Chem 3511 Test 3

Front 1

What are cell receptors made of?

Back 1

Proteins

Front 2

What are ligands typically made of?

Back 2

Small molecules or peptides

Front 3

What is an agonist?

Back 3

A drug or chemical that can bind to a receptor to produce a physiologic reaction.

Front 4

What is an antagonist?

Back 4

A chemical substance that interferes with the physiological action of another, especially by combining with and blocking its nerve receptor.

Front 5

What is histamine? What does it do? When is it secreted?

Back 5

A His without the carboxylate group.

Binds to cell surface receptor.

Triggers immune response.

Secreted in response to an allergen.

Front 6

Name 2 types of extracellular signals, their class, source, and physiological function.

Back 6

Epinephrine, amino acid derivative, adrenal gland - prepares the body for action.

Growth hormone, Polypeptide, Pituitary gland - stimulates growth and metabolism

Front 7

Back 7

1. Protein Growth Factor/Hormone/Ligand

2. Ras*GDP/Monomeric G Protein OFF state

3. GAPs / GTPase activating proteins

4. Raf (Ser/Thr kinase)

5. MAPK (Mitogen-Activated Prtein Kinase)/ERK

6. Gene Expression

Front 8

Back 8

7. GPCR

8. G_alpha*GTP / G prtein alapha subunit with GTP (ON state)

9. Adenylate Cyclase

10. PKA / Protein kinase A

Front 9

Name 3 nuclear receptor ligand.

Back 9

Estrogen

progesterone

Testosterone

Glucocorticoids

Retinoic acid

Vitamin D

Thyroid Hormones

Front 10

Draw a hathworth projection of D-mannose

Back 10

?

Front 11

What is an epimer

Back 11

A single change in a stereocenter

Front 12

Of the 3 major cell surface signal transduction pathways, which has a single transmembrane helix?

Back 12

RTK linked to Ras (signaling/kinase cascade)

Front 13

Of the 3 major cell surface signal transduction pathways that we discussed, which has 3 second messengers?

Back 13

GPCR linked to PLC

(equivalently: GPCR linked to PKC, or PLC/PKC)

Front 14

What is an anomer?

Back 14

A chiral center that arises from cyclization (producing alpha- and beta- entantiomers called anomers)

Front 15

What is a ketose?

Back 15

?

Front 16

What is an aldose?

Back 16

?

Front 17

Lactose is a disaccharide of what 2 monomers?

Back 17

Galactose and glucose

Front 18

Sucrose is a disaccharide of what 2 monomers?

Back 18

Glucose and fructose

Front 19

Cellulose is a polymer of what monomers?

Back 19

glucose

Front 20

What is the function of cellulose?

Back 20

structural / Energy storage

Front 21

Name 2 ways that carbohydrates are conjugated to proteins.

Back 21

N-linked to ASN side chains or O-linked to Ser or Thr Side Chains.

Front 22

Name 2 functions of glycoproteins

Back 22

Major component of bacterial cell walls,

Bacterial surface for cell surface proteins,

in animal cells in membranes for cell-cell signaling,

Determins blod types,

Gives cartilage it's mechanical properties

Front 23

Draw the structure of palmitic acid

Back 23

CH3(CH2)14COOH

Front 24

Name and draw an omega-3 fatty acid

Back 24

Any fatty acid with a double bond at the third bond from the omega end. The one that was assigned for memorization is alpha-linolenic acid: CH3(CH=CHCH2)3(CH2)6COOH.

Front 25

What is the function of triacylglycerol?

Back 25

Energy storage

Front 26

What is the funciton of a glycerophospholipid?

Back 26

Membrane component (structural)

Front 27

Draw and label the core sturcture of cholesterol and steroids

Back 27

?

Front 28

Rank the melting poings of the following fatty acids:

Stearic acid, oleic acid, linoleic acid, docosanoic acid

Back 28

docosanoid acid>stearic acid>oleic acid>linoleic acid

Front 29

Describe the fluid mosaic model of biological membranes

Back 29

Protein "icebergs" floating in a sea of lipids (bilayer)

Front 30

What is amphipathic?

Back 30

?

Front 31

What type of molecules can form bilayers?

Back 31

?

Front 32

In what way do nuclear receptors differ from cell surface receptors in their action after they have bound their cognate ligand?

Back 32

Nuclear receptors are ligand-activated transcription factors, they directly regulate transcription whereas membrane receptors act indirectly by activating intermediary proteins triggering cascades of enzymatic activity.

Front 33

An equilibrium mixture of D-glucose contains 63% beta-D-glucopyraonse and 36% alpha-D-glucopyranose. There are trace amounts of 3 other forms. What are they?

Back 33

The open chain for, alpha-D-glucofuranose and beta-D-glucofuranose (analogous to possible forms of fructose)

Front 34

Although beta-D-glucopyranose is the predominant form of glucose in solution, crystalline glucose consists almost exclusively of alpha-D-glucopyranose. What accounts for this difference?

Back 34

The alpha anomer of glucose is less soluble than the beta anomer and therefore comes out of solution more readily. As it crystallizes, the beta-glucose remainin in solution interconverts with alpha-glucose thereby maintaining the 36% alpha- 63% beta equilibrium ratio. Thus the alpha anomer is continually generated and deposited in the crystal.

Front 35

Explain why a type AB individual can receive a transfustion of type A or type B blood, but a type A or B individual cannot receive a tranfustion of type AB blood.

Back 35

Type AB ind. have both type A and B carbohydrate sturcture on their cell surfaces, so they do not recongize either type A or B blood cells as forein. Consequendtly, they can receive either type A or B blood. Type A ind. synthesize antibodies to type B antigens, so transfused blood cells bearing the type B carbohydrate antigen will agglutinate the blood vessels and vice versa.

Front 36

Rank the melting poings of the following fatty acids:

cis-oleate, trans-oleate, linoleate

Back 36

trans-oleate>cis-oleate>linoleate

Front 37

Steroid hormones expert their physiological effects through what type of receptors?

Back 37

Nuclear receptors

Front 38

Cholesterol is commonly found in:

Back 38

Mammals

Front 39

What 2 compounds are combined to form sphingosine?

Back 39

serine and palmitate (palmitic acid)

Front 40

Why does the consuption of excessive amounts of vitamins D and A cause adverse health effects, whereas consumption of vitamin C well in excess of the recommened daily allowance generally not lead to toxicity?

Back 40

Vitamins A and D are lipid soluble and therefore accumulate in the fatty tissue. Vitamin C is water soluble and any excess is excreted in the urine.

Front 41

Spicy indian dishes flavored with hot peppers are often served with a side dish made from whole-milk yogurt. Why is a spoonful of yogurt preferable to a dring of water after a mouthful of spicy food?

Back 41

The spicy ingredient in the food is a powder made from peppers that contains the hydrophobic compound capsaicin. Yogurt containing whole milk also contains hydrophobic ingredients that con cleanse the palate of the irritating capsaicin. Water is polar, so it does not dissolve the capsaicin and cannot effectively cleanse the palate.

Front 42

How is a Protein Tyrosine Kinase turned on?

Back 42

ATP adds a phosphate group in place of the H on the OH.

Front 43

What is autophosphorylation?

Back 43

?

Front 44

How is receptor-ligand binding quantified?

Back 44

Plotting [RL]/[R]T vs [L] at the halfway point you can find Kl or affinity. In a plot of Bound/Free vs Bound the slope of the line is -1/Kl. The x intercept is Bmax and the y intercept is Bmax/Kl

Front 45

How does most signalling occur?

Back 45

alpha kinase cascades

G protein coupled receptors

Front 46

How many transmembrane alpha helicies does a g protein coupled receptor have?

Back 46

7

Front 47

What are the 3 G protein domains?

Back 47

Alpha - binds to GDP

Beta

Gamma

Alpha and Beta re covalently attached to lipids (anchored to plasma membrane)

Front 48

How does a G protein release GDP?

Back 48

Association of a G protein with a GPCR induces release of GDP and binding of GTP.

Front 49

What generates the second messenger cyclic AMP?

Back 49

Adenylate cyclase produces cAMP from ATP?

Front 50

What do kinases do in signal transduction?

Back 50

Use ATP to phosporylate substrates

Front 51

How are signalling pathways switched off?

Back 51

Phosphatases counteract kinases and break the P-O bond in cAMP to generate AMP.

Front 52

How does heterotrimeric G protein-dependent signaling work?

Back 52

Front 53

What drugs and toxins affect cell signalling ?

Back 53

Caffine: R=CH3, X =CH3

Theophylline R=H, X=CH3

Theobromine: R=CH3, X=H

Front 54

What is the ultimate result of a kinase cascade?

Back 54

Gene Expression

Front 55

What are emergent properties?

Back 55

Novel properties that arise when a certain level of structural complexity is formed from components of lower complexity.

Front 56

What are sugars formed from?

Back 56

CO2 and H2O

Front 57

What are monosacharides, disaccharides, and trisaccharides?

Back 57

1 sugar, 2 sugars linked by glycosidic bond, and 3 linked sugars.

Front 58

How are monosaccharides descirbed based on number of Cs in the molecule?

Back 58

Triose - 3 Carbons

Tetrose - 4 Carbons

Pentose - 5 Carbons

Hexose - 6 Carbons

Front 59

What are aldoses?

Back 59

Sugars made from aldehydes. An aldehyde is a Carbon double bonded to one organic group and one hydrogen.

Front 60

What are ketoses?

Back 60

Sugars made from ketones. A ketone is a Carbon double bonded to an O and 2 organic groups.

Front 61

How do you draw Fischer projections?

Back 61

1. Aldehyde or ketone at the top

2. Identify lowest chiral center in molecule

3. Classify configuration based on OH group

OH is on the right - D

OH is on the left - L

4. Most sugars in nature have the D configuration.

Front 62

What are isomers and epimers?

Back 62

Isomers - Different compounds that have the same chemical formula.

Epimers - Are sugars that differ only by the configuration around one carbon atom.

Front 63

What are enantiomers?

Back 63

Fischer projection about a mirror plane cannot be superimposed upon the other by rotation.

Front 64

Hathworth Projections

Back 64

Left is upwards.

Right is downwards.

Bottom OH -> O connects to first C.

Alpha - OH group is downward

Beta - OH group is upward

Front 65

3 Common disaccharides:

Back 65

Lactose: Galactose + Glucose

Sucrose: Glucose + Fructose

Maltose: Glucose + Glucose

Front 66

2 Types of polysaccharides:

Back 66

Glycogen: homopolysaccharide of glucose

Glycosaminoglycans: heteropolysaccharides

Front 67

What sort of bond does Lactose have?

Back 67

Beta 1-4 glycosidic bond

Front 68

What are the storage forms of glucose in plants and animals?

Back 68

Starch - Plants

Glycogen - Animals

Front 69

[T or F] Glycoproteins are proteins with covalently attached carbohydrates.

Back 69

T

Front 70

[T or F] Glycoproteins occur in all forms of life.

Back 70

T

Front 71

[T or F] Glycoproteins almost all secreted and membrane associated eukaryotic proteins are glycosylated.

Back 71

T

Front 72

[T or F] Glycoproteins glycosylation occurs more frequently than all other types of post-translational modification combined

Back 72

T

Front 73

[T or F] Glycoproteins vastly increases protein diversity.

Back 73

T

Front 74

[T or F] Glycoproteins complicates analysis of protein structure and function

Back 74

T

Front 75

[T or F] Glycoproteins glycosylation of proteins is not as well controlled as transcription or translation: microheterogenity

Back 75

T

Front 76

[T or F] Glycoproteins glycosylation can be N-linked or O linked

Back 76

T

Front 77

How are glycoproteins N-Linked?

Back 77

Through Asn.

?

Front 78

How are glycoproteins O-Linked?

Back 78

Through Ser or Thr

?

Front 79

What are some functions of glycoproteins?

Back 79

Plasma membrane for external surface for cell-cell signalling.
gives cartilage it's mechanical properties
Provides viscoelastic properties of mucus
Major component of bacterial cell walls
Bacterial surfaces for binding cell surface proteins
Many not understood

Front 80

What are the 3 types of membrane lipids?

Back 80

Phospholipids, Glycolipids, and Cholesterol

Front 81

What are lipids

Back 81

Biological molecules that are soluble in nonpolar solvents and poorly soluble in water.

Front 82

What are 4 classes of lipids?

Back 82

Fatty acids - triacylglycerols

Glycerophospholipids

Sphingolipids

Isoprenoids

Cholesterol

Front 83

What are fatty acids?

Back 83

Long chain hydrocarbons.

Polar Head Group: Carboxy acids

Nonpolar tail: Hydrocarbon chain - hydrophobic

Front 84

How do double bonds form in fatty acids?

Back 84

Trans - No kink

Cis - Kinked molecule

Front 85

How thick are lipid bilayers?

Back 85

60-100 A

Front 86

What drives lipid bilayer formation?

Back 86

Spontaneous

Hydrophobic effect drives formation

Front 87

What are biological membranes composed of and are they symmetric?

Back 87

Lipids, Proteins, and carbohydrates

Asymmetric: inside =/= outside

Front 88

Conventions for fatty acids:

Back 88

Multiple unsaturations occur every 3 bonds so they are not conjugated

x is the last double bond counting from the methy terminal (omega - w) end

Front 89

When are double bonds trans?

Back 89

All double bonds are cis unless they are produced by hydrogenation, "trans fats"

Partial hydrogenation

Front 90

What are the benefits of omega 3 fatty acids

Back 90

Decrease hypertension

Decrease depression

Decrease ADHD

Decrease rheumatoid arthritis

Boost immunity

Decrease negative side effects of omega-6 fatty acids

Front 91

What is a triglycerol composed of and what is their purpose?

Back 91

glycerol + fatty acids = triacylglycerol (=triglyceride)

Triacylglycerols function as energy reserves in animals. They are the most abundant class of lipids (but do not make up cellular membranes)

Front 92

What is an adipocyte?

Back 92

A cell that contains a fat gobule that occupies nearly the entire cell.

Highest energy density form of energy storage.

Front 93

What are glycerophospholipids and what is their major function?

Back 93

Phosphoglycerides

Major lipid components of biological membranes

Based on glycerol

Amphiphilic molecules with polar phosphoryl "heads" and nonpoal, aliphatic "tails"

Front 94

What do unsaturations do in fatty acids?

Back 94

Induce a rigid 30 degree bend

Decreases the melting point

Front 95

What are sphingolipids?

Back 95

Use a sphingosine instead of glycerol as a backbone.

Front 96

Where is sphingomyelin found?

Back 96

In the myelin sheath around nerves

Front 97

What are sphingolipids?

Back 97

Ceramindes with a phosphocholine or phosphoethanolamine moiety. Electrical insulation of nerve cells.

Front 98

What is a cerebroside?

Back 98

A sphingolipid with a monosaccharide head group

Front 99

How is cholesterol transported into tissues?

Back 99

By low density lipoproteins (LDLs) - "bad"

Front 100

How is cholesterol transported out of tissues?

Back 100

High density lipoproteins (HDLs) - "good"

Front 101

What does high cholesterol lead to?

Back 101

Heard disease

Atherosclerosis (plaque build up in the arteries)

Front 102

What vitamins are fat soluble?

Back 102

Vitamins A, D, E, and K - isoprenoid derivatives

Front 103

What vitabin requires sunlight for formation?

Back 103

Vitamin D

Front 104

What does vitamin E do?

Back 104

Acts as an antioxidant

Binds to biological membranes

Front 105

What does vitamin D allow for?

Back 105

Ca2+ absorption

Front 106

What does vitamin A do?

Back 106

Retinol plays a role in light reception in the eye.

Derives from beta-carotene (commonly found in carrots)

Front 107

What does vitamin K do?

Back 107

Plays a role in blood coagulation.

Front 108

What role does arachidonic acid play?

Back 108

Involved in pain and fever, blood pressure, blood coagulation, and reproduction.

Front 109

How do the rates of lateral and transverse diffusion differ?

Back 109

Rates of lateral diffusion is rapid

Transverse diffusion is very slow (flip-flop)

Front 110

What is the fluid mosiaic model?

Back 110

Integral membrane proteins float in a sea of lipids.

Front 111

What do glycosylphosphatidylinositol do?

Back 111

Associate in sphingolipid-cholesterol rafts on cell exterior

C-terminal linkage

Front 112

What is freeze fracture used for?

Back 112

To examine the proteins in a lipid bilayer

Front 113

What does Na, K-ATPase do?

Back 113

Allows for active transport.

Maintains different Na+ and K+ concentrations inside and outside of euk cells

Pumps Na+ out and K+ in

Front 114

What do ABC transporters do?

Back 114

Pump small molecules out of euk and prokaryotic cells.

Front 115

What are the characteristics of triacylglycerols?

Back 115

Nonpolar, water insoluble

Front 116

What molecules and structures are amphipathic?

Back 116

Micelles

Bilayers

Cholesterol

Front 117

Types of membrane transport systems:

Back 117

Uniport - One molecule in one directions.

Symport - Two molecules in one directions.

Antiport - Two molecules in opp. directions.

Front 118

Glucose Transport:

Back 118

Front 119

How does metabolism work?

Back 119

Front 120

Where does free energy come from?

Back 120

Hydrolysis of ATP

Front 121

What is the difference between ATP, ADP, AMP, and Adensosine?

Back 121

Front 122

What is the energy associated with ATP going to ADP and P?

Back 122

-30.5 Kj/mol

Front 123

What are "low-energy" phosphate compounds?

Back 123

Glucose-6-phosphate

Glycerol-3-phosphate

Front 124

What are "high-energy" phosphate compounds?

Back 124

Phsphoenolpyruvate

1,3-Bisphosperoglycerate

Phosphocreatine

Front 125

Delta relation at equilibrium:

Back 125

Delta G = -RT ln(Keq)

Front 126

How is acetyl CoA formed?

Back 126

Acetyl CoA is formed from the decarboxylation of pyruvate in a reaction that precedes the citric acid cycle

Front 127

What is produced in metabolism?

Back 127

CO2, H2O, ATP, and NH3

Front 128

What is glycolysis?

Back 128

Breakdown of glucose (C6) into 2 3C molecules (pyruvate)

Front 129

What is gluconeogenesis?

Back 129

Synthesis of glucose from molecules other than carbohydrates

Reverse of glycolysis

Front 130

What is glycogen?

Back 130

The storage form of glucose

Front 131

How many ATP are gained per each glucose?

Back 131

2 ATP

Front 132

How many NADH are produced per glucose?

Back 132

2 NADH

Front 133

What happens to cofactors in redox reactions?

Back 133

They are recycled.

Front 134

How many electrons does NADH carry?

Back 134

2

Front 135

How many electrons can FAD and FADH2 carry/donate?

Back 135

1 or 2

Front 136

How many electrons can Ubiquinone carry?

Back 136

1 or 2

Front 137

What is NADH used for?

Back 137

Generation of ATP
2.5 ATPs (from ADPs and Ps) in oxidative phosphorylation

Front 138

What is NADPH used for?

Back 138

Reductive biosynthesis (anabolic)

EAch FADH2 produces 1.5 ATPs i oxidative phosphorylation

Front 139

Acetyl-CoA facts:

Back 139

Contains high energy thioester - > high acetyl-group transfering potential

CoA can be charged with acyl groups other than acetyle

Uncharged CoA often written as CoA-SH to emphasize reactive thiol

Front 140

Glycolysis Step 1:

Back 140

Glucose is phosphorylated

Enzyme: Hexokinase

Classification: Transferase

ATP -> ADP

Forward only

Front 141

Glycolysis Step 2:

Back 141

G6P is isomerized

Enzyme: Phosphoglucose Isomerase

Classification: Isomerase

Front 142

Glycolysis Step 3:

Back 142

F6P is phosphorylated

Enzyme: Phosphofructokinase

Classification: Transferation

ATP -> ADP

Forward rxn only

Key regulation and rate determining step

Front 143

Glycolysis Step 4:

Back 143

F1, 6BP is cleaved

Enzyme: Aldoase

Classification: Lyase

Front 144

Glycolysis Step 5:

Back 144

DHAP is isomerized

Enzyme: Triose Phosphate Isomerase

Classification: Isomerase

Catalytically perfect

kcat/Km = 2.4X10^8 1/(Ms)

Front 145

Glycolysis Step 6:

Back 145

GAP is phosphorylated uniquely: NADH is formed

Enzyme: Glyceraldehyde 3-Phosphate Dehydrogenase

Classification: Oxidoreductase

2P + 2NAD+ -> 2NADH + 2H+

Front 146

Glycolysis Step 7:

Back 146

1,3-BPG is dephosphorylated; ATP is produced

Enzyme: Phosphoglycerate Kinase

Classification: Transferase

2ADP -> 2 ATP

Front 147

Glycolysis Step 8:

Back 147

3-PG is isomerized to 2-PG

Enzyme: Phosphoglycerase Mutase

Classification: Isomerase

Front 148

Glycolysis Step 9:

Back 148

2PG is dehydrated to form an enol

Enzyme: Enolase

Classification: Lyase - group elimination to form a double bond

-> 2 H2O

Front 149

Glycolysis Step 10:

Back 149

PEP is dephosphorylated to form pyruvate and ATP

Enzyme: Pyruvate Kinase

Classification: Transferase

Final step of glycolysis

Metabolic hub

2 ADP -> 2 ATP

2 Pyruvate

Front 150

Describe and emergent property and give one example:

Back 150

Novel properties that arise when a certain level of structural complexity is formed from components of lower complexity.

Matter giving rise to consciousnes

Front 151

Name 2 biological molecules that include isoprene as a precursor

Back 151

Vitamin D

Vitamin K

Front 152

What are the 2 types of high energy bonds in ATP

Back 152

Phosphoester

Phosphoanhydride

Front 153

From left to right, name the oxidized then reduced forms of NAD+

Back 153

NAD+, NADH

Front 154

From left to right, name the oxidized then the reduced forms of FAD

Back 154

FAD, FADH, FADH2

Front 155

Catabolism

Back 155

Process of breaking down molecules from complex to simple compounds

Front 156

Anabolism

Back 156

Process of building more complex molecules from simple compounds

Front 157

Meaning of DeltaGstd and DeltaG

Back 157

Delta G std - measure of how far eq. is from standard state.

Delta G - measure of how far given conditions are from eq.

Front 158

diff between normal and chem std state

Back 158

pH = 7.0 vs 0.0

[H+std] = 10^-7M, [OH-] = 10^-7M, [H2O] = 55.5 M vs 1 M for chem std state