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Tim's Cards > Metabolism > Flashcards

Metabolism Flashcards

1
Q

What does Catabolism/Anabolism do?

A

Catabolism - breaking down/exergonic/oxidation

Anabolism - building/endergonic/reduction

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2
Q

Define Catabolism/Anabolism:

A

Catabolism - generation of energy to drive vital reactions

Anabolism - synthesis of biological molecules

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3
Q

What are 3 properties of Catabolic pathways?

A
  1. Exergonic (release energy)
  2. Oxidative (e- transferred to NAD+ or NADP+_
  3. Energy captured as ATP
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4
Q

What are the 3 stages of Catabolism?

A
  1. hydrolysis of complex molecules to monomers
  2. conversion of building blocks to acetyl CoA in the mitochondria
  3. oxidation of acetyl CoA to carbon dioxide and water in ATP through Oxidative Phosphorylation (ETC)
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5
Q

Name 3 properties of anabolic pathways:

A
  1. Endergonic
  2. Reductive (hydride ion from NADPH used)
  3. ATP consumed
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6
Q

What type of reactions are carried out by dehydrogenase reactions?

A

oxidize a substrate by transfering Hydride ion to NAD+ and FAD

(dehydrogenase = think oxidation and NAD+ and FAD)

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7
Q

What are the major differences between Catabolism and Anabolism?

A

Catabolic products are similar, low molec. weight, and energy poor

Anabolic products are diverse, large, and energy rich

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8
Q

What is futile cycling?

A

Simultaneous synthesis and degradation

think Sisyphean

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9
Q

At least one of the steps in paired anabolic/catabolic pathways has a different…

A

enzyme

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10
Q

T/F

Paired pathways often occur right next to each other

A

False

they are often in different cellular compartments
i.e. - Fatty acid degradation occurs in Mitochondria
Fatty acid synthesis occurs in cytoplasm

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11
Q

Delta G Exergonic

Delta G Endergonic

A

less than 0

greater than 0

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12
Q

When delta G=0, then

A

equilibrium

forward rate=reverse rate

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13
Q

What 3 things do free energy changes predict?

A
  1. Direction of chemical reactions
  2. Equilibrium positions
  3. Amount of work that can be performed
    (the further from equilibrium the more work can be performed)
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14
Q

What can’t free energy changes tell us?

A

anything about the RATE of rxn

and is independent of the PATH of rxn

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15
Q

Can a rxn proceed if delta G(not) is positive

A

yes.

If delta G is negative

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16
Q

How can a thermodynamically unfavorable reaction be driven in the forward direction?

A

If coupled to highly exergonic rxn through a common intermediate.

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17
Q

What 3 things facilitate ATP hydrolysis?

A

Charge separation

Inorganic phosphate product stabilzed by resonance

direct product of hydrolysis ADP is ionized

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18
Q

Does ATP provide energy through hydrolysis?

A

NO

by group transfers

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19
Q

What are 2 ways to produce ATP?

A

Substrate level phosphorylation (minority)

Oxidative phosphorylation (mitochondria - ETC)

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20
Q

What are 3 levels of metabolic pathway regulation?

A

Allosteric (non-covalent bonding)

Hormonal

Concentration of enzyme (longest time frame)

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21
Q

What are two practical principles of bioenergetics (in terms of delta G and delta G0)?

A

A rxn can move forward even if delta G0 is positive (delta G has to be negative)

chemical rxns can be additive (coupling)

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22
Q

What are the 3 families of lipids?

A

Glycerophospholipids
Sphingolipids
Cholesterol

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23
Q

What is the prefix for a Glycerophospholipid?

A

Phasphatidyl… (or phosphatidic)

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24
Q

What are the 4 Sphingolipids?

A

Ceramide
Sphingomyelin
Glucosylcerebroside
Ganglioside

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25
Q

What molecule is both a phospholipid and a sphingolipid?

A

sphingomyelin

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26
Q

What are the microdomains made up of cholesterol and sphingomyelin in the bilayer?

A

Lipid Rafts

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27
Q

What is a transmembrane protein called?

A

Integral

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28
Q

The membrane spanning part of an IMP (integral membrane protein) is usually ________(property) and ________ (structurally)?

A

Hydrophobic

alpha - helices

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29
Q

An aquaporin is an example of

A

An IMP

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30
Q

What substances easily permeate membranes?

A

Gases and ethanol

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31
Q

What substances are slightly permeable to membranes?

A

Urea and water

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32
Q

Are ions permeable?

A

no

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33
Q

What are 6 ways to get something across a membrane?

A

Simple diffusion - gases and ethanol

Facilitated diffusion - down electrochemical gradient

Primary active transport (ATP)

Secondary active transport (driven by ion moving down gradient carrying substrate)

Ion channel

Ionophore-mediated ion transport

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34
Q

Is ATP required for secondary active transport?

A

No. Not directly.

because it relies on a concentration gradient set up by Na/K pump which does rely on ATP

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35
Q

What type of transport goes against a concentration gradient?

A

Active Transport and Cotransport (with ions)

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36
Q

What are the 3 major types of membrane anchors?

Which are on the cytosolic side?

A

Acylation - fatty acyl to Gly
Prenylation - NH3+ to Cys
(both cytosolic)

GPI anchor - PI, PE, and several sugars anchored through Asp
(exterior cell)

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37
Q

How does glucose enter a cell?

A

Facilitated diffusion

Membrane protein changes conformation (simple hand movement)

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38
Q

What are the 3 general classes of cell-surfaced receptors?

A

second-messenger

catalytic

intracellular

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39
Q

What are 4 approaches to cell signalling?

A

Endocrine
Paracrine
Autocrine
plasma membrane-attached proteins (to adjacent cell)

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40
Q

What are 2 G protein coupled second messengers?

A 
Adenylate Cyclase pathway (glucagon and epinepherine)
Phosphoinositide pathway (growth hormone)
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41
Q

What is the function of the Nitric Oxide pathway?

A

Relaxation of smooth muscle

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42
Q

Give an example of a Sell-Surfaced Receptor and an Intracellular Receptor.

A

Insulin

Steroids

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43
Q

What is another name for 7TM receptors?

A

G protein coupled receptors (GPCR)

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44
Q

G-protein coupled receptor:

A

Hormone binds receptor in plasma membrane
G-protein binds receptor
GDP > GTP
dissolution of complex, conformational change in G alpha
G alpha to effector in plasma membrane
GTP > GDP puts back together

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45
Q

Explain the Adenylate Cyclase cAMP pathway:

A

Epinephrine binds Beta-andrenergic receptor
GDP > GTP
activated Adenylate cyclase (protein/protein interaction)
Adenylate cyclase causes ATP > cAMP,

which activates Protein Kinase A

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46
Q

How do stimulatory and inhibitory (Gs and Gi) heterotrimers work in regards to cAMP

A

Gs activates cAMP
Gi inhibits cAMP

(through separate stimulatory/inhibitory receptors and G-complexes), affecting Adenylyl cyclase

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47
Q

T/F

cAMP inhibits Protein Kinase A

A

False

cAMP activates the regulatory subunits of PKA to release its catalytic subunits
it phosphorylates the targets Ser and Thr, and stimulates transcription activator CREB

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48
Q

Describe how Acetylcholine opens an ion channel (in neurotransmitter)

A

Acetylcholine binds,
GDP > GTP in G-complex dissociates the complex
G-beta binds adjacent channel, allowing K to flow out

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49
Q

How does the inactivation of a receptor work (two steps)?

A
  1. Dissociation of signalling molecule

2. phosphorylation of cell-side of receptor, followed by binding of Beta-Arrestin

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50
Q

How are GTP and cAMP inactivated?

A

GTP - hydrolyzed by intrinsic GTPase

cAMP - by cAMP phosphodiesterase

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51
Q

What are two pathologies arising from a failure to inactivate signal?

A

Cholera and whooping cough (pertussis)

both cases activate G-proteins, which increases cAMP, which leaves ion channels open

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52
Q

8 steps of phosphoinostide cascade

alternative 2nd messenger system for 7TM Receptors

A
  1. GCPR/ligand dissociates G-beta inside cell,
  2. PIP2 (phosphatidylinositol) > IP3 (inositol)
  3. IP3 binds Ca+ ion channel
  4. IP3- gated Ca2+ channel open
    5-8. PKC (protein kinase C) activated by Ca, phosphorylates substrates
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53
Q

What does IP3 cause?

A

rapid release of Calcium from the endoplasmic reticulum

which further activates PKC and Calmodulin

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54
Q

Flow of Nitric Oxide pathway:

A

Ach > Ach GPCR > Phospholipase C > Ca/Calmodulin > NO synthase > NO receptor > PKG

relaxation of muscle cell

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55
Q

What is the function of NO

A

Relaxes smooth muscle
prevents platelet aggregation
neurotransmitter in brain
mediates tumoricidal/bactericidal actions of macrophage

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56
Q

What type of receptor is the insulin receptor?

A

Catalytic

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57
Q

What receptor has a protein kinase as part of its structure and is a good example of transduction?

A

Insulin

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58
Q

Describe 2 ways how a signal is relayed via intracellular receptors:

A

Hormone enters nucleus > binds receptor > transcription > translation > new protein >altered cell function

Peptide or amine binds outside of cell and acts via 2nd messengers to alter gene expression

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59
Q

Name 5 Glycerophospholipids

A 
Phosphatidic acid
Phosphatidylethenolamine
Phosphatidylcholine
Phosphatidylserine
Phosphatidylinositol
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60
Q

What is the free energy of a reaction?

A

Energy available to do work

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61
Q

NADH serves to carry…

A

electrons

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62
Q

[conc] 10 -2 M to 10 -4 M

A

Spontaneous

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63
Q

Which lipid is both a phospholipid and sphingolipid?

A

Sphingomyelin

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64
Q

Which variety of membrane transport coupling involves one species in and another out?

A

Antiporters

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65
Q

T/F

Signal transduction by catalytic receptors and intracellular receptors are both mediated by G-proteins

A

False

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66
Q

Which rxn pathways transform fuels into energy?

A

Catabolic

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67
Q

Exergonic rxns are:

A

spontaneous

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68
Q

Which enzyme begins the phosphoinositol cascade?

A

Phospholipase C

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69
Q

cAMP releases inhibition of, thereby activating…

A

PKA

Protein Kinase A

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70
Q

Glc enters most cells via

A

Facilitated diffusion

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71
Q

3 ways metabolism can be regulated:

A

Hormone
Allosteric
Compartmentalization

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72
Q

Ceramide is a…

A

Sphingolipid

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73
Q

What do both active transport and facilitated diffusion require?

A

Integral membrane protein

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74
Q

AA review. What 2 things does every Amino Acid have?

A

Amino group and Carboxyl group attached to alpha-C

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75
Q

pH=

A

-log [H+]

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76
Q

Why is pH biologically important?

A

charges in environment affect charge of molecule (and therefore shape)

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77
Q

Which acid is stronger,
Formic acid pKa=3.75
Acetic acid pKa=4.76

A

Formic

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78
Q

Henderson-Hasselbach equation:

A

pH = pKa + log [A-]/[HA]

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79
Q

When is buffering optimal?

A

when acid = base

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80
Q

When acid = base,

A

pH = Pka

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81
Q

What is the term for an amino acid that can act either as an acid or a base?

A

Amphoteric

aka - zwitterion

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82
Q

What does an Amino Acid titration curve look like, and what is in the middle?

A

Two plateaus, each representing the pKa of the carboxyl and amino group.

pI = average of the pKa’s

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83
Q

Generally, the pKa’s of carboxyl groups are around ______ , while the pKa’s of Amino groups tend to be around ___.

A

carboxyl = around 2

amino = around 9

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84
Q

The pI, or isoelectric point, is defined as the _________.

What will a molecule do in an electric field (like electrophoresis) at the isoelectric point?

A

point in which there is no net charge on a molecule

won’t move

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85
Q

In terms of charge, how is Histadine different than other AA’s?

A

It has three dissociations (and therefore 3 pKa’s)

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86
Q

Around how many polar and non-polar R groups are there for AA’s?

A

10 polar

10 non-polar

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87
Q

Which amino acid makes serotonin?

which makes dopamine?

A

Tryptophan

Tyrosine

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88
Q

What are the 5 amino acids that carry a charge?

A

Lysine, Arginine, and Histidine (positive)

Aspartate and Glutamate (negative)

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89
Q

What is special about a peptide bond?

A

partial double bond character
rigid and planar
trans configuration
uncharged but polar

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90
Q

What is the conventional direction of an Amino Acid?

A

From N (amino) to C (carboxyl)

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91
Q

Primary, secondary, and tertiary structure

A

AA sequence

Beta sheets, alpha helix (can be parallel or antiparallel), Beta bends and turns.

Folding (intra-structural interactions) - nonpolar usually inside, polar outside

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92
Q

What are structural motifs?

A

This is a supersecondary structure in which individual elements of secondary structure are combined into stable, geometrical arrangements (like helix bundles)

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93
Q

What stabilizes tertiary structure?

A

Non-covalent interactions (hydrophobic, ionic, and H-bonds)

Covalent interactions (peptide bonds, disulfide bonds)

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94
Q

What is the difference between a polypeptide and a protein?

A

Polypeptide is one chain of AA’s

Protein can be made from multiple polypeptides.

(this is Quaternary Structure)

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95
Q

What is the main driving force for the assembly Quaternary Structure?

A

Hydrophobic interactions

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96
Q

What is the difference between a fibrous and globular protein?

A

Fibrous - water insoluble, lack tertiary structure (think hair)

Globular - water soluble (most proteins, etc)

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97
Q

If a molecule has a pKa, it is by definition a…

A

weak acid

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98
Q

At a pH below the pI, proteins carry a net ______ charge, and above the pI, proteins carry a net _____ charge.

A

positive

negative

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99
Q

What does a large pKa tell you about an acid?

A

It is very weak

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100
Q

What is in a conjugated protein?

A

a Prosthetic Group, such as lipids, metal (blood), phosphate groups, etc.

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101
Q

How do temperature and pH affect enzymes?

A

Temp - increase rate of rxn up to point

pH - change charge, conformation, shape

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102
Q

What is the turnover number?

A

The maximum number of molecules of substrate an enzyme can convert to product

(molecules converted/sec.)

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103
Q

How is catalytic efficiency determined?

A

Kcat/Km

low Km means high efficiency/high affinity for substrate

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104
Q

T/F

Enzymes only bind one substrate

A

False.

Enzymes have a range of specificity

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105
Q

Give an example of an enzyme with high specificity.

Low specificity?

A

Urease - absolute specificity

Chymotrypsin - breaks peptide bonds in a broad range (most specific for phenylalanine)

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106
Q

What is the additional ingredient many enzymes require to function?

A

A cofactor

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107
Q

Define Holoenzyme, Apoenzyme

A

Holoenzyme - Enzyme with its cofactor

Apoenzyme - protein portion of the holoenzyme (no cofactor and inactive)

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108
Q

T/F

Coenzymes are non-protein organic molecules

A

True

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109
Q

What is the term for a tightly bound nonpolypeptide non-dissociating structure in an enzyme?

A

Prosthetic Group

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110
Q

Define:
Vmax
Km
Kcat

A

max rate enzyme activity at substrate saturation

substrate [conc] at 1/2 Vmax

turnover number (substrate converted/time)

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111
Q

What term defines catalytic efficiency (how effective an enzyme is at catalyzing rxns)

A

Kcat/Km

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112
Q

What are 3 types of enzymatic reactions?

A

Random (creatine kinase)

Sequential displacement (defined order)

Double Displacement (enzyme > intermediate > enzyme)

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113
Q

What are the 5 key landmarks of a Michaelis-Menten graph

A 
Vmax
1/2 Vmax
Km
1st Order linear rxn zone
0 Order
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114
Q

The Km is referred to as the:

A

Michaelis constant

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115
Q

In a Lineweaver-Burke plot, what do the following indicate
The x-intercept
the y-intercept
the slope

A

-1/Km
1/Vmax
Km/Vmax

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116
Q

Describe the rxn when [S] is less than, equal to, and greater than Km

A

[S] less - optimal rxn velocity

[S]=Km - half max velocity

[S] greater - rxn approaches Vmax

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117
Q

What are the 3 types of enzyme inhibition?

What are their effects on a lineweaver-burke plot

A

Competitive - goes for same active site (Vmax same, Km increases)
Increase slope around the y-axis

Noncompetitive - binds other site on Substrate, changes conformation
Increase slope, but rotates at x-axis

Uncompetitive - Vmax and Km decrease (traps enzyme)
parallel slope

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118
Q

What are the effects of Allosteric positive and negative modifiers?

A

Allosteric positive - Increases affinity of enzyme for substrate

Allosteric negative - Decreases affinity for enzymes to substrate

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119
Q

What is a proenzyme (aka zymogen), and what is an example?

A

Inactive enzyme precursor

pancreatic and blood-clotting pathways (Trypsinogen)

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120
Q

What are isoenzymes?

A

Alternate forms of enzymes existing in different proportions in different tissues (tissue specificity)

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121
Q 
Define:
Aldose
Ketose
Enantiomer
Epimer
Glycosidic bond
A

aldose - carbohydrate with aldehyde as oxidized functional group
ketose - carb with keto as oxidized functional group
enantiomer - non-super imposable mirror images (hands)
epimer - single carbon atom configuration difference
glycosidic bond - carb/carb bond (hemiacetal to hydroxyl)

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122
Q

What is an oligosaccharide?

A

2-12 monosaccharides

under - mono
over - poly

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123
Q

What is a pyranose?

Furanose?

A

pyranose - hexagonal sugar

furanose - pentagonal sugar

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124
Q

What is an anomer?

example?

A

special type of epimer

alpha and beta-D-Glucose are anomers

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125
Q

Where is the hydroxyl group oriented in Alpha D glucopyranose?
Beta D glucopyranose?

A

alpha - hydroxyl on bottom

beta - hydroxyl on top

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126
Q

What can humans digest, alpha or beta glc?

A

Alpha = glycogen chains

Beta = cellulose

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127
Q

How is glycogen branched?

A

Alpha 1,4 (linear) AND Alpha 1,6 (branched) linkages

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128
Q

What is starch made from?

A

Amylopectin (highly branched Alpha 1,4 and Alpha 1,6) and

Amylose (spiral polymer of D glc)

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129
Q

What is cellulose made from

A

Linear chain of Beta 1,4 D Glucose

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130
Q

What makes up the disaccharides Maltose and Lactose?

Sucrose?

A

Maltose - 2 glc (Alpha 1,4)

Lactose - 2 BETA D glc (Beta 1,4)

glc/frc (Alpha 1, Beta 2)

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131
Q

What calcium dependent enzyme is found in saliva and what does it break down?

A

Salivary Amylase

breaks down Alpha 1,4

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132
Q

What breaks Alpha 1,4 glycosidic bonds in the mouth?

What breaks them in the small intestine?

A

Salivary Amylase

Pancreatic Amylase

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133
Q

What 4 brush border enzymes break down disaccharides?

A

Isomaltase, maltase, lactase, and sucrase

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134
Q

What does Isomaltase break down?

A

Alpha 1,6 glycosidic bonds

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135
Q

How does glc move from the lumen to the blood?

A

Symporter (secondary active transport) into enterocyte (cytosol)

Glc then moves through basolateral membrane through GLUT2 transporters (integral membrane proteins) by Facilitated Diffusion

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136
Q

Describe the role of glc transporters in sugar metabolism.

A

GLUT2 IMP’s move glc down concentration gradient through Facilitated Diffusion

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137
Q

What are 4 effects of fiber in the the diet?

A

Increase stool volume
Increase stool softness
Decrease transit time
Increase satiety

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138
Q

What 2 things does passage of undigested carbohydrate into the large intestine cause?

A

Osmotic diarrhea

Bacterial fermentation of carbohydrate to 2 and 3 C fragments (plus carbon dioxide and hydrogen gas)

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139
Q

What is the most common disaccharide enzyme deficiency?

What disaccharide enzyme deficiency hasn’t been observed?

A

Lactase

Maltase

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140
Q

What oral bacteria attaches to the tooth surface and is a precursor to plaque?
What occurs after attachment?

A

S. mutans

biofilm wall builds and acidic bacterial waste leeches calcium out of enamel

141
Q

What makes up the bacterial biofilm wall of S. mutans?

A

Dextran - made from Alpha 1,3 glycosidic linkage (no known enzyme)

142
Q 
What type of linkages are in the following:
Glucose
Starch
Glycogen
Cellulose
Dextran
A

glc: Alpha 1,4 (mostly) and Alpha 1,6 (some)

starch: Alpha 1,4
glycogen: Alpha 1,4

cellulose: Beta 1,4

Dextran: Alpha 1,3

143
Q

What two disaccharide species are synthesized together?

A

Sucrase-Isomaltase

they are one unit

144
Q

Where does glycolysis occur, and what are its aerobic and anaerobic products?

A

cytoplasm

glucose > pyruvate (aerobic)
glucose > pyruvate > lactate (anaerobic)

145
Q

What does 1 molecule of glucose yield in glycolysis?

A

2 ATP (net)
2 pyruvate
2 NADH

146
Q

What does the energy investment phase of glycolysis consist of?

A

Phosphorylation of glc > glc 6 phosphate (Step 1) - costs 1 ATP

Frc-6-phosphate > Frc 1,6 bisphosphate (via PFK-1) - costs 1 ATP

(this results in TWO Glyceraldehyde 3 phosphates)

147
Q

Explain the energy payoff phase of glycolysis.

A

Glyceraldehyde-3-phosphate > 1,3 bisphosphoglycerate
(this step requires the reduction of NAD to NADH)

> 3 - Phosphoglycerate 1 ATP
(two steps)
Phosphoenolpyruvate > Pyruvate 1 ATP

148
Q

What type of phosphorylation occurs in Glycolysis?

A

Substrate-level phosphorylation

149
Q

What is the chief role of glycolysis in skeletal muscle?

Liver?

A

supply ATP for muscle contraction

excess glc in liver converted to fat

150
Q

Why do erythrocytes only derive ATP through anaerobic glycolysis?

A

No mitochondria (or other organelles)

151
Q

What happens to glc in the brain?

A

It is oxidized completely to carbon dioxide and water (process begins with glycolysis)

152
Q

Where are GLUT 1-5 found?

glucose transporters

A

GLUT1 - brain and rbc
GLUT2 - liver, kidney, intestine, beta cells
GLUT3 - nearly all cells
GLUT4 - muscle/adipose (insulin-dependent isoform)
GLUT5 - small intestine

153
Q

What are some insulin-insensitive (insulin independent) tissues?

A

rbc’s, leukocytes, lens of eye, cornea, liver, brain

154
Q

What is the name of the cotransport symporter of glucose from lumen?

155
Q

What are 3 main regulators of Glycolysis?

A

Hexokinase
Pyruvate Kinase
PFK1

156
Q

What enzyme is allosterically inhibited by Glucose-6-Phosphate?

A

Hexokinase (aka Glucokinase)

157
Q

What are the 3 irreversible steps in glycolysis?

A

hexokinase
phosphofructokinase I
pyruvate kinase

158
Q

What is the major committing step of glycolysis, and what is its enzyme?

A

Step 3 (frc-6-phosphate > frc-1,6-bisphosphate)

PFK-1

159
Q

What 2 things regulate hexokinase activity in muscle cells?

A

Inhibited by high [conc] glc in blood

Inhibited by high [conc] glc-6-phosphate

160
Q

What is hexokinase called in the liver?

Does it saturate?

A

Glucokinase

no

161
Q

What activates PFK-1?

What de-activates PFK-1?

A

activated by:
frc-6-phosphate, ADP, AMP, frc-2,6 bisphosphate

decreased by:
ATP, citrate

162
Q

What is the last irreversible step of glycolysis?

What enzyme catalyzes?

A

PEP (phosphoenolpyruvate) > pyruvate

Pyruvate Kinase

163
Q

What inhibits Pyruvate Kinase activity?

A

ATP
covalent modification
high [conc.] Acetyl CoA
long chain fatty acids

164
Q

Describe the differing kinetic characteristics of Hexokinase and Glucokinase.

A

Hexokinase has a low Km, which means a high affinity for glc

Glucokinase has a high Km, which means a low affinity for glc in liver cells

(why? cells need glc for fuel. excess goes to liver for storage)

165
Q

What do all GLUT transporters have in common?

A

All are IMP’s using facilitated diffusion and allow glc to travel down its concentration gradient.

166
Q

GLUT 1-4

Is their Km high or low, what does that mean?

A

GLUT1 - low Km, high affinity for glc
GLUT2- highest Km, low affinity for glc
GLUT3- low Km, high affinity for glc
GLUT4- low Km, high affinity for glc

167
Q 
Describe the tissue specific roles glc plays in the following:
Skeletal muscle
Liver cells
Erythrocytes
Brain
A

Muscle - glc chief in supplying ATP for contraction
Liver - excess glc stored
RBC’s - anaerobic glycolysis of glc only
Brain - exclusively glc (using glycolysis, TCA, and oxidative phosphorylation)

168
Q

What type of channels are found in the outer membrane of mitochondria, and what do they allow to pass through?

A

Porins

Allow Pyruvate through

169
Q

What is found in the double layered inner membrane in the mitochondria and what is allowed to pass through?

A

Electron carriers I-IV, ATP synthase, Cristae

Impermeable to pretty much everything, even gases and especially H+

170
Q

What is contained in mitochondrial matrix?

A

Pyruvate dehydrogenase complex
TCA enzymes
Fatty acid Beta-oxidation enzymes
AA oxidation enzymes

171
Q

At the end of glycolysis, what are the 4 metabolic options for pyruvate?

A

Pyruvate can be converted to:

Lactate (anaerobic)

Alanine (AA)

Acetyl CoA (then TCA) *pyruvate dehydrogenase complex

Oxaloacetate (then TCA or Gluconeogenesis - anaplerotic)

172
Q

Under what conditions does the metabolite (pyruvate) proceed to the Citric Acid Cycle?

A

When there isn’t much Acetyl CoA

Acetyl CoA either upregulates or downregulates Pyruvate conversion into Acetyl CoA, depending on its concentration

173
Q

What happens to pyruvate if the Acetyl CoA concentration is low?

A

Pyruvate > Acetyl CoA

174
Q

What happens to pyruvate if the Acetyl CoA concentration is high?

A

Pyruvate > Oxaloacetate

175
Q

How does pyruvate enter the mitochondrial matrix?

A

Antiports (secondary active transport) with -OH via a Porin

catalyzed by Pyruvate Translocase

176
Q

What happens to pyruvate upon entry into the mitochondria?

A

Attaches to PDHC

pyruvate dehydrogenase complex

177
Q

What are the 5 co-enzymes for the PDHC, and what are they derived from (4/5)?

A 
TPP     Thiamine (B1)    
Pantothentate     CoA-SH (B5)
FAD      Riboflavin (B2)
NAD     niacin (B3)
Lipoic acid
178
Q

Describe the conversion of Pyruvate into Acetyl CoA.
What enzyme does this?
Is it reversible?

A

PDHC (pyruvate dehydrogenase complex) is enzyme.

decarboxylation (loss CO2)
NAD > NADH
S-CoA (power pack)

Not reversible (very negative delta G)

179
Q

Name 5 allosteric inhibitory molecules for PDHC.

A 
ATP
Acetyl CoA
NADH
GTP
long chain fatty acids
180
Q

Name 4 allosteric activating molecules for PDHC.

A

AMP
CoA
NAD+
Ca2+

181
Q

Describe the two covalent regulatory mechanisms of PDHC.

A

Phosphorylation of PDHC (inhibition)
Glucagon > GCPR > cAMP > PKA > phosphorylates

Dephosphorylation of PDHC (activation)
Insulin > Tyrosine Receptor Kinase > phosphatase > PDHC

182
Q

Each turn of the Citric Acid Cycle feeds in ___ Carbons in the form of Oxaloacetate, and gives off ____ Carbons in the form of Carbon dioxide.

183
Q

The 4 redox rxns in the citric acid cycle yield:

A

3 NADH

1 FADH2

184
Q

What is the 1 high energy phosphate bond formed with every turn of the citric acid cycle?

185
Q

What are the 4 mechanisms of regulation in the citric acid cycle?

A

PDHC rxn
Citrate Synthase rxn
Isocitrate Dehydrogenase rxn (decarboxylation)
Alpha - Ketoglutarate Dehydrogenase rxn (decarboxylation)

(these are in order)

186
Q

What inhibits the strongly exergonic steps in the CAC?

A

high ATP, NADH, and Citrate concentrations

187
Q

Why is the CAC important for biosynthesis?

A

Citrate, alpha-ketoglutarate, succinyl CoA, and Oxaloacetate all create 4C and 5C intermediates that serve as precursors for a variety of products.

188
Q

What pathways do the precursors Citrate and Oxaloacetate enter from the CAC?

A

Citrate - Fatty acids and steroids

Oxaloacetate - Aspartate, AA’s, purines, pyrimidines, GLC

189
Q

How is Sorbitol created?

A

Glc > Mannose > Frc-6-P > Sorbitol

190
Q

What cells create Sorbitol and why?

What are the effects of too much sorbitol?

A

Cells, like lens of eye and schwann - that allow easy import of glc but have no way of converting sorbitol to frc

Osmotic effects and swelling

191
Q

What happens if a cell doesn’t want to give up its phosphates when glucose enters?

A

It converts glucose to Sorbitol

192
Q

What does the PPP (pentose phosphate pathway)

(aka - Hexose monophosphate shunt and phosphogluconate pathway) produce?

A

NADPH

Ribose-5-Phosphate

193
Q

What tissues have active PPP’s?

A

Mammary, testes, ovary, adrenal cortex (steroid)
Adipose
Liver
RBC’s

(any tissue synthesizing fatty acids and steroids)

194
Q

What is the oxidative pathway of the PPP?

A

G-6-P > lactone > Ribulose-5-P

isomerization changes to ribose-5-P

195
Q

What occurs in the PPP if cells need NADPH more than ribose-5-P?

A

The Non-Oxidative pathway

Carbon atoms of ribose-5-P can be recycled/rearranged

196
Q

What does reduced glutathione do?

A

detoxifies hydrogen peroxide to water

197
Q

What is the enzyme that rids the cell of hydrogen peroxide?

A

Glutathione peroxidase

198
Q

How does the cell regenerate glutathione?

A

Reduces it with NADPH (from the PPP)

199
Q

T/F

Gluconeogenesis is a universal pathway.

200
Q

What is the major function of gluconeogenesis?

3 Additional functions?

A

Major: provides glc to brain, nervous system, etc when blood sugar low

Minor:
Control acid/base balance
Maintain AA balance
Provide biosynthetic precursors

201
Q

Name 4 important precursor molecules to glucose.

A

lactate
pyruvate
glycerol
most AA’s

202
Q

What is the major site of GNG in the body?

A

Liver

but also kidney

203
Q

T/F

GNG is the reverse of glycolysis

A

False

there are 3 irreversible steps of glycolysis GNG needs to get around

204
Q

Where do lactate and some AA’s enter the GNG pathway?

A

Step 1

pyruvate > oxaloacetate

205
Q

Where two places do AA’s enter the GNG pathway

A

Step 1
(pyruvate > oxaloacetate)

Step 2
(oxaloacetate > phosphoenolpyruvate)

206
Q

Where does glycerol enter the GNG pathway?

A

Step 7

Glyceraldehyde-3-P > dihydroxyacetone phosphate

207
Q

In the beginning of GNG, what enzyme initiates the molecule’s exit from the mitochondria?
(this is a key enzyme - bypass 1)

A

Pyruvate carboxylase

208
Q

What are the steps the pyruvate molecule takes to exit the mitochondria in GNG?

A

Pyruvate (pyruvate carboxylase) > oxaloacetate > Maltase > oxaloacetate

(maltase can cross the IM)

209
Q

What enzyme simultaneously decarboxylates and phosphorylates oxaloacetate in GNG?

A

PEP carboxykinase

210
Q

What does anaplerotic mean?

A

replenishing

211
Q

What is lactate converted to in the liver?

A

Pyruvate

then goes to mitochondria and enters GNG path

212
Q

In GNG, what catalyzes Frc 1,6 bisP > Frc-6-P?

bypass 2

A

Fructose 1,6 bisphosphatase

213
Q

What is the enzyme that coverts Glc-6-P to D-Glc?

this is bypass 3 and allows molecule to exit cell

A

Glucose 6-Phosphatase

214
Q

From whence comes glycerol in the GNG pathway?

what is it broken down into?

A

triacylglycerol (fat)

glycerol > glycerol 3-P (by glycerol kinase)

215
Q

How many high energy bonds are required to synthesize glucose from pyruvate?

How many generated from breakdown from glucose to pyruvate?

A

4 ATP + 2 GTP = 6 bonds (also 2 NADH required)

2 ATP

216
Q

What stimulates pyruvate carboxylase (and thus pyruvate dehydrogenase (and thus GNG)?

this is control point 1!

A

Acetyl CoA

217
Q

What moves the GNG/Glycolytic pathway (control point 2!) between frc-1,6-bisphosphate and frc-6-P?

A

low energy (high levels AMP/ frc-2,6-BP depressed citrate/ATP/H+) moves toward Frc-1,6BP (glycolytic)

high energy (low frc-2,6-BP/AMP and high Citrate) moves toward Frc 6-P (GNG)

218
Q

How does fructose 2,6-BP play a role in whether glc will be degraded or synthesized?

A

Starvation > glucagon > frc 2,6-BP drops

this encourages GNG by decreasing activity of PFK1 and increases activity of phosphatase

219
Q

T/F

Glucagon decreases the activity of pyruvate kinase.

220
Q

What is the Cori Cycle?

A

(muscle) glc > lactate
(liver) lactate > glc

and back to muscle

221
Q

What is glc 2,6-BP regulated by?

A

Insulin/Glucagon ratios

222
Q

What does liver do with glc and what does muscle do with glc?

A

Liver: converts glycogen > G-6-P > Glc > blood
(maintains blood glc levels)

Muscle: glycogen > G-6-P > Glc > ENERGY

223
Q

T/F

Glycogen is in almost every cell of the body

224
Q

Describe the structure of glycogen.

A

Glc connected by Alpha 1,4 bonds and branches of Alpha 1,6 bonds

Reducing ends inside, non-reducing (C1) outside

225
Q

Where is most glycogen stored in the body?

A

Skeletal muscle

but liver stores 4-7x more/weight

226
Q

What is the key enzyme in glycogen synthesis?

A

Glycogen synthase

227
Q

Glycogen synthesis pathway:

key enzyme:

A

Glc > G-6-P > G-1-P > UDP > Glycogen

Glycogen synthase

228
Q

What makes the Alpha 1,6 linkages in glycogen?

A

Glycosyl 4,6 transferase

229
Q

Glycogen breakdown pathway plus 3 options:

A

glycogen > G-1-P > G-6-P then,

  1. glycolysis > pyruvate
  2. glucose (via glc-6-phosphatase)
  3. PPP
230
Q

What is the key enzyme in the breakdown of glycogen?

A

Glycogen Phosphorylase

231
Q

What primer does Glycogen Synthase need to carry out glycogen synthesis?
What bond does it catalyze?

A

Glycogenin

Alpha 1,4 glycosidic

232
Q

What helps glycogen synthase by acting as a sort of scaffolding on which to build glycogen?

A

sugar nucleotides

233
Q

What enzyme do glycogenesis and glycogenolysis have in common?

A

phosphoglucomutase

234
Q

What are the 2 forms of Glycogen Synthase, and how are they regulated hormonally?

A

A (active): insulin + OH = not phosphorylated (make glycogen)

B (inactive): Phosphate + glucagon

235
Q

What are the 2 forms of Glycogen Phosphorylase, and how are they regulated hormonally?

A

A (active): Phosphate + glucagon (make glucose)

B (inactive): Insulin + OH

236
Q

Describe the allosteric regulation of glucose.

A

Increasing glc concentration stores glycogen

Increasing AMP concentration liberates glycogen

237
Q

Why is Von Gierke’s disease so detrimental to the liver but not to muscle cells?

A

defect in G-6-Phosphatase won’t allow glc to leave liver.

muscle uses it all

238
Q

What are some symptoms of Von Gierke’s?

A

hypoglycemia
hyperlipidemia
lactate acidosis
enlargement of liver

239
Q

Why can we make fat from carb but not carb from fat?

A

Pyruvate > Acetyl CoA via pyruvate dehydrogenase is irreversible

240
Q

T/F

the Citric Acid Cycle is regulated by availability of NAD+

241
Q

Ratio of NAD+/NADH

Ratio of NADP+/NADPH

A

1000/1 (lots NAD+)

0.1 (lots NADPH)

242
Q

What is the purpose of NADPH?

A

defeats free radicals and biosynthesis

243
Q

What is a rate limiting step (PPP) with lots of clinical implications (think RBC’s)

A

G-6-P Dehydrogenase

favaism

244
Q

How much ATP is made from each NADH and FADH2 molecule in the ETC?

A

NADH - 2.5
FADH2 - 1.5

(each donate 2 electrons)

245
Q

What enzymes are involved in NADH/FADH2 reduction/oxidation

A

oxidoreductase/dehydrogenase

246
Q

From what vitamin is NAD synthesized?

247
Q

FADH2 is considered to be…

A

a redox cofactor

248
Q

What 3 places is NADH is formed in catabolism?

A

glycolysis
pyruvate dehydrogenase complex
CAC

249
Q

What structure in the outer membrane of mitochondria make it permeable to most ions and small molecules?

250
Q

T/F

The inner mitochondrial membrane is impermeable to most ions and small molecules.

251
Q

What two molecules have transporters to cross the IMM?

A

G-3-P and Malate

252
Q

What molecules are paired to make the malate shuttle run?

A

Oxaloacetate > Malate (NADH > NAD+) > (NAD+ > NADH) Oxaloacetate > Alpha-ketoglutarate (comes back out)

Glutamate > Aspartate (comes out)

253
Q

Where is the low pH found in the mitochondria?

A

Intermembrane Space

254
Q

The IMM is folded into:

and is only permeable to:

A

Cristae

CO2, O2, H2O

255
Q

What is the destination of NADH and FADH2 (both products of the CAC) in the ETC?

A

NADH - Complex I

FADH2 - Complex II

256
Q

What are the two prosthetic groups in Complex I of the ETC?

How many H- are moved to the IMM with each NADH?

A

FMN > Fe-S

4 H-

257
Q

What prosthetic group is found in Complex I, II, and III?

258
Q

What complex doesn’t move hydrogen into the IMM?

A

Complex II

FADH2 complex

259
Q

How do electrons in Complex I travel straight to Complex III?

260
Q

Complex I:

Effector molecule, enzyme, prosthetic groups, number Hydrogens transported to IMM

A

NADH
NADH-Q oxidoreductase
FMN (Flavin Mononucleotide), Fe-S
4

261
Q

Complex II:

Effector molecule, enzyme, prosthetic groups, number Hydrogens transported to IMM

A

FADH2
Succinate Q dehydrogenase/reductase
FAD, Fe-S
0

262
Q 
Complex III:
receives electrons via
transports electrons via
prosthetic group
Hydrogens transported to IMM
A

CoQ
Cytochrome C
Fe-S, Heme groups
4

(the Q cycle)

263
Q

What is oxidized to Q in complex III?

A

Ubiquinol (QH2)

264
Q

What is the last enzyme in the ETC?

A

Cytochrome C oxidase complex

265
Q

Complex IV:

effector molecule, enzyme, prosthetic groups, number hydrogens transported to IMM

A

CoQ
Cytochrome C oxidase
Heme a & a3, CuA & CuB
2

(only one doesn’t use Fe-S clusters)

266
Q

Explain the Q cycle that occurs in Complex III:

A

Q pool > QH2 > Q

from QH2, e- either

  1. Cyt C1 and Cyt C
  2. Q radical > QH2 > Q pool
267
Q

What is the final receptor in Complex IV?

268
Q

How are electrons passed to oxygen in complex IV?

A

2 cytochrome C pass electrons through CuA/CuB, HemeA/HemeA3/CuB

HemeA3 to CuB (iron copper) peroxide bridge

2 more cytochrome C, and more electrons to the system cleaves off the oxygens when 2 Hydrogens cleave the peroxide bridge.

2 more hydrogens added releases 2 water molecules

269
Q

What is a reduction potential?

A

Tendency of species to acquire electrons

the more positive, the greater the affinity

270
Q

What electron receptor has the largest and most positive reduction potential?

271
Q

What enzyme universally converts free radicals to hydrogen peroxide?

A

Superoxide dismutase

commonly found as tetramer with Mn in reactive center

272
Q

What hypothesis involves ATP being synthesized via electrochemical gradient?

A

Chemiosmotic hypothesis

273
Q

Can ATP synthase run in reverse?

274
Q

What two molecules have transporters to move across the IMM?

A

G-3-P (glycerol-3-phosphate)

Malate

275
Q

What enzyme is used in the Glycerol-3-Phophate shuttle and what is exchanged?

A

Glycerol-3-Phosphate dehydrogenase

exchanges FADH2 for NADH

276
Q

What is the defining feature of connective tissue?

A

Extra cellular matrix

277
Q

What are the four main classes of molecules found in the ECM?

A

Fibers
Glycoproteins
Glycosaminoglycans
Proteoglycans

278
Q

What is the ground substance?

A

ECM without the fibers

composed of glycoproteins, glycosaminoglycans, proteoglycans

279
Q

What is calcified ECM called?

280
Q

What are the two main classes of macromolecules making up the ECM?

A

Proteoglycans (GAG’s)

Fibrous/Multi-adhesive proteins (collagen/fibronectin)

281
Q

What are the 4 major classes of GAG disaccharides?

A

Hyaluronan
Chondroitin sulfate
Heparan sulfate
Keratan sulfate

282
Q

What class of GAG does not form proteoglycans?

A

Hyaluronan

283
Q

What is the most abundant GAG in the body?

A

Chondroitin sulfate

284
Q

What molecule is a long unbranched chain of polymers of repeated disaccharides containing an amino sugar?

A

Glycosoaminoglycans

285
Q

What makes GAG’s gels?

A

sulfate and carboxyl groups - for volume

high density of negative charge (attracts water)

286
Q

What is the overall function of GAG’s?

A

maintains homeostatic environment

287
Q

What is Heparin?

A

strong anticoagulant

not to be confused with Heparan - part of GAG structure

288
Q

What is a proteoglycan?

A

A chain of GAG’s (joined covalently to a membrane or protein structure)

mostly carbohydrate by mass

289
Q

What is the major structural proteoglycan found in cartilage?

290
Q

What molecule can be bound to but does not form Proteoglycans?

A

Hyaluronic acid

291
Q

What strengthens the ECM and what gives it resilience?

A

Collagen

Elastin

292
Q

What are 3 classes of Proteoglycans?

What are some of their structural motifs?

A

Small leucine-rich (SLRP’s) - biglycan, decorin

Modular - perlecan, agrin, aggrecan

Cell-surface - syndecan

293
Q

Describe a proteoglycan aggregate.

A

GAG’s attached to long fibers forming Proteoglycans attached to Hyaluronate backbone

(feathers on Hyaluronate)

294
Q

Are Proteoglycan aggregates linked to a protein core?

A

NO

Hyaluronate is apparently not protein

295
Q

What molecule is considered the biological shock absorber?

A

Hyaluronate

296
Q

How is Hyaluronan unique among the GAG’s?

A

No sulfate

297
Q

How are proteoglycans anchored to membranes?

A

Syndecan-1 (part of PG) binds to Chemokines (on cell)

298
Q

Describe Proteoglycan synthesis.

A

tetrasaccharide linker connects GAG to Ser residue (O-linked) in the core protein.

Then sugar nucleotides add sequentially by glycosy transferases

Epimerizations/sufations occur prior to exocytosis

299
Q

What is the result of abnormal proteoglycan catabolism?

A

arthritis, tumor invasions

300
Q

What makes proteoglycans suseptible to proteases?

A

linear conformation

but they have a range of inhibitors

301
Q

What ingredients are required to lysosomally catabolize proteoglycans?

A

3 Exolglycosidases
4 Sulfatases
1 Acetyl trasferase

and step-wise removal of monosaccharides

302
Q

What pathology is defined by enzyme deficiency, autosomally recessive or x-linked, severe and mild forms, and not apparent at birth?

A

Mucopolysaccharide (GAG) defects

aka Lysosomal storage disease

303
Q

What molecules do not accumulate in Lysosomal storage disease?

A

Chondroitin sulfate

Hyaluronate

304
Q

What molecule has both a GAG form and a proteoglycan form?

A

Hyaluronate

305
Q

What two components of the ECM provide strength, shape and elasticity?

A

Collagen and Elastin

306
Q

What two components of the ECM are multi-adhesive, providing attachment for matrix components as well as cells?

A

Fibronectin and Laminin

307
Q

What integral membrane proteins connect ECM to cells?

308
Q

What is the most abundant protein in the body?

309
Q

What purposes do the major proteins found in the ECM serve?

A

Structure and Adhesion

310
Q

Structure in the ECM is provided by…

A

Collagen and Elastin

311
Q

Adhesion in the ECM is provided by…

A

Fibronectin and Laminin

312
Q

Collagen is a glycosylated protein rich in what 4 AA’s?

A

Glycine
Proline
Hydroxyproline and Hydroxylysine

313
Q

The normal AA sequence of collagen is:

A

Gly-Pro-Y
Gly-X-Hyp (Hydroxyproline)

X,Y = any AA

314
Q

How many types of collagen are there?

How many “major” types?

315
Q

Where are the 4 major types of collagen found?

A

I Skin, bone, tendon, bv’s, cornea
II Cartilage, intervertebral discs
III Blood vessels, fetal skin
IV Basement membrane

316
Q

What type of collagen accounts for 90% found in body?

317
Q

What 5 steps of collagen synthesis occur in the ER and Golgi complex?

A
  1. Synthesis of pro-alpha chain
  2. Hydroxylation (pro and lys)
  3. Glycosylation (selected hydroxylysines)
  4. Pro-alpha chains self assemble
  5. Procollagen triple helix forms
318
Q

What are the 4 steps of collagen synthesis that occur outside the cell?

A
  1. Secretion
  2. Cleavage of propeptides
  3. Self-assembly into fibril
  4. Aggregation of fibrils into fiber
319
Q

What type I collagen post translational modification stabilizes the triple helix?

A

Disulfide bond formation

320
Q

What occurs in the propeptide cleavage step of collagen synthesis?

A

Cleavage of N- and C- terminals

321
Q

What AA’s form the cross linking residues that create the fiber in collagen synthesis?

322
Q

What does the hydroxylation rxn of proline and lysine residues require?

A

Vitamin C

scurvy

323
Q

What is the extracellular copper enzyme that catalyzes formation of aldehydes from lysine residues in collagen synthesis?

A

Lysyl Oxidase

324
Q

How does aldehyde formation from lysyl oxidase form collagen?

A

Aldehydes are highly reactive and spontaneously form bonds with other aldehydes (results in cross-linking)

325
Q

How do non-fibrillar collagens differ in their primary structure?

A

No regular Glycine for tight helix

326
Q

Are non-fibrillar collagens cleaved after secretion?

A

NO

so retain propeptides

327
Q

Type IV collagen has lateral interactions between…

A

helical segments

328
Q

Type IV collagen has what type of interactions between the globular domains?

A

head to head

tail to tail

329
Q

Type IV is a ______ forming collagen found in ______.

A

sheet

basal lamina

330
Q

What are the 3 steps of collagen degradation?

A
  1. Enzyme binding
  2. Unwinding triple helix
  3. Cleavage of collagen peptides
331
Q

What 2 enzymes have collagenase property?

A

Matrix metalloproteinases (MMP’s)

Cathepsins (L and K)

332
Q

What does initial cleavage of collagen yield?

How is it cleared?

A

gelatin

denaturation and protease digestion and phagocytosis

333
Q

Which collagen pathology is characterized by long bone fractures prior to puberty?
Which has perinatal lethality?

A

Osteogenesis imperfecta 1 (decreased type I synth)

Osteogenesis imperfecta 2

334
Q

What collagen pathologies result in translucent skin, hyperextensive skin, and joint hypermobility?

A

Ehlers-Danlos IV, VI, VII

335
Q

What ECM fiber has a half life of 74 years?

336
Q

How is elastin assembled?

A

tropoelastin (soluble form) associates with fibrillin to assemble elastic fibers

337
Q

What are tropoelastin cross-linkages formed between?

A

Lysines (catalyzed by LOX)

338
Q

Where is elastin commonly found?

A

lungs, large bv’s, elastic ligaments

339
Q

What AA’s are commonly found in elastin?

A

nonpolar - glycine, alanine, valine

Proline (hydroxyproline) and lysine (no hydroxy form)

340
Q

What protease inhibitor prevents emphysema, COPD, and liver cirrhosis by preventing elastin breakdown?

A

Alpha1-antitrypsin

341
Q

What is the function of fibronectin?

A

binds cells to the ECM

342
Q

What does fibronectin bind?

A

Integrin, collagen, fibrin, and heparan sulfate proteoglycans

(syndecans)

343
Q

T/F

Fibronectin is important for wound healing?

A

True

fibronectin connects cytoskeleton to matrix

344
Q

What is the name of the Type IV collagen pathology?

A

Allports syndrome

345
Q

What are the 4 ECM proteins found in all basal laminae?

A

Laminin
Perlecan
Type IV collagen
Entactin/Nidogen (glycoprotein)

346
Q

What is a cross-shaped protein that is a major part of the basal lamina?

347
Q

What do the short and long arms of laminin bind to?

A

short - other laminin molecules

long - bind to cells

348
Q

What serve as receptors for fibronectin, collagen, laminin, fibrinogen, vitronectin, and lg superfamily?

Tim's Cards (140 decks)

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