Biochem Week 1+2+3 Flashcards
1
Q
Hydrophobic, aliphatic amino acids
A
Alanine, Ala, A Glycine, Gly, G Isoleucine, Ile, I Leucine, Leu, L Methionine, Met, M Proline, Pro, P Valine, Val V
GLAMorous VIPs stay inside so they don’t get wet (hydrophobic)
2
Q
Hydrophobic, aromatic amino acids
A
Phenylalanine, Phe, F
Tryptophan, Trp, W
3
Q
Basic amino acids
A
Arginine, Arg, R
Histidine, His, H
Lysine, Lys, K
HAL
4
Q
Acidic amino acids
A
Apsartic acid, Asp, D
Glutamic acid, Glu, E
Acidic Glue
5
Q
Polar, uncharged amino acids
A
Asparagine, Asn, N Cysteine, Cys, C Glutamine, Glu, Q Serine, Ser, S Threonine, Thr, T Tyrosine, Tyr, Y (aromatic)
G CATS
6
Q
Bond that stabilizes tertiary structures
A
Cysteine-cysteine disulfide bond
7
Q
Secondary structures are the result of
A
Hydrogen bonds formed between carbonyl O of one atom and the amide H of another
8
Q
Alpha-helix
A
Type of secondary structure
3.6 residues per turn.
Carbonyl oxygen atom points in one direction toward the amide group four residues away. They form a hydrogen bond
9
Q
Beta-sheets
A
Composed of a flat segments of several beta strands-a stretch of polypeptide chain typically 3-10 amino acids long with the backbone in an extended conformation, can be hydrogen binds between different segments of the chain,
Parallel if N terminus to C terminus direction is the same in two beta strands in a sheet
Antiparallel if they do not face same direction
10
Q
Intrinsically disordered proteins (IDPs)
A
Proteins that lack a fixed or ordered 3D structure, random could and large multi domain proteins connected by flexible linkers. In random coils, the only fixed relationship between amino acids is that between adjacent residues through the peptide bond
11
Q
Domains
A
Functional and structural units that can fold, function, and exist. Ex: transcription factors have dna binding domains that are found in various other proteins that also bind to dna
Homologous domains different proteins from different organisms may share a common domain that performs a similar function
12
Q
Collagen
A
Most abundant fibrous protein 25% body mass. Structural strength for tissues, flexibility, tendons and ligaments.
Made up of repeating three stranded polypeptide procollagen units in parallel.
Primary amino acid sequence is Gly-X-Y (X and Y are often hydroxyproline or hydroxylysine)
One strand of repeating sequence forms the alpha chain (not helix!)
13
Q
Collagen synthesis
A
Prepro alpha chains synthesized in rER. Have N terminal signal sequence guides them to lumen
Signal sequence cleaved off to produce pro alpha chains
Post translationally modified
mRNA to get primary sequence (preprocollagen )
Proline and lysine are hyroxylated with vitamin c as cofactor
Glycosylation of polypeptide results in procollagen and triple helix formation
Procollagen is exocystosed, N and C terminals are cleaved, resulting in tropocollagen
Several tropocollagen molecules are cross linked via lysyl oxidase, resulting in collagen fibers
14
Q
Diseases of collagen synthesis
A
Osteogenesis imperfecta -brittle bone disease, autosomal dominant. Manifests in children as multiple fractures. Blue sclera, choroidal veins visible due to translucent connective tissue. Also abnormal dentition, hearing loss. (BITE, Bone, Eye, Teeth, Ear
Ehlers- Danlos syndrome- hyper extensible skin, hyper mobile joints, tendency to bleed easily , autosomal dominant and recessive. (I, III, or V)
Scurvy - deficiency of vitamin c (cofactor for hydroxylation). Low hydroxylation of proline and lysine = poor assembly and cross linking of collagen= weak blood vessels and poor wound healing
Osteolathyrism- osteolathrogens that inhibit lysyl oxidase. Grass pea consumed in poorer areas, has toxic chemicals
Stickler syndrome - myopia, hearing loss, joint problems, poor bone formation, distinctive facial appearance
15
Q
Type 1 collagen defects
A
Cause osteogenesis imperfecta
Blue sclera
Hearing loss
Dental imperfections
16
Q
Type 2 collagen
A
Cartilage formation
More severe
17
Q
Type 3 collagen
A
Ehlers-danlos syndrome, easily bleeding
18
Q
Type 5 collagen defects
A
Skin hyper extension and joint hyper mobility subtype of ehlers-danlos syndrome
19
Q
Henderson hasselbalch equation
A
pH= pK1 + log (II/I)
When pH=pKa, [HA]=[A-]. 50% of HA dissociates to H+ and A-
20
Q
21st amino acid
A
Selenocysteine
21
Q
Amino acids with hydroxyl group side chains
A
Serine, threonine, tyrosine
22
Q
Amino acids with carboxylate side groups
A
Aspartate and glutamate
23
Q
Histidine side chain
A
Imidazole, can bind to copper and iron
24
Q
Deleterious amino acid mutation
A
Polar a.a.<—> non polar a.a.
Charged a.a.<—> non charged a.a.
Others
Sickle cell anemia: mutation in the beta subunit of hemoglobin. Glutamate-6 (neg charged, polar)—> valine-6 (non polar) (Glu6Val, or E6V)
25
Native structure
Active, functional structure of polypeptide. Usually stable in a narrow range oh pH and temperature in aq. Environments
26
Motif
Combining secondary structural elements locally and producing geometric patterns
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Alpha-alpha( helix-loop-helix)
beta-alpha-beta
Beta-meander
Beta-barrel
Come together and form domains
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27
Co-translational folding
Polypeptide chains seem to fold into the native structure even as they are being synthesized
28
Chaperones
Correct folding of some proteins require help of these proteins
29
Protein conformational disorders
Alzheimer’s, Huntington, Parkinson’s
Transmission spongiform encephalopathies (creautzfeldt-Jacob disease)
Amyloids: accumulation of insolute aggregating proteins. Deposit in tissues and organs and contributes to pathophysiology of disease
Prions
30
Formation of amyloid plaques found in Alzheimer’s
Enzymes cleavage of amyloid protein precursor in cell membrane
Spontaneous aggregation to form insoluble fibrils of beta-pleated sheets
31
Protein modifications
Phosphorylation: serine, threonine, tyrosine
Methylation: lysine, arginine
Acetylation: lysine, arginine
Hydroxylation: lysine, proline-collage
Ubiquitination:lysine
Glycosylation: O-linked (Ser, Thr, Tyr) and N linked (Asn, Arg)
32
Nitrogen balance
Positive N balance: greater intake than loss; growing child, pregnant women
Balanced: equal intake and loss; adult needs 0.8g/kg/day
Negative N balance: illness, trauma, surgery
Diseases:
- kwashiorkor protein but not calorie deficient(edema due to deficient serum albumin-Hypoalbuminemia)
- marasmus: protein and calorie deficient (muscle wasting- arrested growth, loss of subcutaneous fat, no edema)
-Anorexia nervosa
-Fasting, starving
-Deficiency of single essential amino acid will lead to protein synthesis defect
33
Essential amino acids of humans
PVT TIM HALL (Phe, Val, Thr, Trp, Ile, Met, **His, **Arg, Leu, Lys)
All branched or aromatic except for Met, provides sulfur, and Lys
**His: plentiful amino acid, humans can’t synthesize it
**Arg: conditional essential; healthy adults make enough in kidney and gut. In times of growth, reproduction or recovery from illness, requirement is increased
34
Hemoglobin
Carries oxygen to body’s tissues from lungs,
35
Cooperativity
Property or hemoglobin. Affinity for oxygen increases for each oxygen molecule that is bound to hemoglobin
36
Hemoglobin dissociation curve
Represents relationship between oxygen saturation (number of hemoglobin binding sites bound to oxygen as a percentage of the total number of hemoglobin binding sites within the arterial blood) and partial pressure of oxygen.
At low partial pressure of oxygen, curve has a steep appearance. Here a small increase in partial pressure (like in the arteries) results in large increase in amount of oxygen bound to hemoglobin. Small drop (like in the target peripheral tissues)= large release of oxygen from hemoglobin
37
p50
Represents partial pressure of oxygen at which 50% hemoglobin is saturated.
38
pCO2, temp, pH on oxygen binding
Increased during exercise+ increased temp. At levels increase, blood becomes acidotic and pH (Bohr effect) lowers. Favors T form. Hemoglobin releases bound oxygen to muscles at higher levels of partial pressure of oxygen than normal.
Shifts curve to the right, p50 increased
Opposite if pCO2 decreased
39
2,3-diphosphoglycerate on oxygen binding
Made by tissues in response to low pH and low O2 environment. Higher affinity for T conformation. When it bind, hemoglobin is stabilized in it’s low oxygen affinity state, causing O2 to dissociate. Drops off extra oxygen when hemoglobin comes across higher
As this molecule increases, binding affinity for oxygen to hemoglobin decreases. Without it, Hb not easily giving up O2 to Mb
Results in right shift of curve
40
Carbon monoxide and hemoglobin
Bind with much higher affinity than oxygen, changes confirmation of hemoglobin to form carboxyhemoglobin. This has higher affinity for binding oxygen.
At a given pO2, more O2 remains bound to hemoglobin and less is released to tissues, leads to tissue hypoxia and cell damage
Shifts hemoglobin dissociation curve to left.
Therapy is hyperbaric oxygen
41
Myoglobin
In muscles accepts oxygen from hemoglobin and releases it to cytochrome oxidase in complex IV of the ETC. should have higher oxygen affinity than hemoglobin but lower oxygen affinity than cytochrome oxidase
Non-cooperative binding
42
Hemoglobin
Binds to oxygen in the higher oxygen region like the lungs and releases oxygen in low oxygen areas like tissues
Hill coefficient around 3, strong positive cooperativity in oxygen binding
43
Heme
In myoglobin and hemoglobin
Planar porophyrin- ring structure with four nitrogen ligands binding to a central iron
Ferrous iron
Degraded through formation of bilirubin
Ferric heme does not bind Fe 3+ (methemoglobin)
44
Myoglobin structure
Eight helical segments, labeled A-H
Hydrophobic pocket binds to single heme
Imidazole nitrogen of histidine residue coordinates to the iron in the heme; called proximal histidine F-8
Histidine E-7 located near heme iron on side opposite to the proximal histidine side, this second histidine (distal) is not coordinated to the heme iron but binds O2.
Single myoglobin chain is structurally similar to individual subunit of hemoglobin, a tetramer
45
Hemoglobin structure
4 subunits and 4 chains, each bound to heme like four myoglobins together
Majority made up of two alpha and two beta chains
Small percentage of adult hemoglobin has two alpha chains and two delta chains
Fetal hemoglobin ( HbF) has two alpha and two gamma chains
Can also transport H+ and CO2 from tissues to lungs
46
Pulse oximeter
Measure light absorption in the 660nm and 910nm ranges; the difference is a measure of hemoglobin oxygenation
47
Positive cooperatively
Oxygen to hemoglobin, one Hb can bind to four oxygens. The first oxygen binds to the Hb weakly, every oxygen after has increasing affinity
48
Negative cooperatively
Binding of a ligand to the first site on a protein results in decreased affinity of protein for another ligand to second site (like CTP synthase)
49
Hill coefficient (nH)
Measures cooperativity, greater than 1 for positive cooperatively, less than 1 for negative, q for non-cooperative
50
R confirmation for hemoglobin
Relaxed, high oxygen affinity.
| Binding of oxygen to one of the subunits triggers conformational change to this form
51
T confirmation for hemoglobin
Tense confirmation, low oxygen affinity, completely deoxygenated
52
Allostery
Biological Molecules mostly proteins transmit the effects of binding at one site to another, often distal, functional site, allowing for regulation of activity
53
Fetal hemoglobin (HbF)
Fetal blood needs to extract O2 from maternal Hb. Must have higher oxygen affinity than adult blood. Fetus expresses the Hb isoform-HbF, made up of two alpha and two gamma subunits. Gamma subunit have only weak affinity for BPG
54
Carbaminohemoglobin
Carbon dioxide can also bind to Hb at the amino terminus forming a carbamate. Can assist oxygen release kn oxygen consuming tissues and organs
55
HbS- sickle cell anemia
Glutamate at position 6 in normal beta is replaced by valine
Results in small hydrophobic patch on surface of HbS
Deoxygenated HbS forms hydrophobic aggregates through this patch.; ppt of aggregates results in red cell breakdown, anemia, capillary occlusion, and pain in extremities
Treated with hydroxyurea (HU), induces excessive synthesis of HbF
56
HbC mutation in hemoglobin
Mutation in sixth position in beta chain , substitute K for E. Mild anemia
57
Hb Hammersmith mutation of hemoglobin
F at position 42 of beta chain replaced by S. Results in heme loss and dysfunctional hemoglobin
58
Hb Savannah mutation of hemoglobin
Substitute of V at a G position 24 of beta chain. Unstable hemoglobin
59
Hb Milwaukee mutation of hemoglobin
Val-67 of beta chain replaced by a E. Results in stabilization of dysfunctional methemoglobin (Fe3+)
60
Methemoglobinemia
Fe3+, NADH methemoglobin reductive reduced methemoglobin to hemoglobin
Deficiency of the enzyme causes this
61
Thalassemias
Imbalance of glob in chains
Alpha thalassemias: normally four copies of alpha globin gene per genome. Less function Hb, silent to mild to severe anemia
Beta thalassemias: synthesis of beta globin chain is reduced. Normally two copies of beta globin chain gene per genome.
Minor: one copy mutated
Major: both copies mutated
62
HbA1c
HbA nonenzymatically glycosylated to produce this. Good indicator of uncontrolled high blood sugar levels (hyperglycemia) in the past couple of months
63
Major type of collagen: I- fibril-forming
I-Skin, tendon, bone, cornea, dentin
Resistance to tension
Pathology: ehlers danlos, osteogenesis imperfecta
II-Cartilage, intervertebral disco, vitreous humor
Resistance to pressure
III-Blood vessels, skin, uterus, fetal tissue, granulation tissue, associates with type I
Structural maintenance in expansible tissues
Pathology: ehlers danlos syndrome, type IV
64
Major type of collagen: II- networking forming
IV- basil lamina (basement membranes)
Support of epithelial cells, filtration
Alport syndrome , goodpasture syndrome
65
Major type of collagen: III-fibril-associated
Collagens with interrupted triple helices
66
Menkes disease
Impaired copper absorption and transport
Copper deficiency= poor lysyl oxidase activity= poor collagen crossing
Floppy muscles, kinky hair, weak bones, deterioration of nervous system, developmental delay
67
Elastin structure
Primary- small non polar residues. Has proline and lysine, small amount of hydroxyproline, no hydroxylysine
Secondary- dense hydrophobic globules rich is Val, Pro, Gly. Connected by cross links hydrophilic alpha helical segments rich is Lys and Ala
Some lysyl resides oxidatively delaminated by lysyl oxidase to allow for cross linking (desmosine)(3 allysine x 1 lysine)
68
Elastin fibers consist of…and location
Stretch-reform cycle
Consist of elastin and glycoprotein microfibrils
Found at lungs, walls of large arteries, elastic ligaments
69
Marfan syndrome
Elastic fiber disease
Results from mutations in FBN1 gene (encodes microfibril fibrillin-1), phenotype is variable
Genetic disorder that affects connective tissue; skeletal deformation, scoliosis, elongated limbs all possible
70
Emphysema
Elastic fiber disease
Lung alveoli cells chronically exposed to low levels of neutrophil elastase (protease) that breaks down elastin
Alpha 1 antitrypsin protease inhibitor; synthesized in liver and secreted into blood=normally counteracts elastase=preserves elastin
In this disease, AAT deficient patients, elastase is unopposed=destruction of connective tissues of alveolar walls
71
Enzyme kinetics
Study of biochemical reactions catalyzed by enzymes
72
Michaelis-menten kinetics
Describes how enzyme velocity changes as substrate is added to the reaction . Change in velocity (V) of an enzymatic reaction (y axis) as the concentration of substrate (S) increases (the x axis)
73
Enzyme saturation
All sites on enzyme are occupied by substrate, shows up as plateau on michaelis-menten plot.
74
Vmax
Point at which plot plateaus , all sites on enzyme are now occupied and reactions can’t proceed any faster
75
Michaelis constant
Km, concentration of substrate when velocity is exactly one half Vmax
76
One enzyme, two substrates
Reaction with the substrate that has lowest Km happens first
77
Rate limiting step
S>Km, enzyme turnover (rate at which enzyme can operate) is rate limiting factor
78
Dissociation constant
Kd, differentiates reversible and irreversible reactions. Is the concentration of the drug when 50% of receptors are bound. Therefore a drug with a lower constant has a higher affinity for an enzyme then does a drug with a higher constant
79
Cytochrome p450 enzymes
Induced by barbiturate sedative drugs, in the liver, reduce blood levels of many drugs
80
Reversible enzyme inhibitors
Bind non-covalently to enzymes, by loose hydrogen bonds, hydrophobic interactions, or ionic bonds. These types of inhibitors can easily be removed by just diluting the system.
81
Irreversible enzyme inhibitors
Bind covalently to an enzyme. These inhibitors cannot easily be removed by dilution, because the nature of their chemical modification is more permanent: it’s can guide therapy
82
Competitive inhibitors
Reversible, compete with substrates to bind to the enzyme. Always binds to active site , can be overcome by increasing concentration of substrate
Don’t change y intercept of enzyme kinetics on line weaver burk plot (Vmax). Does increase x intercept (Km)
More substrate is required to achieve the same reaction
Statins are competitive inhibitors of HMG-CoA reductase, which is the rate limiting enzyme during the biosynthesis of cholesterol.
83
Non competitive inhibitors
Irreversible-bind covalently to enzymes active site
Allosteric- changes entire shape of the enzyme and reduces its ability to bind to substrate
Increase y intercept (decrease Vmax) without a change in Km. Enzyme will never be functioning at a maximum level if it has been irreversibly bound to an inhibitor
Aspirin is an irreversible inhibitor of prostaglandin synthetase bit prostaglandin and thromboxane synthesis
84
Uncompetitive inhibitors
Decrease both Km and Vmax (decrease x intercept, increase y intercept on lineweaver burk). Dependent on substrate concentration. Reduce Km because they stabilize the enzyme in complex with substrate. Since substrate can’t dissociate, less of its required to reach Vmax
85
Holoenzyme
Entire active enzyme
86
Apoenzyme
Protein part of enzyme (inactive without cofactors)
87
Prosthetic groups
Coenzymes strong bound to the enzyme (like heme in Hb)
88
Isozymes
Different molecular forms (amino acid sequence) of the same enzyme synthesized by different tissues in the same organism, also called isoenzymes
Catalyze the same reaction but with different kinetic properties
Often have different subunit compositions
89
Oxidoreductases
Catalyze redox rxns
90
Transferases
Transfer functional groups
91
Hydrolases
Catalyze cleavage of bonds by addition of water (hydrolysis)
92
Lyases
Cleave carbons-carbon or C-S, or C-N bonds
93
Isomerases
Catalyze racemization of optical or geometric isomers (isomerize)
94
Ligases
Remote bond formation with concomitant expenditure of energy in the form of ATP
95
Phophatase
Uses water to remove phosphoryl groups
96
Phosphorylase
Uses inorganic phosphate to break a bond and generate a phosphorylation product
97
Dehydrogenase
NAD+ or FAD+ as an electron acceptor
98
Oxidase
Oxygen is acceptor of electrons; oxygen is not incorporated into substrate
99
Oxygenase
One or both oxygen atoms are incorporated into substrate
100
First order
Substrate concentration is less than Km, thus Km + [S] is close to Km, this Vo=Vmax[S]/Km, thus Vo is proportional to [S]
101
Zero order
[S] is greater than Km, thus Km+[S] is close to [S], thus Vo= Vmax [S]/[S], thus Vo=Vmax
102
Feedback inhibition
Occurs to initial enzyme and is equential biochemical event by the final product is very common, the final product is a negative effector of an earlier enzyme.
103
Non polar hormones
Like steroid hormones enter the nucleus of the target cell and binds to specific protein receptors in the nucleus (For complex with the receptor in the cytosol and then enter the nucleus) (nuclear receptor)
104
Sources of plasma enzymes (serum enzymes)
1. Alpha 1 antitrypsin (AAT or A1AT) for coagulation
2. Normal turnovers , levels constant
3. Damaged tissue, releases abnormal levels of intracellular enzymes into the blood. Result of disease of trauma
105
Tissue specific enzymes- ALT and AST for liver damage
Alanine aminotranferase and aspartate aminotransferase
Abundant in liver for amino acid biosynthesis
Elevated ALT and AST in plans signal possible liver damage
106
Tissue specific enzyme- alkaline phosphatase
Cholestasus is any condition in which flow of bile from liver slowed or blocked. Blood test will show elevated levels of this enzyme
Bone related disease, rickets, and in bone tumors, enzyme levels are increased
107
Muscle damage results in increase in enzyme levels of
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Aldolase (glycolysis)- carb metabolism
Aspartate aminotransferase (AST)
Alanine aminotransferase (ALT)
Creatine kinase (CK- creatine biogenesis)
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108
Muscle damage in pancreas causes
Increased level of serum amylase (digestion of carbs)
109
Lactate dehydrogenase (LDH)
Serum isoenzyme
Four subunits
M (skeletal muscle) and H (heart) forms of the subunit (amino acid seq. about 75% identical)
Type 5 (M4) mostly found in liver (will migrate slowest in electrophoresis)
Type 1 (H4) mostly found in heart (will migrate fastest in electrophoresis)
Can be separated by electrophoresis or chromatography
110
LDH 2
Acute leukemia
| HHHM
111
LDH 3
acute leukemia
| HHMM
112
LDH 4
muscle and liver (anaerobic tissues)
| HMMM
113
Creatinine kinase (CK)
Also called creatinine phosphokinase, cpk
Serum isoenzyme
Isozyme is a dimer composed of a B (brain) subunit and M (muscle) subunit
114
CK1
CK-BB found mostly in brain
115
CK 2
CK-MB, found in heart and rises when cardiac muscle is damaged
116
CK3
CK-MM, skeletal muscle and cardiac muscle (1/3 CK2 and 2/3 CK3)
117
myocardial infarction (MI)
Heart attack, interruption of blood supply to heart, leads to reduced oxygen supplies to heart muscle (ischemia) Myocardium (heart muscle) could be permanently damaged if persistent ischemia
118
Blood test for MI
Increase in serum cardiac troponin I and T (cTnl and cTnT) released in 2-4 hours, peak around 24-48 hrs and returns to normal in 7-11 days
CK-MB (CK 2), rise 4-6 hours after infarction, leaks at 24 hrs, returns to normal by 72 hours. Most commonly used before adoption of troponin, not longer used.
119
Electron transport chain
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Moves electrons along series of steps to produce energy
This plus complex V are largest ATP producers for most cells, but not part of the chain
Complexes I-IV, coenzyme Q, and cytochrome C receive electrons from reduced compounds made in glycolysis, citric acid cycle, and beta oxidation and pass them through chain . Energy is released and this pumps H+ into mitochondrial intermembrane space, creates electrochemical gradient
Delta G (free energy) is negative
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120
Oxidation reduction rxns
Transfer of electrons
OIL RIG
Oxidation Is Losing, Reduction Is Gaining
121
Delta G
Free energy
Rxns with negative change in free energy means concentration of products is higher than reactants, so rxn proceeds spontaneously from reactants to products
122
Delta Eo
Reduction potential of a reaction
Delta E of redox rxn is derived from zero values of its component oxidation and reduction rxns as well as the concentrations of the reactant and oxidant species
123
Delta E relation to delta G
Delta E indirectly proportional to delta G
| Positive Delta E means negative delta G and spontaneous oxidation reduction rxns
124
Complex 1 of ETC
Also called NADH dehydrogenase
Coenzyme: flavin mononucleotide (FMN) group as tightly bound prosthetic group
accepts electrons from NADH, oxidizing it to NAD+ with reduction of FMN to FMNH2. Then transfers electrons to CoQ, reducing it while FMNH2 is reoxidized to FMN
ATP yield is 3, pumps out 4 protons
125
Complex 2 of ETC
Also passes electrons to CoQ. Called succinate dehydrogenase, citric acid enzyme that catalyzes oxidation of succinate to fumarate by transferring electrons from FADH2 (originally FAD) to CoQ
ATP yield is 2, smaller proton gradient, does not pump out protons
Only complex that does not have mitochondrial DNA, encoded entirely by nuclear DNA. NOT a trans membrane protein
126
CoQ of ETC
Uniquinone, Travels through inner mitochondrial membrane to complex 3, accepts electrons and passes them to cyt c
127
Cyt C of ETC
Travels through inner mitochondrial membrane to complex IV, called cytochrome oxidase, accepts electrons and passes them to oxygen (final electron acceptor), forms water.
Also has 2 copper ions and 2 heme group
Pumps out 2 protons
128
Chemiosmotic hypothesis
States that ATP synthase synthesizes ATP by using energy released from allowing protons to move from the inter membrane space into the matrix down the electrochemical gradient
Inter membrane space has higher H+ concentration, thereby making it more acidic than the matrix
129
Complex inhibitors of ETC
toxic substances
Rotenone-complex 1 inhibitor. Insecticide
Amytal- sedative
Antimycin A- complex 3 inhibitor. Fungicide, miticide, insecticide
Cyanide and carbon monoxide- complex 4 inhibitors
Reduce ability of ETC to pass electrons along , all prevent NADH oxidation
Oligomycin- complex 5 inhibitor. Binds to F0. Does not directly prevent electrons from moving down chain to oxygen like the others listed. Does stop electrons transfer, NADH not oxidized, proton motive force diminished, oxygen consumption decreased like the ones above
130
Cyanide
Inhibits complex 4 by binding to iron, thereby inhibiting it. Prevents cell from using etc for energy production. Leads to cell death.
Binds more strongly to the Fe3+ form of heme iron than to Fe2+
Administration of thiosulfate to facilitate the rhodanese reaction (conversion of cyanide to thiocyanate) and the administration of nitrate. Nitrate oxidizes hemoglobin to Methemoglobin which binds to cyanide thus Lifting cyanide inhibition of cytochrome oxidase
Treatment: hydroxocobalamin, bind cyanide. Produces cyanobalminin (vitamin B12).
131
Uncouplers
Class of agents that cause dysfunction of ETCs ATP producing ability. Ruin proton gradient by making inner mitochondrial membrane permeable to protons. Protons equilibrate across membrane. ATP cannot be formed. ETC begins to be supplied with substrate and runs faster. This increases rate of oxygen consumption
132
Nonshivering thermogenin
Uncoupling agent of ETC
| ramped up ETC generated more heat, produced in brown adipocytes. Uncoupling in brown fat allows babies to generate heat
133
Pharmacological uncouplers
Dinitrophenol- weight loss. Increase in catabolic pathways, more breakdown of fats and sugars.
Pentachlorophenol- industrial pesticide
Aspirin- uncoupling property partially accounts for hyperthermia seen in aspirin overdose
134
Collection of electrons by NADH and FADH2
Glycolysis producers 2 moles NADH and pyruvate. Pyruvate converted to acetyl CoA with reduction of one mole NAD+ to NADH inside mitochondria
Beta oxidation of fatty acid to produce acetyl CoA, oxidized to carbon dioxide through TCA cycle, produces 3 NADH and one FADH2 inside mitochondria
135
Glycerol phosphate shuttle
1NADH —> 1 FADH2
dihydroxy acetone phosphate reduced to glycerol 3 phosphate by NADH and glycerol phosphate dehydrogenase
Glycerol 3 phosphate diffuse through outer mitochondrial membrane, reoxidized to DHAP and FADH2 in mitochondria by glycerol phosphate dehydrogenase
FADH2 electrons brought to complex II (quinone pool) in inner mitochondrial membrane. Flow through complex III, produced 1.5 ATP per pair of electrons per FADH2
Secondary
136
Malate aspartate shuttle
1 NADH—> 1NADH
Bring electrons into mitochondria at NADH level to complex 1, produced 2.5 ATP per NADH
Primary
137
Iron sulfur proteins
Frequent components of ETC. Different proteins contain different, very labile, clusters of iron atoms alternating with sulfur atoms derived from cysteine residues, many iron sulfur proteins function as one electrons reagents
138
Complex 5 (ATP sythase)
Mushroom shaped part F1 projects into mitochondrial matrix from mitochondrial inner membrane. Base is F0, membrane integral proton channel through which protons are pumped into matrix. F1 non covalently bound to F0
139
Inhibitors of ATP/ADP exchange
Atractyloside, bongkrekic acid. Deplete intra-mitochondrial ADP, hence decreases the rate of phosphorylation, increasing the mitochondrial pH gradient and decreases the rate of respiration
140
Anabolic pathways
Synthesize complex molecules from simple molecules. Consume energy
141
Catabolic pathways
Breakdown complex molecules. Produce energy and building blocks for other biosynthetic processes
142
Acetyl CoA
Point of convergence of metabolism
Oxidized to carbon dioxide through TCA cycle with production of NADH and FADH2
Can be converted to ketone bodies
Cannot be converted to pyruvate
Sugar can be turned into fat but fat alone cannot be turned into sugar
143
Glycolysis
Coverts glucose to pyruvate
Does not need oxygen, needs NAD
when oxygen is not present, pyruvate is converted into lactate to regenerate NAD+
144
Lactic acidosis
If lactate accumulates, increased anaerobic glycolysis due to tissue ischemia (lack of oxygen), body pH will decrease (pH below 7.35 is acidemia)
Results in anion gap becoming larger = sodium ion - (chloride ion+HCO3-). Gap between sodium and negative ions increases
Acidosis will induce rapid shallow breathing in effort to expel carbon dioxide
145
Gluconeogenesis
Body makes sugar from amino acids and TCA cycle intermediated when glucose is not available due to low sugar diet, starvation, or diabetes.
Leads to decreased ability of TCA cycle to process far derived acetyl CoA, which increased acetyl CoA, which increases ketone bodies (ketone acidosis)
146
Urea cycle
Converts ammonia (created from amino acid catabolism) to urea and is excreted. Consumes energy thus proteins are not the preferred molecules to store energy for long term use
147
Long term storage of energy
Glycogen and as triglyceride (called triacylglycerol-TAG)
148
Glycogen
Normally broken down to glucose 6-phosphate, can’t cross membranes
Liver removes the phosphate and produces free glucose
Muscle glycogen can only provide glucose to the muscle itself and not to other tissues
Brain does not store glycogen, hypoglycemia is harmful to brain. Can also use ketone bodies as energy
149
Pentose phosphate pathway
Generation of reducing agents, in the form of NADPH, used in reductive biosynthesis rxns within cells (fatty acid synthesis)
Production of ribose 5-phosphate, used in the biosynthesis of nucleotides and nucleic acids
150
Insulin
Produced by pancreatic beta cells, works through transmembrane protein kinase receptor (insulin receptor, IR)
Storage hormone
-most active after feeding
-stimulates uptake of glucose, decreases blood sugar levels
-stimulates glycogen synthesis
-synthesis of fat (lipogenesis), inhibits mobilization of fats (lipolysis)
-protein synthesis
- glycolysis after feeding
Diabetes- lack of, or low sensitivity to, insulin results in higher blood glucose levels (hyperglycemia), lower intracellular sugar availability
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Glucagon and epinephrine
Produced by pancreatic alpha cells, work through G protein coupled receptors
Mobilizing hormone, most active during fasting or well after meal, increases glycogen breakdown (goycogenolysis) and de novo glucose synthesis (gluconeogenesis), stimulates fat breakdown (lipolysis) to release fatty acid for fuel
Epinephrine- produces in addition higher blood glucose, higher blood flow to mobilize body for fight or flight respond
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Corticosteroids and thyroid hormones
Long acting hormones, work through intracellular receptors (nuclear receptor)
Affect gene expression and protein synthesis
Cortisol has effects similar to norepinephrine, but on chronic basis
Thyroid hormones are essential for growth- stimulate basal metabolic rate and thermogenesis through partial uncoupling of mitochondria (thermogenin, UCP1)
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FED metabolic state (2-4hrs after meal)
High insulin, low glucagon, blood glucose if high (from diet) (glycogen in liver, glycogen in muscle, fuel in brain and kidney), amino acids taken up by liver and other tissues for protein synthesis (some used for fuel), fatty acids taken up by adipose cells and stored as fat
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Fast metabolic state (more than 4hrs after meal)
Low insulin, high glucagon, liver breaks down glycogen and releases glucose to blood and makes glucose from amino acids (gouconeogenesis), muscle breaks down stores glycogen for fuel, triglycerides are hydrolysis and fatty acids released into blood (taken up by liver for fuel and release some ketone bodies for muscles)
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Starvation metabolic state (more than 2-3 weeks after a meal)
Low insulin, high glucagon, glycogen depleted, liver makes glucose from amino acids and exports to brain and red blood cells, triglycerides broken down and fatty acids released to blood (liver take up, uses some as fuel and converts rest to ketone bodies for muscles and brain when high enough)
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Muscle metabolism
Principle sites for degradation of branched chain amino acids Leu, Ile, Val (BCAAs)
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Adipose tissue
Often enough to meet out needs for 3 months without eating
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Liver metabolism
Venous drainage of the gut and pancreas passes through the hepatic portal veins before entry into circulation.
After a meal the liver is bathed in blood containing absorbed nutrients and elevated insulin secreted by pancreas
Glycogenesis, glyconeogenesis , gluconeogenesis, lipogenesis, ketogenesis
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Locations of different metabolic pathways in a cell
Beta oxidation and ketogenesis and oxidative phosphorylation inside mitochondria
Gluconeogenesis and urea cycle partly in mitochondria and cytosol
Glycolysis and fatty acid synthesis in cytosol
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Important steps in regulation of metabolic pathways
Rate limiting step
First committed step
Irreversible reactions
Feedback regulation
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Carbohydrates structure and function
Energy source, storage form of energy, cell membrane components, structure components, intercellular communication
(CH2O) n
An aldehyde or ketone group
At least two other carbons (minimum etc), each of the other carbons contains a hydroxyl group
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Epimers
Carbohydrate isomers (same formula but different structure) that differ in configuration around only one specific carbon atom
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Enantiomer
Isomers with mirror image
D-isomeric form:OH group on asymmetric carbon farthest from carbonyl carbon is on the right
L- isomeric form: OH group on asymmetric carbon farthest from carbonyl carbon is on the left
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Racemases
Interconvert D and L isomers
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Anomeric carbon
Former carbonyl group , alpha (below the plane) or beta (above the plane)
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Hemiacetal
Formed by reaction of aldehyde with an OH group
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Hemiketal
Formed by reaction of ketone with OH group
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Reducing end
The OH group of anomeric carbon is not conjugated to another sugar, this kind of sugar can act as a reducing agent is termed a reducing sugar
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Linking carbohydrates to non carbohydrates
N linked- sugar linked to amine group (asparagine, glutamine, arginine, lysine )
O linked - sugar linked to OH group (serine, threonine, tyrosine)
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Oligosaccharides
3-10 monosaccharides
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Glycosylaminoglycans
GAG, heteropolysaccharides, mucopolysaccharides
| 50-100 repeating disaccharides
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Disaccharides
Two monosaccharides
Lactose- galactose to glucose
Maltose- glucose to glucose
Sucrose- glucose to fructose
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Heteropolysaccharides
```
Composed of repeating disaccharides units (acidic sugar- amino sugar)n except keratan sulfate
One component is an amino sugar, one monosaccharide contains a carbonyl acid group, one of the two monosaccharides residues may contain one or more sulfate groups
Negatively charged (carboxylate, sulfate)
```
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Glycosylaminoglycan properties
Repel each other due to negative charges
Extended in solution and surrounded by water (hydrated)
Viscous, serve as lubricants and fillers in tissues and joints
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Mucopolysaccharides(MPS)- GAG degradation deficiency diseases
Hurler syndrome
Hunter syndrome
San Filipino syndrome
Sly syndrome
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Glycoproteins
Proteins conjugated to saccharides lacking serial repeat unit
Proteins contain covalently bound carbohydrate chain (often oligosaccharides, 2-10 monosaccharides)
No repeating units in carbohydrates
Carbohydrate is often branched
Cell surface recognition, antigenicity, components of ECM
Synthesis in golgi
Degradation in lysosome
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Proteoglycans
Proteins conjugated with polysaccharide serial repeat units (major part)
Synthesized in golgi, degraded in lysosome
Form mesh with glycoproteins between cells to create space for diffusion and prevent bulk flow of ECF by keeping interstitial fluid in gel state
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I-cell disease
Certain lysosomal digestive enzymes failed to be targeted by lysosome
Deficiency in ability to phosphorylate mannose
Skeletal abnormalities, restricted joint movement, coarse facial features
Death usually occurs by age 10
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Hydrolysis of glycosidic bonds
Main digestion sites are mouth and intestinal lumen
Done by glycosides or glycoside hydrolase
Salivary or pancreatic Alpha-amylase briefly and randomly hydrolysis some alpha (1–>4) glycosidic bonds. Indicates disaccharide at the branching point
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Digestive enzyme deficiencies
Disaccharide intolerance caused by
Hereditary
Intestinal disease
Malnutrition drugs that injure mucosa
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Lactose interolerance
65% of human population has reduced ability to digest lactose after infancy,
Lactase accumulated in GI tract, in large intestine bacteria releases gases to lead to bloating, diarrhea, dehydration
Reduce consumption of milk, use lactase treated products, take lactase pills before eating
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Sucrose isomaltase deficiency
Form single protein
Splits sucrose, maltose, Mal tortoise
Intolerance of ingested sucrose
Treatments to without sucrose or enzyme replacement
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Fructose intolerance
50% adults can’t absorb large amounts, 10% can’t absorb moderate amount (deficiency of GLUT-5 fructose transporter)
Unabsorbed fructose metabolized by colonic bacteria to form gas, GI distress
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Diagnosis of abnormal degradation of dietary carbohydrates
Oral tolerance testing with individual disaccharide
| Measure H2 gas in breath
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Carbohydrate in colon
Metabolized by bacteria in colon to gases, and acids
Acids absorbed into colon epithelial cells and used for energy
Gases H2, CH4, CO2 cause flatulence
Osmotic gradient potentially causes diarrhea
186
GLUT 4
Adipose tissue, skeletal muscle, heart muscle
| Insulin sensitive transporter. In presence of insulin, number of transporters increases on cell surface
187
GLUT 5
Intestinal epithelium and spermatozoa
| Fructose transporter
188
GLUT 3
Once glucose in CSF, taken up by neurons via this
189
GLUT 1
Uptake of glucose
190
Dietary fiber
Insoluble cellulose, hemicellulode, lignins
Soluble: plant gums, mucilages, pectins
Decreases bile acid reabsorption (lower cholesterol)
