Biology Notes: Membranes, Transport Proteins, and Cellular Respiration, Quizzes of Cellular and Molecular Biology

Download Biology Notes: Membranes, Transport Proteins, and Cellular Respiration and more Quizzes Cellular and Molecular Biology in PDF only on Docsity!

recombinant DNA technology

-various techniques to isolate, replicate and manipulate specific DNA-molecular cloning is a set of experimental methods in molecular biology that are used to assemble recombinant DNA molecules and to direct their replication within host organisms. TERM 2

restriction nuclease

DEFINITION 2 -A restriction enzyme is an enzyme that cuts DNA at or near specific recognition nucleotide sequences known as restriction sites. -cuts "unmethylated" or foreign DNA TERM 3

gel electrophoresis

DEFINITION 3 -method for separation and analysis of macromolecules and their fragments, based on their size and charge. TERM 4

hybridization

DEFINITION 4 identical DNA fragments grouped and separated to find specific DNA fragments TERM 5

DNA cloning

DEFINITION 5 process of extracting DNA from a host cell and implanting it to function in another type of cell

DNA ligase

used to catalyze covalent bonds between the fragment and vector TERM 7

transformation

DEFINITION 7 genetic alteration of a bacterial cell resulting from the transfer of foreign DNA TERM 8

plasmid vector

DEFINITION 8 plasmid manipulated by genetic engineering to serve as s tool to produce the desired products in the target cell through a biomolecular process such by the expression of gene of interest TERM 9

genomic DNA

library

DEFINITION 9 a collection of DNA fragments that is stored and propagated in a population of micro-organisms through the process of molecular cloning. TERM 10

cDNA

library

DEFINITION 10 -copies of mRNA-a cDNA library is a combination of cloned cDNA fragments inserted into a collection of host cells, which together constitute some portion of the transcriptome of the organism.

Polymerase Chain Reaction (PCR)

-technique for amplifying DNA sequences in vitro by separating the DNA into two strands and incubating it with oligonucleotide primers and DNA polymerase-it can amplify a specific sequence of DNA as many as 1 billion times TERM 12

reverse transcriptase

DEFINITION 12 -an enzyme coded by some virus genomes that uses RNA as a template and with a primer at the 3' end of the RNA will make DNA copy TERM 13

bioinformatics

DEFINITION 13 -interdisciplinary scientific field that develops methods for storing, retrieving, organizing and analyzing biological data. TERM 14

DNA sequencing

DEFINITION 14 -process of determining the precise order of nucleotides within a DNA molecule-it includes any method or technology that is used to determine the order of the four bases- adenine, guanine, cytosine, and thymine-in a strand of DNA. TERM 15

expression vectors

DEFINITION 15 -a plasmid containing the required regulatory sequences specifically used for the expression of a particular gene into proteins within the target cell

reporter gene-green fluorescent protein

• a protein obtained from the jellyfish Aequorea victoria that emits a bright green fluorescence when illuminated, GFP is used to monitor gene expression, gene transfer across plasma membranes, and cell surface activity TERM 17

site-directed mutagenesis

DEFINITION 17

• a method that is used to make specific and intentional changes to the DNA sequence of a gene and any gene products. TERM 18

gene

knockout

DEFINITION 18 -a genetic technique in which one of an organism's genes are made inoperative ("knocked out" of the organism). TERM 19

genetically modified organism

DEFINITION 19 -an organism whose genetic material has been altered using genetic engineering techniques. TERM 20

transgenic organism

DEFINITION 20 -contains a gene or genes which have been artificially inserted instead of the organism acquiring through reproduction

RNA interference

-process in which the introduction of double-stranded RNA into a cell inhibits the expression of genes TERM 22

plasma membrane

DEFINITION 22

• separates the interior of all cells from the outside environment. -semi-permeable TERM 23

lipid bilayer

DEFINITION 23 -a thin polar membrane made of two layers of lipid molecules.-made of phospholipids; hydrophilic heads and hydrophobic tails (fatty acids) TERM 24

amphipathic

DEFINITION 24 -having both hydrophilic and hydrophobic properties TERM 25

membrane fluidity

DEFINITION 25 -dependent on temp and membrane composition (saturated and unsaturated)-viscosity of the lipid bilayer

fatty acids: unsaturated vs.

saturated

-unsaturated: double bond in fatty acid tail which results in a kink (or "dogleg") in the physical layout of the fatty acid because Van der waals forces are strongest with a straight (saturated) fatty acid-saturated: every carbon in the tail has associated with it the maximum number of hydrogens TERM 27

cholesterol

DEFINITION 27

• a 4-ring steroid structure with a hydrocarbon tail-comprised of hydroxyl group (the only hydrophilic aspect of molecule) TERM 28

membrane proteins: integral vs. peripheral

DEFINITION 28 -integral: permanently attached or firmly anchored in the plasma membrane via its hydrocarbon domains interacting with the membrane phospholipids-peripheral: protein temporarily adheres to the membrane, either to lipid bilayer or integral protein by combination of hydrophobic, electrostatic, and other non-covalent interactions TERM 29

transporters

DEFINITION 29 -proteins that need to expand the membrane; be able to open up on the interior side of membrane and exterior side to allow charged particles and molecules to pass throughp TERM 30

poikilotherm

DEFINITION 30 -organisms have internal temperatures that very within the ambient temperature (cold-blooded)

homeotherm

-organisms have constant internal temperatures (warm- blooded) TERM 32

essential fatty acids: linoleic acids (18:2);

linolenic acid (18:3)

DEFINITION 32 -linoleic acid (18:2): a liquid polyunsaturated fatty acid abundant in plant fats and oils; not naturally produced (makes soap)-linolenic acid: essential for humans in the diet TERM 33

semi-permeable membrane

DEFINITION 33 -allows certain molecules or ions to pass through it by diffusion and occasionally specialized "facilitated diffusion". TERM 34

membrane transport proteins

DEFINITION 34 -membrane protein involved in the movement of ions, small molecules, or macromolecules, such as another protein across a biological membrane. TERM 35

transport: active vs. passive

DEFINITION 35 -active: requires energy (usu. ATP); involves movement against concentration gradient-passive: no direct energy; relies on concentration gradient

active transporter: coupled, ATP-driven, light-

driven

-coupled: use the gradient of one molecule to transport another molecule against a gradient symport: movement of both ions in the same direction antiport: movement of ions in opposite direction -ATP driven: ATP hydrolyzed to ADP, energy is released-light- driven: electromagnetic radiation captured by electrons TERM 37

membrane potential

DEFINITION 37 -requires energy (usu. ATP) to establish; can involve movement with or against a concentration gradient TERM 38

electrochemical gradient

DEFINITION 38 -a gradient of electrochemical potential, usually for an ion that can move across a membrane. TERM 39

osmosis

DEFINITION 39 -the spontaneous net movement of solvent molecules through a partially permeable membrane into a region of higher solute concentration, in the direction that tends to equalize the solute concentrations on the two sides. TERM 40

osmotic pressure

DEFINITION 40 -the pressure which needs to be applied to a solution to prevent the inward flow of water across a semipermeable membrane.

H+ (proton), K+ (potassium), Ca2+ (Calcium)

pumps

-H+ (proton) pump: integral membrane proteins that transport proteins across a membrane against a concentration gradient; driven by hydrolysis of ATP by hydrogen-transporting ATP synthase-K+ (potassium) pump: enzyme-based mechanism that removes excess ions from inside a cell and replacing them with ions from outside the cell-Ca2+ (calcium) pump: active transport of calcium across a membrane; driven by enzymatic hydrolysis of ATP TERM 42

ion channel

DEFINITION 42 -pore-forming membrane proteins whose functions include establishing a resting membrane potential, shaping action potentials and other electrical signals by gating the flow of ions across the cell membrane, controlling the flow of ions across secretory and epithelial cells, and regulating cell volume. TERM 43

patch clamp

recording

DEFINITION 43 -technique is a laboratory technique in electrophysiology that allows the study of single or multiple ion channels in cells. TERM 44

channel: voltage-gated, ligand-gated, stress-

gated

DEFINITION 44 -voltage-gated: open and close in response to change in the electrical potential across the plasma membrane of the cell important for conduction action potentials along nerve cell processes -ligand-gated: transmembrane ion channel whose permeability is increased by the binding of a specific ligand, typically a neurotransmitter at a chemical synapse no ions through when shut -stress-gated: TERM 45

Nernst equation

DEFINITION 45 -equation relating the electrical potential and concentration gradient of an ion across a permeable membrane at equilibrium E = [RT/nF]

neuron

-a neuron is an electrically excitable cell that processes and transmits information through electrical and chemical signals. TERM 47

action potential

DEFINITION 47 -a short-term change in electrical potential on the surface of a cell in response to stimulation, and then leads to the transmission of an electrical impulse that travels across the cell membrane TERM 48

catabolism

DEFINITION 48 -the process involving a series of degradative chemical reactions that break down complex molecules into smaller subunits, usually releasing energy in the process TERM 49

acetyl-CoA

DEFINITION 49 -a 2-carbon enzyme intermediate in which cell synthesize, breakdown, or use nutrient molecules for energy production, growth , etc. TERM 50

NAD+/NADH

DEFINITION 50 -NAD+: oxidized electron carrier-NADH: reduced electron carrier; produced in glycolysis and is oxidized to NAD+

glycolysis

-series of reactions in cytosol with conversion of glucose into pyruvate and production of ATP (net gain of 2 ATP and 2 NADH) TERM 52

substrate level phosphorylation

DEFINITION 52 -a type of metabolic reaction that results in the formation of adenosine triphosphate or guanosine triphosphate (GTP) by the direct transfer and donation of a phosphoryl (PO3) group to adenosine diphosphate (ADP) or guanosine diphosphate (GDP) from a phosphorylated reactive intermediate. TERM 53

fermentation

DEFINITION 53 -converts sugar to acids, gases and/or alcohol-produces ATP in the absence of oxygen-NADH produced in glycolysis is oxidized to NAD+ pyruvate reduced to lactate by lactate dehydrogenase or pyruvate is decarboxylated and reduced to ethanol -regeneration of NAD+ resupplies it for further glycolysis TERM 54

glyceraldehyde 3-phosphate

DEFINITION 54 -G3P is a chemical compound that occurs as an intermediate in several central metabolic pathways of all organisms. TERM 55

pyruvate dehydrogenase complex

DEFINITION 55 -3 different enzymes; about 60 polypeptide chains that converts pyruvate into acetyl-CoA by pyruvate decarboxylation-if oxygen is PRESENT

citric acid cycle

-pyruvate concerted to acetyl-CoA and is completely oxidized and broken down into carbon dioxide and water to produce high energy phosphate compounds, which are the source for cellular energy-per cycle 2 carbon dioxide (carbon from glucose and carbon from water) 3 NADH 1 GTP (ATP in plants/bacteria) 1 FADH TERM 57

FADH

DEFINITION 57 -electron acceptor produced during citric acid cycle TERM 58

electron transport chain

DEFINITION 58 -ETC (oxidative phosphorylation):a series of compounds that transfer electrons from electron donors to electron acceptors via redox reactions, and couples this electron transfer with the transfer of protons (H+ ions) across a membrane. TERM 59

gluconeogenesis

DEFINITION 59 -a metabolic pathway that results in the generation of glucose from non-carbohydrate carbon substrates such as pyruvate, lactate, glycerol, glucogenic amino acids, and fatty acids (both even-chain and odd-chain). TERM 60

chemiosmotic coupling

DEFINITION 60 -couples or links the electron transport chain to ATP synthsis- chemiosmosis is the movement of ions across a selectively permeable membrane, down their electrochemical gradient.

mitochondrion

-organelle that generates most of the cell's ATP through cellular respiration-"powerhouse of the cell" TERM 62

intermembrane space

DEFINITION 62 -the region between the inner membrane and the outer membrane of a mitochondrion-great place for lypophylic molecules to freely travel, generating easy electron transport systems TERM 63

inner membrane

DEFINITION 63 -forms internal compartments known as "cristae" which allow greater space for proteins to function properly and efficiently-ETC located here-transport proteins transport a highly controlled manner metabolites across this membrane TERM 64

matrix

DEFINITION 64 -space enclosed by inner membrane-composed of enzymes, DNA filaments, granules, protein crystals, glycogen, and lipids TERM 65

ATP synthase

DEFINITION 65 -enzyme that catalyzes formation of ATP from the phosphorylation of ADP with inorganic phosphate, using a form of energy, such as the energy from a proton gradient

mitochondrial electron transport chain

-3 transmembrane protein complexe use electron energy to pump protons (H+) into the intermembrane space-a membrane bound mobile carrier transfer electrons from the first to the second complex-terminal acceptor of electron flow is oxygen, generation H2O TERM 67

respiratory enzyme complexes: NADH

dehydrogenase, cytochrome b-c1,

cytochrome oxidase

DEFINITION 67 -NADH dehydrogenase: flavoprotein that contains iron-sulfur centers-enzyme that catalyzes this reaction: NADH + H+ + acceptor <-- --> NAD+ + reduced acceptor -cytochrome b-c1: component of ubiquinol-cytochrome c reductase complex part of the mitochondrial respiratory chain involved in redox-linked proton pumping -cytochrome oxidase: an oxidizing enzyme containing iron and a porphyrin, found in mitochondria and is important in cell respiration as an agent of electron transfer from certain cytochrome molecules to oxygen molecules TERM 68

mobile electron carries: ubiquinone & soluble

cytochrome c

DEFINITION 68 -ubiquinone: a quinone molecule that serves as a electron carrier between flavoproteins and in cellular respiration; lipid soluble and accepts electrons from complexes I and II of ETC-soluble cytochrome c: protein which carries electrons and is central to the process of respiration in mitochondria; transfers electrons from complex III and IV, does not bind oxygen TERM 69

photosynthesis

DEFINITION 69 -the synthesis of complex organic material using carbon dioxide, water, inorganic salts, and light energy captured by light absorbing pigments such as chlorophyll-consists of light reactions and dark reactions-process in which CO2, H2O, and light energy are utilized to synthesize an energy-rich carbohydrate like glucose and to produce O2 as a byproduct 6CO2 + 12H20 + energy --> C6H12O6 +6O2 + 6H2O TERM 70

chloroplast

DEFINITION 70

• organelle with double membrane (outer and inner) that defines the interior stroma-stroma had independent membrane vesicles (thylakoids) usually stacked like pancakes (a granum)-conduct photosynthesis

intermembrane space

-accumulates a large positive charge difference (a membrane potential) and an H+ gradient (pH difference)-ETC located here TERM 72

stroma

DEFINITION 72

• a thick fluid that makes up the matrix in between the grana where various enzymes, molecules and ions can be found- dark reaction of photosynthesis occurs here TERM 73

thylakoid-grana

DEFINITION 73 -membranous cisternae found as part of the grana and also as single cisternae interconnecting the grana-contains the photosynthetic pigments, reaction centers and ETC-each thylakoid consists of flattened sac of membrane enclosing a narrow intra thylakoid space TERM 74

chlorophyll

DEFINITION 74 -the green pigment found in chloroplast of higher plants and in cells of photosynthetic microorganisms-primarily involved in absorbing light energy for photosynthesis TERM 75

antenna complex

DEFINITION 75 -chlorophyll pigments arrayed in thylakoid membrane-photon of light energy (hv) absorbed with energy shifting an electron into a more energetic orbital-captures and transfers light energy to the photochemical reaction center

reaction center

chlorophyll

-transfer their electrons to electron carrier proteins TERM 77

enzyme complexes: Photosystem II,

cytochrome b-f, Photosystem I

DEFINITION 77 -photosystem II: the photosystem that absorbs light for use to drive the oxidation of water and the reduction of plastoquinone when it releases an excited electron, it returns to its ground state by accepting an electron from the oxidation of H2O -cytochrome b-f: enzyme found in thylakoid membrane catalyzing the transfer of electrons from plastoquinol to plastocyanin- Photosystem I: photosystem that use of light to transfer electron particularly from plastocyanin to ferredoxin receives electron from the ETC that received it from photosystem II TERM 78

Enzyme complexes: NADP+ reductase

DEFINITION 78 -serves as an electron carrier being alternately oxidized (NADP) and reduced (NADPH) TERM 79

NADPH

DEFINITION 79 -the main reducing agent in cells and provides a source of energetic electrons for other reactions TERM 80

mobile electron carriers: plastoquinone,

soluble plastocyanin, soluble ferredoxin

DEFINITION 80 -plastoquinone: a quinone present in chloroplasts forming a part of the photosynthetic ETC; closely associated with photosystem II- soluble plastocyanin: copper containing protein that acts as an intermediary in photosynthetic electron transport-soluble ferredoxin: low molecular weight iron sulphur proteins that transfer electrons from one enzyme system to another without themselves having enzyme activity

calvin cycle

-converts carbon dioxide into a 3-carbon compound that is chemically stable and biologically unseable Phase 1: CO2 fixed (attached) to the compound, ribulose bisphosphate; the enzyme ribulose bisphosphate carboxylase does the carbon fixation; the product (6-carbon compound) breaks down into two 3-carbon compounds Phase 2: chemical energy is added to the 3-carbon compounds using NADPH and ATP Phase 3: reactions to regenerate ribulose bisphosphate for more carbon fixation