Exam Ii, Chpt. 5-8, 12

Front 1

Vesicles

Back 1

Small membrane enclosed sacs that transport substances

Front 2

Endomembrane system

Back 2

Nuclear envelope, Endoplasmic reticulum, Go.gi apparatus, lysosomes, plasma membrane, and the vesicles that move between these organelles

Front 3

Exocytosis

Back 3

A way for a vehicle to empty its contents to the extra cellular space

Front 4

Endocytosis

Back 4

When a vehicle buds off from the plasma membrane, bringing with it material from outside the cell

Front 5

Nuclear envelope

Back 5

Defines boundary of the nucleus, regulates which molecules move in and out of the cell, nuclear pores allow for inward and outward movement of RNA and other necessary molecules

Front 6

ER lumen

Back 6

Interior of the ER, the ER can be large or small depending on how much protein the cell secretes, within, quaternary structure is stabilized and disulfide bonds form, N linked glycosylation

Front 7

rough ER

Back 7

Associated with ribosomes, ribosomes can either be free in the cytosol or be associated with the ER

Front 8

smooth ER

Back 8

Lacks ribosomes, used to bud off and form vesicles, also the site of fatty acid and phospholipid biosynthesis - this type of ER dominates in cells that are specialized for lipid production - cholesterol, hormones

Front 9

The Golgi Apparatus

Back 9

Further modifies proteins and lipids, sorting station, carbohydrates of the cell are synthesized here, cis to medial to trans Golgi

Front 10

Cisternae

Back 10

Series of flattened membrane sacs that make up the Golgi Apparatus

Front 11

Glycosylation

Back 11

Occurs in the ER (N linked) and Golgi Apparatus, sugars are covalently linked to lipids or specific amino acids of proteins, the attached sugars can protect the protein from enzyme digestion by blocking access to the peptide chain

Front 12

Movement from Golgi to ER

Back 12

Retrieve proteins that are accidentally moved forward, retrograde transport

Front 13

Lysosomes

Back 13

Specialized vesicles derived from the Golgi Apparatus that degrade damaged or unneeded macromolecules, Golgi apparatus also delivers proton pumps and other proteins needed by the lysosome to maintain pH conditions and to break down molecules

Front 14

Protein sorting

Back 14

Process by which proteins end up where they are needed to perform their functions

Front 15

How are proteins from free ribosomes sorted to their destinations?

Back 15

Start off in the cytosol and sorted after translation, signal sequences direct the protein to their cellular compartment, proteins with no signal sequence stay in the cytosol

Front 16

Most proteins with a signal sequence are targeted to...

Back 16

Mitochondria or chloroplasts

Front 17

Nuclear localization signal

Back 17

Signal sequence for the nucleus, enables proteins to move through pores in nuclear envelope, located internally

Front 18

How do proteins from non free ribosomes, get to their destinations?

Back 18

They are sorted as they are translated, signal recognition particle - RNA-protein complex that threads the polypeptide chain through, into the ER lumen

Front 19

Proteins that remain in the ER membrane...

Back 19

Have a signal anchor sequence in their interiors, these transmembrane proteins may end up in plasma membrane as pumps, channels, etc. Carboxyl end is on cytosol side and amino side is in ER lumen

Front 20

Gel electrophoresis

Back 20

Electric current passed through a gel and DNA molecules move towards positive end, smaller DNA strands go through the gel further

Front 21

Non secretory proteins

Back 21

Stay in the cell, go to nucleus, mitochondria, cytoplasm

Front 22

Secretory proteins

Back 22

Proteins that go out into the environment

Front 23

Tay Sachs disease

Back 23

No creation of enzymes to break down lysosomal products

Front 24

Pulse chase experiments

Back 24

Proteins labeled briefly, then labeling is stopped and can see where the cells you labeled, go - more work than just continuous pulsing

Front 25

Autoradiography

Back 25

Normal processes continue, but now radioactive

Front 26

Metabolic labeling

Back 26

Sample denatured, all proteins coated in S-Met (unless disulfide bonds), cells broken up, immuno precipitation to get proteins you want, mixture loaded into gel and proteins separate by size

Front 27

Experimental Methods

Back 27

Look at notes

Front 28

Phototrophs

Back 28

Obtain energy from the sunlight (plants)

Front 29

Chemotrophs

Back 29

Derive energy from organic molecules like glucose (animals)

Front 30

Autotrophs

Back 30

Make their own organic sources of carbon (plants)

Front 31

Heterotrophs

Back 31

Rely on other organisms for carbon

Front 32

Metabolism

Back 32

Entire set of chemical reactions that convert molecules into other molecules and transfer energy in living organisms

Front 33

Catabolism and Anabolism

Back 33

C - break down of molecules to produce ATP

A - creation of molecules from smaller units that uses ATP

Front 34

Food contains what type of energy?

Back 34

Chemical energy, a type of potential energy

Front 35

First Law of Thermodynamics

Back 35

Law of conservation of energy

Front 36

Second Law of Thermodynamics

Back 36

Amount of disorder is always increasing (entropy)

Front 37

Gibbs' free energy

Back 37

Amount of energy available to do work

Front 38

Exergonic

Back 38

- delta G, occurs spontaneously

Front 39

Endergonic

Back 39

Requires an energy input, + delta G

Front 40

Enthalpy (H)

Back 40

Total amount of energy

Front 41

Delta G =

Back 41

Delta H - T * delta S

Front 42

Energetic coupling

Back 42

A spontaneous reaction drives a non spontaneous one with its thermodynamic driving force

Front 43

Enzymes

Back 43

Proteins that catalyze reactions

Front 44

Transition state

Back 44

Intermediate stage between reactants and products, highly unstable and has great free energy

Front 45

Activation energy

Back 45

Energy input required to reach the transition state

Front 46

How do enzymes work?

Back 46

They stabilize the transition state, the substrate forms a complex with the enzyme and is converted to product, R groups are sources for protons from the substrate

Front 47

Active site

Back 47

Portion of the enzyme that binds the substrate and converts it to product, size is very small

Front 48

So why are enzymes so large?

Back 48

The amino acids from the enzyme are very spaced out and come together to form the active site

Front 49

Are enzymes specific?

Back 49

Yes, they catalyze only one or a very limited number of reactions, can discriminate between structures and bond types

Front 50

Inhibitors

Back 50

Decrease enzyme activity

Front 51

Activators

Back 51

Increase enzyme activity

Front 52

Irreversible inhibitors

Back 52

Form covalent bonds with enzymes and permanently inactivate them

Front 53

Reversible inhibitors

Back 53

Form weak bonds with enzymes and easily dissociate

Front 54

Competitive inhibitors

Back 54

Bind to the active site and prevent the substrate from binding, structurally similar to the substrate, reduce the enzyme's affinity for the substrate, but can be overcome by increasing the substrate concentration, maximum rate of reaction remains the same

Front 55

Non-competitive inhibitors

Back 55

Bind to enzyme at site other than the active one, slows down the reaction by altering the enzyme's shape and reducing its activity, maximum rate of reaction is different

Front 56

Allosteric enzyme

Back 56

Binds to activators and inhibitors at sites other than active site and results in a change in shape and activity of an enzyme, depending on concentration of substrate (negative feedback), most common non competitive inhibitor

Front 57

Cofactor

Back 57

A substance that associates with an enzyme and plays a key role in its function (ex. iron, magnesium, metal ions)

Front 58

Does temperature increase lessen activation energy?

Back 58

Yes

Front 59

So, why don't we just increase temperature to catalyze reactions in the body?

Back 59

Not good for us, non specific, whole body will get heated

Front 60

ATP hydrolysis

Back 60

Exergonic, create ADP and a phosphate group, less energy than ATP and water

Front 61

Cellular respiration

Back 61

A series of catabolic reactions that conver energy stored as fuel molecules to ATP, can occur in presence of oxygen (aerobic respiration) or not in the presence of oxygen (anaerobic respiration)

Front 62

Glycolysis

Back 62

Break down of glucose to make pyruvate, takes place in cytoplasm, anaerobic

Front 63

Why do reduced molecules have so much energy?

Back 63

The further away electrons are from the nucleus, the more potential energy they have

Front 64

Electron transport chain (basic definition)

Back 64

Used to extract energy from fuel molecules like glucose or sunlight, NADH and FADH2

Front 65

Substrate level phosphorylation

Back 65

A phosphate group is transferred from an organic compound to ADP, only accounts for a small amount of ATP

Front 66

Glycolysis (more specific)

Back 66

Glucose (6C) -> phosphorylated -> 2 3C compounds, only one can be broken down, other rearranges to form the degradable one -> Pyruvate - net gain 2 ATP and 2 NADH

Front 67

After glucose is phosphorylated in the cell, can it leave the cell?

Back 67

No, the channels for glucose will not accept phosphorylated glucose

Front 68

What is the next step in cell respiration, after glycolysis?

Back 68

The 2 Pyruvates are transported to the mitochondrial matrix, where they are converted to acetyl-CoA with O2, releasing 2 CO2 and 2 NADH in the process

Front 69

The Citric Acid Cycle (basic definition)

Back 69

Fuel molecules completely oxidized, chemical energy in acetyl-CoA is transferred to ATP by substrate level phosphorylation and to the electron carriers, takes place in mitochondrial matrix

Front 70

Citric Acid Cycle (more specific)

Back 70

Cycle because oxaloacetate is reformed at the end, 4 C molecule end product because 2 CO2 are formed, overall, 2 acetyl-CoA produced from 1 glucose yield 2 ATP, 6 NADH, 2 FADH2

Front 71

Electron transport chain

Back 71

Electrons passed from high energy FADH2 and NADH to O, the final electron acceptor, the electrochemical gradient created by the electrons and the protons brought out from solution in the mitochondrial matrix to the intermembrane space, drives the final conversion of ADP to ATP, through the ATP synthase - O is reduced by the electrons to form water - oxidative phosphorylation

Front 72

ATP synthase

Back 72

Enzyme through which protons flow, this flow causes the synthase to rotate and this rotational mechanical energy is converted into the chemical energy of ATP

Front 73

Overall amount of ATP produced by the complete oxidation of glucose

Back 73

32 ATP

Front 74

Fermentation

Back 74

An anaerobic metabolic process in which pyruvate can be broken down, used by organisms that have no access to oxygen and by aerobic organisms when oxygen cannot be delivered fast enough, yields 2 ATP

Front 75

Lactic acid fermentation

Back 75

Used by animals and bacteria, electrons from NADH are transferred to pyruvate to produce lactic acid and NAD+, cyclical, no net gain of NADH

Front 76

Ethanol fermentation

Back 76

Occurs in plants and fungi, Pyruvate converted to Acetaldehyde to Ethanol, NADH -> NAD+

Front 77

Anaerobic respiration

Back 77

Occurs in some bacteria, sulfate or nitrate is the final electron acceptor instead of oxygen

Front 78

Glycogen

Back 78

Storage form of glucose in animals

Front 79

Starch

Back 79

Storage form of glucose in plants

Front 80

This organ is the central storage center in the body

Back 80

The liver

Front 81

What happens when glucose from glycogen is needed for use?

Back 81

One glucose is cleaved and 3 ATP are produced by glycolysis since the first step of glycolysis that requires 1 ATP is bypassed

Front 82

This type of fat is common and stored in fatty tissue

Back 82

Triacylglycerol

Front 83

Beta oxidation

Back 83

Fatty acids are shortened, releasing NADH and FADH2 molecules, yields a huge amount of ATP

Front 84

Metabolic pathways in exercise

Back 84

First few minutes of a run: muscles convert stored glycogen to glucose, lactic acid fermentation occurs, Sustained running: aerobic respiration ATP used, Even longer exercise: liver supplies glycogen, fatty acids broken down via beta oxidation

Front 85

ATP produced by FADH2 and NADH

Back 85

about 2 and 3 respectively

Front 86

Chloroplasts

Back 86

Enclosed by a double membrane, with a third folded membrane called the thylakoid membrane which includes the electron transport chain

Front 87

Lumen (chpt. 8)

Back 87

Fluid filled interior of the thylakoid membrane

Front 88

Stroma

Back 88

Region surrounding the thylakoid membrane

Front 89

Three steps of the Calvin Cycle

Back 89

Carboxylation, Reduction, and Regeneration

Front 90

Carboxylation

Back 90

CO2 added to RuBP (5C sugar), catalyzed by rubisco, 6C compound broken down into 3 PGA

Front 91

Reduction

Back 91

ATP used to phosphorylate 3 PGA, NADPH transfers 2 high energy electrons to the phosphorylated compound, glyceraldehyde 3-phosphate produced (GAP)

Front 92

Regeneration

Back 92

RuBP is regenerated, triose phophates were produced (only one can leave the Calvin Cycle)

Front 93

Absorption of light energy by cholorphyll

Back 93

Absorbed light energy is transferred from chlorophyll to chlorophyll until the reaction center is reached, where the light energy is converted to electron transport (oxidized), activates photosynthetic electron transport chain

Front 94

Z scheme

Back 94

Photosynthetic electron transport chain, absorption of light energy by Photosystem II energizes electrons pulled from water, allowing them to enter the transport chain, occurs again with Photosystem I so electrons have enough energy to reduce NADP+

Front 95

Net energy gain from photosynthesis

Back 95

9 ATP, 6 NADPH

Front 96

Grana

Back 96

Stacks of thylakoid membrane sacs

Front 97

What kinds of cells would you expect to have a large smooth ER?

Back 97

Ones that produce a lot of lipids