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Biochem 6200 > E1 > Flashcards

E1 Flashcards

1
Q

The most critical function of an enzyme

A

catalyze reactions.

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2
Q

Common features of enzymes

A
  1. Catalyze – reaction still could occur.
  2. Enzyme not permanently altered by rxn.
  3. Can catalyze both forward and reverse rxn.
  4. Highly specific for substrate.
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3
Q

Influence of temperature and PH on enzyme

A

Denatures, folding, stability

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4
Q

Composition of complex enzyme

A

Quarternary structure ** more on this?

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5
Q

Oxidoreductase

A

Catalyze transfer of electrons from one molecule (reductant) to another (oxidant). Oft uses NAD+/NADH.

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6
Q

Transferase

A

Transfer a group from one molecule to another.

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7
Q

Hydrolase

A

Add H20

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8
Q

Isomerase

A

Rearange molecules to differing isomers

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9
Q

Ligase

A

Remove H20, bring two molecules to one.

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10
Q

Active site(s) of enzymes

A

fisher, other

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11
Q

Absolute (only 1 rxn) and relative (more than 1) specificities of enzymes

A

*

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12
Q

Definition of enzyme activity

A

1 unit (U) is the amount if enzyme that catalyses the reaction of 1 nmol of substrate per minute under standard conditions.

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13
Q

Km

A

amount of substrate needed for the enzyme to obtain half of its maximum rate of reaction, Max velocity respectively

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14
Q

Reversible and irreversible inhibition of enzyme

A

competitive, noncomp, uncomp, suicide, group-specific reagents (react with specific AA R-groups), substrate analogs (covalently modify site, like substrate)

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15
Q

Regulation of enzyme activity

A

(allosteric (2nd site from active site), reversible covalent (phosphate group most common), isoenzymes, proteolytic (cleavage, can activate, can destroy).

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16
Q

Metabolic channeling

A

Occurs when the product of one reaction is transferred directly to the next active site without entering the bulk solvent. Can greatly increase rate of a reactions

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17
Q

Channeling is possible in

A

Channeling is possible in multienzyme complexes and multifunctional enzymes

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18
Q

Glycolysis starts from glucose and ends at

A

lactate

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19
Q

Glucose can be used to generate

A

ATP, glycogen, ribose, lipid molecules, and NADPH*

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20
Q

Glucose can be trapped in a cell in the form of

A

Glc-6-P

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21
Q

The rate limiting enzyme of glycolysis is

A

PFK-1

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22
Q

Enzymes for glycolysis yield

A

PGK and pyruvate kinase catalyze the yield of ATP in glycolysis

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23
Q

Pyruvate can be transformed to

A

lactate in order to regenerate NAD+

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24
Q

Glc-6-P

A

Hexokinase can be inhibited by Glc-6-P

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25
Q

PFK-1

A

PFK-1 can be inhibited by ATP, activated by AMP

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26
Q

Pyruvate kinase

A

Pyruvate Kinase can be activated by Fructose-1,6-BP

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27
Q

Pentose phosphate pathway is important for the generation of

A

NADPH, Ribose

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28
Q

UDP-glucose is used as the building block for

A

glycogen

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29
Q

Glycogen synthase extend the chain of glycogen

A

extend the chain of glycogen

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30
Q

Glycogenin

A

initiates glycogen synthesis

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31
Q

Glycogen phosphorylase

A

Glycogen phosphorylase catalyze the breakdown of glycogen

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32
Q

Inhibition of glycogen phosphorylase can be used to treat

A

diabetes

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33
Q

Glucagon is an enzyme that

A

stimulate glycogenolysis

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34
Q

Epinephrine and glucagon act to increase the activity of

A

glycogen phosphorylase

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35
Q

Where does TCA cycle occur

A

matrix of mito.

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36
Q

The two major functions of TCA cycle

A

energy production, biosynthesis

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37
Q

Acetyl-CoA and oxaloacetate can both be derived from

A

pyruvate

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38
Q

Pyruvate dehydrogenase catalyze the synthesis of

A

acetyl-CoA

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39
Q

The 4 oxidative enzymes in the TCA cycle are

A

isocitrate DH, AKG DH, succinate DH, and malate DH

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40
Q

The pyruvate DH is negatively regulated by

A

ATP, Acetyl-CoA, and NADH

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41
Q

Which of the following reduces oxygen to water:

A

B. Cytochrome C oxidase

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42
Q

There are two major types of complex carbohydrates

A

glycoproteins and proteoglycans

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43
Q

Glycoproteins are proteins that contain

A

short glycan (or sugar) chains

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44
Q

Glycan chains in glycoproteins are usually about

A

3 to 15 sugars long and often highy branched. They do not have a repeating unit and usually contain about 10-15% carbohydrate by weight.

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45
Q

Glycoproteins are found on the

A

cell surface proteins, the ER and the golgi or they are secreted

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46
Q

Carbohydrates on glycoproteins

A

: 1. assist in protein folding to the correct conformation, 2. enhance protein solubility, 3. stabilize the protein against denaturation, 4. protect the protein from proteolytic degradation, 5. target the protein to specific subcellular locations, 6. serve as recognition signals for carbohydrate binding proteins (lectins).

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47
Q

The major sugar found in glycoproteins are

A

the Amino sugars - N-acetylglucosamine and N-acetlygalactosamine, Neutral sugars – galactose, mannose and fucose, and the Acidic sugar - sialic acid (N-acetylneuraminic acid).

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48
Q

Proteoglycans contain as much as

A

50-60% sugars. Sugarchains are usually long unbranched polymers than can contain hundreds of monosaccharides usually having a repeating disaccharide unit.

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49
Q

There are two types of linkages of carbohydrates to proteins

A

. 1. N – linked where the sugar is attached to an asparagine. 2. O – linked where the sugar is attached to a serine, threonine or hydroxylysine

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50
Q

More than a 100 complex carbohydrate structures have been identified

A

each containing a core of 2 N-acetylglucosamines and 3 mannose residues

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51
Q

Many proteins have both

A

N-linked and O-linked structures.

52
Q

There are no essential sugars because

A

cells can use glucose (or another common sugar) to make all other sugars needed.

53
Q

Lectins on the surface of endothelial cells recognize

A

carbohydrate signals on leukocytes. This is one example of interact of different cell types through carbohydrates.

54
Q

Complex carbohydrates are found on

A

the surface of bacteria. Gram positive bacteria have a thick layer of peptidoglycan on their surface. Gram negative bacteia have a thin layer of peptidoglycan between two lipid bilayers.

55
Q

The carbohydrate portion of peptidoglycan is made up of

A

the alternating co-polymers or N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM).

56
Q

The synthesis and deposition of peptidoglycan is

A

the target of several antibiotics including penicillin

57
Q

Some bacteria are surround by a thick

A

polysaccharide capsule

58
Q

The glucans of S. mutans help bacteria

A

stick to each other to form plaque on the surface of teeth.

59
Q

anabolism

A

Synthesis of biological compounds is called anabolism

60
Q

Catabolism

A

Breakdown of compounds is catabolism

61
Q

R groups within a class

A

ID are they nonpolar, aromatic, polar, aromatic, charged.

62
Q

Understand structures between primary second, tert, quat.

A

a

63
Q

What a pI is of an AA

A

Isoelectric points** https://quizlet.com/2855398/amino-acids-structure-to-full-name-flash-cards/

64
Q

protein purification**

A

expand on this

65
Q

Protein analysis

A

s (SDS page, Mass spec, 2D, Isoelectric focusing).

66
Q

The two components of the clot:

A

Platelets, Fibrin

67
Q

Platelets

A
  • Cell fragments, produced by megakaryocytes
  • Platelet activation, what that entails*

-Cellular fragments
Activated when vessel breeched
Membrane, granules

68
Q

Fibrin

A 
•	Cascade reactions
•	Different subpathways
•	Central components
     o	Thrombin
     o	Fibrin
•	Vitamin K pathway
69
Q

Mechs of:

A
  • Aspirin
  • Warfarin
  • Plavix
  • Heparin
  • EDTA
70
Q

Fibrinolysis

A

TPA
Plasminogen/plasmin

Fibrinolysis is the cleavage of fibrin that can lead to dissolution of the clot
It is carried out the enzyme plasmin
Plasmin is synthesized as the inactive form plasminogen, which is cleaved by plasminogen activators, tPA and urokinase
recombinant tPA is used as treatment for clotting diseases

71
Q

• Inflammation

A

order of cells , types of cytokines

Cytokines and factors from platelet granules
Signals from cellular damage
Presence of foreign microorganisms

Tissue macrophages
Dendritic cells
Mast cells
Gamma-delta T cells

72
Q

Specific oral/dental wound healing

A
  • Growth factors
  • Membranes
  • Substrates
  • “Guided tissue regeneration”
73
Q

Dietary protein is the

A

main source of amino acids

74
Q

There is no dedicated

A

storage form of amino acids.

75
Q

Mammals acquire most of there energy from

A

carbohydrates, fats and proteins. Carbohydrate breakdown is the most efficient but yields that lowest amount of energy. Protein releases an intermediate amount of energy, however nitrogen containing byproduct must be eliminated.

76
Q

The liver synthesizes

A

nonessential amino acids, removes and breaks down excess amino acids, removes ammonia from the blood and converts it to urea and makes other nitrogen-containing compounds.

77
Q

Amino acids feed into

A

other pathways (especially carbohydrate metabolizing pathways) at several locations including pyruvate, acetyl CoA and TCA intermediates

78
Q

Amino acids can be converted to

A

pyruvate and therefore glucose, while fatty acids cannot.

79
Q

The first step in converting amino acids into glucose or other intermediates is

A

deamination. The most common mechanism for deamination is transamination that exchanges the amino group with the keto group on alpha- keto glutarate resulting in glutamic acid.

80
Q

Glutamate is a key intermediate in

A

amino acid metabolism. Glutamate can be deaminated to give free ammonia. There is no net loss of nitrogen or ammonia during transamination.

81
Q

Approximately half of the 20 amino acids that make proteins are

A

essential or they are required in the diet. The other half are non-essential and we are able to synthesize them.

82
Q

The general scheme for amino acid catabolism is first to

A

remove the amino group that is used to synthesize new nitrogen compounds or excreted as urea. This is followed by incorporation of the carbon atoms into compounds that can enter the TCA cycle

83
Q

Some of the major compounds that derive nitrogen from amino acids are

A

Nitric oxide, hormones, neurotransmitters, nicotinamide, heme, creatin phosphate and nucleotides.

84
Q

Transaminase reactions are

A

reversible. This allows the inter-conversion between amino acids keeping their concentrations balanced

85
Q

Ammonia is highly

A

toxic to living organisms and must be eliminated safely

86
Q

Conversion of ammonia to urea takes place in

A

the liver

87
Q

The urea cycle converts one

A

molecule of free ammonia (from glutamic acid) and one amino group from aspartate into urea and fumarate.

88
Q

There is a connection between the urea cycle and the TCA cycle through the product of

A

fumarate during the urea cycle

89
Q

Alanine is used to transport

A

nitrogen from peripheral tissues to the liver. In the liver, alanine is converted to pyruvate with the nitrogen incorporated into urea. This glucose-alanine cycle facilitates that conversion of amino acids into glucose.

90
Q

Alanine and glutamine account for about

A

50% of amino acids released by muscle into the blood

91
Q

The conversion of ammonia into carbamoyl phosphate occurs in

A

the mitochondria

92
Q

A total lack of urea cycle activity is

A

lethal. Treatment can include the use of compound that react with amino groups and remove them from the body.

93
Q

Glucogenic amino acids are those that can be metabolized into

A

3 carbon molecules that can be used to synthesize glucose

94
Q

Ketogenic amino acids are metabolized into

A

2 or 4 carbon structures

95
Q

There are several inherited diseases caused by defects in amino acid metabolism:

A

Maple syrup urine disease (MSUD) is an inability to metabolize branch chain amino acids. Phenylketonuria is a deficiency of phenylalanine hydroxylase that converts phenylalanine to tyrosine. Alkaptonuria (black urine disease) and Albinism are caused by other defects in aromatic amino acid metabolism

96
Q

The first step in polyamine synthesis is the

A

decarboxylation of ornithine to make putrescine

97
Q

Ornithine decarboxylase (ODC) is the

A

rate-limiting step in polyamine synthesis and has been the target for a number of cancer drugs.

98
Q

What is the solid storage form of lipids that is found primarily in adipose tissue?

A

Triglycerides.

99
Q

What molecule is central to both carbohydrate and fat metabolism?

A

Acetyl CoA

100
Q

Extra cards

A

https://quizlet.com/96090634/98-924-carbohydrates-and-lipids-craig-bartling-flash-cards/

101
Q

Relationship between fatty acid structure and physical properties (e.g., melting point)

A

Longer the chain, lower solubility

  • Longer the chain, higher the melting point
  • Fewer double bonds (saturated), lower solubility in water
  • More double bonds (unsaturated), lower melting point
102
Q

Know what phospholipids are

A

glycerol + 2 fatty acids + 1 phosphate group; makes up membrane bilayers of cells; hydrophobic interiors and hydrophillic exteriors

103
Q

Fatty acids are esterified to what molecule?

A

glycerol to form triacylglycerol

104
Q

How is lipid metabolism regulated?

A

by hormones (insulin, glucagon, epinephrine, and cortisol)

105
Q

What is the carnitine shuttle

A

long chain Fatty Acids are activated in the cytoplasm and transported via carnitine shuttle

106
Q

What are the products of β-oxidation of odd-numbered, even numbered, saturated,
unsaturated, branched, etc?

A

Occurs in mitochondria, releases two carbon acetyl coA units each turn of cycle

oxidation of B-carbon (to keto group) followed by cleavage between a and b carbons by thiolase.

107
Q

What is a ketone body?

A

Ketones are made in the liver. Intermediate is HMG-CoA (also an intermediate in cholesterol synthesis). Consists of 3 compounds: acetoacetate, beta-hydroxybutyrate, and acetone. Occurs during conditions when fat oxidation is overly active and leads to an accumulation of Acetyl-CoA. Because Acetyl CoA is present in larger amounts than OAA, the extra Acetyl CoA is used to produce ketones in the mitochondria of the liver.

108
Q

Acetyl-CoA carboxylase: what is the reaction, how is it regulated, etc.

A

Rate limiting step of fatty acid synthesis.

a biotin-dependent enzyme that catalyzes the irreversible carboxylation of acetyl-CoA to produce malonyl-CoA through its two catalytic activities, biotin carboxylase (BC) and carboxyltransferase (CT).

109
Q

• What is the malate shuttle?

A

allows transfer of two-carbon units from the mitochondria to the cytosol

1) pyruvate decarboxylated into acetyl coA in the mitochondria
2) reacts with oxaloacetate to form citrate
3) citrate moved to cytosol via malate shuttle
4) citrate cleaved to acetyl coA and oxaloacetate by citrate lyase
5) Acetyl CoA carboxylated to malonyl coA for the synthesis of fatty acids

110
Q

What is leptin?

A

main fat storage molecule, hormone that signals the hypothalamus and brain stem to reduce appetite and increase the amount of energy used.

leptin deficient animals are obese and lethargic

111
Q

Understand the steps of fatty acid synthesis

A

1) Acetyl CoA:ACP transacylase: Activates acetyl CoA for reaction with malonyl-ACP
2) Malonyl CoA:ACP transacylase: Activates malonyl CoA for reaction with acetyl-ACP
3) 3-ketoacyl-ACP synthase: Reacts priming acetyl-ACP with chain-extending malonyl-ACP.
4) 3-ketoacyl-ACP reductase: Reduces the carbon 3 ketone to a hydroxyl group
5) 3-Hydroxyacyl ACP dehydrase: Removes water
6) Enoyl-ACP reductase: Reduces the C2-C3 double bond.

112
Q

What is a lipase?

A

An enzyme secreted in the digestive tract that catalyzes the breakdown of fats into individual fatty acids that can be absorbed into the bloodstream

113
Q

What is a statin

A

any of a group of drugs that act to reduce levels of fats, including triglycerides and cholesterol, in the blood.

114
Q

What are bile acids, where are they produced, how are they regulated, what are their functions, etc.?

A

Bile acids are steroid acids found predominantly in the bile of mammals and other vertebrates. Different molecular forms of bile acids can be synthesized in the liver by different species.[1] Bile acids are conjugated with taurine or glycine in the liver, forming bile salts.

Activation of FXR in the liver inhibits synthesis of bile acids, and is one mechanism of feedback control when bile acid levels are too high.

115
Q

Furci

A

https://quizlet.com/96212474/bioenergetics-furci-929-flash-cards/

116
Q

Furci

A

https://quizlet.com/96212420/membranes-and-transport-furci-928-flash-cards/

117
Q

Carbohydrate chirality, anomeric carbon

A

Numbering begins at end containing aldehyde or ketone group.

D= OH group of highest C on the Right
L= OH group of highest C on the Left

Stereoisomers: =2^n
n=number of asymmetric centers (middle C’s)
Anomeric = The only carbon attached to two oxygens and its hydroxyl group can point down or up, giving the α (axial-below ring) or β (equatorial-above ring) anomer.

118
Q

• What is the most abundant carbohydrate in nature?

A

Cellulose

119
Q

Difference between starch and glycogen?

A

Starch can be in the form of amylose, with hundreds of glucose rings hooked together by a-1,4 linkages, or amylopectin, which might contain thousands of glucose rings hooked together with a combination of a-1,4 and a-1,6 linkages.

Glycogen is the means by which animals store glucose for later use. It has both a-1,4 and a-1,6 linkages, like amylopectin, allowing for many molecular branches and consequently a greater surface area for more rapid conversion by hydrolysis back to glucose.

120
Q

Which amino sugar is found in bacterial cell walls and in connective tissues as hyaluronate (coupled with glucuronate)?

A

Glycosaminoglycan

Repeating disaccharide of glucuronic acid and N-acetyl-glucosamine
b(1-3) & b(1-4) glycosidic linkages
Widely throughout connective, epithelial, and neural tissues and component of bacterial capsules where it plays a role in virulence

121
Q

Do lipids or carbohydrates yield more energy? Why?

A

Lipids b/c Fatty acids are more “reduced” than carbohydrates.

122
Q

Why has glucose been evolutionarily selected as blood sugar?

A

So, really, the answer is that our body is better at processing glucose than lipids or proteins for use in respiration. Chances are this is a result of evolutionary biology - i.e. plants are easier to come by and consume, and they store their energy as glucose chains, so we developed alongside plants in that our digestive tract specializes in breaking down glucose rather than fats or proteins. Also not very reactive (reducing sugar).

123
Q

Relationship between sugars and blood types?

A

the ABO epitopes were conferred by sugars, to be specific, N-acetylgalactosamine for the A-type and galactose for the B-type.

124
Q

Relationship between sugars and blood types?

A

the ABO epitopes were conferred by sugars, to be specific, N-acetylgalactosamine for the A-type and galactose for the B-type.

125
Q

Lens Dislocation in Homocysteinuria

A

The most common ocular manifestation of homocystinuria is lens dislocation occuring around age 10 years. Fibrillin, found in the fibers that support the lens, is rich in cysteine residues. Disulfide bonds between these residues are required for the crosslinking and stabilization of proteins and lens structure. Homocysteine-dependent disulfide exchange

Another equally rare sulfur amino acid disorder – sulfite oxidase deficiency – is also associated with lens dislocation by a similar mechanism (usually presenting at birth with early refreactory convulsions). Marfan’s syndrome, also associated with lens dislocation, is associated with mutations in the fibrillin gene.

126
Q

Cytokines

A

Secreted proteins acting in cell communication (freq for immune responses)
Interleukins – “IL-(Number)” leukocytes (and others)
Growth factors – stimulate cell division “(Letter)GF”
Chemokines – structurally related, small, chemotaxis “CXCL8” “CCR2”

Made during inflammation
Examples
Tumor Necrosis Factor (TNF)
IL-1
IL-6
IL-8
Interferon-gamma (IFN-γ)
Anti-inflammatory cytokines include Transforming Growth Factor-β (TGF-β)

Biochem 6200 (18 decks)

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