Exam 1 Flashcards

Question

Polysaccharides

Answer 1

Polymers composed of monosaccharides joined by glycosidic linkages

Answer 2

**Starch-** primary form of energy storage in plant cells, form granules known as *plastids* which include chloroplasts, composed of *a-*glucose monomers * Amylose- simplest form of starch, _unbranched_ * Amylopectin- a more complex starch, _somewhat branched_ **Glycogen-** primary form of energy storage in animal cells * Stored mainly in liver and muscle cells, _extensively branched_

Answer 3

**Cellulose-** major component of cell walls in plant cells * Composed of ß-glucose molecules making every glucose monomer "upside down" with respect to their neighbor * Never branched, held together laterally by hydrogen bonds **Chitin-** structural carbohydrate used by arthropods to build their exoskeletons * Also provides structural support for the cell walls of many fungi

Answer 4

Small hydrophobic molecules generally not big enough to be considered as macromolecules

Answer 5

**Glycerol-** an alcohol whose three carbons each bear a hydroxyl group **Fatty acid-** has a long carbon skeleton, usually 16 to 18 carbon atoms in length * Relatively non-polar C—H bonds are the reason why fats are hydrophobic

Answer 6

Three fatty acids linked to one glycerol molecule by a dehydration reaction

Answer 7

Process of converting unsaturated fats to saturated fats by adding hydrogen

Answer 8

Two fatty acids and a phosphate group attached to glycerol The oxygen of the phosphate opposite of the attachment site to the glycerol is connected to an additional small charged or polar molecule such as choline but can vary

Answer 9

Lipids characterized by a carbon skeleton consisting of four fused rings Different steroids are distinguished by the particular chemical groups attached to the rings Cholesterol, a type of steroid, is a component in animal cell membranes and a precursor from which other steroids are synthesized

Answer 10

Is an organic molecule with both an amino group and a carboxyl group At its center is an asymetric carbon called an *alpha carbon* whose four different partners are and amino group, a carboxyl group, a hydrogen atom, and a variable R-group called a side chain Amino groups are usually ionized in a cell

Answer 11

**Peptide bond-** covalent bond between the carboxyl group of one amino acid and the adjacent amino group of another, formed through a dehydration reaction Forms the *polypeptide backbone* of an amino acid

Answer 12

**Globular-** roughly spherical in shape **Fibrous-** shaped like long fibers

Answer 13

Is the actual sequence of individual amino acids that make up a protein, dictates the secondary and tertiary structure

Answer 14

Repeated coils and folds that form in a protein as the result of hydrogen bonds between repeating constituents of the **polypeptide backbone**, NOT the side chains Two main structures: * *a* helix- delicate coil held together by hydrogen bonding between every *fourth* amino acid * ß pleated sheet- two or more segments of the polypeptide chain lying side by side (called *ß strands*) connected by hydrogen bonds

Answer 15

Overall shape of the polypeptide resulting from the interactions between the side chains of the constituent amino acids Stabalized by three interactions: * Hydrophobic interactions- hydrophobic side chains are clustered in the core of the protein, held together by *van der Waals* interactions * Hydrogen bonds form between exterior polar side chains * Disulfide bridges can reinforce the structure of the protein where two cysteine monomers are brought close together by folding

Answer 16

The ocerall protwin structure that results from the aggregation of seperate polypeptide subunits, not all proteins have multiple subunits

Answer 17

**Chaperonins-** keep the nascent polypeptide segregated from the disruptive chemical conditions in the cytoplasm while it folds *spontaneously*

Answer 18

Exist as polymers called **polynucleotides** made up of monomers calles *nucleotides*

Answer 19

Composed of three parts: * Pentose- five carbon sugar * Nitrogenous base- a nitrogen containing base * Phosphate group The portion of a nucleotide without any phosphate group is called a *nucleoside*

Answer 20

**Deoxyribose-** the sugar molecule in DNA, _lacks_ an oxygen molecule on the second carbon in the ring **Ribose-** the sugar molecule in RNA- _has_ an oxygen molecule on the second carbon in the ring

Answer 21

**Pyrimidines-** has _one_ six-membered ring of carbon and nitrogen atoms * Cytosine (C) * Thymine (T)- only in DNA * Uracil (U)- only in RNA **Purines-** are larger with a six-membered ring fused to a five-membered ring * Adenine (A) * Guanine (G)

Answer 22

**Phosphodiester linkage-** a phosphate group that links the sugars of two nucleotides, results in a repeating pattern of sugar-phosphate units called the *sugar-phosphate backbone* * One end has a phosphate attached to a 5' carbon and the other end has a hydroxyl group on the 3' carbon * Nucleotide has built-in directionality along the sugar-phosphate backbone from 5'to 3'

Answer 23

1. **Magnification-** ratio of an object's image size to its real size 2. **Resolution-** measure of clarity; minimum distance two points can be separated and still be distinguished as seperate points 3. **Contrast-** the difference in brightness between the light and dark areas of an image

Answer 24

_Scanning Electron Microscope_ Used to look at the **surface** of a specimen by focusing a beam of electrons onto it Provides images that look 3-D

Answer 25

**Transmission Electron Microscope** Used mainly to study the internal structure of cells Focuses a beam of electrons through a specimen

Answer 26

Takes cells apart and separates the major organelles from one another Enables scientists to determine the functions of organelles

Answer 27

1. Plasma membrane 2. Semifluid substance called *cytosol* 3. Chromosomes (carry genes) 4. Ribosomes (make proteins)

Answer 28

A _double membrane_ composed of two sepearte lipid bilayers with associated proteins called *pore complexes*

Answer 29

A netlike array of intermediate protein filaments on the inside (nuclear side) of the envelope that maintains the shape of the nucleus my mechanically supporting the nuclear envelope

Answer 30

A framework of protein fibers that extends throughout the nuclear interior May help organize genetic material so that it functions efficiently

Answer 31

A prominent structure within the nondividing nucleus where _ribosomes_ are assembled *Ribosomal RNA* is synthesized in the nucleolus and combined with proteins imported from the cytoplasm to form large and small ribosomal subunits These subunits exit to the cytoplasm and a large and a small subunit combine into a ribosome

Answer 32

Complexes made of ribosomal RNA and protein Carry out protein synthesis in two locations: * Free ribosomes are present in the *cytosol* * Bound ribosomes are on the outside of the endoplasmic reticulum or the nuclear envelope

Answer 33

* Nuclear envelope * Endoplasmic reticulum * Golgi apparatus * Lysosomes * Vacuoles * Plasma membrane These components are either continuous or connected via transfer by *vesicles*

Answer 34

Synthesizes lipids Metabolizes carbohydrates Detoxifies drugs and poisons Stores calcium ions

Answer 35

Has bound ribosomes, which secrete *_glycoproteins_*- proteins covalently bonded to carbohydrates Distributes _transport vesicles_- secretory proteins surrounded by membranes Is the _membrane factory_ of the cell- as the ER expands, portions are transferred in the form of transport vesicles to other components of the endomembrane system

Answer 36

Functions of the Golgi apparatus: * Modifies products of the ER * Manufactures certain macromolecules * Sorts and packages materials into transport vesicles The shipping and receiving center of the cell Consists of flattened membranous sacs called *cisternae* (cisterns)

Answer 37

**Cis face-** is usually located near the ER and accepts transport vesicles that bud from the ER **Trans face-** is on the opposite side and gives rise to the vesicles that pinch off and travel elsewhere As products of the ER migrate through the Golgi apparatus they are modified and refined

Answer 38

A membranous sac of hydrolytic enzymes that can digest macromolecules Lysosomal enzymes work best in the acidic environment inside the lysosome Hydrolytic enzymes and lysosomal membranes are made by rough ER and then transferred to the Golgi apparatus for further processing

Answer 39

Process in which an organism engulfs and consumes a smaller organism or food particles Extends pseudopodia around a particle which is then pinched off to form a *food vacuole* Food vacuole fuses with a lysosome which digests it

Answer 40

Process by which a cell's lysosomes recycle the cell’s own organelles and macromolecules

Answer 41

Diverse maintenance compartments Large vesicles derived from the ER and Golgi apparatus Perform a variety of functions in different kinds of cells: * *Food vacuoles* are formed by phagocytosis * *Contractile vacuoles* are found in many freshwater protists- pump excess water out of cells * *Central vacuoles* are found in many mature plant cells- hold organic compounds and water

Answer 42

Have a smooth outer membrane and an inner membrane folded into **cristae** Cristae present a large surface area for enzymes that synthesize ATP Inner membrane creates two compartments, the intermembrane space and **mitochondrial matrix**

Answer 43

**Thylakoids-** flattened interconnected membranous sacs **Granum-** stacks of thylakoids that resemble poker chips **Stroma-** the fluid outside of the thylakoids which contains the chloroplast's DNA, ribosomes, and enzymes

Answer 44

A family of closely related plant organelles which include: * Chloroplasts * Amyloplast- organelle that stores starch * Chromoplast- contains the pigments that give fruits and flowers their orange and yellow hues

Answer 45

Specialized metabolic compartments bounded by a single membrane Produce hydrogen peroxide and convert it to water Have many different functions: * Use oxygen to break down fatty acids which can be used for cellular respiration * Detoxify alcohol and othe poisons by transferring hydrogen from the poison to oxygen * Specialized peroxisomes called *glyoxysomes* convert fatty acids to sugar in seeds as an energy source until a plant can initiate photosynthesis

Answer 46

Network of fibers extending throughout the cytoplasm Helps to support the cell and maintain its shape Interacts with motor proteins to produce motility Vesicles can travel along tracks provided by the cytoskeleton

Answer 47

**Microtubules-** thickest of the three components of the cytoskeleton **Microfilaments-** also called *actin filaments*; thinnest components **Intermediate filaments-** fibers with diameters in a middle range

Answer 48

Composed of *tubulin*-a dimer consisting of *a*-tubulin and ß-tubulin 25 nm with a 15 nm lumen Functions of microtubules: * Shaping the cell * Guiding movement of organelles * Separating chromosomes during cell division * Control the beating of flagella and cilia

Answer 49

Region of the cell where the microtubules originate from Often located near the nucleus Location of the centrioles Only present in animal cells

Answer 50

Organize microtubule assembly in animal cells Aid in the seperation of chromosomes during mitosis Located as a pair in the centrosome perpendicular to each other Composed of nine sets of triplet microtubules arranged in a ring

Answer 51

Differ in their beating patterns but share a common structure Composed of a core of microtubules sheathed by the plasma membrane * Nine doublets of microtublues arranged in a ring with two single microtubules in its center in a "9+2" pattern * This pattern is found in nearly all eukaryotic flagella and motile cilia **Basal body**- anchors the cilium or flagellum * Structure similar to a centriole with nine triplets of microtubules in a "9+0" pattern **Dyneins-** motor proteins that are responsible for movement that attach each outer tubule doublet

Answer 52

*Actin* filaments Structural role: * Bear tension by resisting pulling forces within the cell * Form a 3-D network called the **cortex** just inside the plasma membrane to help support the cell’s shape Motile role: * Function in cellular motility in conjunction with the protein **myosin** * Thicker filaments composed of myosin interdigitate with the thinner actin fibers * Involved in *amoeboid* (crawling) movement by extending **pseudopodia** **Cytoplasmic streaming-** the induced circular flow of cytoplasm within a cell which speeds distribution of materials within a cell

Answer 53

Most common in vertebrates Specialized for bearing tension Various types are constructed by particular molecular subunits; includes **keratin** Some make up the **nuclear lamina** which lines the interior of the nuclear envelope

Answer 54

Extracellular strucutre posesed by: * Plant cells * Prokaryotes * Fungi * Some unicellular eukaryotes Plant cell walls are made of cellulose fibers embedded in other polysaccharides and protein

Answer 55

**Primary cell wall-** relatively thin and flexible outtermost wall * First secreted by young plant cells * When a plant cell is done growing it can secrete a hardening substance into the primary wall **Middle lamina-** a thin layer between primary walls of adjacent plant cells * Layer is rich in sticky polysaccharides called **pectins** * Serves to glue cells together **Secondary cell wall-** between the primary cell wall and the plasma membrane * Strong and durable matrix that affords the cell protection and support * Often deposited in several laminated layers * Wood consists primarily of secondary cell walls **Plasmodesmata-** channels that perforate the cell wall that join adjacent cells

Answer 56

Protects the cell Maintains its shape Prevents excessive uptake of water

Answer 57

Composed of glycoproteins and other carbohydrate-containing molecules: * Collagen * Proteoglycans * Fibronectin Bind to receptor proteins in the plasma membrane called *integrin* The ECM around a cell can influence the activity of gene in the nucleus Mechanical signaling through cytoskeletal changes trigger chemical signals in the cell

Answer 58

Most abundant glycoprotein in animal cells Form strong fibers outside of the cell embeded in a web of *proteoglycan complexes* Accounts for 40% of total protein in the human body

Answer 59

Can consist of hundreds of proteoglycan molecules attached noncovalently to a single long polysaccharide molecule Proteoglycan molecules consist of a small core protein with many carbohydrate chains covalently attached; about 95% carbohydrate

Answer 60

Proteins that bind to cell surface receptor proteins called *integrins* which are built into the plasma membrane

Answer 61

Span the cell membrane Bind to microfilaments of the cytoskeleton on their cytoplasmic side and *fibronectins* of the ECM on their extracellular side Based on the word "integrate" Transmit signals between the ECM and the cytoskeleton to integrate changes occuring outside and inside the cell

Answer 62

Perforations in plant cell walls that unify most plant cells Channels allow cytosol to pass through Join the internal chemical environments of adjacent cells

Answer 63

Plasma membranes of neighboringcells are tightly pressed against each other Bound together by specific proteins Forms a continuous seal around cells Establish a barrier that prevents leakage of extracellular fluid between cells

Answer 64

Function like rivets, fastening cells together into strong sheets Intermediate filaments made of keratin anchor desmosomes in the cytoplasm Attach muscle cells to each other * Some muscle tears involve the rupture of desmosomes Also called *anchoring junctions*

Answer 65

Provide cytoplasmic channels from one cell to an adjacent cell; similar to plasmodesmata of plant cells Consist of membrance proteins that surround a pore and allow ions, sugars, amino acids, and other small molecules to pass Necessary for communication between cells in tissue such as the myocardium Also called *communicating junctions*

Answer 66

Views the membrane as a mosaic of protein molecules bobbing in a fluid bilayer of phospholipids Proteins are not randomly distributed in the membrane but are gropued in long-lasting specialized patches that carry out common functions

Answer 67

**Peripheral proteins-** bound to the surface of the membrane **Integral proteins-** penetrate the hydrophobic core * Integral proteins that span the membrane are called transmembrane proteins * The hydrophobic regions of an integral protein consist of one or more stretches of nonpolar amino acids, often coiled into alpha helices

Answer 68

1. Transport 2. Enzymatic activity 3. Signal transduction 4. Cell-cell recognition 5. Intercellular joining 6. Structural integrity

Answer 69

**Channel proteins-** provide a hydrophilic channel through the membrane that allow for the passage of certain molecules or ions * Many function as gated ion channels that open or close in response to stimulus * **Aquaporins-** speed the passage of water molecules; allow entry of up to 3 billion water molecules per second **Carrier proteins-** hold onto their passengers and change shape to ashuttle them across the membrane * Are specific to the substance that they are designed to transport * Allow for directionality of membrane permissibility * Some actively hydrolyze ATP to pump *against* a concentration gradient

Answer 70

The control of solute concentrations and water balance

Answer 71

When the membrane pulls away from the cell wall causing the plant to wilt; usually lethal

Answer 72

Oscillates between two shapes that result in the removal of **3 Na⁺** from the cell for every **2 K⁺** brought back into the cell

Answer 73

Voltage difference across a membrane Ranges from about –50 to –200 millivolts (mV)

Answer 74

Combination of two forces that drive the diffusion of ions across a membrane 1. **Chemical force**- the ion’s concentration gradient 2. **Electrical force-** the effect of the membrane potential on the ion’s movement

Answer 75

A transport protein that generates voltage across a membrane Help store energy that can be used for cellular work * The *sodium-potassium pump* is the major electrogenic pump of animal cells * The *proton pump* is the main electrogenic pump of plants, fungi, and bacteria cells * Actively transports protons _out_ of the cell

Answer 76

Occurs when active transport of a solute indirectly drives transport of other substances Couples the downhill diffusion of one solute to the uphill transport of another Plants use hydrogen ion gradient to drive nutrients

Answer 77

Secretion of certain molecules from the cell Transport vesicles migrate to the membrane, fuse with it, and release their contents outside the cell Many secretory cells use exocytosis to export their products The loss of membrane by exocytosis seems to be offset the addition of membrane via endocytosis

Answer 78

The cell takes in macromolecules by forming vesicles from the plasma membrane Small area of the plasma membrane sinks inward to form a pocket which gets pinched-off The addition of membrane by endocytosis seems to be offset by the loss of membrane via exocytosis Three types of endocytosis 1. *Phagocytosis* (cellular eating) 2. *Pinocytosis* (cellular drinking) 3. *Receptor-mediated endocytosis*

Answer 79

Continuous process in which the cell forms tiny vacuoles of extracellular fluid Cell obtains molecules dissolved in the droplets Nonspecific for the substances brought into the cell Parts of the membrance that form vesicles are lined with proteins on their cytoplasmic side; resulting vesicles are said to be *coated*

Answer 80

Specialized type of pinocytosis that enables the cell to acquire bulk quantities of specific substances that may not be highly concentrated in the extracellular fluid Proteins embedded in the membrane act as receptor cites exposed to the extracellular fluid and bind to specific solutes The receptor proteins then cluster in coated pits which form a vesicle containing the bound solutes After the vesicles are emptied, the receptors are recycled to the outter membrane by the same vesicle Binding of *ligands* to receptors triggers vesicle formation

Answer 81

Any molecule that binds specifically to a receptor site on another molecule

Answer 82

Energy cannot be created or destroyed, only transferred or transformed

Answer 83

Every energy transfer or transformation increases the entropy of the universe

Answer 84

The study of how energy flows through living organisms

Answer 85

The portion of a system's energy that can do work when temperature and pressure are uniform throughout the system

Answer 86

For a reaction to be spontaneous the change in Gibb's free energy must be negative As a reaction proceeds towards equilibrium the free energy decreases A system at equilibrium is at the lowest possible energy state for that system

Answer 87

Proceeds with a net _release_ of free energy and is **spontaneous** Magnitude of energy released represents the *maximum* amount of work that the reaction can perform

Answer 88

_Absorbs_ free energy from its surroundings and is **nonspontaneous** Magnitude of energy absorbed is the quantity of energy required to *drive* that reaction

Answer 89

The use of an exergonic process to drive an endergonic one

Answer 90

Phosphates are crowded together and their mutual repulsion contributes toward instability in that region; equivalent to a compressed spring Energy is released by the hydrolysis of the third phosphate group * Can drive endergonic reactions as long as the energy required to drive the reaction is less than the energy released by the hydrolysis of ATP Usually involves the phosphorylation: * Phosphate group covalently bonds to a recipient molecule called a **phosphorylated intermediate** * This phosphorylated intermediate is more reactive than the original unphosphorylated molecule

Answer 91

**Ribose-** five-sided monosaccharide **Adenine-** nitrogenous base **Triphosphate group-** chain of three phosphate groups bonded together

Answer 92

The ATP cycle is a revolving door in which energy passes from catabolic to anabolic pathways It couples energy yielding exergonic reactions to energy consuming endergonic ones ATP is regenerated by a dehydration reaction between ADP and a phosphate group

Answer 93

Intermediate chemical stage a reactant must reach prior to the formaion of a product Has a higher free energy than that of the initial reactants

Answer 94

The reactant that an enzyme acts on

Answer 95

1. Increase reaction rates by lowering the E_A requiredf 2. Form transient, reversible complexes with substrate molecules 3. Change the **rate** at which equilibrium is achieved, _not the position of the equilibrium_

Answer 96

An enzyme and substrate as a singular structure

Answer 97

**Template-** when there are two or more reactants the enzyme can provide a _template_ on which the substrates can come together in the proper orientation for a reaction to occur **Bond distortion-** the enzyme may stretch the substrate molecules toward their transition state by stressing and bending the chemical bonds, thus reducing the free energy required for the reaction **Proton transfer-** increases reactivity of substrate **Microenvironment-** the active site may provide a more conducive environment than the solution it is in for the reaction to take place **Electron transfer-** a brief covalent bond may form between the substrate and a side chain of an amino acid of the enzyme which is returned to its original state after completion

Answer 98

Nonprotein helpers for catalytic activity, often by functioning as electron acceptors May be permanently bound to the enzyme bind loosely and reversibly along with the substrate Called **prosthetic groups**, there are two main types: 1. Inorganic metals such as zinc, copper, or iron 2. **Coenzymes-** organic molecules often derived from vitamins

Answer 99

Under the Enzyme Commission (EC), enzymes are divided into six major classes based on general function: **O**ver **T**he **HILL** **O**xidoreductases **T**ransferases **H**ydrolases **I**somerases **L**ysases **L**igases

Answer 100

Substrate binding at the active site induces a conformational change in the shape of the enzyme The active site recognizes and binds to the substrate and activates it by providing the right environment for catalysis Called *substrate activation* which proceeds via several possible mechanisms In opposition to the "lock and key model" which viewed this interation as more static

Answer 101

1. The random collision of a substrate molecule with the active site results in it binding there 2. Substrate binding induces a conformational change that tightens the fit, facilitating the conversion of substrate into products 3. The products are then released from the active site 4. The enzyme molecule returns to the original conformation with the active site available for another molecule of substrate

Answer 102

Describes the quantitative aspects of enzyme catalysis and the rate of substrate conversion into products Reaction rates are influenced by factors such as the concentrations of substrates, products, and inhibitors

Answer 103

**Initial reaction velocity (*v*)-** rate of change in product concentration per unit time is dependent on: the _substrate concentration [S]_ * At low [S], doubling [S] will double *v* * As [S] increases though, each additional increase in [S] results in a smaller increase in *v* * When [S] becomes very large the value of *v* reaches a maximum

Answer 104

As [S] tends toward infinity, *v* approaches an upper limiting value; **maximum velocity (*V*_max)** *V*_max is an upper limit determined by: * The time required for the actual catalytic reaction * How many enzyme molecules are present The value of *V*_max can be increased by adding _more enzyme_ **Saturation-** the state where increasingly higher substrate concentrations will no longer increase the reaction velocity beyond a finite upper value

Answer 105

At very low [S], the initial velocity of the reaction is roughly proportional to [S]

Answer 106

At very high [S] the initial velocity of the reaction is independent of variation in [S] *V*_max is the velocity at saturating substrate concentrations

Answer 107

Shows that *K*_m is the specific substrate concentration at which the reaction proceeds at one half its maximum velocity

Answer 108

The lower the *K*_m value for a given enzyme and substrate, the lower the [S] range in which the enzyme is effective *V*_max is important, as a measure of the potential maximum rate of the reaction By knowing *V*_max, *K*_m, and the *in vivo* [S] we can estimate the likely rate of the reaction under cellular conditions

Answer 109

Enzymes are influenced (mostly inhibited) by products, alternative substrates, substrate analogs, drugs, toxins, and allosteric effectors The inhibition of enzyme activity plays a vital role as a control mechanism in cells Drugs and poisons frequently exert their effects by inhibition of specific enzymes

Answer 110

**Reversible inhibitors-** bind enzymes noncovalently and can dissociate from the enzyme **Irreversible inhibitors-** bind to the enzyme covalently; cause permanent loss of catalytic activity and are generally toxic to cells * Heavy metal ions, nerve gas poisons, some insecticides * Nerve agents block acetylcholinesterase which breaks down acetylcholine

Answer 111

Bind to the enzyme molecule outside of the active site Inhibit activity indirectly by causing a conformation change in the enzyme either by: * Inhibits substrate binding at the active site * Reduces catalytic activity at the active site

Answer 112

Bind the active site of an enzyme competing with substrate Enzyme activity is inhibited directly because active sites are bound to inhibitors which prevents the substrate from binding Can only be overcome by increasing the _substrate concentration_

Answer 113

**Allosteric regulation-** a protein's function at one site is affected by the binding of a regulatory molecule at a seperate site Allosteric enzymes have two conformations, one in which it has affinity for the substrate and one in which it does not May be an activator or inhibitor: * The binding of an **activator** to a regulatory site stabalizes the shape that has _functional_ active sites * The binding of an **inhibitor** to a regulatory site stabalizes the _inactive_ form of the enzyme

Answer 114

A substrate molecule binding to one active site in a multisubunit enzyme triggers a shape change in all subunits Increases catalytic activity at other active sites One substrate molecule thus primes an enzyme to act on additional substrate molecules more readily A kind of *allosteric activation*

Answer 115

Enzymes can be regulated by the addition or removal of chemical groups Activity is regulated by addition or removal of groups such as phosphate, methyl, or acetyl groups, etc The reversible addition of phosphate groups by protein kinases is a common covalent modification

Answer 116

Metabolic pathway is halted by the inhibitory binding of its own end-product to an enzyme that acts early in the pathway Prevents overproduction or overaccumulation of metabilic products

Answer 117

The reversible addition of phosphate groups by protein kinases is a common *covalent modification* **Phosphorylation-** occurs most commonly by transfer of a phosphate group from ATP to the hydroxyl group of Ser, Thr, or Tyr residues in a protein **Dephosphorylation-** the removal of phosphate groups from proteins; catalyzed by protein phosphatases

Answer 118

Glycogen phosphorylase exists as two inter-convertible forms * **Glycogen phosphorylase–a-** the active, phosphorylated form * **Glycogen phosphorylase–b-** the inactive non-phosphorylated form The enzymes responsible: * *Phosphorylase kinase* phosphorylates the enzyme * *Phosphorylase phosphatase* removes the phosphate

Answer 119

The activation of a protein by a one-time, irreversible removal of part of the polypeptide chain Proteolytic enzymes of the pancreas: trypsin, chymotrypsin, and carboxypeptidase are examples of enzymes synthesized in inactive form (*zymogens*) and activated by cleavage as needed

Answer 120

**G**ood **M**en have **R**egular **G**irl**F**riends **G**lucose **M**annose **R**ibose **G**alactose **F**ructose

Answer 121

Not all redox reactions involve the complete transfer of electrons Pure covalent bonds such as between C–H share electrons EQUALLY Oxygen being much more elctronegative “hogs" electrons Electrons are much closer to oxygen in CO₂ so the oxygen has partially gained the electrons, oxidizing the carbon Electrons thus lose energy and free energy is released

Answer 122

Mode of ATP synthesis where an enzyme transfers a phosphate group from a *substrate molecule* to ADP In contrast to oxidative phosphorylation which transfers an *inorganic* phosphate group **Substrate molecule** refers to an organic molecule that is generate as an intermediate during the catabolism of glucose

Answer 123

Glycolysis occurs in the *cytoplasm* and has two major phases 1. Energy investment phase- _consumes_ two ATP 2. Energy payoff phase- _yields_ four ATP, four NADH, and two pyruvate Glycolysis occurs whether or not O₂ is present

Answer 124

Harvesting of energy from glucose has three stages * **Glycolysis-** breaks down glucose into two molecules of pyruvate * **Citric acid cycle-** completes the breakdown of glucose * **Oxidative phosphorylation-** accounts for most of the ATP synthesis * The process that generates most of the ATP because it is powered by redox reactions * Almost 90% of the ATP generated by cellular respiration

Answer 125

_Intermediates_ **G**irls **G**et **F**ine **F**ood, **G**entlemen **D**ine **G**irl(*s*) 1. Glucose 2. Glucose 6-phosphate 3. Fructose 6-phosphate 4. Fructose 1,6-bisphosphate 5. Glyceraldehyde 3-phosphate (G3P) * Dihydroxyacetone phosphate (DHAP) * DHAP converts to *second* molecule of G3P _Enzymes_ **H**elen **P**aints **P**ictures **A**long **I**solated **T**rails 1. Hexokinase 2. Phosphoglucoisomerase 3. Phosphofructokinase 4. Aldolase 1. Isomerase- converts DHAP to G3P 5. Triose phosphate dehydrogenase- leads to energy payoff phase *Primary rate limiting enzymes highlighted in red*

Answer 126

_Intermediates_ **B**oys **P**refer to **P**ick-up **P**epperoni **P**izza 1. 1,3-Bisphosphoglycerate (BPG) 2. 3-Phosphoglycerate (PG) 3. 2-Phosphoglycerate (PG) 4. Phosphoenolpyruvate (PEP) 5. Pyruvate _Enzymes_ **P**retty **P**eople **E**njoy **P**arties 1. Phosphoglycerokinase 2. Phosphoglyceromutase 3. Enolase 4. Pyruvate kinase *Primary rate limiting enzymes are highlighted red*

Answer 127

Links glycolysis to the citric acid cycle Pyruvate is a charged molecule and must enter the mitochondria via active transport Pyruvate is converted to a compound called *acetyl CoA* in a series of three reactions catalyzed by several enzymes called the **pyruvate dehydrogenase complex** 1. Pyruvate's carboxyl group is already fully oxidized and is thus removed and given off as **one** molecule of CO₂ 2. Remaining two-carbon group is oxidized forming acetate 1. Extracted electrons are transferred to NAD⁺ forming one molecule of NADH 3. Coenzyme a (CoA) is attached via its _sulfur_ atom to the acetate forming acetyl CoA

Answer 128

**Pyruvate oxidation-** yields one NADH, one acetyl CoA, and one CO₂ as waste **Citric acid cycle-** yields one ATP, three NADH, one FADH₂, and two CO₂ as waste Inputs and outputs shown are for _each_ pyruvate molecule thus, each glucose molecule nets: * 2 ATP * 8 NADH * 2 FADH₂

Answer 129

Also called the *Krebs cycle*, completes the break down of pyruvate to CO₂ The citric acid cycle has eight steps, each catalyzed by a specific enzyme * The acetyl group of acetyl CoA joins the cycle by combining with oxaloacetate, forming citrate * The next seven steps decompose the citrate back to oxaloacetate, making the process a cycle The NADH and FADH₂ produced by the cycle relay electrons extracted from food to the electron transport chain

Answer 130

The ETC is in the *cristae* of the mitochondrion * Most of the chain’s components are proteins which exist in multiprotein complexes The carriers alternate reduced and oxidized states as they accept and donate electrons Electrons drop in free energy as they go down the chain and are finally passed to O₂, forming H₂O * The ETC generates no ATP directly

Answer 131

_Intermediates_ **C**an **I K**eep **S**elling **S**ex **F**or **M**oney **O**fficer? 1. Citrate 2. Isocitrate 3. *a*-Ketoglutarate 4. Succinyl CoA 5. Succinate 6. Fumarate 7. Malate 8. Oxaloacetate

Answer 132

_Enzymes_ **C**overt **A**tropian **I**nfidels **K**eep **S**tealing **S**uper **F**unny **M**emes 1. Citrate synthase 1. Inhibited by citrate and ATP 2. Aconitase 3. Isocitrate dehydrogenase- rate limiting 1. Inhibited by NADH 2. Stimulated by ADP and Ca²⁺ 4. *a*-ketoglutarate dehydrogenase 1. Inhibited by NADH, succinyl CoA, and acetyl CoA 2. Stimulated by Ca²⁺ 5. Succinyl CoA synthetase 6. Succiniate dehydrogenase 7. Fumarase 8. Malate dehydrogenase

Answer 133

PDH is allosterically _inhibited_ by: * ATP * NADH * acetyl CoA * High ATP:ADP ratio PDH is _activated_ by: * AMP * NAD⁺ * Free CoA * Low ATP:ADP ratio

Answer 134

1. **Flavoproteins-** have a prosthetic group called *flavin mononucleotide* (FMN) 2. **Iron-sulfur proteins-** family of proteins with both iron and sulfur tightly bound 3. **Ubiquinone (coenzyme Q)-** small hydrophobic molecule 1. Only enzyme in ETC that is NOT a protein 2. Is individually mobile within the membrane 3. Occur as large assemblies of proteins called *respiratory complexes* 4. **Cytochromes-** electron carriers between ubiquinone and oxygen 1. Prosthetic group called a *heme* group has an iron atom that accepts and donates electrons 2. Each cytochrome has a slightly different heme group 3. Last cytchrome *Cyt a₃* passes its electrons to oxygen which picks up a pair of hydrogen ions, forming water All enzymes except ubiquinone are proteins with prosthetic groups capable of being _reversibly_ oxidized and reduced

Answer 135

Gold arrows trace the transport of electrons which are finally passed to a terminal acceptor As the complexes shuttle electrons they pump protons from the mitochondrial matrix into the intermembrane space NADH deposits its electrons in complex I FADH₂ deposits its electrons via complex II which is at a lower energy level than complex I * Consequently, results in fewer protons pumped into the intermembrane space

Answer 136

The use of the energy in a H⁺ gradient to drive cellular work The H⁺ gradient results in a **proton-motive force** which drives H⁺ back across the membrane During chemiosmosis protons flow back down their gradient via *ATP sythase* In general terms chemiosmosis is an energy coupling mechanism that uses the proton-motive force to drive cellular work

Answer 137

Protein complex that functions as a mill powered by the proton-motive force Makes ATP from ADP and *inorganic* phosphates Multiple ATP sythases reside in eukaryotic mitochondrial and chloroplast membranes * Located in cellular membrane in prokaryotic cells **Dinitrophenol (DNP)** is known to uncouple ATP synthesis from electron transport * Allows protons to cross the membrane freely so that no proton gradient can be formed

Answer 138

_Per molecule of **glucose**_ **Glycolysis** * 2 ATP via *substrate-level phosphorylation* * 2 NADH * 2 Pyruvate **Pyruvate oxidation** * 2 NADH * 2 Acetyl CoA **Citric acid cycle** * 2 ATP via substrate-level phosphorylation * 6 NADH * 2 FADH₂ **Oxidative phosphorylation** * Roughly 26-28 ATP _Total ATP_ Maximum 30-32 ATP

Answer 139

Without oxygen glycolysis couples with anaerobic respiration or fermentation to produce ATP Anaerobic respiration uses an ETC with a final electron acceptor other than oxygen such as *sulfate* * Some sulfate-reducing marine bacteria use the sulfate ion at the end of their respiratory chain

Answer 140

Fermentation uses *substrate-level phosphorylation* instead of an ETC to generate ATP Consists of glycolysis plus reactions that regenerate NAD⁺ by transferring a hydride from NADH to pyruvate or derivatives of it Two common types: 1. **Alcohol fermentation-** pyruvate is converted to alcohol in two steps 1. The first releases CO₂ from the pyruvate which is converted to a two-carbon compound acetaldehyde 2. Acetaldehyde is reduced by NADH to ethanol, forming NAD⁺ 2. **Lactic acid fermentation-** method of fermentation used by human muscle cells when oxygen is scarce 1. Pyruvate is reduced directly by NADH to form lactate as an end product with no release of CO₂

Answer 141

Amino acids with _polar_ side chains **S**anta's **T**eam **C**rafts **N**ew **Q**uilts **Y**early S- serine- Ser T- threonine- Thr C- cysteine- Cys N- asparagine- Asn Q- glutamine- Gln Y- tyrosine- Tyr Santa's workshop IS near the North Pole

Answer 142

Amino acids with a _non-polar_ side chain **G**randma **A**lways **V**isits **L**ondon **I**n **M**ay **F**or **W**instons's **P**arty G- glycine- Gly A- alanine- Ala V- valine- Val L- leucine- Leu I- isoleucine- Ile M- methionine- Met F- phenylalanine- Phe W- tryptophan- Trp P- proline- Pro London is NOT near the North Pole

Answer 143

**D**ragons **E**at acid D- asparate E- glutamate *Asp*iring G*lu*ttons Also, suffix -*ate* associated with dragons *eating*

Answer 144

**K**nights **R**ide **H**orses K- lysine- Lys R- arginine- Arg H- histidine- His Knights riding horses in a very BASIC literary motif

Answer 145

Only carry out fermentation of anaerobic respiration Organisms cannot survive in the presence of oxygen

Answer 146

Species that can make enough ATP to survive by either fermentation or respiration Human muscle cells behave in a similar way * Under aerobic conditions pyruvate is converted into acetyl CoA and oxidation continues to the citric acid cycle * Under anaerobic conditions lactic acid fermentation occurs and pyruvate is diverted from the citric acid cycle to serve as an electron acceptor to recycle NAD⁺

Answer 147

Begins with peptide bond hydrolysis or **proteolysis** * Enzymes responsible for it are called *proteases* * Products are small peptides and free amino acids Free amino acids can be catabolized for energy * Amino group must first be removed via process of **deamination** * Nitrogenous refuse is excreted in the form of ammonia (NH₃) * Converted into intermediates of mainstream catabolism in as few steps as possible

Answer 148

Fats are highly reduced compounds that liberate more energy per gram upon oxidation than carbohydrates Triacylglycerol catabolism begins with their hydrolysis to glycerol and free fatty acids * The glycerol is channeled into the glycolytic pathway by oxidative conversion to dihydroxyacetone phosphate * Fatty acids are linked to coenzyme A to form fatty acyl CoA which is then degraded by **ß-oxidation**

Answer 149

Each cycle involves 1. Oxidation 2. Hydration 3. Reoxidation 4. Thiolysis The result is the production of one (1) FADH₂, one (1) NADH, and one (1) acetyl CoA **per cycle**

Answer 150

Begins with an activation step in the cytosol (FA-1) that requires the energy of ATP hydrolysis * **FA-1**⇢ drives the attachment of a CoA molecule to the fatty acid forming FA-1 The *fatty* acetyl CoA is then transported into the mitochondrion by a translocase in the inner membrane

Answer 151

**FA-2**⇢ An integral membrane *dehydrogenase* oxidizes the fatty acetyl CoA, forming a double bond between the α and ß-carbons * The two electrons and protons removed are transferred to FAD, forming FADH₂ **FA-3**⇢ water is added across the double bond by a *hydratase* **FA-4**⇢ another *dehydrogenase* oxidizes the ß-carbon, converting the hydroxyl group to a keto group **FA-5**⇢ the bond between the α and ß-carbons is broken by a *thiolase* and a two-carbon fragment is transferred to a second acetyl CoA The steps FA-2 to FA-5 are repeated until the original fatty acid is completely degraded * Most fatty acids have an even number of carbons and are completely degraded * Unsaturated fatty acids require one or two additional enzymes

Answer 152

Catabolic pathways funnel electrons from many kinds of organic molecules into cellular respiration Glycolysis accepts a wide range of carbohydrates Proteins must be digested to amino acids; amino groups can feed glycolysis or the citric acid cycle Fatty acids are linked to coenzyme A, to form fatty acetyl CoA which is then degraded by **β-oxidation**

Answer 153

Pyruvate and lactate are the most common starting materials Simple reversal of glycolysis using the same enzyme in both directions Gly-1, Gly-3, and Gly-10 are accomplished by other means * These are the most exergonic reactions of glycolysis

Answer 154

**Gly-10** * Pyruvate carboxylase (PC) * Phosphoenolpyruvate carboxykinase (PEPCK) **Gly-3** * Fructose 1,6-bisphosphatase (FBPase) **Gly-1** * Glucose 6-phosphatase

Answer 155

Control of catabolism is based mainly on regulating the activity of enzymes at strategic points in the catabolic pathway Feedback inhibition is the most common mechanism for metabolic control * If ATP concentration begins to drop respiration speeds up * When there is plenty of ATP respiration slows down