BioChem Flashcards
(153 cards)
1
Q
Oxidoreductases
A
Transfer elecltrons from a donor to an acceptor
2
Q
Transferases
A
Transfer a functional group
3
Q
Isomerases
A
Rearrange / isomerase a molecule
4
Q
Lyases (syntheses)
A
Add or remove atoms to or from a double bond
5
Q
Ligases “synthetases”
A
Form (C-O C-S C-N C-C) bonds with the hydrolysis of atp
6
Q
Hydrolases
A
Cleave bonds via the addition of water
7
Q
Enzyme that uses Cu as a cofactor
A
Cytochrome c oxidase
8
Q
Enzyme that uses Fe as cofactor
A
Heme proteins (hemoglobin and myoglobin) need Fe to bind O2
9
Q
Enzyme that requires Mg as a cofactor
A
ATPases
10
Q
Enzyme that requires Se as a cofactor
A
Glutathione peroxidase- detoxifies hydrogen peroxide
11
Q
Enzyme that requires Zn as a cofactor
A
Superoxide dismutase - binds the free radical of molecular oxygen
12
Q
2 types of coenzymes
A
Co substrate - temporary association such as NAD+
Prosthetic - permanent association Heme
13
Q
Ideal temp for enzyme activity
A
37 degrees C
14
Q
Ideal pH for enzyme activity
A
4-8 with the exception of pepsin
15
Q
Gastric proton pumps are on what type of cell
A
Parietal cells
16
Q
What variable stands for enzyme - substrate affinity?
A
Km
17
Q
/What shape is a Michaelis menten plot?
A
Hyperbolic
18
Q
/What shape is a lineweaver Burke plot?
A
Linear
19
Q
Competitive inhibitor
A
Resemble substrate - compete for the active site on an enzyme
No effect on vmax - increase Km
20
Q
1/2 vmax
A
Km
21
Q
Lineweaver Burke x intercept
A
-1/Km
22
Q
Y intercept lineweaver Burke
A
1/Vmax
23
Q
Slope lineweaver Burke plot
A
Km/Vmax
24
Q
Non competitive inhibitor
A
Bind to E or ES complex not at the active site
Decreases Vmax
Unchanged Km
Effect cannot be altered by increasing substrate concentration
25
Uncompetitive inhibition
Decrease in vmax and Km by the same factor - lineweaver Burke plot with and without inhibitor yields parallel lines
26
How can you inhibit metaloenzymes
Use metal cofactor - chelating the cofactor will inhibit enzyme activity
This can be used to stop lead poisoning through using edta which is a lead chelator (lead normally will bind heme rendering it useless)
27
```
Enzyme inactivation
VMax? Up or down
Km? Up or down
Reversible or not?
Similar lineweaver Burke plot to what type on inhibition?
```
Vmax decreased
Unchanged Km
Irreversible
Non competitive is similar but is reversible
28
Allosteric enzymes
Type of bond ?
Location of bond?
Positive or negative effect?
Noncovalent bond
Not at the catalytic site
Induce conformational change to create a positive or negative impact
Utilize feedback inhibition where product of enzyme is a negative effector
29
What shape plot does a allosteric enzyme create
Sigmoidal
30
What is an Isozyme?
Same catalytic function, different primary sequence. Different binding sites. Can be used as marker for myocardial infarction - creatine kinase, aspartate, aminotransferase and more. Different isozymes can be used based on time after myocardial event.
31
Troponin in myocardial infarction
It is a 3 subunit protein in muscles one of these is Tn-1 of which there are 3 types of Tn-1. The heart version is called cTn-1 which can be used as a bio marker for myocardial infarction. Best used as a marker 10-24 hours after the event.
32
Proenzymes or zymogens
inactive precursor of enzymes that allow for enzyme regulation.
33
6 Roles of membranes
Protective barrier, characteristic shape, separates intracellular and extracellular, selective permeability, transport, cell recognition,
34
What type of bond attaches carbohydrates to membrane lipids and proteins?
Covalent attachment
35
3 different types of membrane lipids
Phospholipids
Glycolipids
Cholesterol
36
2 types of phospholipids
Glycerophospholipids and sphyngolipids
37
Describe the structure of glycolipids
shingosine backbone with carbohydrate residues Found in outer leaflet of the lipid bilayer.
38
Describe structure of cholesterol and where it is found
Embedded in lipid bilayer. Steroid nucleus with a hydroxyl group and hydrocarbon side chain.
39
Phosphatidylserine is found in outer or inner sheet of membrane
And what does it mean when it is found in each
Inner bilayer - normal healthy cell
| Outer - this happens during apoptosis - phagocytes use this to recognize these cells.
40
Niemann-Pick Disease
| Cause
Deficiency in activity of acid sphingomyelinase A-SMase (breaks down sphingomyelin ). This SM then builds up in liver and spleen and causes neurological damage. Also causes a cherry red spot in the eye.
41
3 types of membrane proteins
Integral membrane proteins - firmly embedded and stabilized by hydrophobic interactions
Peripheral proteins- loosely bound to membrane through electrostatic interactions with proteins or lipids
Lipid-anchored proteins - tethered to membranes via covalent attachment to lipid
42
Polytopic transmembrane proteins
Integral membrane protein that span entire bilayer weave in and out of membrane several times and interact with internal and external environment includes transporters, ion channels, and receptors.
43
Starch structure
Polysacharide of glucose
44
Sucrose structure
Disaccharide of glucose and fructose
45
Lactose structure
Disacharide of glucose and galactose
46
Fatty acid structure
Saturated or unsaturated with a carboxilic acid group on one end.
47
Triacylglycerol structure
3 fatty acids with glycerol backbone (glycerol is 3 saturated carbons that each have a oxygen on them.)
48
Cholesterol esters structure
A cholesterol esterified to a fatty acid
49
What is Isoprenoid and what it do.
synthesized from acetyl coa via IPP intermediate - IPP used to make steroids, vitamins, and more
Steroids have characteristics ABCD ring system counting from the bottom up.
Ex; cholesterol - component of bile, important precursor, and membrane component
50
Essential amino acids 9 of them
VLT Tim hall (we apparently don’t count arginine like some online sources do). Isoleucine, leucine, valine, phenylalanine, tryptophan, Hystidine, lysine, threonine, methionine, they are essential because we need to get them in our diet.
51
3 roles of proteins
Fuel - in the tca cycle they make atp
Structure - key component in connective tissue
Activity - enzymatic , transport, and cell signaling
52
Non polar amino acids
Alanine, glycine, isoleucine, leucine, methionine, phenylalanine, proline, tryptophan, valine Mnemonic ; pt avg limp
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Polar uncharged amino acids
Asparagine, cysteine, glutamine, serine, threonine, tyrosine,
Mnemonic is sgt cat
54
Negatively charged acidic amino acids
Aspartic acid, glutamic acid. No mnemonic sorry
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Positively charged basic amino acids
Arginine , histidine, lysine no mnemonic
56
How are carbs used in membranes
Covalently attached - outer sheet of many membranes covered in carbs shell called glycocalyx - glycocalyx protects, provides cell adhesion, and cell identification
57
Primary active transporters
P. Type atpases and abc transporters - only difference is that abc transporters don’t get phosphorylation in the process.
P type is phosphorylated on a aspartame residue always.
58
Antiporter, uniporter, and symporter
Anti - 1 in 1 out. Sym- 2 in uni - 1 in one direction
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Sodium glucose transporter 1
Moves Na+ into the cell with Glucose or galactose due to a Na+ gradient caused by Na+ atpase uniporter secondary active transporter
60
Ncx
Antiporter of 3x Na+ and 1Ca2+
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GLUT2
Simple diffusion of sugars main transporter in the liver low affinity
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Glut 5
Moves fructose into the cell via facilitated diffusion
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Cystnuria
Defect in transport of cysteine and other dibasic amino acids;arg lys and orn. Results in cys Chrystals in the kidney
64
Hartnup disease
Defect in transporter for non polar or neutral AA’s alanine valine threonine leucine trypophan etc. mostly in kidneys and intestine. Tryptophan is precursor for serotonin and niacin manifests as failure to thrive cerebellum ataxia (lack of muscle coordination), nystagmus, and light sensitivity
65
Jejunum
Sugars, peptides and amino acids, calcium, water, electrolytes
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Absorbed in the Ileum
Bile acids vitamin b12 water electrolytes
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B1 / thiamine defficiency
From alcoholism - ataxia, nystagmus, weak eye movement
Psychosis
Dry beriberi Paralysis
Wet beriberi- cardiac failure edema in peripheral
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B2 / riboflavin deficiency
Caused by poor diet - red thing on eye, magenta colored tongue and rash around mouth
69
Niacin / B3 deficiency
Hartnup disease causes it through a tryptophan deficiency which is used to make niacin
Clinical - rash/pellagra , diarrhea , dementia , dermatitis, death
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Pantotheic acid /B5 deficiency
Caused by extreme starvation - dermatitis, numbness, paresthesia (tingling skin), muscle cramps, enteritis(intestine inflammation), alopecia, hypoglycemia
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Pyridoxine / B6 defficiency
Deficiency from isoniazid therapy - sideroblastic anemia, Cheilosis (inflamed corners of mouth), convulsions
72
Biotin / B7 deficiency
Caused by excessive consumption of raw eggs - alopecia , rashes, bowel inflamation, muscle pain
73
Folic acid / B9 deficiency
Side effect from several drugs, also pregnancy and alcoholics - macrocytic megaloblastic anemia homocysteinemia (cardio vascular disease )
74
Cobalamin / b12 deficiency
Pernicious anemia, chronic pancreatitis, long term vegetarian, resection of ilium - megaloblastic anemia, neuropathies, cardio vascular disease
75
Ascorbate/ vit C deficiency
Diet deficient in citrus fruit and green vegetables
Leads to scurvy
Poor wound healing, easy bruising, bleeding gums, glossitis
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Vitamin A// retinol
Extreme malnutrition or fat malabsorption and liver cirrhosis
Night blindness,
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Vitamin D deficiency
Childhood rickets, delayed growth, pain in spine and legs, muscle weakness, bowed legs, breastbone projection
78
Glut 1
Ubiquitous but high in RBCs and brain high affinity
79
Glut 3
Main transporter in neurons high affinity
80
Glut 4
Present in skeletal muscle, heart, adipose tissue
Insulin dependent
Sequestered in vesicles until insulin signals for it to fuse with the membrane
81
Hexokinase is inhibited by what
| And has high or low affinity for glucose?
High affinity and is inhibited by g6p (product)
82
Glucokinase high or low affinity for glucose , inhibited by what, is sequestered by what protein to where?
Low affinity, lightly inhibited by g6p, sequestered by GK - regulatory protein to the nucleus
83
Phophofructokinase I regulation
This is rate limiting in glycolysis. Activated by ; insulin , AMP, (F2,6 BP), NH4+, AMP, Pi
Inhibited by; ATP ,Citrate, PEP, H+, glucagon
When dephosphorylated it is active
84
Regulation of Pyruvate kinase
Activated by = f 1,6 bp and insulin
Inhibited by ATP , alanine, and glucagon
Active when dephosphorylated
85
What effect does physical exertion have on glycolysis
Glycolysis is activated during exertion to meet energy requirement
86
Glucose 6 phosphate is a intermediate in glycolysis. It is also used in what other pathways?
Precursor for Pentose phosphate pathway and also converted to glucose 1 phosphate which is used in galactose metabolism and used in glycogen synthesis
87
Fates of pyruvate
Tca or Krebs cycle turned into acetyl coa and then CO2.
Converted to alanine in gluconeogenesis and protein synthesis
Reduced to lactate which generates NAD+
88
Most disorders of glycolysis cause ? Why?
Hemolytic Anemia
| This is because atp driven ion concentrations are messed up which causes water to rush into the cell.
89
Absorbed in the duodenum
Fat sugars peptides and amino acids, iron folate calcium water electrolytes
90
Tarui disease gsd VII
Deficient in pfk 1
Hemolytic anemia
High bilirubin and jaundice
91
Pyruvate carboxylase is an enzyme in glyconeogenesis that does what?
Helps skip a irreversible step of glycolysis by turning pyruvate into oxaloacetate
92
Lipid rafts are composed of what type of lipid
Cholesterol
93
PEP carboxykinase is an enzyme used in glyconeogenesis that does what?
Turns oxaloacetate into pep. This contributes to avoiding the irreversible step of pep to pyruvate in the glycolysis steps
94
Fructose 1,6 bisphosphatase
Turns fructose 1,6 bisphosphate into fructose 6 phosphate which overturns the irreversible work of step 3 by pfk1
95
Glucose 6 phosphatase is an enzyme involved in glyconeogenesis. What do it do?
Turns G6P into Glucose
96
When is glycolysis favored and when is glyconeogenesis favored
Positive regulation glycolysis - glucose, insulin, amp, fru 2,6 bp, fru 6 p, alanine. Positive regulation glyconeo - glucagon, citrate, cortisol, thyroxine , acetyl coa
Neg reg glycolysis - glucagon, atp, citrate, glc 6 p , fru 6 p , alanine
Neg reg glyconeo - adp amp fru 2,6 bp
97
What enzyme from glyconeogenesis is found in the mitochondria
Pyruvate kinase
98
Pyruvate decarboxylase requires what cofactor
Biotin
99
How does oxaloacetate escape the mitochondria
First reduced to maleate by malate dehydrogenase. Then exits, then is reoxidized by malate dehydrogenase in the cytosol.
100
Which enzyme is part of the rate limiting step in glyconeogenesis
Fructose 1,6 bisphophatase
101
Where is the glucose 6 phosphatase protein located which is involved in glyconeogenesis
In the lumen of the endoplasmic reticulum.
102
What is the cori cycle
2 pyruvate at the end of glycolysis are turned into lactate which diffuses into the blood and then into the liver. Lactate is then turned back into pyruvate to start glyconeogenesis.
103
What is Von gierke disease
Deficiency in glucose 6 phosphatase
104
Franconi - Bickel syndrome
Mutation in glut2 transporter which is located in liver and pancreas which makes them unable to uptake glucose, fructose, and galactose
105
Polyol pathway
Converts glucose to fructose via converting glucose to sorbitol with aldose reductase. Sorbitol is oxidized to fructose by sorbitol dehydrogenase. Sorbitol accumulation can lead to water influx which can cause cataracts
106
Fructose metabolism
Fructose can avoid the rate limiting step of glycolysis through fructokinase which leads to fast and easy fat production.
107
Galactose metabolism
Galactose is converted to galactose 1 p by galactokinase. Then GALT turns it into
108
Galactosemia
Deficiency in GALT leads to accumulation of galactitol
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Deficiency in galactokinase
Accumulation of galactose and galactitol in blood and urine
110
Pentose phosphate pathway
Produces no nrg, makes the sugar for dna and rna, makes NADPH
G6P to ribulose 6 P
2 parts, reversible oxidative / catabolic and irreversible non-oxidative /anabolic step
111
PPP - oxidative step
G6P dehydrogenase is the rate limiting step which makes NADPH and an intermediate. NADPH is used to regenerate glutathione which is used to detox H2O2.
112
Function of liver glycogen
Regulate blood sugar
113
Function of glycogen in muscle
Reservoir of fuel
114
Phosphoglucomutase does what in glycogenesis
Glucose 6 phosphate to glucose 1 phosphate
115
UDP glucose pyrophosphorylase does what in glycogenesis
Makes udp glucose out of glucose 1 phosphate
116
Glycogen synthase
Takes udp glucose and adds it in a 1-4 bond to glycogen chain - rate limiting step
117
Branching glycogen chains
When glycogen reaches about 11 links, about 7 links are broken off and reattached somewhere in a 1-6 manner by glucosyl 4:6 transferase. Branching increases solubility
118
Glycogen phosphorylase
Releases a g1p from non reducing end and uses B6 pyridoxal phosphate as a cofactor - this continues until it gets within 4 residues of a branch point - rate limiting step in degradation
119
Debranching enzyme - glycogenolysis
Moves 3 of the 4 remaining residues and puts them on the end of the main chain
120
Glycogen synthesis and degradation regulation?
Glycogen synthase
Glycogen phosphorylase when are each active and inactive
gp- when phosphorylated it is active
| GS - when not phosphorylated it is active
121
Does glucagon promote glycogenolysis in the liver or the muscle tissue
Liver - has no effect in muscle.
122
4 key proteins in insulin regulation of glycogen synthesis
GLUT 4 , protein kinase B, Protein phosphatase 1, glycogen synthase kinase 3, net result is that insulin activates glycogen synthesis.
123
Blood glucose criteria for diabetes
Normal is 70-100 fasting and less than 140 when fed.
Prediabetes is 100-125 and greater than 140 when fed
Diabetes is greater than fasting values and greater than 199 when fed
124
Regulation of glycogenolysis by glucagon
Key enzymes?
Net result?
```
G protein
Adenylate Cyclase and camp
Protein kinase A
Protein phosphatase 1
Phosphorylase kinase
Net ; Glycogen breakdown
```
125
GSD 0
Deficiency in glycogen synthase - rely in glucose in diet
126
Gsd 3 cori disease
Deficiency in a 1-6 glucosidase enzyme which is the debranching enzyme
127
GSD IV Anderson disease
Deficiency in glucosyl 4:6 transferase which is the branching enzyme
128
GSD V mcardle disease
Deficient in muscle glycogen phosphorylase which is rate limiting step in glycogen break down.
129
GSD VI Hers disease
Deficiency in liver glycogen phosphorylase - prevents glycogen break down in the liver
130
Pompe disease GSD II
Defect in acid Maltase - used in lysosomal degradation pathway
131
Function of lipids
Fuel stores, structural components, signaling molecules, other roles like providing insulation
132
What is more energy per pound, carbs or lipids>?
Lipids
133
3 phases in synthesis of fatty acids
Cytosolic entry of acetyl coa, generation of Malonyl coa, fatty acid chain formation
134
What does atp citrate lyase do ?
What inhibits it ?
What activates?
Citrate -> OAA and acetyl coa
Inhibits by; pufa’s and lepton - if you have fat then don’t make more
Activated by; glucose and insulin - if to much sugar than take it up and store it
135
Acetyl coa carboxylase - what does it do ?
What inhibits it
What activates it
Acetyl coa to malonyl coa
Glucagon and epinephrine inhibit
Citrate and insulin activate
136
Name 2 tca disorders
2-oxoglutaric aciduria and fumarase deficiency
137
What drugs inhibit complex 1 in oxphos
Amytal, rotenone, myxothiazol, piericidin
138
What drug inhibits complex 2 in oxphos
Malonate
139
What drug inhibits complex 3 in oxphos
Antimycin
140
What inhibits complex 4 in oxphos
CO cyanide h2s
141
What inhibits complex 5 in oxphos
Oligomycin
142
4 steps of fatty acid synthesis
Condensation, reduction, dehydration, reduction
| You add a 3 carbon with a 2 carbon and end up with a 4 carbon after loosing CO2
143
Atp citrate lyase is stimulated by phosphorylation or not phosphorylation?
Phosphorylation
144
Acetyl Coa Carboxylase is stimulatated or inhibited by phosphorylation?
Inhibited
145
When lengthening longer fatty acids where does it happen and what is used to lengthen
SER - malonyl COA
| Mitochondria - acetyl coa
146
What forms desaturated fatty acids and where can they form
Acyl coa desaturases - can desaturated at the 4 5 6 and 9
147
2 essential fatty acids
Linoleic acid and linolenic acid
148
4 steps in beta oxidation of fatty acids
Oxidation (done by ACAD (specifically know MCAD)), hydration, oxidation, thiolysis
149
How do you finish off odd numbered fatty acids
Propionyl coa carboxylase
Methylmalonyl Coa mutase
Metabolize normally until just 3 left.
Use first enzyme to attach a 4th carbon
Second enzyme rearranges the molecule so that the carbons are all in a row
150
How does metabolism handle an unsaturated bond
Reductase will reduce a double bond and isomerase will move the disruptive bond.
151
Where is metabolism for extremely long fatty acids >20 in length
Peroxisome until it is less than 20 and then and instead of acad enzyme it uses acyl coa oxidase
152
3 types of ketone bodies and where produced
Acetoacetone
Acetone
Beta hydroxybutyerate
All produced in the liver
153
Exopeptidase
Proteolysis at c or n terminus
