEFINITION 114 plasma membrane; cytosol; chromosomes (carry genes); ribosomes(make proteins) TERM 115

Nucleus

DEFINITION 115 contains most of the cell's genes and is usually the most conspicuous organelle

Nuclear Envelope

encloses the nucleus, separating it from the cytoplasm TERM 117

Nuclear Membrane

DEFINITION 117 a double membrane; each membrane consists of a lipid bilayer. TERM 118

Nuclear Lamina

DEFINITION 118 netlike array of protein filaments TERM 119

Chromatin

DEFINITION 119 genetic material formed in the nucleus by DNA and proteins; the DNA that is unwound and spread out throughout the nucleus. TERM 120

Chromosomes

DEFINITION 120 discretely formed when chromatin condenses.

Nucleolus

located within the nucleus and is the site of ribosomal RNA (rRNA) synthesis. TERM 122

Ribosomes

DEFINITION 122 particles made from ribosomal RNA (rRNA) and protein; carry out protein synthesis in two locations: cytosol and outside of the endoplasmic reticulum or the nuclear envelope. TERM 123

Endomembrane System

DEFINITION 123 Nuclear Envelope, Endoplasmic Reticulum, Golgi Apparatus, Lysosomes, Vacuoles, Plasma Membrane; Continuous or connected by vesicles. TERM 124

Endoplasmic Reticulum (ER)

DEFINITION 124 accounts for more than half of the total membrane in many eukaryotic cells; continuous with the nuclear envelope; smooth or rough. TERM 125

Smooth ER

DEFINITION 125 lacks ribosomes; synthesizes lipids; metabolizes carbohydrates; detoxifies poison; stores calcium; SLIDE 35 Lesson 14