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Biochemistry 2 > Labs > Flashcards

Labs Flashcards

1
Q

What is special about protein interaction with its ligand?

A

specificity which is accomplished by an extremely precise and complementary interaction between a signal and its receiver

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2
Q

Specificity of the enzyme is due to

A

Their structure

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3
Q

Influence of temperatures on enzyme activity

A

High temperatures->denaturing

Low temperatures-> inactive, but not permanently denatured

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4
Q

Lactose has been shown to aid the absorption of

A

Calcium
Magnesium
Zinc

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5
Q

The gene for the production of lactase is located on

A

Chromosome 2

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6
Q

What is the difference between the person with lactose intolerance and without

A

Not DNA difference, but the difference in the messenger RNA

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7
Q

Predominant sugar in cow’s milk

A

Lactose

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8
Q

Predominant sugar in soy milk

A

Sucrose

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9
Q

Predominant sugar in rice milk

A

Glucose

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10
Q

At what pH and temperature lactase was the most efficient

A

The optimal temperature for lactase is 37̊C and pH range of 4-9

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11
Q

What happened with lactase when exposed to boiling for 1 hour or to pH 2 and pH 12

A

High temperature and pH outside the optimal pH range disrupted intra- and intermolecular forces (e.g. hydrogen bonds) that hold the quaternary, tertiary and the secondary structure of the enzyme, which allows the tight bonding between the substrate and the enzyme, making the enzyme ineffective.

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12
Q

Sugars in lactose and the bond connecting it

A

Lactose is a disaccharide Lactose is the result of condensation reaction between two monosugars: D-galactose and D-glucose, which are connected by beta 1-4 glycosidic linkage.

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13
Q

Lactose has ___

A

a reducing end

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14
Q

Characterization of glucose and galactose

A

aldohexose and they are epimers at C-4.

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15
Q

What is the name of the reaction breaking down lactose

A

Hydrolysis

Hydroxyl group is added on the first carbon in D-glucose and hydrogen to oxygen on carbon 4 in D-galactose.

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16
Q

Why lactase cannot break other sugars

A

Lactase can hydrolyze only β-1-4-glycosidic bond between D-galactose and D-glucose. To bind to its substrate, lactase recognizes hydroxyl groups on carbon 2 and 3 on the galactopyronase moiety in lactose. Thus, it cannot hydrolyze sucrose, for instance, because this disaccharide consists of fructose and glucose molecules with 2β α1 linkage.

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17
Q

After exposing lactase to different temperatures, when the glucose level rose after the waiting period and why

A

The glucose concentration rose when ice treated lactase combined with lactose stayed at room temperature for 30 minutes. Initially, the temperature for the enzyme activity was very low and the reaction occurred at very slow rate. The test for free glucose level was negative. When the test tube remained at room temperature for some time, the activity of the enzyme increased, as the molecule movement and the collision between the substrate and the enzyme became more frequent.

The tube with room temperature lactase

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18
Q

Lipids include

A

oils, waxes, phospholipids, steroids (like cholesterol), and some other related compound

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19
Q

Solubility of fat

A

Hydrophobic

But dissolve in fat solvents:hexane or acetone

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20
Q

Lipids break into ___ when hydrolyzed with alkali like NaOH

A

Glycerol and FAs

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21
Q

The process of breaking down lipids into FAs, glycerol and producing sodium salts of FAs is called

A

Saponification, production of salt

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22
Q

Saturated fats are coming from __

A

Animal sources

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23
Q

Why saturated fat is solid at room temperature?

A

Its tails are straight and it can pack together

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24
Q

How can you discover the degree of bond saturation

A

A halogen solution such as iodine and bromide-> the extend of decolourization

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25
Q

What is iodine number

A

The more double bonds a fat contains, the more halogen is required; thus, a high iodine number means a high degree of unsatu

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26
Q

How can you determine the length of FAs

A

Differences in chain length can be distinguished by the differences in intensity of colour due to the absorption of a chemical known as Sudan III. Longer fatty acid chains give more intense and deeper colour

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27
Q

H2O,Soap,NaoH,EtOH,Acetone,Chloroform: fat miscibility

A

Do not mix with water

Mix with ethanol,acetone,soap,chloroform,NaOH

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28
Q

How to count saponification number

A

Mol of KOH in the solution*(HCL used for titration-ml(blank) -HCL used for titration-test)->Mol of KOH reacted

Mol KOH56.110^3->saponification number

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29
Q

What type of soap produced jojoba and coconut is hard/soft

A

Jojoba-soft

Coconut- hard

30
Q

Why oil did not mix with water

A

. Water does not mix with oil and stay separate from it, because it is thermodynamically favorable. As oil and water has two different kinds of bonds and the intermolecular forces in oil (the London dispersion force) is weaker and do not have enough energy to mix with high energy water molecules. Water is more attracted to each other because of hydrogen bond-dipolar interactions.

31
Q

How the soap does its job

A

The dirt is a hydrophobic particle that dissolves in oil. Oil and water do not mix together, making the dirt hard to wash off. The soap has both a hydrophobic tail (an aliphatic chain) and a hydrophilic head (carboxylate group). This dual nature allows the soap mix well with both water and oil and from micells.

32
Q

What is the job of phenyalalnine and how does it turn form pink to colorless

A

Phenolphthalein is a chemical that is used to determine the pH of the solution. In the basic environment it turns pink. It changes the color to transparent in the acidic environment. The change of the color is the process called ionization. During this process the molecule loses or gain electrons. In the case of phenolphthalein, ionization results in conformational change, when added to alkaline solution. Usually, phenolphthalein is colorless, because it allows the light to come through. But when added to the basic solution, OH- takes off hydrogen from phenolphthalein (and electron as well), changing the shape and thus resulting in color change to pink.

33
Q

The primary and the secondary role of carbohydrates

A

Source of energy

Intermediate source of energy (starch and glycogen)

34
Q

Sucrose is a disaccharide of

A

Glucose and fructose

35
Q

Major source of carbohydrates for humans are

A

Starch and sucrose

36
Q

Connectivity in glycogen

A

1-4 alpha

1-6 alpha

37
Q

Benedict’s test is for

A

The detection of the presence of reducing sugars.

38
Q

Reducing sugars have either ___ or ___

A

Free aldehyde group or free ketone group

39
Q

What are the components of Benedict’s solution and how the reaction happens

A

Benedict’s solution is the mixture of copper sulfate, sodium citrate, and sodium bicarbonate, which is used to determine the reducing end in sugars. Sodium citrate keeps Cu2+ in the solution, which otherwise would precipitate. Sodium bicarbonate provides an alkaline environment, required for the redox reaction to occur. The color of Benedict’s solution is blue due to the presence of Cu2+. In the hot alkali environment, upon addition of sugar that has a free aldehyde group or a free ketone group (reducing sugars), the color of the solution changes its color to red brick due to cuprous oxide (Cu2O). When combined with sodium bicarbonate and heated, a reducing sugar is converted to enediols, a molecule with two adjacent hydroxyl groups to the double bond. Enediols react with Cu2+ in Benedict’s solution to form Cu2O.

40
Q

Glucose is what sugar, the same for fructose, xylose and sucrose

A

Glucose is an aldohexose reducing monosaccharide. Fructose is a ketohexose reducing monosaccharide. Sucrose is not a ketose or aldose, because it is a disaccharide. Also, sucrose is a non-reducing hexose sugar. Xylose is an aldopentose reducing monosaccharide

41
Q

Bial’s reagent is used to detect

A

For pentoses

42
Q

The content of Bial’s reagent and indication of the positive result, how the reaction happens

A

Bial’s reagent is the solution of orcinol, concentrated hydrochloric acid and ferric chloride. In an acidic medium with the presence of heat, pentoses form furfural molecule, which in turn reacts with orcinol and ferric ion to from bluish product. This product gives the solution its color, indicating positive results for the presence of a pentose sugar. When a hexose is put into Bial’s solution and heated, 5-hydroxy-furfural is formed, which then reacts with Fe3+ and orcinol, resulting in green or yellow color.

43
Q

Seilwanoff’s test is used for

A

A test for ketoses

44
Q

The content of Seilwanoff’s reagent and how the reaction happens and what is the positive reaction

A

Seilwanoff’s reagent consists of resorcinol and hydrochloric acid. When sugar is added to the reagent and heated, hydrochloric acid hydrolysis poly- and disaccharides to monosaccharides and then converts ketoses to 5-hydroxymethylfurfural. The latter reacts with resorcinol within 5 minutes to give a deep red wine color. Aldoses undergo the same reactions but more slowly.

45
Q

Molish’s test is used for

A

detection of mono, di, poly saccharides

46
Q

Components of molish’s reagent and what happens

A

Molisch’s reactant is 1-naphthol dissolved in ethanol. All sugars will give a positive result to Molisch’s reactant. When the reagent is combined with sugars and sulphuric acid is added gradually to form a layer on top, the acid dehydrates hexoses to 5-hydroxymethylfurfural and pentoses to furfural. Also, the acid breaks di- and polysaccharides into smaller subunits. Furfural reacts with 1-naphthol, resulting in a purple product. As di- and polysaccharides need an extra step of breaking down before to be converted to furfural, monosaccharides will form a purple band faster than di- and polysaccharides.

47
Q

What cow has the highest amount of sugar in the blood: lactating, heifer,pregnant

A

Heifer is the highest, then pregnant and then peak lactation

48
Q

Chromotography is used to

A

Separate mixtures of substances into their components

49
Q

What was the stationary phase and the mobile phase in the experiment

A

Stationary phase: water and nitrocellulose

the mobile phase is a solvent, which consists of 72% Propanol, 8% Acetic Acid and 20% dH2O

50
Q

What is important with the solvent level and the line where amino acids were put

A

The solvent should be below this line

51
Q

why we covered the beaker with the aluminum foil where chromotography was

A

To saturate with vapor-> rise more quickly

52
Q

What is done in the end of the experiment so we can see AAs

A

When the solvent has migrated almost to the end, the paper is dried and sprayed by ninhydrin solution. At 100°C, ninhydrin reacts with α-amino acids to form a purple colour, allowing the amino acids to be visualized

53
Q

How to count Rf

A

Distance traveled by compound/distance traveled by solvent

54
Q

What AAs travel the highest and the lowest

A

Least to highest

Lysine, aspartic acid, glutamic acid, phenyalalnine, isoleucine

55
Q

Diet Pepsi had what sugar

A

Aspartame= aspartic acid and phenylalanine

56
Q

Gel electrophoresis is used for

A

or the separation of deoxyribonucleic acid, ribonucleic acid, or proteins using an electric current applied to a gel matrix

57
Q

Why it is called electrophoresis

A

Electrophoresis” refers to the electromotive force (EMF) that is used to move the molecules through the gel matrix. By placing the molecules in the gel and applying an electric current, the molecules will move through the matrix at different rates, usually based on size. Nucleic acids have a net negative change and move from negative electrodes located near the top of the gel to positive electrodes at the bottom of the gel. Movement is based on charge and size

58
Q

The migration rate of the fragment in gel is inversely proportional to

A

the log10 of their size

59
Q

What is gel in electrophoresis and example of one of those and how it is made

A

el is a cross linked polymer whose composition and porosity is chosen based on the specific weight and composition of the target to be analysed. One example of gel usedto separate nucleic acidsis Agarose. Agarose isa long chain polysaccharideisolated from seaweed. Itis heated in a buffer solution and then cooled it forms a matrix (gel) with buffer solution trapped inside. This gives rise to a porous lattice in the buffer solution which enables nucleic acidmolecules to slip through the lattice holes in order to move toward the positive pole

60
Q

Characteristics that influence the travelling capacity of the nucleic acid

A

conformation, charge, size

61
Q

Aragose size can changed from 0.5 to 2%, influencing

A

ges. Higher percentage gels have smaller pores which retards nucleic acidsmovement. High percentage gels are excellent for allowing the separation of small fragments of nucleic acidand lower percentage gels are typically used to separate larger fragm

62
Q

What is the comb

A

fragments. A “comb” is used to create wells in the gel to allow for the loading of nucleic acids. These wells are small grooves in the gel where the nucleic acidis placed before running the gel to hold it in place. The well size determines how much of the nucleic acidsample can be loaded.

63
Q

The most common buffer for electrophoresis

A

Tris Bonate EDTA

64
Q

Why do we need EDTA

A

The Trismaintains a slightly basic condition (pH 7.3). EDTA prevents enzymatic degradation of nucleic acids as it chelates magnesium ion

65
Q

What does loading dye has and the purpose of it

A

g glycerol and tracking dyesis mixed in with the nucleic acid sample.The high density of glycerol aids the nucleic acid solution in settling in the well when loading. The dye moves more quickly than the nucleic acids and allows tracking the movement of the fragments. It is used as an indicator to alert the researcher to turn off the power.

Makes the solution more visible, to make the handling of the solution easier

66
Q

The use of ethidium bromide and the precaution

A

. Ethidium bromide is commonly used in molecular biology laboratories for visualizing nucleic acids using electrophoresis and other gel-based nucleic acid separation methods. Ethidium bromide fluoresces when exposed to ultraviolet light and exhibits a vivid red-orange color when bound to nucleic acids.UV-transilluminator are usedto visualize the nucleic acidbands after running the gel.Ethidium Bromide however is quite dangerous to use as it is a carcinogenand a mutagen.

67
Q

We tested the chromosome of what species and what gene

A

Gallus gallus

CHD-1

68
Q

What is PCR

A

PCR, or polymerase chain reaction, is a method used for amplifying of a specific DNA region in a test tube. Taq Polymerase, primers that are complementary to the DNA sequence of interest, DNA, nucleotides together with cofactors required for the enzyme function are put in the test tube and are subjected to cycles of cool and hot temperature that allow DNA to be multiplied.

69
Q

Explain how PCR is performed

A

The first step is to expose the solution to 96 ̊ C, so DNA strand denature and single DNA strands would be available. The second step is to cool the solution to 55-65 ̊ C, so the primers can bind to the complementary sequence on single-stranded DNA. Finally, the solution is heated to 72 ̊ C, so the extension by Taq polymerase of the required DNA sequence occurs more quickly. The cycle is repeated 25-35 times.

70
Q

Why do we use Taq polymerase and what is it

A

Taq Polymerase is a DNA Polymerase that was excreted from heat-tolerant bacterium Thermus aquaticus. This species can be found in hydrothermal vents and hot springs. Its DNA Polymerase is heat-stable and has peak activity at 70 ̊ C

Biochemistry 2 (17 decks)

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