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Biochemistry > Week 3 > Flashcards

Week 3 Flashcards

1
Q

What role do regulatory enzymes play in pathways?

A

They effect the overall rate of a serious of metabolic reactions

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2
Q

What causes the levels of regulatory enzymes to change?

A

They change levels in response to transcriptional regulation

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3
Q

When do regulatory enzymes control rates of enzyme-catalyzed reactions?

A

When more of a substance is needed so the reaction rates increase
Or when a substance is no longer needed so the rate decreases

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4
Q

What ability allows the cell to adapt to its changing needs?

A

The ability to control the rate of the overall metabolic pathway

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5
Q

In what part of a pathway do regulatory enzymes catalyze a reaction (speed up)?

A

The rate-limiting or slowest step in the pathway

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6
Q

How does substrate concentration affect the enzyme rate in a pathway?

A

The more substrate there is the faster the reactions will occur due to the enzyme’s active site being saturated with the abundant amounts of substrate

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7
Q

What are the two types of regulation?

A

Stimulatory and inhibitory

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8
Q

What are the two ways to mediate regulation?

A

Control of catalytic efficiency through protein modification (increasing the speed of reaction more efficiently)
Bioavailability (the amount of the enzyme in different tissues and cellular compartments)

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9
Q

What are the 5 ways enzymes are regulated?

A

Allosteric control (non-covalent)
Having multiple forms of the enzymes (isozymes)
Reversible covalent modification
Proteolytic activation
Controlling the amount of enzyme present (transcriptional level of control)

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10
Q

Where is the allosteric site?

A

On the enzyme separated from the active site (not competing with substrate)

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11
Q

What does non-covalent binding to the allosteric site cause for the active site?

A

A conformational change (shape changes) and can increase or decrease the enzymes affinity for the substrate (ability of binding)

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12
Q

What structure protein is an allosteric enzyme (primary, tertiary, etc.)?

A

Quaternary structures (remember this means there is more than one subunit)

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13
Q

Are allosteric effectors modified when binding to the enzyme’s allosteric site?

A

No - this is a NON-covalent interaction so no modifications are made - all weak interactions

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14
Q

What happens when an allosteric effector is a homotropic effector?

A

The enzyme’s substrate is serving as the effector (homo=same, so the substrate and effector are the same)

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15
Q

Are homotropic effectors usually activators or inhibitors?

A

Usually activators (having the substrate binded in one active site increases the catalytic properties at the other sites (positive cooperation))

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16
Q

What is happening when the allosteric effector is a heterotropic effector?

A

The effector is different than the substrate (hetero=different or not same)

The binding to the allosteric site has a different effect than the substrate at the active site

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17
Q

Do heterotropic effectors usually serve as allosteric inhibitors or activators?

A

Inhibitors (important in negative feedback)

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18
Q

What is positive cooperativity?

A

When the binding of one substrate makes it easier for other substrates to bind to different subunits

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19
Q

What is T conformation?

A

When there is low affinity for the substrate (taut or tight)

In a conformation that makes it hard for the substrate to fit into the binding site

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20
Q

What is the R conformation?

A

The relaxed state - high affinity conformation - easy to bind

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21
Q

Do allosteric activators bind more tightly to the R state or the T state?

A

When the enzyme is in the R or relaxed state (higher affinity for substrate or activator in this case)

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22
Q

In what way do allosteric activators stimulate a reaction?

A

They increase the amount of enzymes in the active state

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23
Q

Do allosteric inhibitors bind more tightly to the R state or the T state?

A

The T tight state

Make it even more difficult for substrates and activators to convert the subunit to the most active conformation

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24
Q

How would one overcome the effects of allosteric inhibitors?

A

By increasing substrate concentration OR the activator concentration

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25
Q

Is the effect of an allosteric effector fast or slow?

A

Fast (not happening at a transcriptional level but on the surface of the enzyme so easily accessible)

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26
Q

What do isozymes allow for?

A

Tissue specific regulation

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27
Q

How do isozymes differ from its regular enzyme?

A

They catalyze the same reaction but have different physical properties and amino acid sequences

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28
Q

How are glucokinase and hexokinase isozymes?

A

They both are kinases (phosphorylation) but glucokinase has a low affinity for glucose and located in the liver while hexokinase has a high affinity for glucose and is found in the red blood cells, skeletal muscle, and most tissues

(phosphorylation of glucose can trap it inside cells)

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29
Q

What does lactate dehydrogenase do?

A

Converts pyruvate to lactate in anaerobic conditions (no oxygen available)
Converts lactate to pyruvate when oxygen is available

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30
Q

How many different isozymes exist of LDH?

A

5 different isozymes that are all tissue specific and differ in structures and kinetic properties

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31
Q

What protein carries out phosphorylation (adding an inorganic phosphate to an enzyme through hydrolysis of ATP to ADP - using energy)?

A

Protein kinase

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32
Q

What protein carries out dephosphorylation (removing an inorganic phosphate group from an inactive enzyme to activate it)?

A

Protein phosphatase

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33
Q

What is the role of serine/threonine kinases?

A

They transfer a phosphate group from ATP to OH group of serine and sometimes threonine on the target enzyme

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34
Q

What is the role of tyrosine kinases?

A

To transfer a phosphate group to the hydroxyl group of a specific tyrosine residue

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35
Q

How does the binding of phosphate groups affect the active site?

A

They are negatively charged and bulky so they change the conformation or shape of the active

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36
Q

How would you reverse effect of phosphorylation?

A

By removing the phosphate group with a phosphatase

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37
Q

What is the main source of phosphate groups for kinases?

A

ATP

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38
Q

Do phosphorylation and dephosphorylation occur fast or slow?

A

Fast (seconds)

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39
Q

What kind of interactions does the addition of phosphoryl groups alter?

A

Electrostatic interactions (it is negative so it alters ionic interactions)

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40
Q

What kind of bonds can a phosphoryl group form?

A

Hydrogen bonds (it is a strong electronegative atom)

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41
Q

How is glycogen phosphorylase activated?

A

Phosphorylation of the Ser side chains

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42
Q

How is glycogen phosphorylase inactivated?

A

Dephosphorylation of Ser residues by phosphorylase phosphatase

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43
Q

What are zymogens?

A

Inactive precursors of enzymes

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44
Q

How do zymogens become fully functional?

A

It must undergo proteolytic cleavage

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45
Q

Does proteolytic cleavage require energy?

A

No (it can occur outside the cell - in blood)

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46
Q

Is proteolytic cleavage reversible?

A

No it is irreversible regulation

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47
Q

How would you tell if a zymogen was in its inactive form from its name?

A

if the prefix is “pro-“ or the suffix was “-ogen”

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48
Q

What are 2 inactive zymogens that have to do with blood clotting?

A

FibrinOGEN and PROthrombin

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49
Q

When would fibrinogen and prothrombin become activated?

A

When they are cleaved by proteases and proteases are activated by their attachment to a damaged region in the vessel wall

(keeps clot formation to the site of injury

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50
Q

How would you reach maximal capacity of a tissue to change?

A

Increased protein synthesis

Increased protein degredation

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51
Q

Is enzyme synthesis fast or slow?

A

Slow (making enzymes - DNA-mRNA-amino acid-folding) takes hours or days

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52
Q

What does cytochrome P450-2EI do?

A

Oxidizes ethanol to acetaldehyde

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53
Q

What happens to proteins in the skeletal muscle during fasting?

A

They are degraded in order to increase the levels of amino acids in the blood for gluconeogenisis (creating glucose)

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54
Q

What happens to proteins during an infection?

A

They are degraded in order to free amino acids to make antibodies and other proteins needed for the immune response

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55
Q

What are 2 pathways that cause protein degredation?

A

Lysosomal degradation and ubiquitin-proteasome system

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56
Q

How does the ubiquitin-proteasome system work?

A

By attaching a ubiquitin polypeptide to proteins targeted for degradation by proteasome

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57
Q

What kind of reactions are metabolic pathways?

A

Sequential reactions (product of one is the substrate for the next and can have branch points)

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58
Q

What is usually the first committed step of a pathway?

A

The rate limiting step (slowest step and not easily reversible)

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59
Q

How does feedback regulation happen?

A

When the end product is high, it can bind to the regulatory enzyme of the pathway and inhibit formation of intermediate substrates in a pathway

When the end product is low, the allosteric inhibitor dissociates from the allosteric site allowing the regulatory enzyme to become active again

(too much product- it inhibits, too little product- inhibitor comes off)

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60
Q

Why would a cell compartmentalize an enzyme?

A

Provide unique conditions
Limit access of enzyme to substrates
Separate anabolic pathways from catabolic pathways (build up from break down)

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61
Q

What are inhibitors and how do they work?

A

They are substances that decrease the rate of an enzyme-catalyzed reaction by binding to the enzyme

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62
Q

What are reversible inhibitors?

A

Substances that non-covalently bind to and enzyme and so can be released
Usually similar in structure to the substrates or products
(competitive, uncompetitive, and mixed competitive)

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63
Q

What are irreversible inhibitors?

A

Substances that cause covalent alterations of the enzyme
(either alters the enzyme itself or irreversibly binds to the enzyme)
PERMANENT SHUT DOWN OF ENZYME

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64
Q

Where do competitive inhibitors bind on the enzyme?

A

To the active site (they are competing with the substrate for the active site)

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65
Q

How do competitive inhibitors look compared to substrates?

A

Very similar - they are analogs

66
Q

How would you overcome competitive inhibition?

A

Increasing the concentration of the substrate

67
Q

What kind of inhibitors are statin drugs?

A

Competitive inhibitors - they have HMG CoA analog (missing a methyl group) attached to it which inhibits the actual substrate from binding to the active site which then decreases the amount of cholesterol produced and present in plasma

68
Q

Where do uncompetitive inhibitors bind on the enzyme?

A

Another site other than the active site

69
Q

How does uncompetitive inhibition work?

A

The substrate binds to the enzyme and creates a conformation change for the inhibitor to bind to the enzyme and the inhibitor prevents the substrate from becoming the product

70
Q

Can you overcome uncompetitive inhibition by increasing substrate concentration?

A

No (the substrate binding actually helps the inhibitor bind to the enzyme)

71
Q

Where do mixed inhibitors bind (noncompetitive)?

A

To the regulatory site which is NOT the active site (can bind to the enzyme or the enzyme substrate complex)

72
Q

What do mixed inhibitors do?

A

Bind to the enzyme with or without the substrate
Inhibits both substrate binding and catalysis by causing conformational change of the enzyme which affects the affinity for the substrate
Reduces functional enzymes

73
Q

Can you overcome mixed inhibition by adding more substrate?

A

No (it can still bind while the substrate is bound)

74
Q

When do irreversible (suicide) inhibitors become reactive?

A

When they bind to the enzyme’s active site

75
Q

How many times can irreversible inhibitors be used?

A

Once

76
Q

How does the body overcome irreversible inhibition?

A

Synthesizing new enzyme molecules (slow process)

77
Q

Can a suicide inhibitor kill an enzyme when it is not active?

A

Yes

78
Q

What are 3 main functions of lipids?

A 
Energy storage (fatty acids and triglycerides)
Cell membrane structure (sphingolipids and glycerophospholipids)
Endocrine signaling (eicosanoids and sterioids)
79
Q

What are lipids soluble in?

A

Organic solvents

80
Q

What are lipids not soluble in?

A

Water

81
Q

What are the types of open-chain compound lipids?

A 
Fatty acids
Triacylglycerols
Sphingolipids
Phosphoacylglycerols
Glycolipids
82
Q

What are the types of fused-ring compound lipids?

A

Cholesterol
Steroid hormones
Bile acids

83
Q

Are most natural fatty acids branched or unbranched?

A

Unbranched

84
Q

Do most fatty acids have an even or odd number of carbons?

A

Even

85
Q

What do unsaturated fatty acid chains have?

A

a carbon-carbon double bond

86
Q

How would you tell the difference structurally between an unsaturated and saturated fatty acid?

A

Unsaturated have double bonds (mono or poly)

Saturated have no double bonds in the carbon chain

87
Q

What type of fatty acid is Stearic acid?

A

Saturated fatty acid

88
Q

What type of fatty acid is alpha-linolenic acid?

A

Unsaturated

89
Q

What type of double bonds are found naturally in fatty acids?

A

cis double bond that creates a kink in the chain

trans looks like a saturated fatty acid

90
Q

Do trans fatty acids or cis fatty acids have a lower melting point?

A

Cis fatty acids due to their kink (less linear and more room)

91
Q

Why would we use trans fatty acids in our foods?

A

To increase the shelf life or stability at high temperatures (oils used in cooking)

92
Q

What kind of fatty acids are more ordered (saturated or unsaturated cis)

A

Saturated fatty acids are more ordered and tightly packed together (explains why they have a higher melting point - they also have more favorable interactions which makes them more stable)

93
Q

What are the major types of lipid components in the membrane?

A

Phospholipids (glycerophospholipids and sphingolipids)

Cholesterol

94
Q

What kind of phospholipid is the most abundant type of membrane lipid?

A

Glycerophospholipids

95
Q

What are phosphate lipids composed of?

A

One or more fatty acid
Glycerol backbone
Polar head group

96
Q

How are fatty acids joined to glycerol (what type of bond)

A

Ester bonds

97
Q

What are the components of a polar head group?

A

Phosphate group with alcohol attached to it

98
Q

What determines the surface properties of membranes?

A

The properties of the polar head groups

99
Q

What molecule is the major component of most eukaryotic membranes (what glycerophospholipid)?

A

Phosphatidylcholine

100
Q

From what molecule are sphingolipids derivatives of?

A

Sphingosine

101
Q

What is the major difference between glycerophospholips and sphingolipids?

A

Instead of the glycerol as the back bone, an 18 carbon amino alcohol is

102
Q

How would a ceramide be formed?

A

When a fatty acid forms an amide linkage with sphingosine

103
Q

What is the role of sphingolipids in membranes?

A

cell signaling transduction

104
Q

What are glycolipids?

A

Carbohydrate-containing lipids derived from sphongosine

105
Q

Where is the carbohydrate in glycolipids attached to on the sphingosine?

A

The primary alcohol

106
Q

What is the simplest glycolipid?

A

Cerebroside (a single sugar)

107
Q

Where would one find spingomyelin?

A

In the plasma membrane of many cells but is enriched in nerve cells

108
Q

What is the difference between a cerebroside and a ganglioside?

A

Gangliosides contain a branched chain of as many as 7 sugar molecules and cerebrosides contain one sugar molecule

109
Q

What part of the membrane would you find the carbohydrate components of glycolipids?

A

On the extracellular surface of the cell membrane (cell-cell recognition)
(they have many OH’s coming off the sugars so they are polar and can be in an aqueous solution)

110
Q

Where are cholesterols found in the plasma membrane?

A

Inside the membranes (to transport them they must be converted to an ester)

111
Q

What is the makeup of a cholesterol?

A

Contains 27 carbons

has a rigid four ringed steroid core

112
Q

How do cholesterols affect the membrane?

A

They affect the fluidity and permeability of the membrane

113
Q

Would you find cholesterol in the membranes of prokaryotic and fungal cells?

A

No they do not exist in them

114
Q

What molecule serves as a precursor for steroid hormones and bile acids?

A

Cholesterol

this is a fused ring lipid so it is the precursor for other fused ring lipids

115
Q

What are three major aggregate structures of lipids found in water?

A

Micelles
Liposomes
Bilayers

116
Q

What do structure forms of lipid aggregates depend on?

A

Type of lipid

Concentration

117
Q

How many polar surfaces do micelles have?

A

Only one (concentration dependent)

118
Q

What role are micelles important in?

A

Intestinal digestion

119
Q

How many polar surfaces do liposomes contain?

A

2 polar surfaces (lipid vesicles)

120
Q

What kind of cavity do liposomes contain?

A

aqueous (enclose dissolved molecules)

121
Q

What are liposomes useful for?

A

Artificial carriers of molecules (drugs, vectors for gene therapy)

122
Q

What are membrane bilayers dependent on?

A

Thy hydrophobic effect

123
Q

What type of interactions stabilize the membrane?

A

van der Waals interactions between the hydrophobic tails

124
Q

What part of the cell synthesizes the membrane lipids?

A

The smooth ER

125
Q

What affects the flexibility of the cell?

A

Lipid composition

126
Q

What are important functions of the membrane?

A

Allow import and export
Retain metabolites and ions within the cell
Sense external signals and transmit info into cell
Compartmentalization in the cell

127
Q

What leaflet are glycolipids found on?

A

Outher leaflet

128
Q

How are integral proteins associated with the membrane?

A

Firmly (many spanning the bilayer)

129
Q

How are peripheral proteins associated with the membrane?

A

Weakly and can be removed easily

either non covalently attached or linked by anchors

130
Q

Where do bulkier molecules tend to predominate in the bilayer?

A

Usually on the outer layer

131
Q

Where do small molecules tend to predominate in the bilayer?

A

Usually in the inner layer (less room or circumference than the outer layer)

132
Q

What are the charges of the inner and outer layers of the membrane?

A

Inner is negative outer is positive (polarity)

133
Q

Explain the gel phase of the lipid bilayer.

A

Liquid ordered state where individual molecules do not move around

134
Q

Explain the fluid phase of the membrane.

A

Liquid disordered state where individual molecules can move around

135
Q

What can cause phase transition from the gel to the fluid?

A

Heat

136
Q

Under physiological conditions are membranes more fluid or gel like?

A

Fluid like (must be fluid for proper function)

137
Q

How is the arrangement of bilayer controlled?

A

By the fatty acid composition and the cholesterol content (more cholesterol means more fluid)- disrupts the tight packing of fatty acids

138
Q

How can lipids and proteins in the membrane diffuse?

A

Laterally but not transversely (to the side but not upside down because the polar heads would have to go through the hydrophobic parts which takes days)

139
Q

What enzymes can catalyze transverse diffusion?

A

Flippases (move from outer to inner)

Floppases (inner to outer)

140
Q

What do lipid rafts contain?

A

clusters of glycosphingolipids with longer than usual tails

141
Q

What do lipid rafts allow?

A

Segregation of proteins in the membrane

142
Q

What are lipid rafts important for?

A

Cell signaling

143
Q

What do receptors do in the membrane?

A

detect signals from outside the cell (hormones, light, neurotransmitters, pheromones)

144
Q

What do channels, gates and pumps in the membrane do?

A

Allow entrance or exit of nutrients, ions, and neurotransmitters

145
Q

What do enzymes in the bilayers do?

A

Lipid biosynthesis

ATP synthesis

146
Q

What are the 2 types of integral membrane proteins?

A

Monotopic (interact with one leaflet)

Polytopic (interact with both leaflets)

147
Q

How can integral proteins be removed from the membrane?

A

Detergents that overcome the hydrophobic effect

148
Q

Where would Tyr and Trp amino acid residues cluster in the membrane?

A

At nonpolar/polar interfaces (have nonpolar rings but also have polar parts N and OH)
They cluster where the tails meet the heads

149
Q

Where would charged amino acids be found in relation to the membrane?

A

On the aqueous domains (since the charges make them polar)

150
Q

Where would you find a Met residue in the bilayer?

A

Inside the bilayer with the nonpolar tails

151
Q

What types of interactions hold peripheral proteins to the membrane?

A

Electrostatic interactions and hydrogen bonding (remember these are in the aqueous parts of the membrane so the outer and inner leaflets)

152
Q

Other than interactions, what can hold a peripheral protein to the membrane?

A 
Lipid anchors (covalently linked to extracellular or cytoplasmic side)
GPI anchors only found in outer leaflet of membrane
153
Q

What are lipid bilayers highly impermeable to?

A

Ions and most polar molecules (lipids are non polar and these are lipid insoluble molecules)

154
Q

What allows for rapid and bulk transportation of water through the membrane?

A

Aquaporins (tetramer with a transmembrane pore - forms hydrophilic transmembrane channels)

155
Q

Why is the energy of activation for diffusion through the bilayer high?

A

Because you have to desolvate the hydration shell and they is very endergonic

156
Q

What reduces the activation energy for diffusion?

A

A transporter protein (forms non covalent interactions with the dehydrated solute to replace the hydrogen bonding with water)

157
Q

What are ionophores produced and excreted by?

A

Microorganisms bacteria fungus

158
Q

What is an ionophore?

A

Hydrophobic peptide toxin that surrounds an ion and shuttles the ion across the membrane

159
Q

What kind of drugs act as ionophores?

A

Antibiotics

160
Q

What are the three types of membrane transporters?

A

Uniport (one solute one way)
Symport (2 solutes same way)
Antiport (2 solutes in opposite directions)

161
Q

What kind of transporter is the bicarbonate transporter?

A

Antiporter (each HCO3- in one direction a Cl- moves the opposite direction)

162
Q

What type of transporter is a GLUT1 (glucose transporter)?

A

Uniporter (moves glucose from outside to inside the cell through 2 conformations)

Biochemistry (10 decks)

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