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Biochemistry Flashcards

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1
Q

Nonpolar amino acids

A

Alanine, glycine, valine, leucine, isoleucine, methionine, proline

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2
Q

Aromatic amino acids

A

Tryptophan, phenylalanine, tyrosine

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3
Q

Polar amino acids

A

Serine, threonine, asparagine, glutamine, cysteine

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4
Q

Negatively charged amino acids

A

Aspartate, glutamate. They are acidic

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5
Q

Postively charged amino acids

A

Lysine, arginine, histidine. They are basic

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6
Q

Peptide bond formation

A

A dehydration reaction in which the electrophilic carbonyl carbon of one amino acid is attacked by the nucleophilic amino group of a second amino acid

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7
Q

Primary structure

A

Sequence of amino acids. Stabilized by peptide bonds

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8
Q

Secondary structure

A

Local structure of neighboring amino acids. Stabilized by H-bonding. Common examples: alpha-helices (CCW), beta-pleated sheets (can be parallel or antiparallel)

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9
Q

Effect of proline on secondary structure

A

Disrupts secondary structure with its rigid cyclic structure

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10
Q

Tertiary structure

A

3D shape of protein governed by hydrophobic interactions. Ex: disulfide bonds occur when two cysteine molecules are oxidized

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11
Q

Quaternary Structure

A

Interaction between peptides in proteins that contain multiple strands

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12
Q

Conjugated proteins

A

Proteins that have prosthetic groups, which may be a metal ion, vitamin, lipid, carb or nucleic acid

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13
Q

Lyases

A

Catalyze cleavage without addition of water and without the transfer of electrons. May also be known as synthases performing the reverse of synthesis

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14
Q

a-ketoglutarate + aspartate

A

Catalyzed by aminotransferase. Forms oxaloacetate and glutamate. A reaction of protein metabolism

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15
Q

Ligases

A

Catalyze addition or synthesis reaction between large, similar molecules. Often use ATP

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16
Q

Apoenzymes

A

Enzymes that require cofactors to function, but currently do not have their cofactor

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17
Q

Holoenzymes

A

Enzymes that contain their necessary cofactors

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18
Q

Cofactors and Coenzymes (and the difference)

A

Nonprotein molecules that some enzymes require for function. Cofactors: inorganic molecules/metal ions, often ingested as dietary minerals. Coenzymes: small organic groups that are mainly vitamins/derivatives of vitamins (NAD+, FAD, and CoA)

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19
Q

Water-soluble vitamins

A

B complex vitamins, vitamin C

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20
Q

Fat-soluble vitamins

A

A, D, E, K

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21
Q

B-complex vitamins

A

Water-soluble. Thiamine, riboflavin, niacin, pantothenic acid, pyridoxal phosphate, biotin, folic acid, cyanocobalamin

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22
Q

Prosthetic groups

A

Covalently bound cofactors or coenzymes. May be organic or inorganic

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23
Q

Hill’s coefficient >1

A

Indicates positive cooperative binding takes place between substrate and enzyme

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24
Q

Hill’s coefficient < 1

A

Indicates negative cooperative binding between enzyme and substrate

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25
Q

Hill’s coefficient = 1

A

Indicates that no cooperative binding occurs

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26
Q

Feedback regulation

A

Regulation of an enzyme by products further down the given pathway

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27
Q

Types of Reversible Inhibition

A

Competitive, noncompetitive, mixed, and uncompetitive

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28
Q

Competitive inhibition

A

Inhibitor binds to the enzyme at the active site.

K_m appears to increase, V_max stays the same

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29
Q

Noncompetitive Inhibition

A 
Inhibitor binds to an allosteric site, which conformationally changes the active site. Binds well to both enzyme and enzyme-substrate complex. Cannot be overcome by adding more substrate.
K_m remains (because non-altered enzymes still function)
v_max decreases
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30
Q

Mixed Inhibition

A

Occurs when an enzyme can bind at an allosteric site to an enzyme OR an enzyme-substrate complex with different affinities for each.
If inhib binds better to enzyme, then K_m increases, but if it binds better to E-S complex, then K_m decreases.
In both cases, v_max decreases

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31
Q

Uncompetitive Inhibition

A

Inhibitor only binds the E-S complex and locks the substrate in, preventing its release and disabling the enzyme from performing its duty.
Both K_m and v_max decrease.
On L-B plot, the lines for with and without this inhib are parallel

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32
Q

Irreversible inhibition

A

Changes to the active site are permanent. Prime drug mechanism. Ex: aspirin

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33
Q

Mechanism of Aspirin

A

Irreversible inhibition of cyclooxygenase-1 in that it can no longer bind arachidonic acid to produce prostaglandins. Prostaglandins usually modulate pain and inflammatory response. The body must synthesize new cyclooxygenase-1

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34
Q

Glycosylation of Enzymes

A

Covalently tags an enzyme for transport within the cell or modifies protein activity and selectivity

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35
Q

Zymogens

A

Inacitve forms of enzymes that are activated when the enzyme is needed. Ex: trypsinogen is the zymogen of trypsin

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36
Q

Collagen

A

Main protein of the ECM. Has a trihelical structure (a helix made up of 3 helices). Provides strength and flexibility

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37
Q

Elastin

A

Also found in ECM. Responsible for stretch and recoil of tissues

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38
Q

Keratins

A

Intermediate filament proteins found in epithelial cells. Make up hair and nails. Aid in mechanical integrity of cells and have regulaotry functions

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39
Q

Motor proteins

A

ATPases that power conformational changes necessary for motor function. Interact with either actin (myosin) or microtubules (kinesin, dynein). Responsible for cellular movement and muscle contraction

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40
Q

Kinesin

A

Brings vesicles towards the positive end of microtubules. Ex: brings full vesicles of NTs to the membrane of pre-synaptic cell for release. Key roles in chromosome alignment during metaphase and depolymerizing MTs during anaphase of mitosis.

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41
Q

Dynein

A

Brings vesicles toward negative end of microtubules. Involved in the sliding movement of flagella and cilia. Bring vesicles of waste/recycled NTs towards the soma

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42
Q

Binding Proteins

A

Transport/sequester molecules by binding to them, increasing stability. Include Hb, Ca-binding proteins, DNA binding proteins, and more

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43
Q

Cell Adhesion Molecules (CAMs)

A

Proteins found on the surface of cells that help the cell bind to ECM or to other cells. 3 classes: cadherins, integrins, and selectins

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44
Q

Cadherins

A

Type of CAM. Glycoproteins. Mediate Ca-dependent cell adhesions. Often hold similar cell types together.

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45
Q

Integrins

A

Type of CAM. Have two membrane-spanning channels: alpha and beta, are essential to communicating/binding with ECM. Play an important role in cell signaling and may help promote cell division or apoptosis, also help with WBC migration and clotting

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46
Q

Selectins

A

Type of CAM. Bind to carbohydrates that originate on other cell surfaces. Weakest form of CAM. Expressed on WBCs and endothelial cells of blood vessels. Important role in inflammation and WBC migration

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47
Q

Immunoglobins

A

AKA antibodies. Work by neutralizing targets in the body like toxins and bacteria, then recruit other cells to help do away with the threat. Each only bind to one antigen at their unique antigen-binding regions (located at the tips of their “Y” structures)

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48
Q

Three possible outcomes of antibody binding to antigen

A
  1. Neutralization (making antigen unable to exert its effect)
  2. Opsonization (marking antigen for destruction by other WBCs)
  3. Agglutination (clumping of the antigen+antibody into large complexes that will be phagocytosed by macrophages)
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49
Q

The 3 main types of G-proteins (and their functions)

A

G_s: stimulates adenylate cyclase, increases cAMP levels
G_i: inhibites adenylate cyclase, decreases cAMP levels
G_q: activates phosphlipase C -> cleaves phosphlipid from membrane to form PIP2, PIP2 gets cleaved into DAG and IP3, IP3 can open Ca-channels of ER, increasing Ca2+ levels in cell

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50
Q

GPCR mechanism of activation

A

Ligand binds to GPCR -> engages G protein -> GDP gets replaced by GTP -> alpha subunit dissociates -> alpha activates adenylate cyclase -> affects levels of cAMP depending on s vs i

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51
Q

Receptor tyrosine kinases

A

Enzyme-linked receptors. Composed of a monomer that dimerizes upon ligand-binding. The dimer then self-phosphorylates AND phosphorylates other enzymes

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52
Q

Electrophoresis

A

Subjects compounds to an electric field for separation. Negatively charged compounds migrate toward positively charged anode. Positively charged compounds migrate to negatively charged cathode. Polyacrylamide gel is the standard medium for proteins

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53
Q

Native PAGE

A

Polyacrylamide gel electrophoresis = PAGE. Analyzes proteins in their native states. Good for comparing molecular size or charge of proteins (better than SDS PAGE or size exclusion chromatography)

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54
Q

SDS-PAGE

A

Usefule for separating proteins based only off size. SDS disrupts all noncovalent interactions, binds to all proteins, and creates a large chain with net negative charges

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55
Q

Isoelectric Focusing

A

Separation of proteins based on pI. Gel has a pH gradient. Anode (+) is acidic , cathode (-) is basic. The protein stops moving when it reaches a portion of the gel wher ethe pH is equal to its pI

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56
Q

Column Chromatography

A

Adsorbent/stationary phase: silica or alumina beads. Separation basedon size and polarity. Less polar compounds have shorter retention times because they interact only weakly with beads

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57
Q

Ion-exchange chromatography

A

Column chromatography, except the beads are coated with a charged substance

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58
Q

Protein structure identification methods

A

X-Ray Crystallography, NMR. X-Ray is more common and reliable

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59
Q

Edman Degradation

A

Sequential digestion of proteins with specific cleavage enzymes in chunks of up to 50-70 amino acids. Removes N-terminal amino acid(s) that can then be run throughmass spec

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60
Q

Concentration Determination of Proteins

A

Method: spectroscopy. UV-spectroscopy is possible because proteins contain aromatic side chains. Also can be performed using colorimetric changes (BCA assay, Lowry reagent assay, Bradford protein assay)

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61
Q

Bradford Protein Assay

A

Measures protein concentration using color. The more blue the dye, the higher the concentration of protein. Most useful when there is only one type fo protein in the solution. Limited by presence of a detergent or excessive buffer

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62
Q

Migration velocity (proteins in PAGE)

A

v = E*z/f

E: electric field strength

z: net charge on the molecule
f: frictional coefficient

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63
Q

Equation to determine the number of stereoisomers with same C-backbone

A

= 2^n, where n is the number of chiral centers

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64
Q

The only stable cyclic carbohydrates

A

Pyranose rings (6 mem) and furanose rings (5 mem)

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65
Q

Anomeric Carbon

A

Carbon in a carbonhyrate that is the carbonyl C in straight-chain form

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66
Q

Anomers

A

alpha and beta forms of cyclized carbs. Alpha form has anomeric OH group trans to the CH2OH group. Beta form has anomeric OH group cis to the CH2OH group

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67
Q

Converting Fischer to Haworth projections

A

Any groups on the right in Fischer will point down in the Haworth projection.

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68
Q

Mutarotation

A

Spontaneous change in configuration between alpha and beta anomers. Can be sped up by addition of acid or base catalyst.

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69
Q

Dominant anomer of glucose (and reason)

A

beta anomer - because in alpha configuration the anomeric OH group is axial, which increases steric strain (decreases stability)

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70
Q

Aldonic acids

A

Aldoses that have been oxidized into carboxylic acids

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71
Q

Reducing sugar

A

Any monosaccharide with a hemiacetal ring (because they can be oxidized, therefore reducing another species)

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72
Q

Lactone

A

A cyclic ester with a carbonl group present on the anomeric C. Results when an aldose is oxidized in ring form.

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73
Q

Reagents used to detece the presence of reducing sugars

A

Tollens’ reagent and Benedict’s reagent

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74
Q

Tollen’s reagent

A

Freshly prepared [Ag(NH3)2]+. Produces a silvery mirror when aldehydes are present.

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75
Q

Benedict’s reagent

A

Indicates the presence of aldehydes when a red precipitate of Cu2O forms

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76
Q

Conversion of a ketose to carboxylic acid

A

Begins with keto-enol shift: tautomerization into an aldose under basic conditions. Aldose is then reacted with Tollens’ of Benedict’s reagent to form carb acid

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77
Q

Alditol

A

A former aldose that has been reduced to an alcohol

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78
Q

Glucokinase

A

Enzyme in the liver and pancreatic beta-islet cells that catalyzes phosphate esterification formation on glucose (ie phosphorylating glucose)

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79
Q

Glycosides (and how they are formed)

A

A form of acetal. Anomeric OH group on a hemiacetal is transformed into an alkoxy group (ether). Reaction of a hemiacetal and an alcohol. Formation is a dehydration reaction

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80
Q

Glycosidic bonds

A

Bonds between monosaccharides in di/polysoaccharides. Formed in the formation of glycosides.

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81
Q

Maltose

A

Disaccharide of two glucose molecules linked by alpha(1->4) linkage

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82
Q

Sucrose

A

Glucose-a-1,2-fructose. Disaccharide

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83
Q

Lactose

A

Galactose -beta-1,4-glucose. Disaccharide

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84
Q

Cellulose

A

Homopolysaccharide of glucose. Linkages: beta-1,4. Main strucutral component of plants. Humans cannot digest it because we lack cellulase, so it is a good source of fiber - draws water to the gut.

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85
Q

Starches

A

Alpha-D-glucose monomers. More digestable by humans.

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86
Q

Amylose vs Amylopectin

A

Both are starches. Amylose is linear. Amylopectin is branched, leading to a helix conformation. Iodine is often used to detect presence of amylose because it associated with the helical structure, forming a starch-iodine complex

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87
Q

Glycogen

A

glucose-alpha-1,4 polymer. Carbohydrate storage in animals. Highly branched (alpha1-6 linkages) –> makes it highly soluble in solution.

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88
Q

Glycogen phosphorylase

A

Cleaves glucose from the nonreducing end of glycogen branch and phosphorylates the freed monomer. Produces glucose-1-phosphate

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89
Q

Phospholipids

A

All contain a polar head group (a phosphate and an alcohol) attached to at least one hydrophobic fatty acid tail by a phosphdiester linkage

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90
Q

Link between polar head and nonpolar tail(s) in phospholipids

A

Phosphodiester linkages

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91
Q

Phosphoglycerides

A

AKA: glycerophosphlipids. Phospholipids with glycerol backbones. Two fatty acids are bound to the backbone by ester linkages

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92
Q

Sphingolipids

A

Phospholipids with sphingosine backbones

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93
Q

Phosphatidylcholine

A

Glycerophospholipids with a choline head group

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94
Q

Steroid hormones

A

Have high-affinity receptors often on the nucleus. Travel in the blood stream from endocrine glands. Simply diffuse through plasma membrane.

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95
Q

Triacylglycerol function and reason

A

Fuel storage. Reason: C’s are highly reduced and yield high amount of energy upon oxidation, they are also dehydrated so they carry no extra water weight

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96
Q

Fat soluble vitamins

A

A, D, E, K

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97
Q

Do all sphingolipids contain a sphingosine backbone?

A

NO! Sphingolipids may contain either a sphingosine or sphingoid backbone

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98
Q

ABO blood-typing is reliant upon lipids of which class of glycolipids

A

Sphingolipids

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99
Q

Isoprene

A

5-Carbon molecules that make up terpene. One terpene has two isoprene units

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100
Q

Prostaglandins

A

Paracrine or autocrine signaling molecules that regulate cAMP production. Major downstream effects: pain, inflammation, smooth muscle contraction, body temp elevation, sleep-wake cycle

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101
Q

Effect of NSAIDs on prostaglandins

A

NSAIDs inihibit the production of COX, an enzyme that helps synthesize prostaglandins. Thus, prostaglandin production is decreased/inhibited

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102
Q

Waxes (and function)

A

Esters of long-chain fatty acids with long-chain alcohols. Function: protection in both plants and animals. Prevent dehydration in animals or repel water from birds’ feathers

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103
Q

Terpenes

A

Odiferous chemicals made of isoprene subunits. Produced mainly by plants and some insects. Ex: Vitamin A, carotenoids, natural rubber

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104
Q

Terpenoids

A

AKA: Isoprenoids. Derivatives of terpenes that have undergone oxidation or rearrangement of the carbon skeleton. Also have functional groups added to the C skeleton

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105
Q

Steroids

A

Signaling lipids that contain 3 cyclohexane rings and 1 cyclopentane ring. Derivatives of terpenes

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106
Q

Which type of hormone at estrogens, testosterone, aldosterone, and cortisol?

A

Steroid hormones

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107
Q

Cholesterol

A

A steroid with hydrophilic and hydrophobic parts. Regulates membrane fluidity. In low temperature environments, cholesterol keeps membrane from getting too solid, and in high temperatures, keeps membrane from getting too fluid. Also a precursor to many steroid hormones, bile acids, and vitamin D

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108
Q

Vitamin A

A

AKA carotene. Important to vision, growth and development, and immune function. Precursor of retinal (light-sensing component in the eye) and retinol (storage-form of retinal)

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109
Q

Vitamin D

A

AKA: cholecalciferol. Active form is calcitrol, which increases uptake of Ca2+ and phosphate in the intestines. Promotes bone production

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110
Q

Rickets

A

Vitamin D deficiency

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111
Q

Vitamin E

A

AKA tocopherols and tocotrienols. Prevents cancer by acting as an antioxidant: attacks free-radicals and thus prevents oxidative damage.

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112
Q

Vitamin K

A

Vital to production of prothrombin, an important clotting factor in the blood.

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113
Q

Saponification

A

Strong base + triacylglycerol –> glycerol + fatty acid salt (soap)

An ester hydrolysis reaction

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114
Q

Surfactant

A

Decreases the surface tension at the surface of a liquid, acting as a detergent or emulsifier. Soaps are surfactants

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115
Q

Heterochromatin

A

Condensed DNA that remains condensed during interphase (only a small portion of total DNA). Transcriptionally silent. Contains highly repetitive sequences. Appears dark under light miscroscopy.

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116
Q

Euchromatin

A

Dispersed chromatin (classic “beads on a string” appearance). Genetically active. Appears light under light microscopy

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117
Q

Higher GC-content indicates ____ melting point because _____.

A

Higher MP because G-C bond has three hydrogen bonds wherease A-T only has two.

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118
Q

Purines

A

Contain two rings in their structures. Adenine and guanine.

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119
Q

Pyrimidines

A

Contain one ring in their structures. Cytosine, thymine, and uracil

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120
Q

Requirements of Aromaticity

A
  1. Cyclic
  2. Planar
  3. Conjugation: alternating single and multiple bonds, or lone pairs, creating at least one unhybridized p-orbital for each atom in the ring
  4. Huckel’s rule: there are 4n + 2 pi electrons
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121
Q

cDNA

A

Complementary DNA that results from reverse transcription of mRNA. Used in DNA libraries and contains only the exons of genes that are transcriptionally active in the sample tissue

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122
Q

Ingredients of PCR

A

DNA sample, primer, free nucleotides, and enzymes (including polymerase from Thermus aquaticusis because it can withstand high temperatures)

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123
Q

Endonucleases

A

Cut DNA in the middle of sequences. Also used by cell from DNA repair. Used in lab for DNA analysis as restriction enzymes (they are used to cleave DNA for electrophoresis, Southern blotting, and to introduce a gene of interest into a viral vector for gene therapy)

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124
Q

Cytosine deamination results in ____

A

Uracil

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125
Q

Probe DNA

A

DNA with a known sequence

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126
Q

Replisome / Replication complex

A

Set of specialized proteins that assist DNA polymerases

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127
Q

Centromere

A

Point at which sister chromatids remain connected. Also can be seen at the “meeting point” of the replication forks

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128
Q

DNA topoisomerases

A

Introduce negative supercoiling by creating nicks in the DNA that allow relaxation of the coils. Then reseal their cuts

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129
Q

Direction of DNA/RNA Synthesis

A

5’ to 3’

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130
Q

Direction that DNA and RNA polymerases read

A

3’ to 5’

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131
Q

DNA Polymerase III

A

Replicates leading strand in prokaryotes

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132
Q

DNA polymerase - alpha, delta, epsilon

A

Work together to synthesize both the leading and lagging strands of DNA. Delta fills in the gaps left behind when the RNA primers are removed

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133
Q

DNA Polymerase - gamma

A

Replicates mitochondrial DNA

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134
Q

DNA Polymerase - beta and epsilon

A

Aid in DNA repair during replication

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135
Q

DNA Polymerase I

A

In prok, adds DNA nucleotides where RNA primer used to be

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136
Q

DNA ligase

A

Seals the ends of DNA newly synthesized DNA molecules together

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137
Q

Mismatch Repair

A

Detects and removes errors in replication. Occurs during G2 phase of cell cycle. Relevant genes are MSH2 and MLH1

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138
Q

Nucleotide Excision Repair

A

Proteins scan the DNA molecule for errors (like Thymine dimers that are induced by UV light), then and exicion endonuclease nicks the phosphodiester backbone of the damaged strand on either sides of the faulty nucleotide(s) and then removes it. DNA polymerase fills in the gaps and DNA ligase patches it all up

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139
Q

Base excision repair

A

First, glycolase enzyme recognizes and removes affected base, leaving an abasic/AP site. AP endonuclease recognizes the AP site and removes the damaged sequence. Repair by DNA polymerase and ligase occurs

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140
Q

DNA Cloning

A

Used to produce large amounts of a desired sequence.

Process: investigator ligates the gene of interest (extracted from a sequence using restriction enzymes) into a viral/bacterial plasmid vector that also contains an antibacterial resistant gene. Recombinant vector is then inserted into host bacterium and grown, isolated, in large quantities. The bacteria can either be made to express the gene of interest or lysed to reioslate the recombinant vectores.

141
Q

Restriction enzymes

A

Recognize specific, palindromic, double-stranded DNA sections and then cuts the DNA backbones at those sequences. Isolated from bacteria, where their original purpose is to protect the bacteria from DNA viruses.

142
Q

DNA libraries: genomic and cDNA

A

Large collections of known DNA sequences. Genomic libraries include exons (coding) and introns (noncoding). cDNA libraries contain sequences of DNA produces via reverse transcription of mRNA, contain no introns, AKA expression libraries

143
Q

Hybridization

A

Joining of complementary base pair sequences. Can be DNA-DNA recognition or DNA-RNA. Vital part of PCR and Southern blotting

144
Q

Gel electrophoresis of DNA

A

All DNA migrates towards positive anode because of neg backbone. Preferred gel is agarose gel. Longer strands of DNA migrate shorter distances

145
Q

Southern blotting

A

Used to detec the presence and quantity of various DNA strands in a sample. After DNA fragments are separated using gel electrophoresis, they are transferred separately to a membrane. Membrane is then probed using many copies of single-stranded DNA. The probe will bind to its complementary sequence and form dsDNA. Probes are labelled with radioisotopes or indicator proteins, both of which can indicate the presence of a desired sequence.

146
Q

DNA sequencing

A

Uses dideoxyribonucleotides and the ingredients of PCR to synthesize many fragments that all end in a dideoxyribonucleotide. Then gel electrophoresis is performed and then bases can then be read in order.

147
Q

Transgenic mice

A

Altered at their germ line by introducing a cloned gene into embryonic stem cells. If the transgene is a disease-producing allele, the mice can be used to study the progression of the disease from early embryonic development through adulthood

148
Q

Knockout mice

A

Mice in which a gene has been intentionally deleted to determine whether the cut-out gene is desease-inducing.

149
Q

Gap Junctions

A

Allow rapid exchange of ions or small molecules between adjacent cells. Cells are held together by pores made of connexin which connect the cytoskeletons of the neighboring cells

150
Q

Tight Junctions

A

Prevent paracellular transport (eg lateral transport through an epithelial layer of cells). Prevents fluid leakage. Consist of a continuous band around the cell. Create a transepithelial voltage difference due to differing ion concentrations

151
Q

Desmosomes

A

Bind adjacent cells by anchoring to their cytoskeletons. Formed by transmembrane proteins associated with internal intermediate filaments. Primarily found between epithelial cells

152
Q

Hemidesmosomes

A

Attach epithelial cells to underlying structures, like basement membrane, or ECM

153
Q

Two essential fatty acids for humans

A

alpha-linolenic acid and linoleic acid

154
Q

Chylomicrons

A

Transport fatty acids in the form of triacylglycerols from the intestines

155
Q

Glycerophospholipids

A

Mainly used for membrane synthesis. Can produce a hydrophilic surface on the layer of lipoproteins, like VLDL, a lipid transporter

156
Q

Pinocytosis

A

Endocytosis of fluids or dissolved particles.

157
Q

Phagocytosis

A

Endocytosis of large particles.

158
Q

Clathrin

A

Vesicle-coated protein that is largely responsible for invagination of endocytosed particles coming into the cells

159
Q

Nernst equation

A

E = RT/(zF) *ln ( [ion_out] / [ion_in] ) = 61.5/z log ( [ion_out] / [ion_in] )

E is the membrane potential

160
Q

Goldman-Hodgkin-Katz equation

A

V_m = 61.5 * log( (P-Na[Na+_out] + P-K[K+_out] +P-Cl[Cl-_in]) / (P-Na[Na+_in] + P-K[K+_in] +
P-Cl[Cl-_out]) )

Calculates voltage of a membrane using the permeability of each ion

161
Q

Cardiolipin

A

Major component of the inner mitochondrial membrane

162
Q

Does the inner mitochondrial membrane contain cholesterol?

A

No, mainly cardiolipin

163
Q

trans-phospholipids ____ the melting points / ____ the fluidity of the plasma membrane

A

increase; decrease

164
Q

Types of sphingolipids

A

Ceramides, sphingomyelins, gangliosides, cerebrosides

165
Q

Role of Waxes in Plasma Membrane

A

Stabilize and enforce rigidity of the plasma membrane by associating with the nonpolar tail region. Serve extracellular functions of waterproofing and protection

166
Q

What type of molecule is responsible for the ABO blood typing system?

A

The ABO antigens on RBCs are sphingolipids than only differ by their carbohydrate sequences

167
Q

GLUT2 transporter protein

A

Glucose transporter protein found in liver and pancreatic cells. Low affinity - cannot be saturated under normal physiologic conditions. Takes glucose into liver cells as a function of blood glucose levels (first-order kinetics). Acts as a glucose sensor in the beta-islet cells of the pancreas in order to signal proper insulin release

168
Q

GLUT4

A

Glucose transport proteins on adipose and muscle cell surfaces. K_m is very close to physiologic glucose concentration, so they are almost always saturated. Cells increase rate of transport through GLUT4s by increasing the number of them on the surface. Insulin triggers vesicles to migrate to the inner surface of the plasma membrane and insert more GLUT4s.

169
Q

Hexokinase

A

First enzyme of glycolysis in most tissues. Phosphorylates glucose to glucose 6-phosphate in order to prevent a GLUT transporter from removing the glucose from the cell.

170
Q

Glucokinase

A

Induced by insulin. Found in liver and beta-islet pancreatic cells - is the first second enzyme involved in glycolysis here. Phosphorylates glucose in order to prevent GLUT from removing it from the cell

171
Q

PFK-1

A

The main rate-limiting enzyme in glycolysis. Converts fructose-6-phosphate to fructose-1,6-bisphosphate using ATP. Inhibited by citrate and ATP, so that the cell stops glycolysis once energy is sufficient. It is activated by AMP, so the glycolysis starts when there is a great need for energy. Activated by insulin and inhibited by glucagon, both indirectly and involving PFK-2

172
Q

PFK-2

A

Indirectly activates PFK-1 by converting fructose 6-phosphate to fructose 2,6-bisphosphate, which then activates PFK-1, regardless of ATP levels, which means that energy production can continue even though energy levels are sufficiently high. Activated by insulin and inhibited by glucagon.

173
Q

Glyceraldehyde-3-phosphate dehydrogenase

A

Catalyzes an oxidation and addition of P_i to glyceraldehyde-3-phosphate. Produces 1.3-bisphosphoglycerate and reduces NAD+ to NADH

174
Q

3-phosphoglycerate kinase

A

Engages in substrate-level phosphorylation to generate ATP, also forming 3-phosphoglycerate from 1,3-bisphosphoglycerate and ADP. The only means of ATP production in anaerobic tissue.

175
Q

Substrate-level phosphorylations in glycolysis

A

Performed on 1,3-bisphosphoglycerate to by 3-phosphoglycerate kinase, as well as on phosphoenolpyruvate to by pyruvate kinase.

Yield ATP. the only ATP-producing mechanism in glycoloysis alone

176
Q

Pyruvate kinase

A

The last enzyme of glycolysis. Uses the high-energy intermediate, phosphoenolpyruvate to phosphorylate ADP, forming ATP. Activated in a feed-forward mechanism by F-1,6-BP (produced by PFK-1).

177
Q

Lactate dehydrogenase

A

Key fermentation enzyme. Reduces pyruvate to lactate while oxidizing NADH to NAD+. This new NAD+ replenishes the supply of coenzymes for glyceraldehyde-3-phosphate dehydrogenase.

178
Q

Dihydroxyacetone phosphate (DHAP)

A

Used in hepatic and adipose tissue for triacylglycerol synthesis. Formed from F-1,6-BPG. It can be isomerized back to glycerol 3-phosphate and then converted to glycerol (backbone of triacylglycerols)

179
Q

Irreversible enzymes of glycolysis

A

Hexokinase, glucokinase, PFK-1, and pyruvate kinase

180
Q

Glycolysis in RBCs

A

Only respiration is through glycolysis because RBCs do not have mitochondria.

181
Q

Bisphosphoglycerate mutase

A

In RBCs, converts 1,3-BPG to 2,3-BPG. 2,3-BPG then binds to the beta-chains of Hb, decreasing its affinity for O2, thus releasing O2. Fetal RBCs do not have this enzyme, so O2-binding affinity of 2,3-BPG is quite high.

182
Q

Sucrose

A

Disaccharide of glucose and fructose

183
Q

Lactose

A

Disaccharide of glucose and galactose

184
Q

Important enzymes of galactokinase

A

Galactokinase and galactose-1-phosphate uridyltransferase (an epimerase that converts galactose-1-phosphate to glucose-1-phosphate for glycolysis)

185
Q

Fructose metabolism

A

Fructokinase, then cleavage into glyceraldehyde and DHAP by aldolase.

186
Q

Pyruvate dehydrogenase complex (def. and cofactors)

A

Irreversible system that converts pyruvate to acetyl-CoA in prep for the citric acid cycle. Inhibited by acetyl-CoA, so that pyruvate is no longer converted to acetyl-CoA, rather, to oxaloacetate to enter gluconeogenesis.

Cofactors: thiamine pyrophosphate, lipoic acid, CoA, FAD, and NAD+

187
Q

The three fates of pyruvate (and the relevant enzymes)

A

Conversion to acetyl-CoA by pyruvate dehydrogenase

Conversion to lactose by lactase dehydrogenase

Conversion to oxaloacetate by pyruvate carboxylase

188
Q

Differing roles of glycogen in liver and skeletal muscle tissues

A

Liver: broken down to replenish blood glucose levels

Skel muscle: broken down for fuel for the muscle during exercise

189
Q

Glycogen synthase

A

The rate-limiting enzyme of glycogenesis. It forms the a-1,4-glycosidic bond in LINEAR glycogen. Stimulated by insulin and glucose-6-phosphate. Inhibited by epinephrine and glucagon.

190
Q

Branching enzyme

A

Enzyme in glycogenesis that forms the a-1,6 glycosidic bond essential for glycogen to branch. Mechanism involves cleavage of existing linear glycogen at an a-1,4 glycosidic bond to free an oligoglucose, then moves the freed piece to a new location and creates the new 1,6 bond.

191
Q

Glycogen phosphorylase

A

Rate-limiting enzyme of glycogenolysis. Breaks a-1,4-glycosidic bonds between glucose using inorganic phosphate, thus releasing glucose from the granules. In liver, it is activated by glucagon. In muscle, it is activated by AMP and epinephrine. It is inhibited by ATP.

192
Q

Debranching enzyme

A

Made up of two enzymes for the multi-step process of breaking down branched glycogen: the first a-1,4 bond on the branch adjacent to the branch point is broken, and then the new oligoglucose is moved to the exposed end of the chain where a new a-1,4 bond is formed. The a-1,6 bond is then cleaved and a single residue is released

193
Q

Isoforms

A

Slightly different versions of the same protein from the same gene. Results from alternative splicing (different combinations of exons), so the nucleic acid and amino acid sequences differ

194
Q

Substrates for Gluconeogenesis

A

Glycerol-3-phosphate from triacylglycerols

Lactate from anaerobic respiration

Glucogenic amino acids (all except Leu and Lys, from muscle proteins)

195
Q

Glucoenogenesis

A

Mainly occurs in the liver. Keeps glucose levels up during fasting.

196
Q

Alanine aminotransferase

A

Converts alanine to pyruvate for gluconeogensis

197
Q

Pyruvate carboxylase

A

Mitochondrial enzyme that converts pyruvate to oxaloacetate due to high levels of Acetyl-CoA (sourced from fatty acids).

198
Q

PEPCK: phosphoenolpyruvate carboxykinase

A

Converts oxaloacetate to phosphoenolpyruvate using GTP for gluconeogenesis. PEP then continues on the F-1,6-BP. Circumvents the pyruvate kinase step of glycolysis.

199
Q

Fructose-1,6-bisphosphatase

A

Key control point of gluconeogenesis, rate-limiting. Reverses the action of PFK-1 in that it converts F-1,6-BP to fructose-6-phosphate. Inhibited by AMP and F-2,6-BP. Activated by ATP (makes sense because sufficient ATP signifies that the cell is energetically well-off and able to produce glucose for other cells in the body).

PFK-2, which is activated by insulin, forms F-2,6-BP, so high amount of sugar in the blood increases insulin levels, which increases F-2,6-BP levels, which decreases the rate of gluconeogenesis by inhibiting F-1,6-bisphosphatase

200
Q

Glucose-6-phosphatase

A

Converts glucose-6-phosphate to glucose. Circumvents glucokinase and hexokinase. Only present in lumen of the ER in liver cells. The fact that it is not present in skeletal muscle cells shows that glycogen in these cells is not a source of glucose for the blood, only for the muscle.

201
Q

Gluconeogenesis requires expenditure of ___ produced by ____ of fatty acids

A

ATP; beta-oxidation

202
Q

Pentose Phosphate Pathway / Hexose Monophosphate Shunt

A

Occurs in cytoplasm. Serves to prodcue NADPH and as a source of ribose-5-phosphate for nucleotide synthesis

203
Q

G6PD in PPP

A

The rate-limiting enzyme of the PPP. Converts glucose-6-phosphate into 6-phosphogluconate. Induced by insulin because PPP is classified as a glucose-storage pathway. It is inhibited by NADP+.

204
Q

Second part of the PPP

A

Starts with ribulose 5-phosphate and ends with ribose 5-phosphate for nucleotide synthesis, as well as products that are also glycolytic intermediates, so they feed into glycolysis.

205
Q

Transketolase and Transaldolase in PPP

A

Synthesize pentoses from glycolytic intermediates

206
Q

Functions of NADPH

A

A potent reducing agent. Aids in synthesis of fatty acids and cholesterol, cellular bleach production in some WBCs, and maintenance of reduced glutathione supply (the body’s natural antioxidant)

207
Q

Glutathione

A

A reducing agent that is the body’s natural antioxidant by reversing radical-formation before they can damage cells (specifically cell membranes). Protects the body from radical oxidative damage caused by peroxides.

208
Q

Formation of Acetyl-CoA from CoA

A

Covalent attachment of an acetyl group to CoA-SH at the sulfur, thus forming a thioester (which is high energy)

209
Q

Pyruvate dehydrogenase

A

PDH. Oxidizes pyruvate, forming CO2, while the remaining two C’s bind covalently to thiamine pyrophosphate (TPP, vitamin B1). Mg2+ is also required

210
Q

Dihydrolipoyl transacetylase

A

Second enzyme in pyruvate dehydrogenase complex. It oxidizes the product of PDH and transfers it to lipoic acid (its coenzyme) where it is oxidized again to create an acetyl group that is thioester-linked to lipoic acid. Then dihydrolipoyl transacetylase catalyzes the CoA-SH interaction with the newly formed thioester, transferring the acetyl group to form acetyl-CoA. Lipoic acid is left in its reduced form

211
Q

Dihydrolipoyl dehydrogenase

A

Third enzyme in the pyruvate dehydrogenase complex. Its coenzyme FAD is used to reoxidize lipoic acid (resetting it), which reduces FAD to FADH2

212
Q

Carnitine

A

Carries an acyl group from a cytosolic CoA-SH to a mitochondrial CoA-SH because the whole molecules cannot traverse the mitochondrial membrane. Group is transferred to and from carnitine via transesterification.

213
Q

Methods of Acetyl-CoA formation

A

Pyruvate dehydrogenase complex (after glycolysis), beta-oxidation, amino acid catabolism, reversal of ketone-body formation, and conversion of alcohol

214
Q

How is Acetyl-CoA formed from amino acids?

A

Ketogenic amino acids lose their amino group via transamination, and then a ketone body can be formed from the C skeleton. Ketone bodies can be converted to Acetyl-CoA

215
Q

Formation fo acetyl-CoA from alcohol

A

Upon buildup of alcohol, it is catalyzed by alcohol dehydrogenase and acetaldehyde dehydrogenase.

216
Q

Substrates of the Citric Acid Cycle

A

PCIKSSFMO:

pyruvate, citrate, isocitrate, a-ketoglutarate, succinyl-CoA, succinate, fumarate, malate, oxaloacetate

217
Q

Citrate formation in CAC

A

Condensation of acetyl-CoA and oxaloacetate to form intermediate citryl-CoA. Hydrolysis of citryl-CoA yields citrate and CoA-SH via citrate synthase. This step helps propel the cycle forward

218
Q

Aconitase

A

Catalyzes the isomerization of citrate to isocitrate by switching an H and an OH on citrate, achieved by dehydration and then re-hydration of a different C. The enzyme requires Fe2+

219
Q

Isocitrate dehydrogenase

A

The rate-limiting enzyme of the citric acid cycle. Catalzyes the formation of oxalosuccinate from isocitrate, which is then decarboxylated to form a-ketoglutarate and CO2. This step also produces the first NADH

220
Q

Mechanism of dehydrogenases

A

Transfer of a Hydride ion to an electron acceptor, usually NAD+ or FAD. Dehydrogenases are a form of oxidoreductases

221
Q

a-ketoglutarate dehydrogenase complex

A

Catalyzes the formation of succinyl CoA from a-ketoglutarate in a method similar to PDH complex. Also results in the second and final CO2 formed in the CAC and reduces another NAD+ to NADH

222
Q

Synthetase vs Synthase

A

Both form new covalent bonds, but synthetases require the input of energy whereas synthases do not

223
Q

Succinyl-CoA Synthetase

A

The reverse of the synthesis reaction of this enzyme forms succinate from succinyl-CoA by hydrolyzing the thioester bond. Since thioesters require high energy input to form, this energy is released upon cleavage and is used to phosphorylate GDP to GTP, which then phosphorylates ADP to ATP.

224
Q

During which reaction is ATP DIRECTLY formed in the citric acid cycle?

A

ONLY during the reaction that forms succinate from succinyl-CoA via the enzyme succinyl dehydrogenase

225
Q

Succinate dehydrogenase

A

Catalyzes the oxidation of succinate to form fumarate, the only step that does not occur in the mitochondrial matrix because this enzyme is an integral membrane protein so it occurs on the inner membrane instead. During this reaction, FAD is reduced to FADH2.

226
Q

Fumarase

A

Catalyzes the formation of an alkene bond in fumarate to yield malate. Both enantiomers are possible, but only L-malate forms in the body

227
Q

Malate dehydrogenase

A

Catalyzes the oxidation of malate to form oxaloacetate. Reduces the third and final NAD+ to NADH.

228
Q

Yield of ATP from one molecule fo glucose

A

25 ATP after CAC and ETC are complete

229
Q

Describe regulation of Pyruvate Dehydrogenase

A

When the cell is energetically satisfied, the high levels of ATP signal pyruvate dehydrogenase kinase to phosphorylate the enzyme, thus inhibiting it. But when ADP levels are high, pyruvate dehydrogenase phosphatase dephosphorylates PDH, thus allowing the production of Acetyl-CoA for progression of the CAC. Also, high levels of Acetyl-CoA iteself can inhibit PDH

230
Q

Control points of the Citric Acid Cycle

A

Citrate synthase, isocitrate dehydrogenase, and a-ketoglutarate dehydrogenase complex.

All are regulated by allosteric inhibitors or activators

231
Q

Inhibitors of citrate synthase

A

ATP, NADH, Acetyl-CoA, and succinyl-CoA. All are allosteric

232
Q

Regulation of isocitrate dehydrogenase

A

All are allosteric

Inhibitors: ATP and NADH
Activators: ADP and NAD+

233
Q

Regualtion of a-ketoglutarate dehydrogenase complex

A

All allosteric.

Inhibitors: succinyl-CoA, NADH, ATP
Activators: ADP, Ca2+

234
Q

Driving force behind the electron transport chain

A

Proton-motive force created by the proton gradient across the inner mitochondrial membrane

235
Q

Describe the general mechanism of the electron transport chain

A

High-energy electron carriers from the citric acid cycle, NADH and FADH2, transfer their electrons to proteins on the inner mitochondrial membrane. Eventually, the electrons are given to O2 as H- ions, which forms water. The energy released from the transporting of electrons facilitates H+ ion transport across the membrane, intensifying the gradient, which allows for ATP synthesis via ATP synthase.

Based on the fact that ATP formation is endergonic and electron transport is exergonic

236
Q

Complex I of the ETC

A

NADH-CoQ oxidoreductase. NADH transfers its electrons over to FMN to form FMNH2, which then becomes oxidized with sulfur. Then the Fe-S subunit is reduced and the electrons are transferred to CoQ (ubiquinone) to form CoQH2. Results in 4 protons being moved into the intermembrane space

237
Q

Complex II of the ETC

A

Succinate-CoQ oxidoreductase. Succinyl-CoA transfers its electrons to FAD, which is covalently bonded to Complex II and is then converted to FADH2. FADH2 then reduces an Fe-S protein. Final step is reoxidation of the Fe-S protein and transfer of electrons to ubiquinone. No H pumping occurs here

238
Q

Complex III of the ETC

A

AKA: cytochrome reductase. Facilitates the transfer of e from ubiquinone to cytochrome c. Each molecule of cytochrome c can only accept one electron, so one molecule of CoQH2 with two electrons requires two cytochrome c molecules. Contributes to the proton gradient through the Q cycle

239
Q

Q cycle

A

Part of Complex III of the ETC that displaces four protons into the intermembrane space

240
Q

Cytochromes

A

Proteins with heme groups that have iron ions that get reduced to Fe2+ and then reoxidized to Fe3+

240
Q

Cytochromes

A

Proteins with heme groups that have iron ions that get reduced to Fe2+ and then reoxidized to Fe3+

241
Q

Cpomplex IV of the ETC

A

Transfer of electrons from cytochrome c to oxygen (the final acceptor) by way of cytochromes a and a3 and Cu2+

242
Q

Why are NADH shuttles required? What are the different types?

A

They are needed because NADH produced in glycolysis cannot directly cross the mitochondrial membrane.

Specific examples include: glycerol-3-phosphate shutter, malate-aspartate shuttle

243
Q

F0 and F1 portions of ATP synthase

A

This is the transmembrane portion of the protein that houses the ion channel. As protons flow through here, F1 portion of the protein utilizes the energy being released from the electrochemical gradient to phosphorylate ADP to ATP

244
Q

Chemiosmotic coupling

A

There is a direct relationship between the electrochemical gradient and the synthesis of ATP

245
Q

Conformational coupling (ATP synthase)

A

Suggests that electrochemical gradient and ATP synthesis are indirectly related in that the F1 portion of ATP synthase is motivated to rotate like a turbine when H+’s pass through F0. The turbine mechanism is a conformational change in the protein that causes P and ADP to be forced together and bonded

246
Q

Key regulators of oxidative phosphorylation (and other side regulators)

A

O2 (key!): when O2 is low, ATP synthase activity is relatively low

ADP (key!): when O2 is in sufficient supply, rate of ATP synthesis is determined by ADP. Low ADP signals ATP synthesis to increase

Others: NADH (buildup causes ATP synthase to

247
Q

How is O2 consumption affected in a patient who was exposed to a toxin that increases permeability of the inner mitochondrial membrane to H+?

A

O2 consumption would increase because the electrochemical gradient will not be as intense due to the increased permeability, so ATP synthesis per molecule of glucose will be less efficient, thus requiring more O2 use to meet the body’s ATP needs

248
Q

Tricarboxylic acid cycle

A

Another name for the Citric Acid/Krebs cycle

249
Q

In what form do fatty acids enter the catabolic pathway?

Describe the mechanism

A

acetyl-CoA

Mechanism: fat from adipose tissue can be hydrolyzed by lipases to form fatty acids and glycerol. Fatty acid can then be activated in the cytoplasm by coupling to CoA-SH and forming acyl-CoA. Acyl-CoA is then attached to a carnitine transporter to cross the inner mitochondrial membrane. Then transfer of from carnitine occurs to reform acyl-CoA, which can then undergo beta-oxidation to form acetyl-CoA that can enter the CAC

250
Q

Nucleosidediphosphate kinase

A

Phosphorylates GDP to GTP during succinate formation in the CAC

251
Q

Digestive enzymes/mixtures that aid in the digestion of dietary fats

A

Bile (bile salts, cholesterol, pigments), pancreatic lipase, colipase, and cholesterol esterase

252
Q

How are lipids absorbed from the digestive tract?

A

After emulsification in the small intestine, the fragments form micelles that are able to diffuse through the brush border of the mucosal cells of the small intestine where they are then absorbed into the mucosa and re-esterified.

The re-resulting triacylglycerols and cholesteryl-esters are then packaged into chylomicrons which can exit the intestine via lacteals (lymphatic system) or enter the bloodstream through the thoracic duct

253
Q

Hormone-sensitive lipase

A

An enzyme that is triggered at night time by a fall in insulin levels. Hydrolyzes triacylglycerols in adipose cells to yield fatty acids and glycerols. May also be activated by epinephrine and cortisol.

NOT subject to regulation by gluagon

254
Q

Lipoprotein lipase (LPL)

A

Metabolizes chylomicrons and VLDL to release free fatty acids

255
Q

Albumin

A

Transport protein that carries free fatty acids (and other nonpolar molecules) through the blood

256
Q

Lipoproteins

Rank them from least to most dense

A

Aggregates of apolipoproteins and lipids. Carry cholesterol and triacylglycerols (varying amounts depending on the type of lipoprotein) around the blood.

Increasing density: chylomicrons, VLDL, IDL, LDL, HDL

257
Q

Chylomicrons

A

Lipoproteins that mainly transport dietary triacylglycerols, cholesterol, and cholesteryl esters from the intestines to tissues. Least dense of the liprproteins

258
Q

VLDL

A

Lipoproteins that carry triacylglycerols and fatty acids from liver to tissues

259
Q

IDL

A

Intermediate density lipoproteins. They are remnants of VLDL. They pick up cholesteryl esters from HDL to become LDL (increase in density). They get picked up by the liver

260
Q

LDL

A

Delivers cholesterol to the cells

261
Q

HDL

A

PIcks up cholesterol accumulating in the blood vessels and delivers it to liver and steroidogenic tissues. Transfers apolipoproteins to other lipoproteins

262
Q

Apoproteins

A

The protein component of lipoproteins. They are receptor molecules involved in signaling

263
Q

De novo cholesterol synthesis

Relevant enzymes and reactants that drive it?

What triggers the process?

A

Occurs in the liver. It is driven by Acetyl-CoA and ATP. The rate-limiting step has the enzyme HMG-CoA reductase that yields mevalonic acid.

Triggers: low cholesterol, high insulin, and upregulation of the HMG-CoA reductase gene

264
Q

LCAT

A

Enzyme activated by HDL in the bloodstream that adds a fatty acid to cholesterol –> yields soluble cholesteryl esters like those in HDL

265
Q

CETP

A

Enzyme that facilitates transfer of cholesteryl esters from HDL to IDL so that it becomes LDL.

266
Q

Fatty acids (def. and nomenclature)

A

Long-chain carboxylic acids

Naming: carbons:double bonds, further specified with the # of the first C of the unsaturated bond and the isomerization

267
Q

Essential fatty acids

A

alpha-linolenic acid and linoleic acid

268
Q

Citrate lyase

A

Splits excess citrate from the citric acid cycle back into acetyl-CoA and oxaloacetate. Located in the cytoplasm

269
Q

Acetyl-CoA carboxylase

A

Key rate-limiting enzyme in fatty acid synthesis. It adds CO2 to acetyl-CoA to form malonyl-CoA. It is activated by citrate and insulin

270
Q

The product of de novo fatty acid synthesis

A

Palmitic acid / palmitate

271
Q

Palmitate synthase

A

Commonly called fatty acid synthase: a large multienzyme complex found in the cytosol that is rapidly activated following insulin-rise after a big meal

Substrates and coenzymes: 8 acetyl-CoA molecules, pantothenic acid (vitamin B5), NADPH

272
Q

Steps of Palmitate Synthase

A

Attachment of acetyl-CoA to acyl carrier protein
Bond formation between activated malonyl-CoA and growing fatty acid chain
Reduction of double bond
Dehydration
Reduction of double bond

273
Q

Fatty-acyl-CoA-synthetase

A

Activates fatty acids for beta-oxidation by attaching them to acyl-CoA

274
Q

Carnitine acytransferase I

A

Rate-limiting enzyme of fatty acid oxidation. Shuttles fatty acids that over 12 Cs long into the mitochondria

275
Q

Products of one round of beta–oxidation

A

1 acetyl-CoA and the freshly reduced NADH and FADH2

275
Q

Products of one round of beta–oxidation

A

1 acetyl-CoA and the freshly reduced NADH and FADH2

276
Q

Steps of beta-oxidation

A
  1. Oxidation of the fatty acid to form a double bond
  2. Hydration of the double bond to form a hydroxyl group
  3. Oxidation of the OH to form a beta-ketoacid (a carbonyl)
  4. Splitting of the beta-ketoacid to form acetyl-CoA and a shortened acyl-CoA
277
Q

What is the three-C product formed at the end of odd-chain beta-oxidation

A

propionyl-CoA

278
Q

Enoyl-CoA isomerase

A

Enzyme that converts a 2,3-cis double bond in unsaturated fatty acids to 3,4-trans, which allows beta-oxidation to occur

279
Q

2,4-dienoyl-CoA reductase

A

Enzyme involved in the oxidation of unsaturated fatty acids. Mechanism involves converted two conjugated double bonds into one double bond, so that it can undergo isomerization by enoyl-CoA isomerase and then beta-oxidation

280
Q

Ketone bodies

What are the major two that arise from acetyl-CoA, yielded by beta-ox?

A

Essentially transportable forms of acetyl-CoA. Can be broken down as fuel by cardiac and skeletal muscle, and in extreme fuel shortages, the brain

Major two: acetoacetate and 3-hydroxybutyrate

281
Q

Ketogenesis (def. and major enzymes)

A

Production of ketone bodies. Occurs in the mitochondria of liver cells. Triggered by buildup of acetyl-CoA in the blood.

Major enzymes: HMG-CoA synthase, HMG-CoA lyase

282
Q

Ketolysis (def. and major enyzmes)

A

Catabolism of ketone bodies. Major enzyme is thiophorase. The liver lacks this enzyme so that it cannot breakdown the keton bodies it produces

283
Q

Pancreatic proteases

A

Trypsin, chymotrypsin, and carboxypeptidases A and B

284
Q

Pepsin

A

Begins breakdown of proteins in the stomach

285
Q

Proteolytic enzymes in the brush-border of the small intestine

A

Dipeptidase and aminopeptidase

286
Q

Method of amino acid transport out of intestinal lumen

A

Secondary active transport linked to Na+

287
Q

Method of transport of amino acids from epithelial cells into bloodstream

A

Facilitated diffusion

288
Q

Glucogenic amino acids

A

Can become glucose via gluconeogenesis

Includes all of them except leucine and lysine

289
Q

Ketogenic amino acids

A

Can be converted into ketone bodies and acetyl-CoA. There are 7 of them:

Leu, Lys, Ile, Phe, Trp, Tyr, Thr

290
Q

Transamination

A

AKA deamination, which is the process by which amino acids lose their amino groups and are left a C-skeletons. The Carbon skeleton can then be used as metabolic fuel

291
Q

Urea Cycle

A

Pathway the body uses to eliminate ammonia in the form of urea because ammonia is toxic

292
Q

Where does the bulk of protein digestion occur?

A

Small intestine (brush-border enzymes!)

293
Q

What is the fate of long-chain fatty acids contained in micells?

A

They are packaged into chylomicrons and then released into the lymphatic system through lacteals

294
Q

In which process is hormone-sensitive lipase active?

A

Fatty acid mobilization

295
Q

Nomenclature of the fatty acid synthesized in the body (C:double bonds)

A

16:0

Palmitic acid

296
Q

Location of ketogenesis

A

In the mitochondria of liver cells during a prolonged fast

297
Q

What ketone bodies does the human body produce? Which are used for fuel?

A

Acetoacetate, 3-hydroxybutyrate, and acetone. Only the first two are used as fuel, whereas acetone is a byproduct

298
Q

Enthalpy

A

Measures overall heat loss or gain of a system. At constant pressure and temp., it is equal to Q

299
Q

Entropy (def and units)

A

Measure of a system’s energy dispersion or degree of disorder. Units are J/K

300
Q

Concentration of H+ at “modified standard state”

A

[H+] = 1e-7 M

pH = 7

301
Q

Amount of energy yielded in combustion per gram of fat

A

9 kcal/g

302
Q

Amount of energy yielded in combustion of one gram of carbohydrates/proteins/ketone bodies

A

4 kcal/g

303
Q

delta G at modified standard state of ATP

A

-30.5 kJ/mol

304
Q

Methods of ATP formation in the cell

A

Substrate-level phosphorylation and oxidative phosphorylation

305
Q

Soluble high-energy electron carriers

A

NADH, NADPH, FADH2, ubiquinone, cytochromes, and glutathione

306
Q

Flavin mononucleotide

A

An example of a membrane-bound electron carrier. Also known as FMN. It is bonded to complex I of the ETC.

307
Q

Flavoproteins

A

Electron carriers that contain modified vitamin B2, or riboflavin. Also function as coenzymes in fatty acid oxidation, decarboxylation of pyruvate, and reduction of glutathione (a soluble electron carrier in the cytoplasm) . They are derived from nucleic acids. Two types: FMN and FAD

308
Q

Postprandial state

A

AKA absorptive or well-fed state. Characterized by anabolism of fuel molecules rather than breakdown. Lasts about 3-5 hours after a big meal. Insulin levels are high and leads first to maximum glycogen synthesis and storage, and then to synthesis of fatty acids in the liver from excess glucose and protein synthesis in muscle

309
Q

Which types of tissues are not sensitive to insulin?

A

Red blood cells, nervous tissue, kidney tubules, intestinal mucosa, and beta-cells of the pancreas

310
Q

Postabsorptive state

A

AKA Fasting state. The following hormones increase in concentration in the body: glucagon, cortisol, epinephrine, norepinephrine, and growth hormone. They promote breakdown of glycogen and the release of glucose. Gluconeogenesis is also triggered in the liver, but is much slower than glycogenolysis

311
Q

Prolonged state

A

AKA Starvation. Characterized by uniquely high levels of glucagon and epinephrine. Gluconeogenesis becomes the main source of glucose after glycogen stores have been depleted (about 24 hours of fasting). The brain adapts ketone bodies as its primary fuel source when levels of fatty acids and ketone bodies are high enough in the blood

312
Q

Amino acid-derived hormones (def. and relative rate of affect)

A

Include thyroid hormones and steroid hormones. They are slower to effect change than peptide hormones but induce longer-lasting effects because their modifications are made at the transcriptional level.

313
Q

Glucokinase

A

Enzyme in the liver that phosphorylates glucose as the first step in glycogen synthesis (increases glycogen storage). It is also the first enzyme of glycolysis in the liver. It is activated by insulin

314
Q

Effect of insulin on fuel storage/mobilization

A

Insulin increases glycogen synthesis by activating glucokinase and glycogen synthase (which is the rate-limiting enzyme), and by inhibiting enzymes of glycogenolysis like glucose-6-phosphatase and glycogen phosphorylase.

Increases the uptake of amino acids by muscle cells to increase protein synthesis. It also decreases the formation of ketone bodies

Increases synthesis of triacylglycerols in the liver and fat tissue and decreases lipolysis in fat tissue.

315
Q

Cells of origin of Glucagon

Primary target cells, too

A

Origin: alpha islet cells of the pancreas

Target: hepatocytes

316
Q

Effects of glucagon

A

Increases in glycogenolysis and gluconeogenesis in order to raise the levels of blood glucose.

Increases ketogenesis and decreases lipogenesis.

Activates hormone-sensitive lipase in the liver, thus increasing breakdown of lipids, although the effect is indirect so glucagon is not considered a major fat-mobilizing hormone.

317
Q

Triggers of glucagon release

A

Low blood glucose level.

High amino acid levels, especially basic amino acids

318
Q

Glucocorticoids

A

Released from the adrenal cortex. Responsible for glucose mobilization for the fight or flight response. Main one is cortisol, released in response to stress – it mobilizes energy stores via degradation. It also elevates blood glucose levels but also inhibits its uptake in tissue including muscle, lymphoid, and fat.

319
Q

Effects of prolonged exposure of the body to cortisol

A

Hyperglycemia which stimulates insulin, which actually promotes fat storage in fat tissue, rather than breakdown.

320
Q

Steroid hormone classes secreted by the adrenal cortex

A

Glucocorticoids, mineralocorticoids, and sex hormones

321
Q

Catecholamines and their effect on metabolism

A

Released from the adrenal medulla and include epinephrine and norepinephrine. They act on the liver and skeletal muscle tissues to promote glycogenolysis, on adipose tissue to promote lipolysis, and epinephrine targets organs like the heart to increase basal metabolic rate

322
Q

Difference in structures of epinephrine and norepinephrine

A

Epinephrine has a secondary amine whereas norepinephrine has a primary amine.

Think: Norepinephrine has the N at the eNd of a chain in its structure

323
Q

Deiodonases

A

Enzymes that remove iodine from a molecule. Convert T4 to T3.

324
Q

Thyroid hormones

A

T4 and T3. They increase BMR. Their specific main effects include increase of glucose uptake in the small intestine for metabolism in the cells. Also affect lipid metabolism and accelerate clearance of cholesterol from the plasma.

325
Q

Sources of C-skeleton for glucose synthesis

A

Lactate (from anaerobic repspiration), glycerol (from triacylglycerols), and amino acids

326
Q

Primary energy fuel for the liver in a well-fed state

A

Excess amino acids

327
Q

Effects of insulin on adipose tissue

A

High insulin activates lipoprotein lipase –> causes release of triacylglycerols from VLDL and chylomicrons. Insulin also suppresses the release of triacylglycerols from adipose cells, thus promoting storage of fat.

Low insulin activates hormone-sensitive lipase, thus causing the release of triacylglycerols from adipocytes

328
Q

Resting skeletal muscle’s sources of fuel

A

Glucose and fatty acids.

329
Q

Type of cellular respiration in skeletal muscle during short bursts of intense exercise

A

Anaerobic respiration reliant on muscle glycogen

330
Q

Primary source of fuel of cardiac muscle cells

A

Fatty acids. May switch to ketones in the event of long fasting

331
Q

Fuel sources of the brain during rest and fast

A

Rest and whenever possible: blood glucose

Fasting: glucose from hepatic glycogenolysis and gluconeogenesis, then ketones

Never fatty acids because they cannot cross the blood-brain barrier

332
Q

Respiratory quotient

A

RQ = CO2 produced / O2 consumed

333
Q

Hormones of hunger

A

Grehlin: increases appetite and stimulates release of orexin

Orexin: further increases appetite and plays a role in alertness/the sleep cycle. Can be triggered by hypoglycemia

Leptin: secreted by fat cells, suppresses orexin which decreases appetite

334
Q

Equation for BMI

A

BMI = mass (kg) / [height (m)]^2

335
Q

T/F: Hormonal control of glycolysis proceeds via noncovalent interactions

A

False - hormones exert their effect on glycolysis main via phosphorylation and dephosphorylation

336
Q

Which tissues are most dependent on insulin for fuel uptake?

A

Resting skeletal muscle and adipose tissue

337
Q

Homotropic regulation

A

Type of enzymatic reaction in which a particular molecule acts as both a substrate and a regulator of the given enzyme

338
Q

O2 is the final electron acceptor in which metabolic process?

A

Electron transport chain

339
Q

Arachidonic Acid

A

An essential fatty acid from which the body synthesizes eicosanoids (20-C omega-6 polyunsaturated fatty acids with four cis bonds), most importantly, prostaglandins.

340
Q

Prostaglandins

A

A specific type of eicosanoids that have a divers range of effects, including the modulation of inflammation

341
Q

Thromboxanes

A

A type of eicosanoid that is involved in the clotting cascade

342
Q

Which of the following will be in high urine concentration during chronic hyperglycemia?

A: proteins
B: glucose
C: ketone bodies

A

B and C

343
Q

Mnemonic for Purines and Pyrimidines (names and structure

A

“Pure As Gold” = adenine and guanine are the purines

so the other ones (cytosine, uracil, and thymine) are the pyrimidines, which are single rings making them more shaped like “pyramids”

344
Q

Order the nitrogenous bases in order of decreasing molecular weight

A

G > A > T > U > C

345
Q

Which amino acid residues are most commonly phosphorylated? Why?

A

Serine, Threonine, and Tyrosine.

Reason: they each bear a hydroxyl group, which is the preferred site of phosphorylation

346
Q

Major products of the pentose phosphate pathway

A

NADPH and ribose-5-phosphate

MCAT (6 decks)

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