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Biochem > BioChem > Flashcards

BioChem Flashcards

1
Q

Oxidoreductases

A

Transfer elecltrons from a donor to an acceptor

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2
Q

Transferases

A

Transfer a functional group

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3
Q

Isomerases

A

Rearrange / isomerase a molecule

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4
Q

Lyases (syntheses)

A

Add or remove atoms to or from a double bond

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5
Q

Ligases “synthetases”

A

Form (C-O C-S C-N C-C) bonds with the hydrolysis of atp

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6
Q

Hydrolases

A

Cleave bonds via the addition of water

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7
Q

Enzyme that uses Cu as a cofactor

A

Cytochrome c oxidase

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8
Q

Enzyme that uses Fe as cofactor

A

Heme proteins (hemoglobin and myoglobin) need Fe to bind O2

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9
Q

Enzyme that requires Mg as a cofactor

A

ATPases

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10
Q

Enzyme that requires Se as a cofactor

A

Glutathione peroxidase- detoxifies hydrogen peroxide

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11
Q

Enzyme that requires Zn as a cofactor

A

Superoxide dismutase - binds the free radical of molecular oxygen

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12
Q

2 types of coenzymes

A

Co substrate - temporary association such as NAD+

Prosthetic - permanent association Heme

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13
Q

Ideal temp for enzyme activity

A

37 degrees C

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14
Q

Ideal pH for enzyme activity

A

4-8 with the exception of pepsin

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15
Q

Gastric proton pumps are on what type of cell

A

Parietal cells

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16
Q

What variable stands for enzyme - substrate affinity?

A

Km

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17
Q

/What shape is a Michaelis menten plot?

A

Hyperbolic

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18
Q

/What shape is a lineweaver Burke plot?

A

Linear

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19
Q

Competitive inhibitor

A

Resemble substrate - compete for the active site on an enzyme
No effect on vmax - increase Km

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20
Q

1/2 vmax

A

Km

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21
Q

Lineweaver Burke x intercept

A

-1/Km

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22
Q

Y intercept lineweaver Burke

A

1/Vmax

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23
Q

Slope lineweaver Burke plot

A

Km/Vmax

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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

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25
Q

Uncompetitive inhibition

A

Decrease in vmax and Km by the same factor - lineweaver Burke plot with and without inhibitor yields parallel lines

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26
Q

How can you inhibit metaloenzymes

A

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)

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27
Q 
Enzyme inactivation 
VMax? Up or down
Km? Up or down
Reversible or not?
Similar lineweaver Burke plot to what type on inhibition?
A

Vmax decreased
Unchanged Km
Irreversible
Non competitive is similar but is reversible

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28
Q

Allosteric enzymes
Type of bond ?
Location of bond?
Positive or negative effect?

A

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

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29
Q

What shape plot does a allosteric enzyme create

A

Sigmoidal

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30
Q

What is an Isozyme?

A

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.

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31
Q

Troponin in myocardial infarction

A

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.

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32
Q

Proenzymes or zymogens

A

inactive precursor of enzymes that allow for enzyme regulation.

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33
Q

6 Roles of membranes

A

Protective barrier, characteristic shape, separates intracellular and extracellular, selective permeability, transport, cell recognition,

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34
Q

What type of bond attaches carbohydrates to membrane lipids and proteins?

A

Covalent attachment

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35
Q

3 different types of membrane lipids

A

Phospholipids
Glycolipids
Cholesterol

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36
Q

2 types of phospholipids

A

Glycerophospholipids and sphyngolipids

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37
Q

Describe the structure of glycolipids

A

shingosine backbone with carbohydrate residues Found in outer leaflet of the lipid bilayer.

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38
Q

Describe structure of cholesterol and where it is found

A

Embedded in lipid bilayer. Steroid nucleus with a hydroxyl group and hydrocarbon side chain.

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39
Q

Phosphatidylserine is found in outer or inner sheet of membrane
And what does it mean when it is found in each

A

Inner bilayer - normal healthy cell

Outer - this happens during apoptosis - phagocytes use this to recognize these cells.

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40
Q

Niemann-Pick Disease

Cause

A

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.

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41
Q

3 types of membrane proteins

A

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

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42
Q

Polytopic transmembrane proteins

A

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.

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43
Q

Starch structure

A

Polysacharide of glucose

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44
Q

Sucrose structure

A

Disaccharide of glucose and fructose

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45
Q

Lactose structure

A

Disacharide of glucose and galactose

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46
Q

Fatty acid structure

A

Saturated or unsaturated with a carboxilic acid group on one end.

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47
Q

Triacylglycerol structure

A

3 fatty acids with glycerol backbone (glycerol is 3 saturated carbons that each have a oxygen on them.)

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48
Q

Cholesterol esters structure

A

A cholesterol esterified to a fatty acid

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49
Q

What is Isoprenoid and what it do.

A

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

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50
Q

Essential amino acids 9 of them

A

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.

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51
Q

3 roles of proteins

A

Fuel - in the tca cycle they make atp
Structure - key component in connective tissue
Activity - enzymatic , transport, and cell signaling

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52
Q

Non polar amino acids

A

Alanine, glycine, isoleucine, leucine, methionine, phenylalanine, proline, tryptophan, valine Mnemonic ; pt avg limp

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53
Q

Polar uncharged amino acids

A

Asparagine, cysteine, glutamine, serine, threonine, tyrosine,
Mnemonic is sgt cat

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54
Q

Negatively charged acidic amino acids

A

Aspartic acid, glutamic acid. No mnemonic sorry

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55
Q

Positively charged basic amino acids

A

Arginine , histidine, lysine no mnemonic

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56
Q

How are carbs used in membranes

A

Covalently attached - outer sheet of many membranes covered in carbs shell called glycocalyx - glycocalyx protects, provides cell adhesion, and cell identification

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57
Q

Primary active transporters

A

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.

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58
Q

Antiporter, uniporter, and symporter

A

Anti - 1 in 1 out. Sym- 2 in uni - 1 in one direction

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59
Q

Sodium glucose transporter 1

A

Moves Na+ into the cell with Glucose or galactose due to a Na+ gradient caused by Na+ atpase uniporter secondary active transporter

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60
Q

Ncx

A

Antiporter of 3x Na+ and 1Ca2+

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61
Q

GLUT2

A

Simple diffusion of sugars main transporter in the liver low affinity

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62
Q

Glut 5

A

Moves fructose into the cell via facilitated diffusion

63
Q

Cystnuria

A

Defect in transport of cysteine and other dibasic amino acids;arg lys and orn. Results in cys Chrystals in the kidney

64
Q

Hartnup disease

A

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
Q

Jejunum

A

Sugars, peptides and amino acids, calcium, water, electrolytes

66
Q

Absorbed in the Ileum

A

Bile acids vitamin b12 water electrolytes

67
Q

B1 / thiamine defficiency

A

From alcoholism - ataxia, nystagmus, weak eye movement
Psychosis
Dry beriberi Paralysis
Wet beriberi- cardiac failure edema in peripheral

68
Q

B2 / riboflavin deficiency

A

Caused by poor diet - red thing on eye, magenta colored tongue and rash around mouth

69
Q

Niacin / B3 deficiency

A

Hartnup disease causes it through a tryptophan deficiency which is used to make niacin
Clinical - rash/pellagra , diarrhea , dementia , dermatitis, death

70
Q

Pantotheic acid /B5 deficiency

A

Caused by extreme starvation - dermatitis, numbness, paresthesia (tingling skin), muscle cramps, enteritis(intestine inflammation), alopecia, hypoglycemia

71
Q

Pyridoxine / B6 defficiency

A

Deficiency from isoniazid therapy - sideroblastic anemia, Cheilosis (inflamed corners of mouth), convulsions

72
Q

Biotin / B7 deficiency

A

Caused by excessive consumption of raw eggs - alopecia , rashes, bowel inflamation, muscle pain

73
Q

Folic acid / B9 deficiency

A

Side effect from several drugs, also pregnancy and alcoholics - macrocytic megaloblastic anemia homocysteinemia (cardio vascular disease )

74
Q

Cobalamin / b12 deficiency

A

Pernicious anemia, chronic pancreatitis, long term vegetarian, resection of ilium - megaloblastic anemia, neuropathies, cardio vascular disease

75
Q

Ascorbate/ vit C deficiency

A

Diet deficient in citrus fruit and green vegetables
Leads to scurvy
Poor wound healing, easy bruising, bleeding gums, glossitis

76
Q

Vitamin A// retinol

A

Extreme malnutrition or fat malabsorption and liver cirrhosis
Night blindness,

77
Q

Vitamin D deficiency

A

Childhood rickets, delayed growth, pain in spine and legs, muscle weakness, bowed legs, breastbone projection

78
Q

Glut 1

A

Ubiquitous but high in RBCs and brain high affinity

79
Q

Glut 3

A

Main transporter in neurons high affinity

80
Q

Glut 4

A

Present in skeletal muscle, heart, adipose tissue
Insulin dependent
Sequestered in vesicles until insulin signals for it to fuse with the membrane

81
Q

Hexokinase is inhibited by what

And has high or low affinity for glucose?

A

High affinity and is inhibited by g6p (product)

82
Q

Glucokinase high or low affinity for glucose , inhibited by what, is sequestered by what protein to where?

A

Low affinity, lightly inhibited by g6p, sequestered by GK - regulatory protein to the nucleus

83
Q

Phophofructokinase I regulation

A

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
Q

Regulation of Pyruvate kinase

A

Activated by = f 1,6 bp and insulin
Inhibited by ATP , alanine, and glucagon
Active when dephosphorylated

85
Q

What effect does physical exertion have on glycolysis

A

Glycolysis is activated during exertion to meet energy requirement

86
Q

Glucose 6 phosphate is a intermediate in glycolysis. It is also used in what other pathways?

A

Precursor for Pentose phosphate pathway and also converted to glucose 1 phosphate which is used in galactose metabolism and used in glycogen synthesis

87
Q

Fates of pyruvate

A

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
Q

Most disorders of glycolysis cause ? Why?

A

Hemolytic Anemia

This is because atp driven ion concentrations are messed up which causes water to rush into the cell.

89
Q

Absorbed in the duodenum

A

Fat sugars peptides and amino acids, iron folate calcium water electrolytes

90
Q

Tarui disease gsd VII

A

Deficient in pfk 1
Hemolytic anemia
High bilirubin and jaundice

91
Q

Pyruvate carboxylase is an enzyme in glyconeogenesis that does what?

A

Helps skip a irreversible step of glycolysis by turning pyruvate into oxaloacetate

92
Q

Lipid rafts are composed of what type of lipid

A

Cholesterol

93
Q

PEP carboxykinase is an enzyme used in glyconeogenesis that does what?

A

Turns oxaloacetate into pep. This contributes to avoiding the irreversible step of pep to pyruvate in the glycolysis steps

94
Q

Fructose 1,6 bisphosphatase

A

Turns fructose 1,6 bisphosphate into fructose 6 phosphate which overturns the irreversible work of step 3 by pfk1

95
Q

Glucose 6 phosphatase is an enzyme involved in glyconeogenesis. What do it do?

A

Turns G6P into Glucose

96
Q

When is glycolysis favored and when is glyconeogenesis favored

A

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
Q

What enzyme from glyconeogenesis is found in the mitochondria

A

Pyruvate kinase

98
Q

Pyruvate decarboxylase requires what cofactor

A

Biotin

99
Q

How does oxaloacetate escape the mitochondria

A

First reduced to maleate by malate dehydrogenase. Then exits, then is reoxidized by malate dehydrogenase in the cytosol.

100
Q

Which enzyme is part of the rate limiting step in glyconeogenesis

A

Fructose 1,6 bisphophatase

101
Q

Where is the glucose 6 phosphatase protein located which is involved in glyconeogenesis

A

In the lumen of the endoplasmic reticulum.

102
Q

What is the cori cycle

A

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
Q

What is Von gierke disease

A

Deficiency in glucose 6 phosphatase

104
Q

Franconi - Bickel syndrome

A

Mutation in glut2 transporter which is located in liver and pancreas which makes them unable to uptake glucose, fructose, and galactose

105
Q

Polyol pathway

A

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
Q

Fructose metabolism

A

Fructose can avoid the rate limiting step of glycolysis through fructokinase which leads to fast and easy fat production.

107
Q

Galactose metabolism

A

Galactose is converted to galactose 1 p by galactokinase. Then GALT turns it into

108
Q

Galactosemia

A

Deficiency in GALT leads to accumulation of galactitol

109
Q

Deficiency in galactokinase

A

Accumulation of galactose and galactitol in blood and urine

110
Q

Pentose phosphate pathway

A

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
Q

PPP - oxidative step

A

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
Q

Function of liver glycogen

A

Regulate blood sugar

113
Q

Function of glycogen in muscle

A

Reservoir of fuel

114
Q

Phosphoglucomutase does what in glycogenesis

A

Glucose 6 phosphate to glucose 1 phosphate

115
Q

UDP glucose pyrophosphorylase does what in glycogenesis

A

Makes udp glucose out of glucose 1 phosphate

116
Q

Glycogen synthase

A

Takes udp glucose and adds it in a 1-4 bond to glycogen chain - rate limiting step

117
Q

Branching glycogen chains

A

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
Q

Glycogen phosphorylase

A

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
Q

Debranching enzyme - glycogenolysis

A

Moves 3 of the 4 remaining residues and puts them on the end of the main chain

120
Q

Glycogen synthesis and degradation regulation?
Glycogen synthase
Glycogen phosphorylase when are each active and inactive

A

gp- when phosphorylated it is active

GS - when not phosphorylated it is active

121
Q

Does glucagon promote glycogenolysis in the liver or the muscle tissue

A

Liver - has no effect in muscle.

122
Q

4 key proteins in insulin regulation of glycogen synthesis

A

GLUT 4 , protein kinase B, Protein phosphatase 1, glycogen synthase kinase 3, net result is that insulin activates glycogen synthesis.

123
Q

Blood glucose criteria for diabetes

A

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
Q

Regulation of glycogenolysis by glucagon
Key enzymes?
Net result?

A 
G protein
Adenylate Cyclase and camp 
Protein kinase A
Protein phosphatase 1
Phosphorylase kinase 
Net ; Glycogen breakdown
125
Q

GSD 0

A

Deficiency in glycogen synthase - rely in glucose in diet

126
Q

Gsd 3 cori disease

A

Deficiency in a 1-6 glucosidase enzyme which is the debranching enzyme

127
Q

GSD IV Anderson disease

A

Deficiency in glucosyl 4:6 transferase which is the branching enzyme

128
Q

GSD V mcardle disease

A

Deficient in muscle glycogen phosphorylase which is rate limiting step in glycogen break down.

129
Q

GSD VI Hers disease

A

Deficiency in liver glycogen phosphorylase - prevents glycogen break down in the liver

130
Q

Pompe disease GSD II

A

Defect in acid Maltase - used in lysosomal degradation pathway

131
Q

Function of lipids

A

Fuel stores, structural components, signaling molecules, other roles like providing insulation

132
Q

What is more energy per pound, carbs or lipids>?

A

Lipids

133
Q

3 phases in synthesis of fatty acids

A

Cytosolic entry of acetyl coa, generation of Malonyl coa, fatty acid chain formation

134
Q

What does atp citrate lyase do ?
What inhibits it ?
What activates?

A

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
Q

Acetyl coa carboxylase - what does it do ?
What inhibits it
What activates it

A

Acetyl coa to malonyl coa
Glucagon and epinephrine inhibit
Citrate and insulin activate

136
Q

Name 2 tca disorders

A

2-oxoglutaric aciduria and fumarase deficiency

137
Q

What drugs inhibit complex 1 in oxphos

A

Amytal, rotenone, myxothiazol, piericidin

138
Q

What drug inhibits complex 2 in oxphos

A

Malonate

139
Q

What drug inhibits complex 3 in oxphos

A

Antimycin

140
Q

What inhibits complex 4 in oxphos

A

CO cyanide h2s

141
Q

What inhibits complex 5 in oxphos

A

Oligomycin

142
Q

4 steps of fatty acid synthesis

A

Condensation, reduction, dehydration, reduction

You add a 3 carbon with a 2 carbon and end up with a 4 carbon after loosing CO2

143
Q

Atp citrate lyase is stimulated by phosphorylation or not phosphorylation?

A

Phosphorylation

144
Q

Acetyl Coa Carboxylase is stimulatated or inhibited by phosphorylation?

A

Inhibited

145
Q

When lengthening longer fatty acids where does it happen and what is used to lengthen

A

SER - malonyl COA

Mitochondria - acetyl coa

146
Q

What forms desaturated fatty acids and where can they form

A

Acyl coa desaturases - can desaturated at the 4 5 6 and 9

147
Q

2 essential fatty acids

A

Linoleic acid and linolenic acid

148
Q

4 steps in beta oxidation of fatty acids

A

Oxidation (done by ACAD (specifically know MCAD)), hydration, oxidation, thiolysis

149
Q

How do you finish off odd numbered fatty acids
Propionyl coa carboxylase
Methylmalonyl Coa mutase

A

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
Q

How does metabolism handle an unsaturated bond

A

Reductase will reduce a double bond and isomerase will move the disruptive bond.

151
Q

Where is metabolism for extremely long fatty acids >20 in length

A

Peroxisome until it is less than 20 and then and instead of acad enzyme it uses acyl coa oxidase

152
Q

3 types of ketone bodies and where produced

A

Acetoacetone
Acetone
Beta hydroxybutyerate
All produced in the liver

153
Q

Exopeptidase

A

Proteolysis at c or n terminus

Biochem (3 decks)

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