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BioChem > Test 3 > Flashcards

Test 3 Flashcards

1
Q

What reactions do proteases control? ON EXAM

A

Hydrolysis of protein bonds

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2
Q

What is a scissile bond?

A

The bond that will be cleaved in a certain proteolytic reaction

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3
Q

What is in the active site of cysteine proteases? What is the carbonyl attacked by?

A

Thiol, His-activated cysteine

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4
Q

What is in the active site of aspartyl proteases? What is the carbonyl attacked by?

A

Carboxyl, Asp-activated water

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5
Q

What is in the active site of metalloproteases? What is the carbonyl attacked by?

A

Metal (Zn) ion, Metal-activated water

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6
Q

What is in the active site of serine proteases? What is the carbonyl attacked by?

A

Serine, His-activated Serine

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7
Q

What kind of enzyme is chymotrypsin?

A

a serine protease

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8
Q

Describe the role of chymotrypsin’s specificity pocket

A

a deep hydrophobic depression in the enzyme that can only fit long hydrophobic side chains, binding of certain AAs in specificity pocket determines enzyme specificity

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9
Q

Where does cleavage of the scissile bond by chymotrypsin occur?

A

on the carboxyl side of Phe, Trp, and Tyr

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10
Q

What is the catalytic triad present in chymotrypsin?

A

Asp, His, Ser 195

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11
Q

What is common to all serine proteases (clotting factors and digestive factors)?

A

They break ester and peptide bonds using His-activated serine in a catalytic triad. They contain a specificity pocket for particular AAs and oxyanion hole that stabilizes the negatively charged Oxygen

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12
Q

Which protease is the HIV protease?

A

Aspartyl protease. Cleaves viral proteins into active forms

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13
Q

Describe feedback inhibition

A

a regulatory mechanism that relies on the inhibition of the first step of the pathway by the final product of the pathway

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14
Q

What are the two types of allosteric enzyme subunits?

A

Catalytic and regulatory

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15
Q

What are the four major regulatory mechanisms that control enzyme activity?

A

Allosteric control, Isozymes, covalent modification, proteolytic activation

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16
Q

What is the concerted model of allosteric enzymes?

A

the enzyme only exists in the T or R state, with no intermediate

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17
Q

What is the sequential model of allosteric enzymes?

A

the binding of the ligand to its subunit changes its conformation from T to R such that each subsequent liand has an easier time binding

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18
Q

What shape is seen in the kinetic plot (substrate by rate) of an enzyme that exhibits cooperative binding and which way do POSITIVE modulators shift this curve?

A

sigmoidal, to the left

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19
Q

Describe allosteric control. Give an example.

A

enzyme regulation involving the binding of a non-substrate molecule at a regulatory site on the enzyme other than the active site. Exhibits cooperativity. Example- ATCase

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20
Q

How can concentrations of lactate dehydrogenase in the blood be used to diagnose a heart attack? ON EXAM

A

an increase of heart subunits (H4) relative to normal blood subunits (H3M)

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21
Q

Describe Covalent modification. Give an example

A

Addition or removal of chemical groups, can influence the properties of the target protein. Can be reversible or irreversible. Examples- Phosphorylation, acetylation, dephosphorylation, ubiquitination

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22
Q

What ways can allosteric control affect enzymes?

A

Can either have a positive or negative effect on enzyme activity or cooperatitivity.

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23
Q

Describe the reaction catalyzed by ATCase aka Aspartyl Transcarbamylase. How is ATCase regulated?

A

ATCase catalyzes the first step in the pyrimidine biosynthetic pathway, formation of carbamoyl aspartate. It is inhibited by CTP, the final product of the pyrimidine pathway. It is activated by ATP (signals that there is energy available for DNA synthesis) (APP stabilizes R state, CTP stabilizes the T state)

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24
Q

Describe isozymes. Give an example

A

Enzymes with identical function but different structure, which allows the to regulate the same reaction at different places, and with potentially different enzyme kinetics. Example- lactate dehydrogenase

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25
Q

Describe Proteolytic activation. Give an example.

A

Activation of an enzyme by peptide cleavage. Inactive precursor (proenzyme or zymogen) is irreversibly cut to yield the active form. Examples- Digestive enzymes, Pepsinogen is cleaved to form pepsin. Formation of trypsin Blood clotting is mediated by a cascade of proteolytic activation.

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26
Q

Describe Covalent modification. Give an example

A

Addition or removal of chemical groups, can influence the properties of the target protein. Can be reversible or irreversible. Examples- Phosphorylation and acetylation

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27
Q

What reaction is catalyzed by protein kinases? (reaction and target) ON EXAM

A

Phosphorylation of serine and threonine (tyrosine phosphorylated by a seperate class of kinases) using the energy from ATP Add phosphate group to hydroxyl group

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28
Q

What basic reaction is catalyzed by protein phosphatases?

A

Dephosphorylation, hydrolysis using water

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29
Q

Describe the subunit composition of ATCase.

A

ATCase has regulatory and catalytic subunits. Only the regulatory are responsible to ATP and CTP. When treated with p-hydroxymercuribenzoate the subunits dissociate.

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30
Q

How is PKA (Protein Kinase A) activated by cAMP? What is the role of PKA?

A

Under normal conditions PKA consists of R2C2 (regulatory, catalytic) subunit with the R2 functioning as a pseudo substrate for both C subunits, blocking activity. In the presence of cAMP the R2 subunit no longer inhibits the C subunits, which dissociate off of the R2 subunit and become active (C-R2-C) Phosphorylates Ser and Thr residues

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31
Q

What reaction is catalyzed by protein kinases? (reaction and target)

A

Phosphorylation of serine, threonine, and tyrosine

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32
Q

Describe the 3D subunit arrangement of ATCase

A

Catalytic subunits consists of 3 chains (c3) and regulatory subunits consists of 2 chains (r2). The active complex (c6r6) consists of two catalytic trimer subunits on “top” and “bottom” surrounded by three regulatory subunits.

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33
Q

Define T state vs R state.

A

T state is compact, low substrate affinity, low catalytic activity. R state is open conformation, high substrate affinity, high catalytic affinity.

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34
Q

Define Zymogen/pro-protein

A

Inactive enzyme precursors that are activated by proteolytic cleavage

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35
Q

Give some examples of zymogens

A

Digestive or pancreatic enzymes such as pepsinogen, chymotrypsinogen, trypsinogen, or procarboxypeptidase. Blood clotting has multiple zymogens.

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36
Q

What is the pathway for secretion of pancreatic zymogens?

A

Pancreatic zymogens are synthesized in exocrine acinar cells of the pancreas and release upon stimulation. They are modified in the ER. RER->Golgi->Granule->Lumen

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37
Q

What is chymotrypsin?

A

A digestive enzyme (breaks down proteins)

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38
Q

How is chymotrypsinogen converted to chymotrypsin? (in detail)

A

Trypsin cleaves a single peptide bond between Arg15 and Ile16. The newly freed alpha-amino group of Ile16 is electrostatically attracted to the carboxylate group of Asp 194. This interaction triggers multiple conformational changes, which result in the formation of the substrate-specificity site.

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39
Q

The substrate specificity site of chymotrypsin codes for which amino acids?

A

Aromatics (Tyr, Phe, Trp), cuts on C side

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40
Q

How is trypsinogen converted to trypsin?

A

Enteropetidase activates trypsinogen.

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41
Q

What is the master activation step for the pancreatic zymogens?

A

Formation of trypsin, the common activator of all pancreatic zymogens.

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42
Q

What inhibits Trypsin formation, and why does it need an inhibitor?

A

Trypsin has a positive feedback loop, it is inhibited by pancreatic trypsin inhibitor and alpha-1 antitrypsin.

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43
Q

How is pepsinogen converted to pepsin?

A

At normal pH the active site is blocked. After eating, acid is released by stomach cells, protonating Asp and breaking the salt link between it and Lys.

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44
Q

What are the general steps of the blood clotting response?

A
  1. Vasoconstriction, diverting and decreasing blood flow 2. Platelet aggregation, platelets adhere and aggregate to the damaged vessel, forming a clump that can plug and stop minor bleeding. 3. Clotting occurs through cascade of zymogen activations 4. Conversion of soft fibrin clots to hard clots by thrombin
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45
Q

What occurs during platelet aggregation?

A

the platelets adhere to the damaged blood vessel and then to each other, forming a clump that can plug and stop minor bleeding. They release chemicals that further potentiate coagulation. As they adhere they change shape and are called “activated”. They finally initiate blood clotting by activating a number of clotting proteins.

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46
Q

Most clotting factors are what?

A

zymogenic serine proteases

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47
Q

What are the two pathways to blood clotting?

A

The intrinsic pathway of blood clotting- activated by exposure of anionic surfaces on rupture of endothelial lining The extrinsic pathway - trauma exposes tissue factor

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48
Q

Describe the activity of Factor XIIIa (Factor 13)

A

Fibrin-stabilizing factor Factor XIIIa joins the C-terminus segments of gamma chains of fibrin monomers by forming cis-peptide bonds between Gln on one gamma unit and a Lys on the other

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49
Q

Differentiate the structure and properties of fibrinogen from fibrin

A

Fibrinogen is a large molecule made up of three globular units. It is soluble and contains many highly anionic/repelling residues. Fibrin is fibrinogen after the release of the anionic residues, it can now bind to other fibrin monomers

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50
Q

Describe the conversion of fibrinogen to fibrin ON EXAM

A

Thrombin converts fibrinogen to fibrin through the releasing of the four highly anionic/repelling residues called fibrinopeptides (lots of Arg and Lys) that also block the binding sites

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51
Q

How does vitamin K and calcium help create blood clots?

A

Thrombin has many Glu residues on its N terminus. Vitamin K carboxylates those into Gla (y-carboxyglutamate). Those function with Ca+ ions to anchor thrombin to the injury site

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52
Q

Describe how fibrin monomers bind to each other

A

The ends of the fibrin chains bind to the binding holes of the central globular domains

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53
Q

Describe prothrombin

A

The three-domained zymogen of thrombin that circulates in the plasma. It is cleaved twice to yield thrombin, a dimer of A and B chains

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54
Q

What is the function of calcium for blood clotting?

A

The binding of calcium by prothrombin anchors it to the phospholipid membranes derived from blood platelets after injury. It brings prothrombin in close proximity to 2 clotting proteins that convert it into thrombin.

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55
Q

Where does Vitamin K function?

A

post translational modification of prothrombin in the ER

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56
Q

Describe the genetic defect in hemophilia and its treatment

A

Defective factor VIII (8), a clotting protein. Also known as anti hemophilic factor (AHF) treated by addition of supplemental factor VIII

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57
Q

What is the general pathway for clotting to occur?

A

Intrinsic/Extrinsic → Common Pathway → Prothrombin to Thrombin → Fibrinogen to Fibrin → Crosslinking

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58
Q

What is the function of plasmin? ON EXAM

A

Splits fibrin clots into peptides, dissolves clots

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59
Q

What is the function of TPA?

A

Tissue Plasminogen Actor, converts plasminogen to plasmin

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60
Q

What are the most common acceptor residues for phosphorylation?

A

Serine, Threonine, Tyrosine (-OH)

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61
Q

What is the physiological role of myoglobin?

A

Binds oxygen in muscle cells, functions for storage

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62
Q

What is the physiological role of hemoglobin?

A

Transports oxygen from the lungs to the tissues.

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63
Q

Which displays cooperativity, myoglobin or hemoglobin?

A

hemoglobin

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64
Q

Describe the heme group

A

Center of myoglobin and the four subunits of hemoglobin. An organic molecule protoporphyrin and a central iron ion.

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65
Q

What state must the iron of the heme group be in to bind oxygen?

A

In its ferrous Fe2+ form.

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66
Q

Where can the iron form additional bonds? What bonds at these sites?

A

Iron can form additional bonds at the fifth and sixth coordination sites. Fifth site binds proximal histidine, sixth site binds oxygen and brings it into the plane of the protoporphyrin

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67
Q

Where does the distal histodine bind?

A

To the oxygen on the sixth site of the iron

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68
Q

When heme is not a part of globin, what is it missing?

A

Its distal histidine

69
Q

What is the function of the distal histidine?

A

Prevents release of superoxide ion. Also lowers affinity towards carbon monoxide by forcing it to bind at an angle

70
Q

Differentiate between the composition of adult and fetal hemoglobin

A

Adult hemoglobin is an alpha dimer and beta dimer. Fetal hemoglobin is an alpha dimer and a gamma dimer

71
Q

Compare oxygen binding in myoglobin to hemoglobin

A

Myoglobin binds oxygen more tightly than hemoglobin, saturation is always higher

72
Q

Describe the two oxygen dissociation curves for myoglobin and hemoglobin

A

Myoglobin has a hyperbolic curve, hemoglobin has a sigmoidal curve

73
Q

Summarize how the cooperative binding of oxygen by hemoglobin makes it a better oxygen transporter

A

Allows for 98% oxygen saturation in blood compared to 32% in tissue, which means 66% loading and unloading capacity. This is compared to 38% unloading capacity with no cooperativity, or 7% for myoglobin.

74
Q

What is the mutation that causes sickle cell anemia?

A

a single point mutation in hemoglobin replaces beta subunit with S, producing the HbS variant

75
Q

Structure of hemoglobin

A

two alpha-beta dimers, with a heme in the center of each subunit

76
Q

Structure of myoglobin

A

a single subunit of mostly compact alpha helices, 8 stretches (A-H), His F8 is proximal histidine on the 8th residue on the F stretch, His E7 is the distal histidine

77
Q

Describe the Bohr effect

A

The production of carbon dioxide and H+ by actively respiring tissues leads to the stimulation of oxygen release by hemoglobin, as the T state conformation is favored lower pH has ionic bonds stabilizing the T state

78
Q

Put simply, how does a lower pH affect hemoglobin?

A

Ionic bonds stabilize the T state

79
Q

What is the effect of 2,3-bisphosphoglycerate on hemoglobins affinity for oxygen?

A

2,3-BPG decreases affinity of hemoglobin for oxygen by stabilizing the T state present in red blood cells, helps facilitate the release of oxygen

80
Q

How does 2,3-BPG stabilize the T state of hemoglobin?

A

The T state tetramer contains a central cavity with which the 2,3-BPG binds to. There, it interacts with three positively charged groups on each beta chain

81
Q

Describe the major structural differences between the oxygenated and deoxygenated forms of hemoglobin

A

-Oxygen binding moves the iron ion into the plane of porphyrin, normally it lies slightly outside -Oxygen binding raises the proximal histidine -The structural changes that moved the iron and histidine also rotate the two alpha-beta dimers, forming the oxyhemoglobin R state

82
Q

What do the concerted/sequential models explain?

A

The cooperativity of hemoglobin

83
Q

Describe how the cooperativity of hemoglobin is explained in the concerted model. What is evidence for this?

A

The concerted model postulates that enzyme subunits are connected in such a way that a conformational change in one subunit is conferred to all other subunits. Therefore, all the subunits must exist in the same conformation. Evidence comes from the fact that when 3 O2 are bound, the last subunit is in R state

84
Q

Describe how the cooperativity of hemoglobin is explained in the sequential model. What is evidence for this?

A

The sequential model postulates that the enzymes subunits do not necessarily have the same conformation. It is the binding of oxygen which causes the conformational change to R state. Evidence comes from the fact that when 1 O2 is bound, the remaining subunits are in T state

85
Q

Structurally, how does H+ affect oxygen binding by hemoglobin?

A

In deoxyhemoglobin three amino acid residues form two salt bridges that stabilize the T state. One of these salt bridges (between His146 and Asp 94) requires an added proton on histidine Beta146. A negative charge on the aspartate Beta94 favors protonation

86
Q

Structurally, how does CO2 affect oxygen binding by hemoglobin?

A

Reacts with water to form carbonic acid, which dissociates to form HCO3- and H+, resulting in a drop in pH inside the cell Some reacts with amino terminal hemoglobin groups, forming carbamate. This carbamate forms salt bridges that stabilize the T state.

87
Q

Explain CO poisoning

A

CO binds to heme with 200x the affinity of oxygen, and prevents oxygen from binding CO also shifts the curve on an oxygen dissociation chart left, as it increases affinity, promoting the R state and preventing delivery of oxygen to tissues

88
Q

Rationalize the existence of fetal hemoglobin

A

Fetal hemoglobin must bind oxygen at the same pO2 at which the mother is releasing oxygen. The gamma chain has less affinity for 2,3-BPG and more affinity for oxygen.

89
Q

Why does fetal hemoglobin have a lower affinity for 2,3-BPG

A

Lowered affinity for 2,3-BPG is due to the replacement of His by Ser

90
Q

What causes sickle-cell anemia?

A

Mutation in hemoglobin replaces valine for glutamate at position 6 of the Beta chains. This valine causes the formation of aggregates, which lead to a “sickle” shaped red blood cell

91
Q

Contrast deoxygenated sickle-cell hemoglobin (HbS) with hemoglobin A (HbA)

A

The substituted valine on HbS is exposed and can interact with other deoxygenated HbS to form aggregates that deform the red blood cells

92
Q

What does neuroglobin do? What about cytoglobin?

A

Neuroglobin is expressed in the brain and retina, protects against oxygen deprivation Cytoglobin is expressed throughout the body and may also protect against hypoxia.

93
Q

Describe the potential of the neuroglobin mutant Ngb-H64Q

A

Could potentially serve as an antidote to carbon monoxide poisoning because: It should bind more tightly to CO than hemoglobin does. It should bind CO more tightly than it does O2 (so that oxygen in blood does not compete away the CO). Its rate of oxidation to the ferric state should be slow (so that it remains in its active form)

94
Q

Differentiate between sickle-cell anemia and the sickle-cell trait

A

If both alleles of the Beta chains are mutated, it can be fatal. However, if only one allele is mutated, that is called sickle-cell trait, and individuals are asymptomatic (with added protection against malaria)

95
Q

How does deoxyhemoglobin S form fibrous precipitates?

A

The exposed valine binds to a hydrophobic patch on another sickle cell hemoglobin, which in turn continues the chain

96
Q

Correlate the genetics of sickle-cell anemia with the geographical distribution of the disease.

A

Significant correlation of malaria and high frequency of HbS allele, although malaria is missing from some high desert areas

97
Q

final step in clotting pathway ON EXAM

A

Prothrombin → thrombin, Fibrinogen → fibrin, crosslinking by transglutaminase

98
Q

What does a hyperbolic curve indicate?

A

MM kinetics

99
Q

What is the P50 of hemoglobin and myoglobin? ON EXAM

A

P50 of hemoglobin is 26 mmHg/Torr P50 of myoglobin is 1 or 2 mmHg/Torr

100
Q

What factors shift pO2 / saturation curves to the right? ON EXAM

A

increases in hydrogen ion concentration, concentration of 2,3-BPG, temperature, and CO2 levels

101
Q

Define carbohydrate in chemical terms

A

Carbohydrates are aldehyde or ketone compounds with multiple hydroxyl groups

102
Q

Define monosaccharide in chemical terms

A

Monosaccharides are the simplest carbohydrates made of aldehydes or ketones with two or more hydroxyl groups and a formula of (C-H2O)n

103
Q

What are the smallest monosaccharides?

A

Trioses (3 carbons) Dihydroxyacetone and D/L glyceraldehyde

104
Q

What are stereoisomers?

A

Stereoisomers are isomeric molecules that have the same molecular formula but which differ only in the three-dimensional orientations of their atoms in space

105
Q

What are enantiomers?

A

Enantiomers are two stereoisomers that are mirror images of each other and non-superimposable (like human hands)

106
Q

What are diastereoisomers?

A

Diastereoisomers are two stereoisomers that are neither superimposable or mirror images of each other

107
Q

What are epimers?

A

Epimers are diastereomers that differ at only one stereogenic center

108
Q

What do the symbols D and L designate in a linear monosaccharide?

A

Symbol D and L designate the absolute configuration of the asymmetric carbon FARTHEST from the aldehyde or keto group. -OH group to the right is D, -OH group to the left is L (If the =O of the aldehyde/ketone is on the top)

109
Q

What do the symbols D and L designate in a ring shaped monosaccharide?

A

If the oxygen is on the top right of the ring, D indicates the R group to the left of the oxygen is pointing up, while L indicates the R group to the left of the oxygen is pointing down

110
Q

What do the symbols alpha and beta designate in a ring shaped monosaccharide?

A

If the oxygen is on the top of the ring, alpha indicates the -OH group pointing down, and beta indicates the -OH group pointing up

111
Q

What is an anomeric carbon?

A

A new chiral center created when a sugar becomes cyclic

112
Q

What is the anomeric center in glucose? Fructose?

A

Glucose- C-1 Fructose- C2

113
Q

What is a 1,4-bond? Differentiate between alpha and beta

A

Most common linkage between two monosaccharides, links them in a chain, with an oxygen in between two bonding carbons. Alpha 1,4-bond has the hydrogens on the bonding carbons facing the same direction

114
Q

What is a 1,6-bond? Differentiate between alpha and beta

A

Branching linkage between two monosaccharide, where one monosaccharide is linked to the chain, with an oxygen in between the two bonding carbons. Alpha is when the bond to the oxygen comes from below to plane of the ring to the C6, beta is when the bond comes from above the plane of the oxygen

115
Q

Differentiate between ketoses and aldoses.

A

Monosaccharides containing ketone groups are ketoses and those containing aldehyde groups are aldoses

116
Q

What do the terms triose, tetrose, pentose, hexose, and heptose indicate?

A

The number of carbon atoms in a monosaccharide

117
Q

Define pyranose. Which carbon is anomeric?

A

Pyranoses are formed when aldohexoses cyclize (six membered ring, one R group), C1 is anomeric

118
Q

Define furanose. Which carbon is anomeric?

A

Furanoses are formed when ketopentoses cyclize (five membered ring, two R groups), C2 is anomeric

119
Q

How do you know which carbon is anomeric in pyranoses and furanoses?

A

The carbon of the aldehyde or ketone is anomeric

120
Q

Fructose and some other sugars are unique in which way? (ring classification)

A

They can form both pyranoses and furanoses, depending on how they cyclize

121
Q

Draw the Fischer structure of D-Glucose

A
122
Q

How do ring structures arise through the formation of hemiacetal or hemiketal bonds?

A

An aldehyde reacts with an alcohol to form hemiacetal, a ketone reacts with an alcohol to form hemiketal. The carbon that was double bonded to the oxygen changes the =O to a -OH and gains a -OR bond

A ring structure can arise if the aldehyde/ketone group on one end of the monosaccharide reacts with the hydroxyl on the opposite end of the monosaccharide.

123
Q

What are anomers of monosaccharides?

A

Anomers are isomers that differ at a new asymmetric carbon atom formed on ring closure. The particular anomer is distinguished with either alpha or beta

124
Q

What is an O-glycosidic bond? What is an N-glycosidic bond?

A

O-glycosidic bonds are formed between the anomeric carbon of a cyclic monosaccharide and the oxygen of an alcohol.

N-glycosidic bonds are formed between the anomeric carbon of a cyclic monosaccharide and the nitrogen of an amine

125
Q

What are the monosaccharide units of sucrose? What is the bond?

A

Sucrose is made of glucose and fructose joined by a 𝞪-1,𝜷-2-glycosidic bond (Uses both anomeric carbons)

126
Q

What are the monosaccharide units of sucrose? What is the bond?

A

Sucrose is made of glucose and fructose joined by a 𝞪-1,𝜷-2-glycosidic bond (uses both anomeric carbons)

127
Q

What are the monosaccharide units of lactose? What is the bond?

A

Lactose is made of galactose and glucose joined by a 𝜷-1,4-glycosidic bond

128
Q

What are the monosaccharide units of maltose? What is the bond?

A

Maltose is made of glucose and glucose joined by a 𝞪-1,4-glycosidic bond

129
Q

What is the structure and biological role of glycogen?

A

Glycogen is a highly branched polymer of glucose residues connected by 𝞪-1,4-glycosidic bonds with 𝞪-1,6-glycosidic branches once every ten units

it is the storage form of glucose in aminals

130
Q

What is the function of starch, and what are the two different types? Describe their structure

A

Glucose storage molecule for plants. Amylose and amylopectin.

Amylose is unbranched and has α-1,4- glycosidic bonds

Amylopectin is branched and has α-1,6- glycosidic bonds about every 30 units

131
Q

What is the structure and function of cellulose?

A

Cellulose is an unbranched polymer of glucose residues joined by 𝜷-1,4-glycosidic bonds, functions in structure

132
Q

Differentiate between alpha/beta-1,4-linkages. Match them to the biological polymer

A

𝜷 bonds form long, straight chains ideal for structural purposes (Cellulose)

𝞪 bonds form bend structures ideal for storage (Starch, Glycogen)

Glycogen also contains alpha-1,6 every ten units, while amylopectin contains alpha-1,6 every thirty units

133
Q

What is a reducing sugar? How are they unique?

A

A reducing sugar is a sugar that can be readily interconverted to a form with a free aldehyde group. They can bind to other molecules such as hemoglobin and react with Ferhlings solution

134
Q

What is the importance of A1C? How is it measured?

A

Levels of A1C or glycosylated hemoglobin correspond to the long-term regulation of glucose levels. It would be higher in diabetics because more hemoglobin would become glycosylated (more reducing sugars in the blood). The glycosylation of Hb has no effect on O2 binding, but glycosylation of other compounds in the body can be detrimental.

Measured by the amount of hydrogen peroxide produced by glucose oxidase enzymes

135
Q

What is the general chemical formula of a fatty acid?

A

CH3-(CH2)n-COOH

(Chains of carbon atoms with a carboxylic acid at one end and a methyl group at the other end)

136
Q

What is the standard notation for representing the number of carbons and double bonds in a fatty acid chain

A

FattyAcidName (#carbons : #double bonds)

Deltan indicates the position of the double bond from the carboxylic acid

137
Q

How many carbons are typically going to be in a fatty acid?

A

An even number, normally around 16-18

138
Q

Distinguish between saturated and unsaturated fatty acids in terms of structure and naming

A

Saturated fatty acids have no double bonds and have a suffix of -anoic (saturated with -H)

Unsaturated fatty acids have 1+ double bonds and have a suffix of -enoic

139
Q

Explain the relationship between fatty acid chain length, degree of saturation, and physical property of melting point

A

As chain length increases, melting point increases

As the number of double bonds increases, melting point decreases

140
Q

A more fluid membrane would have what type of fatty acids

A

Unsaturated and short

141
Q

What is the definition of lipids and how are they a diverse class? Give some examples

A

Lipids are organic molecules that are characterized by low solubility in water.

They can be branched or unbranched, cyclic or linear, alcohols, phosphates, cholines, or sulfates are all lipids

142
Q

What are the biological functions of lipids?

A

Structure - Plasma Membrane

Storage - Triglycerides, Fatty Acids

Cofactors - Vitamins

Signaling - Cholesterol, Other Hormones

Pigments, Antioxidants

143
Q

Match the makeup with the group

Makeup:

Glycerol + 3 Fatty Acids

Glycerol + 2 Fatty Acids + PO4 + Alcohol

Glycerol + 2 Fatty Acids + (Mono/Di)Saccharide + SO4

Sphingosine + Fatty Acid + PO4 + Choline

Sphingosine + Fatty Acid + (Mono/Oligo)Saccharide

Group:

Phos-phosphingolipids

Glycero-phospholipids

Sphingo-glycolipids

Galacto- or Sulfo-lipids

Triacylglycerols

A

Glycerol + 3 Fatty Acids -> Triacylglycerols

Glycerol + 2 Fatty Acids + PO4 + Alcohol -> Glycero-phospholipids

Glycerol + 2 Fatty Acids + (Mono/Di)Saccharide + SO4 -> Galacto- or Sulfo-lipids

Sphingosine + Fatty Acid + PO4 + Choline -> Phos-phosphingolipids

Sphingosine + Fatty Acid + (Mono/Oligo)Saccharide -> Sphingo-glycolipids

144
Q

What is the chemical basis of the colorful feathers of birds?

A

The diet of birds and how they uptake and process certain compounds leads to different colors based on the production of compounds with long conjugated systems that absorb visible light

145
Q

How are fatty acids numbered?

A

The carbon next to the -COOH group is designated alpha, the next one is beta, then gamma, etc.

The most distant carbon is indicated ω, and the double bond location can be indicated from its position from ω

146
Q

What are omaga-3 and omega-6 fatty acids and why are they important?

A

Fatty acids with double bonds between carbons 3-4 for omega-3 and 6-7 for omega-6. These are essential fatty acid used to make mylein in the brain

147
Q

What is the structure of triacylglycerol? What do they do?

A

Triacylglycerols are three fatty acids each in ester linkage with a single glycerol. They store energy and are good for long-term needs because they carry more energy per carbon and less water per gram

148
Q

How do you differentiate between the subcategories underneath phospholipids and Glycolipids?

A

Phospholipids contain the subcategories glycerophospholipids and sphingolipids, they contain a phosphate group

Glycolipids contain the groups sphingolipids and sulfolipids, which contain mono- or oligosaccharide

149
Q

What is the formula of palmitic acid?

A

Palmitic acid = palmitate, a saturated 16-carbon fatty acid (16:0)

150
Q

What is the formula of linoleic acid?

A

Linoleic acid = linoleate, an unsaturated 18-carbon fatty acid (18:2)

Double bonds at 9 and 12

151
Q

What is the formula of linolenic acid?

A

linolenate, an unsaturated 18-carbon fatty acid (18:3)

Double bonds at 9, 12, and 15

Linoleic= 2 double bonds

Linolenic = 3

152
Q

What is arachidonic acid? (MIGHT NOT BE ON THE TEST)

A

Arachidonic acid = arachidonate, an unsaturated 20-carbon fatty acid (20:4)

Double bonds at 5, 8, 11, and 14

153
Q

What are essential fatty acids?

A

Fatty acids with double bonding beyond carbon number 9 (from hydroxyl) that cannot be made by the human body and must be found in the diet

154
Q

Are the double bonds in fatty acids conjugated? Are they in the cis configuration in naturally occurring fatty acids?

A

Almost all naturally occuring fatty acids have cis-double bonds and polyunsaturated fatty acids have double bonds seperated by at least one methylene group (not conjugated, which is every other)

155
Q

What are trans fatty acids?

A

Trans fatty acids were created by people for a long shelf-life or deep-frying, they have trans double bonds instead of cis

156
Q

Describe the general chemical formula of a phosphoglyceride (phosphatidic acid), primary constituent of cell membrane.

A

A phosphoglyceride is a phospholipid with a glycerol platform, formed when an alcohol is added onto phosphatidate

Their structure is two fatty acids RC(=O)- attached to glycerol OCH2CH(O)CH2O which is attached to a phosphate PO3 and an alcohol (O from phosphate - R)

157
Q

Recognize the structure of cholesterol

A

3 six membered carbon rings and 1 five membered carbon ring with an OH group and an extended carbon chain. Methyl groups are attached.

158
Q

What is a steroid nucleus? Where is it found?

A

A steroid nucleus is four fused rings (3 hexagons and one pentagon)

Found in cholesterol, hormones, and vitamin D

159
Q

How does pH affect enzyme activity?

A

ionizing amino acid side chains

160
Q

What are the components of signal transduction cascade?

A

Release of the Primary Messenger → Reception of the Primary Messenger → Delivery of the Message Inside the Cell by the Second Messenger → Activation of Effectors that Directly Alter the Physiological Response → Termination of the Signal

161
Q

How do most signal molecules deliver their information?

A

Most signal molecules bind to membrane receptors and transmit information across a membrane without traversing the membrane

162
Q

What are the roles of molecular receptors, ligands, primary messengers, second messengers, and protein phosphorylation in the process of signal transduction

A

Molecular receptors are proteins in the cell membrane that bind the signal molecules and transfer the information that the molecule has bound from the environment to the cell’s interior

Ligands are a signal molecule that binds to a (extracellular) receptor

Primary messengers are the singal released by the stimulus

Secondary Messengers are intracellular molecules that change in concentration in response to environmental siganls and aplify the signal throughout the cell. They may alter the concentration of other second messengers (cAMP and calcium ions are examples)

Protein phosphorylation occurs in different ways for each cell in signal transduction, but functions to activate various things

163
Q

What are the advantages of fats over polysaccharides?

A

Fatty acids carry more energy because they are more reduced, and less water because they are nonpolar

164
Q

Membrane formation is a consequence of what property of the constituent lipid molecules?

A

Their amphipathic nature (hydrophobic tails and polar heads)

165
Q

What are lipid rafts? What do they do?

A

When cholesterol forms complexes with sphingolipids, glycolipids, and some GPI-anchored proteins. These complexes concentrate in small, defined regions of the membrane.

They help to moderate membrane fluidity and appear to function in signal transduction

166
Q

What are G-proteins? What is the significant function?

A

Hetreotrimers consisting of an alpha, beta, and gamma subunit. The alpha subunit will activate Adenylate Cyclase, which converts ATP to cyclic AMP

167
Q

Where are the G-proteins bound at the start? What occurs at this location?

A

Bound to the 7M receptor (aka GPCR). This GPCR catalyzes the exchange of GTP for bound GDP at the alpha subunit. The beta and gamma subunits dissociate.

168
Q

What is the function of cAMP?

A

A second messenger released from adenylate cyclase after the binding of the alpha subunit. The allosteric binding of 4 cAMPs to the regulatory portion of Protein Kinase A releases the catalytic sites so they can phosphorylate specific serine and and threonine residues of cellular proteins

169
Q

What are the ways the GTP signal can be terminated?

A

Dissociation of signal molecule from receptor

GTPase activity of 𝞪 subunit that causes it to reassociate with the 𝜷𝜸 dimer

Hydrolysis of cAMP to AMP by phosphodiesterase

BioChem (6 decks)

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