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Biochemistry 450 > Midterm 2 > Flashcards

Midterm 2 Flashcards

1
Q

How can enzymatic reactions be inhibited?

A

Reversible and irreversible processes.

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2
Q
  • Reversible processes:

- Irreversible processes:

A
  • Involve binding of an inhibitor and its subsequent release.
  • Involve covalent attachment of a molecule to an enzyme followed by its inactivation.
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3
Q

Competitive Inhibition:

A

Reversible Inhibition. Inhibitor competes with substrate. Greater inhibitor concentration = greater inhibition.

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4
Q

How can competitive inhibition be overcome?

A

Increasing amount of substrate.

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5
Q

What happens to Vmax and Km in competitive inhibition compared to uninhibited? Why is Km different?

A

Vmax does not change. Apparent Km does vary, requires more substrate to get the same velocity. This is because only active enzymes are measured.

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6
Q

Non-competitive Inhibition:

A

Reversible Inhibition. Occurs when inhibitor binds to enzyme at unrelated site to substrate binding site. Inhibitor not similar structure to substrate. don’t compete.

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7
Q

Can the effects of a non-competitive inhibitor be eliminated by adding substrate? Why?

A

No, the inhibitor can inhibit the enzyme without interference from the substrate. They don’t compete. Same number of enzymes inhibited no matter how much substrate is added.

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8
Q

What happens to Vmax and Km in non-competitive inhibition compared to uninhibited?

A

Vmax is lowered because they don’t compete. Km does not change.

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9
Q

Lineweaver-Burk plot in competitive inhibition:

X and Y intercepts.

A

line crosses y-axis at the same spot as uninhibited enzyme (1/Vmax stays the same). X-intercept is closer to zero because -1/Km is closer to zero as Km rises (appears to rise).

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10
Q

Lineweaver-Burk plot in non-competitive inhibition:

X and Y intercepts.

A

Same x-intercept because Km does not change so (1/Km) doesn’t change. Y-intercept is higher because Vmax is lower and therefore, (1/Vmax) is higher. Enzyme affinity doesn’t change according to adding substrate.

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11
Q

What do chemicals such as DIPF and iodoacetate do?

What type of inhibition is this?

A

Covalently and Irreversibly bind to the side chains of specific amino acids (serine and cysteine, respectively).

  • If side chains essential, these chemicals will inhibit reaction catalysis.
  • Nonspecific covalent modification.
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12
Q

What is Penicillin like? How does it inactivate enzymes?

A 
Resembles substrate of enzyme in bacteria that makes cell wall.
Inactivates enzyme (after binding) by covalently bonding to active site. Destroys enzyme and kills bacteria in it.
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13
Q

What is a suicide inhibitor? What is an example of one?

A

An enzyme that commits suicide by binding to its inhibitor. Penicillin is an example.

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14
Q

Proteases:

A

catalyze hydrolysis of peptide bonds in polypeptides and are usually fairly specific for amino acids they cut near.

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15
Q

Chymotrypsin:

A

Protease that can be studied using an artificial substrate which releases yellow product when cleaved by an enzyme. Cuts adjacent to phenylalanine.

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16
Q

Two rates of color released by chymotrypsin:

First step-

A

First very rapid release due to initial burst of activity. This step cleaves bond to produce yellow, covalently linked substrate remains.

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17
Q

Two rates of color released by chymotrypsin:

Second step-

A

To bind to another substrate the enzyme releases covalently bound molecule slowly, so yellow is released slowly in second step.

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18
Q

What is chymotrypsin an example of? What chemical can inactivate it?

A

Serine protease (protease with reactive serine in active site). DIPF chemical links to serines and inactivates enzyme.

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19
Q

What do serine proteases do with polypeptide substrates?

A

they form covalent intermediates with them

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20
Q

3 Steps of Serine proteases:

A
  1. Nucleophilic attack of an alkoxide ion on polypeptide substrate. (Forms acyl-enzyme intermediate).
  2. Acyl-enzyme intermediate formation cleaves peptide bond. (Releases one polypeptide fragment)
  3. Acyl-enzyme intermediate resolved by addition of water to release original polypeptide along with regeneration of original enzyme active site. (occurs slowly)
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21
Q

What does the active site of serine proteases (such as chymotrypsin) contain?

A

A catalytic triad of amino acids, include serine hydrogen (SH) bonded to histadine. Histadine is H-bonded to aspartic acid residue in active site.

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22
Q

How is nucleophilic attack of the alkoxide ion on serine made possible?

A

By interactions in the catalytic triad and hydrogen bonds.

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23
Q

Subtilisin

A

A serine protease that has a catalytic triad just like chymotrypsin.

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24
Q

Two important sites of the enzyme other than the catalytic triad?
What do they do and where are they located?

A

Oxyanion hole: stabilize a tetrahedral intermediate that arises during the catalysis.
S1 pocket: where substrate binds.
Both located adjacent to the active site (catalytic triad).

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25
Q

What is the specific role of the S1 pocket?

A

Determines a serine protease’s specificity.

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26
Q

Describe the S1 pocket of chymotrypsin:

Describe the S1 pocket of trypsin:

A

Chymotrypsin has large and hydrophobic S1 pocket, binds to phenylalanine.
Trypsin has negatively charged group in the bottom of S1 pocket, allowing it to bind to lysine and argenine.

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27
Q

Cysteine proteases:

Group used and what it does-

A

Use cysteine and histidine in active site. Use ion like SH group of cysteine to be nucleophile. This attaches carbonyl peptide bond and facilitates breakage of peptide bond. There is a covalent intermediate.

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28
Q

Aspartyl Proteases:

Groups used and method of attacking peptide bond-

A

Aspartic acids and water in active site. Two aspartic acid side chains hold water in place. Use ion of it to act as nucleophile to attack peptide bond. No covalent intermediate.

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29
Q

Metalloproteases:

Groups used and method of attacking peptide bond-

A

Metal ion (usually zinc) and water in active site. Metal ion holds water in place so it can be ionized and be nucleophile to break peptide bond.

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30
Q

Carbonic Anhydrase:

A

Enzyme that catalyzes joining of carbon dioxide and water to form carbonic acid.

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31
Q

What role does zinc play in carbonic anhydrase?

A

Zinc ion held in place in active site by 3 histadines. It binds a water molecule and subsequent loss of a proton of water is necessary for catalysis.

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32
Q

When does carbonic anhydrase have the max activity?

A

At high pH because protons are easily removed. Low activity in low pH (acidic = 6.0)

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33
Q

What is the limiting step in the action of carbonic anhydrase?

A

Abstraction of proton from water. Buffer/bases help facilitate this and speed up reaction.

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34
Q

What are restriction enzymes?

A

Bacterial enzymes that cleave DNA by breaking phosphodiester bonds between adjacent nucleotides.

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35
Q

How do restriction enzymes work?

A

Bind to enzyme (at specific sequences), change/bend DNA shape which provides “pocket” for water and magnesium ion to be positioned properly.
Water activated as nucleophile to attack and cleave phosphodiester bond.

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36
Q

What do restriction enzymes protect against? What are they paired with?

A

They protect against DNA viruses (bacteriophages).

They are paired with modification system that consists of methylase.

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37
Q

What does methylase do?

A

Methylase puts methyl on same sequence as restriction enzyme and prevents it from recognizing and cutting sequence.

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38
Q

What is Aspartate transcarbamoylase (ATCase)?

A

enzyme that catalyzes first step in pyrimidine biosynthesis.

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39
Q

Equation for ATCase:

A

Aspartate + carbamoyl phosphate N-carbamoylaspartate

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40
Q

How is ATCase regulated?

A

It is allosterically regulated in both positive and negative fashion. It responds to binding of the substrate (aspartate) to it.

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41
Q

What inhibits ATCase?
What activates it?
What is this phenomenon called?

A

CTP (end product of pyrimidine biosynthesis) inhibits enzyme.
ATP activates the enzyme.
Its called feedback inhibition.

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42
Q

Feedback Inhibition

A

When a small molecule binds to a protein and affects the protein’s activity. (end product inhibits first enzyme).

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43
Q

How many subunits does ATCase have? What are these called and what do they bind to?

A

12 subunits.
6 Catalytic and 6 Regulatory.
The 6 regulatory are smaller and bind to CTP, catalytic do not.

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44
Q

What happens when CTP binds to ATCase?

A

CTP binds to regulatory subunits to stabilize (lock) enzyme in T state =reduced affinity for substrate.

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45
Q

What happens when ATP binds to ATCase?

A

It binds to regulatory subunits and stabilizes the R state = relaxed state, more reactive, increased activity and affinity for substrate.

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46
Q

What happens to ATCase in absence of ATP and CTP?

A

Enzyme flips freely from T state to R state randomly. But T state predominates.

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47
Q

If CTP and ATP absent and more aspartate substrate is added to ATCase, what can be observed?

A

A sigmoidal plot, enzyme changing as more aspartate added which is flipping from T state to R state since aspartate stabilizes R state.

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48
Q

What are the two models for enzyme flipping R to T and vice versa?

A

1) Sequential model: Allosteric effector causes flip (ie hemoglobin)
2) Concerted model: Flip occurs independently of effector. Binding only stabilizes the state when bound. (ie. CTP and ATP binding to ATCase)

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49
Q

PALA

A

Artificial substrate which binds (covalently) to ATCase and inhibits enzyme by locking it in R state, can’t catalyze reaction. Like suicide inhibitor. but Small amount added increases catalysis.

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50
Q

Protein kinase A

A

Enzyme involved in covalent modification of enzymes. Catalyzes addition of phosphate to a molecule (like all kinases), specifically to proteins.

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51
Q

Where do phosphates get attached to when using protein kinase A? What can others attach phosphates to?

A

Hydroxyl side chains of serine or threonine.

Others can attach phosphate to tyrosine side chains.

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52
Q

What is protein kinase A controlled by?

A

Controlled allosterically.

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53
Q

Structure of Protein Kinase A:
What inactivates the enzyme?
What activates it?

A

2 regulatory subunits, 2 catalytic subunits (called R2C2).

  • Inactive when catalytic subunits bound to regulatory subunits.
  • Active when cAMP binds to regulatory subunits and releases catalytic subunits. Then can add phosphates.
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54
Q

What trigger more purines to be made?

A

If more pyrimidines are being made by the ATCase enzyme because they need to be balanced in cell. Both made in same pathway.

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55
Q

Phosphotase:

A

Takes phosphates off of molecules/proteins

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56
Q

Zymogens:

A

enzymes synthesized in an inactive form whose activation requires covalent modification (ie. proteolytic cleavage).

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57
Q

Examples of zymogens

A

trypsin, chymotrypsin, elastase, carboxypeptidase

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58
Q

Trypsin:

What can improper activation of trypsin lead to?

A 
primary activator of class of proteolytic enzymes. 
Improper activation close to pancreas can lead to pancreatitis (proteases attack proteins in pancreas)
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59
Q

What does the activation of chymotrypsinogen to chymotrypsin require?

A

Requires trypsin.

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60
Q

Explain how trypsin coverts chymotrypsinogen to chemotrypsin.

A
  1. Trypsin cleaves between amino acids 15 and 16. A disulfide bond keeps pieces from coming apart. This creates chymotrypsin intermediate pi-chymotrypsin.
  2. Pi-chymotrypsin cleaves into two dipeptides, resulting in full chymotrypsin activity.
    Three pieces held by disulfide bond.
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61
Q

Alpha-one-antitrypsin:

A

Inhibitor of many proteases such as trypsin and elastase. Normally binds to elastase, prevent tissue damage.

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62
Q

What often happens to people deficient in Alpha-one-antitrypsin?

A

They have protein in their alveolar walls of the lung (and other connective tissue) destroyed, resulting in emphasema.

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63
Q

What affect does smoking have on Alpha-one-antitrypsin?

A

smoke reacts with healthy Alpha-one-antitrypsin, causing methionine residue to be oxidized. This prevents Alpha-one-antitrypsin from binding to elastase, allow tissue damage.

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64
Q

What is blood clotting controlled by?

A

Tightly controlled by zymogens. Activated by two diff cascades of protease activation and both converge by converting prothrombin zymogen to thrombin (active). These are called extrinsic and intrinsic pathways.

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65
Q

Cascades:

What are cascades great for?

A

One enzyme activates another which activates hundreds and in turn millions.
Ampifying signals.

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66
Q

Cascade of blood clotting:

A
  1. Prothrombin zymogen converted to thrombin.
  2. Thrombin protease converts fibrinogen into fibrin, which involves clipping small portions off of fibrinogen.
  3. Pieces left behind intertwine with “pockets” on adjacent fibrin to form 3-D meshwork (a soft clot).
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67
Q

What role does transglutaminase play in blood clotting?

A

It forms covalent bonds between fibrin classes to harden the clot.

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68
Q

How is prothrombin activated?

A

It must bind calcium in to be held near the site of the wound. Allows prothrombin to anchor itself to the phospholipid membranes derived from blood platelets after injury. Converted to thrombin at this site.

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69
Q

How can you enable prothrombin binds to calcium strongly?

A

glutamine residues are carboxylated (added carboxyl group) which is catalyzed by enzyme that uses Vitamin K as a cofactor.

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70
Q

What do compounds like Coumarin and Warfarin do?

A

They block vitamin K sites on enzyme and cat as blood thinners. Prothrombin cannot be activated to thrombin and blood clots are less likely to form.

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71
Q

What is plasmin? What is it synthesized as?

A

An enzyme involved in the removal of blood clots. Synthesized as zymogen called plasminogen.

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72
Q

How is plasminogen converted to plasmin?

A

Converted to plasmin by tissue-type plasminogen activator (t-PA), which initiates the cascade to dissolve unwanted blood clot in stroke or heart attack.

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73
Q

What are simple carbohydrates? What do they include?

A

They are monosaccharides (sugars). Include glucose, galactose, mannose.

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74
Q

What is suffix for saccharides?

What are prefixes?

A

suffix: ose
prefix: tri, tetr, pent, hex, hept, oct (for 3-8 C)

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75
Q

Monosaccharides with aldehyde group=

Monosaccharides with ketone group=

A

Aldose (more reactive)

Ketose (more stable)

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76
Q

What are the simplest saccharides we call carbohydrates?

A

Glyceraldehyde and dihydroxyacetone.

77
Q

If a carbon has 4 different molecules attached to it, it is?

A

It is chiral.

78
Q

What is a stereoisomer?

A

Stereoisomers is when same molecules are attached to a carbon but the spacial arrangement is different.

79
Q

What do D and L tell you about saccharide?

How are D isomers written?

A

Which way it rotates in polarized light (right (D) or left (L)). D is when hydroxyl group in lowest carbon is on the right.

80
Q

What configuration are most biological molecules in?

A

D configuration.

81
Q

Stereoisomers that are mirror images of each other are called:

A

Enantiomers

82
Q

When sugars differ in their stereoisomeric configuration but are not mirror images they are called:

A

Diastereomers.

83
Q

When sugars differ by only one carbon, they are called:

A

Epimers

84
Q

When sugars (cyclic only) differ in configuration of anomeric carbon, they are called

A

anomers.

85
Q

Cyclization of sugars gives rise to what two structures typically? What forms from aldoses and ketoses?

A

Furanoses (five membered rings) and Pyranoses (six membered rings). Hemiacetals come from aldoses and hemiketals come from ketoses.

86
Q

How does cyclization affect the new anomeric (asymmetric) carbon?

A

It can create an alpha (hydroxyl down position) or beta (hydroxyl up position) configurations. Reversibly forms and can flip from alpha to beta by going from ring to cycle.

87
Q

How can the flipping of an anomeric carbon from alpha to beta be stopped?

A

If the hydroxyl of the anomeric carbon is altered (ie. by methylation) linear structure cannot form and flipping doesn’t occur.

88
Q

What does alteration of the hydroxyl group on the anomeric carbon of a sugar create? When is this common?

A

Creates a glycoside. Glycosides commonly created during formation of disaccharides and longer carbohydrates.

89
Q

What are the two forms of a cyclic sugar? which is preferred and why?

A

Chair and boat confirmations. Chair is preferred because of less steric hinderance.

90
Q

Fructose and Ribose are usually found in what type of ring?

A

Commonly form 5 membered ring

91
Q

Galactose usually found in what type of ring

A

6 membered ring.

92
Q

Higher order saccharides which involve linking together of more than one sugar residue:

A

Disaccharides, trisaccharides, oligosaccharides (several sugars), and polysaccharides (many)

93
Q

Higher order linkages involve what kind of bond?

A

Glycosidic bonds.

94
Q

What are three types of disaccharides and what sugars do they contain?

A

Sucrose (glucose + fructose): non-reducing sugar, which means it has a no free anomeric hydroxyl.
Lactose (glucose + galactose): reducing sugar, has a free anomeric hydroxyl
Maltose (two glucoses)

95
Q

Oligosaccharides are components of:

A

glycoproteins

96
Q

4 most common polysaccharides and where they are found:

A
  1. Glycogen: energy storage in animals
  2. Cellulose: structure of plants
  3. Starch: energy storage in plants by combining amylopectin and amylose.
  4. Chitin: Exoskeleton of insects.
97
Q

What are homopolymers?

A

Polysaccharides that contain only one sugar residue.

98
Q

What are heteropolymers?

A

Polysaccharides that contain more than one sugar residue.

99
Q

5 examples of homopolymers:

A
  1. Glycogen
  2. Cellulose
  3. Amylose
  4. amylopectin
  5. chitin
100
Q

Examples of homopolymers:

  1. Glycogen
  2. Cellulose
A
  1. glucose in alpha 1-4 linkages and extensive alpha 1-6 branches
  2. Glucose in beta 1-4 linkages
101
Q

Examples of homopolymers:

  1. Amylose
  2. Amylopectin
  3. chitin
A
  1. glucose in alpha 1-4 linkages
  2. glucose in alpha 1-4 linkages + some alpha 1-6 branches.
  3. N-acetyl-D-glucosamine in beta 1-4 linkages.
102
Q

What is cellulase? Where are they found?

A

The enzyme required to digest beta 1-4 linkages of cellulose. Ruminants and ungulates contain bacterium that make cellulase.

103
Q

What are glycosaminoglycans?

A

Polysaccharides containing either N-acetylgalactosamine or N-acetylglucosamine as one of their monomeric units. Interesting chem properties.

104
Q

examples of glycosaminoglycans:

A

Chondroitin sulfates, keratan sulfates of connective tissue, dermatan sulfates, heperin, hyaluronic acid, and others. Make slimy fluid in joints and sometimes snot.

105
Q

What are proteoglycans?

A

Complexes of proteins and glycosaminoglycans that form feathery structures.

106
Q

What do glycoproteins consist of?

A

A protein linked to an oligosaccharide, usually via an ‘N’ or ‘O’ linkage.

107
Q

What do N linkages occur through?

A

Asparagine of the protein

108
Q

What do O linkages occur across?

A

Serine or Threonine of a protein.

109
Q

What is the function of oligosaccharides on proteins (glycoproteins) and lipids (glycolipids)? What are they recognized by?

A

They have functions in cellular identity. They are recognized and bound by immunoglobulins.

110
Q

What is an example of oligosaccharides giving cellular identity?

A

A, B, and O blood group antigens give rise to different blood types. They come from carbohydrates (oligosaccharides) on their cell surface.

111
Q

What is glycosylation?

A

Addition of carbohydrate residues (oligosaccharides) to a protein

112
Q

Where does glycosylation occur for N-linked glycoproteins?

A

In the ER and the Golgi complex

113
Q

Where does glycosylation occur for O-linked glycoproteins?

A

In the Golgi complex only.

114
Q

Proteins are modified in the ER, then move to the Golgi complex for addition modifications. What are the three possible locations that the protein will target next?

A

1) the cell membrane
2) release from the cell
3) the lysosome

115
Q

Oligosaccharides that are to be linked to glycoproteins are made in what portion of the ER?

A

Built on the dolichol phosphate (amphiphilic) on the outer portion of the ER, which then flips to the inside for attachment to the protein.

116
Q

How does the flu viruses effect glycoproteins?

A

Specific carbohydrate residues on the surface of glycoproteins of blood cells are the target binding sites for hemagluttanin proteins on surface of flue virus.

117
Q

How does the flu virus exit a cell?

A

The virus cleaves the salic acid off a neuraminidase enzyme (on the flu virus’s surface).

118
Q

What do anti-flu drugs do? What is the name of the drug?

A

Tamiflu: acts by inhibiting the action of the neuraminidase.

119
Q

Describe the actions of the first messenger (hormone) in cell signaling-

A

Released by one cell. Travels though bloodstream. Interacts with receptor of another cell. Initiates series of events inside new cells including changing inside of cells.

120
Q

Describe the actions of the second messenger in cell signaling-

A

It is made and released inside the target cell (which has received a signal from the first messenger) and is what causes changes inside the target cell.

121
Q

~Signaling system of beta-adrenergic receptor~

Describe the actions of the first messenger:

A

A ligand (ie epinephrine/adrenalin) released into bloodstream in response to a stimulus. It binds to target cell receptor and changes its shape slightly.

122
Q

~Signaling system of beta-adrenergic receptor~

Describe the changes inside the cell after the first messenger binds:

A

There is a change in shape of the receptor, which acts on a G-protein to activate it. Activated G-protein activates enzyme adenylate cyclase and begins to synthesize cAMP.

123
Q

~Signaling system of beta-adrenergic receptor~

Describe the actions of second messenger:

A

cAMP (the second messenger) binds to Protein kinase A to activate it. This begins phosphorylating a set of enzymes (turning them on or off according to enzyme)

124
Q

What does phosphorylating transcription factors do?

A

Activates or inactivates them. Meaning that it turns on or off transcription of specific genes in the DNA.

125
Q

What are the rapid effects in cell signaling?

What are the slow effects in cell signaling?

A
  • Controlling enzyme activities

- Controlling gene expression by controlling transcription

126
Q

What are the structure of first messenger receptors often like? What are the receptors called?

A

The receptors consist of a polypeptide chain that spans the cell membrane 7 times. They are called 7TM proteins.

127
Q

Where do G-proteins get their name?

A

From the fact they bind to guanine nucleotides (GDP and GTP)

128
Q

Describe the structure of G-proteins and how there is such variety of them (how cells attain G-protein “families”)

A

Complexes have three subunits - alpha, beta, gamma. There are multiple slightly different subunits in the genome and can be paired many ways.

129
Q

When/ How is a G protein inactivated?

A

When the alpha subunit is bound to GDP, it also is bound to beta and gamma and it is inactivated.

130
Q

When/How is a G protein activated?

A

When the cell receptor binds to first messenger (ie beta-adrenergic receptor binding to ligand), the receptor stimulates GTP to load onto the alpha subunit, displacing GDP and dissociating from beta and gamma subunits. alpha subunit can then bind to other target proteins and is active.

131
Q

What ensures that the G protein will not be left in the “on” state?

A

Enzymatic activity (of GTPase) in the cell slowly breaks down GTP to GDP within the alpha subunit.

132
Q

In the beta-adrenergic receptor signaling. What does the alpha subunit of the G-protein binding to GTP allow?

A

Allows it to bind to adenylate cyclase (enzyme embedded in the cell membrane) and activate it.

133
Q

How is protein kinase A activated?

A

Binding of cAMP (the second messenger in the beta adrenergic receptor signaling) to the R subunits causes them to dissociate from C subunits. Free C subunits are active.

134
Q

What effect does signaling through the adrenergic receptor have on blood glucose?
What does insulin do?

A

Increases blood glucose.

Insulin counters effect of epinephrine (first messenger) and lowers blood glucose.

135
Q

What does increasing cAMP concentration in the adrenergic receptor signaling pathway do?
What breaks down cAMP?

A

Increasing cAMP results in an increase of blood glucose.

Phosphodiesterase breaks down cAMP

136
Q

What does caffeine do, and what effect does it have on blood glucose?

A

Caffeine inhibits phosphodiesterase and increases blood glucose.

137
Q

What are activated intermediates?

A

Molecules that have high energy bonds and use the energy of that bond to transfer a part of itself to someone else.

138
Q

2 ways beta-adrenergic receptor can be turned off:

A
  1. Simple dissociation of epinephrine ligand from receptor.
  2. Phosphorylation of the ligand receptor by receptor kinase. It is bound to beta-arrestin and inhibites G-protein activation.
139
Q

In cell signaling, some receptors stimulate Phospholipase C enzyme activity. Describe this activity.

A

Phospholipase C cleaves a membranous molecule phophatidyl inositol (PIP2), results in 2 second messengers.

140
Q

Describe the two messengers coming from Phospholipase C cleaving PIP2:

A
  1. Diacylglycerol (DAG) remains near/in lipid bilayer and stimulates Protein Kinase C, which phosphorylates many enzymes to activate/inactivate them.
  2. Inositol 1,4,5 triphosphate (IP3) is soluble in cytoplasm stimulates release of calcium from storage.
141
Q

Describe the role of calcium in cell signaling:

What is the concentration normally and what is it essential for?

A

Can be thought of as third messenger. Normally cell keep concentration low to prevent it from binding to proteins and DNA. Essential for muscular contraction.

142
Q

What are EF hands?

A

Important structural domains of calcium binding proteins such as calmodulin.

143
Q

Describe what Calmodulin does. What is an example of a class that binds to calmodulin to keep calcium concentration low?

A 
It binds to calcium and keep concentration low. When bound to calcium it changes shape, allow it to bind to other proteins.
-CaM kinases (large) are a class stimulated to phosphorylate proteins when bound to calmodulin and calcium.
144
Q

Describe the structure of the insulin receptor?

What does it not involve in signaling?

A

Not 7TM. Normally present in dimeric form. Consists of two extracellular alpha subunits and two intracellular beta subunits.
Does not involve G-proteins.

145
Q

When is insulin receptor inactive?

When is it active?

A

When insulin not bound, subunits are not phosphorylated and kinase is inactive.

146
Q

When is insulin receptor active?

A

Insulin binding moves dimer closer. 2 tyrosine kinase sites phosphorylate tyrosine residues on opposite one, activating it. Also phosphorylate tyrosines on each beta subunit.

147
Q

Phosphorylated tyrosines on the insulin receptor are binding sites for what proteins?
What does this protein contain?

A

Insulin receptor substrates (IRS-1)

Protein contains a SH2 domain (common domain), that recognizes and binds to phosphorylated tyrosines.

148
Q

When IRS-1 binds to insulin receptor, it get phosphorylated tyrosines. These tyrosines are bound by the SH2 domain of what enzyme?

A

Phosphatidylinositide-3-kinase, binds to IRS-1 protein and stimultes phosphorylation of PIP2 in membranes to PIP3.

149
Q

PIP3 is the membrane binding target for what? What does binding do to it?

A

PDK1 (PIP3-dependent protein kinase), binding activates it.

150
Q

What does activated PDK1 do (what is the pathway)?

A
  1. Phosphorylates kinase known as Akt, activates it.
  2. Akt moves through the cell and phosphorylates/activates other pathways.
  3. One pathway: GLUT4 (glucose transport) protein moves to cell surface.
151
Q

What is the EGF and receptor and what does it stimulate?

A

epidermal growth factor (EGF) is a small polypeptide which stimulates cell to divide and grow. The EGF receptor exists as a monomer, but binding of EGF causes it to dimerize.

152
Q

How is EGF receptor similar to insulin receptor?

A

It has an intracellular domain this is a tyrosine kinase. Dimerization of it causes carboxy terminal portion to become phosphorylated at tyrosines. Which then bind to Sos and Ras g-protein

153
Q

Oncogenes:

A

Genes that have been mutated to lead to uncontrollable growth/cancer.

154
Q

Proto-oncogenes:

A

Unmutated forms of genes that perform important signaling or control functions.

155
Q

Example of a proto-oncogene:

A

Ras is a G-protein in EGF signaling are what control cell division signal inside the cell. Mutations can interfere with its ability to cleave GTP to GDP and cause uncontrolled cell growth.

156
Q

What is the name of a receptor than can dimerize the EGF receptor other than EGF?
How much of this is usually made?

A

HER, which when dimerizes with EGF, can stimulate cell division.
Usually made in low levels in the cell. Not big role in cell division.

157
Q

What can mutation of HER do?

A

Mutation in HER causes it to be made it large amounts and cell divides uncontrollably, an oncogene.

158
Q

How are HER-caused tumors treated?

A

With a monoclonal antibody called herceptin that binds to HER and stops it from stimulating cell division.

159
Q

What is leukemia (CML) caused by?

A

a DNA rearrangement that joins together BCR and ABL genes. ABL is tyrosine kinase important to cell division. When fused, ABL made in greater quantities, cell divides uncontrollably.

160
Q

How are BCR-ABL tumors treated? Who advanced the treatment.

A

Treated with tyrosine kinase inhibitor known as Gleevac, advanced by Dr. Bian Druker at OHSU.

161
Q

Catabolism:

A

Breakdown of complex substances to simpler ones (releases energy) Involves oxidation

162
Q

Anabolism:

A

Synthesis of complex substances from simpler ones (taken up energy) Involves reduction

163
Q

Free energy of a process is energy available to do:
What is free energy of a process called?
What are we most concerned with?

A

Work
Gibbs Free Energy
Change in free energy of a system

164
Q

What is favored for each of the below scenarios:
▵G = negative
▵G = positive
▵G = zero

A

▵G negative = forward process favored (A –> B)
▵G positive = reverse process favored/forward unfavorable (B –> A)
▵G zero = process is at equilibrium. Forward and reverse equally favored.

165
Q

Equation for calculating ▵G

A

▵G = ▵G^(0’) + RTln[B/A]

where T is absolute temp in kelvin (standard is 273) and R is gas constant: 8.314 J/molxK

166
Q

What do phosphates do?

A

Store energy in molecules. Electrons shift and stabilize adjacent phosphates.

167
Q

ATP:

A

source of energy in cell because of ▵G of hyrdolysis reaction in very negative.

168
Q

How is ATP used to drive a reaction?

A

It is not given directly to the reaction, but is coupled to an energetically unfavorable reaction to help it proceed.

169
Q

Substrate level phosphorylation:

How much of a contributor of ATP is it?

A

High energy phosphates (such as on creatine phosphate) allow molecules containing hem to transfer phosphate directly to ADP to make ATP.
Minor contributor to amount of ATP in body.

170
Q

Where do oxidative phosphorylation and photophosphorylation occur?

A

oxidative phosphoryltaion: in mitochondria

Photophosphorylation: in photosynthetic organisms

171
Q

What are some of the reasons why cells need ATP?

A
  • Accomplish work (muscular action)
  • Transmit information (nerve signals)
  • Signal/communicate to each other (cell signaling)
  • Synthesizing important biochemicals.
172
Q

What is oxidation state of a molecule related to?

Higher oxidation state has what effect on energy?

A

It energy availability.

Means less energy can be obtained from it.

173
Q

What has higher energy? Glucose or Fatty acids?

A

Glucose has higher oxidation state and provides less energy to cells than fatty acids.

174
Q

What are the three electron carriers and they roles?

A
  1. NAD+/NADH (accept electrons in redox reactions) catabolic electron carrier
  2. FAD/FADH2 (accept electrons in redox reactions)
  3. NADP+/NADPH (used mostly in anabolic reactions).
175
Q

Examples of metabolic carrier molecules:

What are their characteristics?

A

Coenzyme A (acetyl-CoA) and UDP (UDP-glucose) are activated carriers that contain high energy between themselves (CoA) and the molecule they carry (acetyl group). Molecule carried is donated to larger molecule.

176
Q

6 classes of reaction catalyzed by enzymes:

A
  1. Oxidation Reduction Reactions (electrons gained/lost)
  2. Ligation Reactions (two molecules put together)
  3. Isomerization Reaction (intramolecular rearrangements)
  4. Group Transfer Reactions (part of one molecule moves to another.)
  5. Hydrolytic reactions (breakdown reactions using water)
  6. lyases (breakdown reactions involving a double bond, not using water).
177
Q

Glycolysis:

A

Breakdown of glucose. A catabolic pathway involving oxidation and yields ATP energy.

178
Q

Glucogenesis:

A

synthesis of glucose. An anabolic pathway involving reduction and requires ATP.

179
Q

How many reactions are in glycolysis?

How many phases are in glycolysis?

A

10 reactions

3 phases

180
Q

What are the three phases of glycolysis?

A
  1. Energy investment phase
  2. molecular rearrangement phase
  3. energy realization phase where ATP is made.
181
Q

Reaction #1 of glycolysis:

A
  1. Hexokinase catalyzes transfer of phosphate to glucose from ATP, forming glucose 6-phosphat/G6P. (energy coupled reaction)
  2. Hexokinase changes shape as it binds to glucose (induced bit of an enzyme during catalysis).
182
Q

Describe Delta G zero prime in Reaction #1

A

Delta G zero prime is strongly negative because of ATP hydrolysis.

183
Q

Reaction #2 of glycolysis:

A

Catalyzed by phophoglucoisomerase. G6P is coverted to fructose 6-phosphate (F6P). Linear intermediate is formed in the process.

184
Q

Describe Delta G zero prime in Reaction #2

A

Delta G zero prime is close to zero.

185
Q

Reaction #3 of glycolysis:

A

Primary regulatory reaction in glycolysis.

  1. Catalyzed by phosphofructokinase (PFK), required ATP.
  2. Fructose 1,6-Biphosphate is made from F6P, and it is a high energy molecule. Energy is needed for next step.
186
Q

Describe Delta G zero prime in Reaction #3

A

It is an energy coupled reaction so Delta G zero prime is strongly negative thanks to ATP hydrolysis.

187
Q

Reaction #4 of glycolysis:

A
  1. Catalyzed by Aldolase.
  2. It is pulled by reactions ahead of it and pushed by reactions behind it.
  3. products are Glyceraldehyde 3-phosphate (GAP), and dihydroxyacetone phosphate (DHAP)
188
Q

Describe Delta G zero prime in Reaction #4

A

Strongly positive Delta G zero prime.

189
Q

How can you tell that a sugar is reducing sugar?

A

If there is at least one free anomeric carbon in an aldose, the sugar is a reducing sugar.

Biochemistry 450 (3 decks)

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