MIDTERMS Flashcards by Jasmine Juit

Working in the laboratory exposes you to various __ which are agents that have the potential to cause harm.

hazards

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__ were established to minimize if not eliminate your exposure to these hazards. It is still highly important for you to know and understand these laboratory safety protocols.

Laboratory safety protocols

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__ are garments and articles that are worn for protection against various kinds of workplace hazards like physical, chemical, and biological hazards.

Personal Protective Equipment (PPE)

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needed PPEs in chemistry laboratory (6)

laboratory gown
safety goggles
face mask
long pants/trousers
closed-toe shoes
gloves

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A __ is usually a white cotton buttoned loose cloth that serves as barrier for your skin and clothing against laboratory hazards. Remember that your gown is not a cape for flying (you are no superman/woman, but you are one promising scientist and/or medical professional in the making) so button down whenever you are wearing it!

laboratory gown

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__ should have a wrap-around splash guard for better protection against chemical spillage and projectiles that may damage your beautiful eyes

Safety googles

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__ is a must for protection against chemical and biological hazards. It will protect you from inhaling respiratory particles, dusts, and microorganisms but not chemical fumes

Face mask

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__ or __ are required for protecting your smooth or hairy legs, so even if you look much better wearing your shorts, sorry they are not allowed if you are doing an experiment in the laboratory!

Long pants
trousers

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__ are likewise the primary protection for your feet, so sandals and slippers are a big no in the laboratory!

Closed-toe shoes

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__, typically the latex or nitrile type, is only required when you are handling acutely toxic chemicals or potentially infectious biological specimens

gloves

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Always remember that the laboratory is not the safest place on earth as it has multiple associated hazards, so you need to strictly comply with wearing of PPE for your own protection irregardless of your fashion sense!

true

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A __ is a step-wise flow chart of the experimental procedures that can be easily understood and followed. The writing of schematic diagram will train you in summarizing and understanding technical procedures in doing scientific experiments. The process of making this flow chart will require an active reading and understanding of the described procedures. This will enhance your skills in interpreting technical procedures and will train you in critiquing existing protocols for improvement. A schematic diagram should be straightforward and brief as illustrated in the Figure below.

schematic diagram

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states that an acid increases proton/hydrogen cation (H+) concentration in water while bases increase the hydroxide (OH-) concentration

Arrhenius concept

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__ is a broader definition of acids and bases wherein an acid donates a proton while a base accepts a proton.

Bronsted-Lowry concept

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Arrhenius and Bronsted-Lowry concept
For both concepts, an acid or a base dissociates or ionizes in water.

true

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mixture of a weak acid/base and its conjugate base/acid with focus on their practical preparation in the laboratory.

buffers

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__ are typically pH sensitive, hence, appropriate buffer is needed to preserve their native conformation or shape.

Biomolecules

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Since buffer has both an acidic and a basic component, it can resist drastic changes in pH

true

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the equation used in calculating the pH of buffers

Henderson-Hasselbalch equation

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A __ is a proton (H+) donor which means that it partially dissociates and donates its hydrogen atom to another substance typically water

weak acid (HA)

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When a weak acid loses its H+ it forms a __

conjugate base (A-)

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Meanwhile, the water molecule that accepted a proton forms a __

hydronium cation (H3O+)

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The physiologic pH is narrowly maintained around __ (7.35-7.45) by biological buffer systems.

7.40

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Deviations from this pH (around 7.40) lead to __ which may result to serious deleterious effects including possible death if left uncorrected

acid-base disorders

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Experiments in Biochemistry typically require the use of appropriate buffer system especially if proteins, enzymes, and nucleic acids are involved because they are highly pH sensitive.

true

The most common inorganic buffer system used

phosphate buffer

is phosphoric acid a weak triprotic acid?

yes

__ an acidic pH is required, then the H3PO4-H2PO4- buffer system should be used. For buffer with pH value near the physiologic pH, the H2PO4—HPO4-2 system should be utilized because the equivalent pKa2 is already at 7.21 which is very near the physiologic pH of 7.40.

phosphate buffer

preparation of phosphate buffer (procedures)

(1) calculate the needed reagents in preparing 250 ml of0.200 M KH2PO4-K2HPO4 buffer with pH of 7.40. wrte your solution on the designated worksheet on the next page. (molecular weight of KH2PO4=136.086 g/mol and K2HPO4=174.176 g/mol) (2) weigh the needed solide reagents in separate 100 ml beaker using an analytical balance (3) add 50 ml of distilled water to each reagent and stir thoroughly until they dissolve completely (4) transfer them into 250 ml volumetric flask and wah the remnants with distilled water in a wash bottle (5) half-fill the flask with distilled water and swirl the contents throughly (6) fill the flask to the mark with distilled water. stopper and invert the flask several times while holding the stopper to mix the content throughly (7) pour the buffer in a storage bottle with label of "0.200 M Phosphate buffer, pH 7.40" (8) transfer 25 ml of the buffer to 2 separate beakers and measure the resulting pH (9) to one flask, add 5 ml of 0.100 M HCl, stir the mixture and measure the resulting pH (10) to the other flask, add 5 ml of 0.100 M NaOH, stir the mixture and measure the resulting pH (11) repeat the procedures 8-10 using 25 ml of distilled water instead of the buffer

__ is a popular amino acid salt seasoning or food flavor enhancer in many Asian countries especially in East and Southeast Asia.

Monosodium glutamate (MSG)

MSG was discovered by the Japanese chemist __ in 1908 founded ajinomoto company

Kikunae Ikeda

He isolated the compound from food sources and identified it as the chemical basis for __, the fifth basic taste which means rich meaty or savory taste

umami taste

Though MSG is a popular seasoning in Asia, it generated a bad reputation in Western countries. It was widely maligned in the 1960s as the cause of the so-called __ which is the alleged symptoms of headache, flushing, and sweating associated with eating of MSG-laden cuisine in Chinese restaurants.

“Chinese restaurant syndrome”

__ is actually an amino acid that is naturally abundant in meat products, mushrooms, cheeses, and fermented products. In fact, a person’s average daily intake of it ranges from 10-20 g with at most 10% coming from seasoning. It binds to the umami receptor in our tongue giving food that characteristic savory flavor.

Glutamate

Glutamate is a __ in the human brain that plays a key role in synaptic plasticity which is associated with cognition or learning

major excitatory neurotransmitter

MSG is generally regarded as safe for use as seasoning

true

The problem with MSG-laden snack foods is not MSG per se but rather their high salt content and empty caloric value, so it is wise to avoid these junk foods

true

building blocks of proteins

amino acids

(3) structural features in amino acids

the α-amino group, the α-carboxylic acid, and the variable functional group (R)

The __ has equal number of positive & negative charges so its net charge is zero.

zwitterion

The α-amino group is located to the left side, hence, the complete designation for amino acids is __

L-α-amino acid

All standard amino acids are therefore said to be __-handed

left

The designation also implies the __ nature of amino acids which make them capable of rotating plane-polarized light in solution.

chiral

The structure of the __ or __ determines the identity of an amino acid.

R group side chain

Alipathic AA (5)

GAVLI

Secondary Amine or Imino Acid (1)

Aromatic AA (3)

FYW

Alcoholic AA (2)

Sulfur-Containing AA (2)

Acidic AA (2)

Amide AA (2)

Basic AA (3)

KHR

Amino acids are __ in nature which means that they can behave both as an acid and as a base.

amphoteric

A __ or ionizable group can accept or donate H+ at a particular pH

prototropic

The value of pKa1 is for the __ which is expected on the acidic pH range

α-COOH group

pKa2 is for the __ which is expected on the basic pH range

α-NH2 group

pKa3 is for the __ which depends on the nature of the amino acid

R group

__ is the most useful way of investigating the acid-base properties of amino acids and peptides. This involves the progressive neutralization of all prototropic groups

titration

(5) steps of titration

(1) Begin with the most acidic form of the amino acid (2) Assign the pKa values for each prototropic group (3) Begin the titration with the lowest pKa value (4) Continue the titration (5) Calculate the isoelectric pH of the amino acid

The __ shows the change in the pH of an amino acid in the process of titration

titration curve

the __ of the prototropic groups can be determined from the titration curve They are taken as the pH value at the various inflection points of the curve which is the point where there is sudden change in the slope of the curve.

pKa values

the __ of the amino acid are the medial zones between two pKa values where pH change is slowest.

buffering regions

The __ is actually within the buffering zone of an amino acid

pI (isoelectric pH)

__ are short amino chain of amino acids which are linked together by amide bond between the α-carboxylic acid group of one amino acid can react with the α-amino group of another

Peptides

The amide bond called is typically called as __

peptide bond

In the process of peptide bond formation the reacting groups condenses with removal of __

water molecule

Notice that aspartic acid has the free α-amino group while phenylalanine has the free α-carboxylic acid, hence, they are referred to as the __ & __ respectively

N-terminal C-terminal amino acids

Peptides are always named from __ to __ and the suffix __ is added with the deletion of –ine/-ic acid except for the C-terminal amino acid, and the number of amino acids is specified as a peptide

N- terminal C- terminal -yl

Peptides exhibit the same acid base-properties as amino acids as they are their building blocks. For the titrimetric analysis of peptides, we follow the same steps as in amino acids. However, since peptides are made up of several amino acids their titration process may be longer and writing their structure throughout the titration process can be tedious. To simplify the process, __ is recommended

structural condensation

The __ reveals which species predominates at a particular pH

titrimetric profile

The __ meanwhile, reveals the pKa of the various prototropic groups in amino acids and peptides, their buffering zones, and of course their respective pI values

titration curve

They can resist drastic changes in pH due to the presence of both acidic and basic components (2)

amino acids peptides

__ is also a useful way of identifying an unknown amino acid based on its pKa values and pI.

Titration

procedure on the experiment on amino acid titration

(1) Weigh 0.25 g of the unknown amino acid sample in a 250 ml beaker using a toploading balance. (2) Add 15 ml of distilled water and stir to dissolve the sample. (3) Using a syringe, add 0.200 M HCl while stirring until the pH of the solution drops to 1.50. (4) Titrate with 0.20 ml increments of 0.200 M NaOH. Stir then measure the pH after each increment and record the volume of NaOH and pH values. (5) Continue the process until the pH of the solution reaches past 11. (6) Using MS Excel, graph the pH against the volume of added NaOH. (7) Analyze the resulting titration curve and estimate the pKa values from the inflection points of the curve. (8) Determine the unknown amino acid based on the identified experimental pKa values. Compare the experimental pka values with the theoretical values and calculate the percent error. (9) Draw the titrimetric profile of the identified amino acid. Calculate the theoretical and experimental pI of the amino acid and determine the percent error.

__ are polypeptides with at least 50 amino acid residues and could have hundreds and even thousands of amino acid residues

Proteins

The structure of proteins is largely determined by their amino acid sequence as postulated in __

Anfinsen’s dogma

The __ is the amino acid sequence of the polypeptide which starts at the N-terminal amino acid and ends at the C-terminal amino acid

primary structure (10)

The __ refers to the local folding of a short segment of the peptide into specific configurations such as α-helix, β-sheet, or random coil.

secondary structure (20)

__ is the over-all three-dimensional shape of the protein which can either be globular or fibrous in conformation.

Tertiary structure (30)

the __ is the association of the various sub-units of a multimeric protein.

quaternary structure (40)

_ is used to detect the presence of peptide bond and uses alkaline/basic copper sulfate reagent. Copper ion (Cu2+) forms a coordination complex with the nucleophilic nitrogen atom of the peptide bond which manifests as violet complex also known as Biuret complex

Biuret test

__ is used for the detection of free amine on amino acids or peptides where ninhydrin reagent forms an intense violet colored complex called Ruhemann's purple

Ninhydrin test

__ is used to distinguish the presence of tryptophan or tyrosine which forms yellow-colored product with nitric acid. The benzene ring of these amino acids reacts with nitric acid forming a yellow by-product.

Xanthoproteic test

__ is used to confirm the presence of tyrosine by the formation of reddish-brown product with mercury in nitrous acid. It detects tyrosine by the reaction of its phenolic group with the reagents, producing a reddish-brown complex.

Millons test

__ is used for the detection of tryptophan which forms a violet ring upon reaction with glyoxylic acid and concentrated sulfuric acid. It detects tryptophan by the reaction of its indole ring reacts with the reagents. This is manifested in the formation of violet ring in between the layer of the sample and sulfuric acid.

Hopkins-Cole test

_- is the disruption of these stabilizing forces and bonds in a protein that results to the disruption of its native conformation and subsequent loss of its biological function.

denaturation

__ like mechanical agitation and heating can denature proteins.

Physical manipulations

__ like acids, bases, salts, organic solvents, detergent, alkaloids, heavy metals, and the so-called chaotropic agents ( e.g. guanidine HCl, urea, and β-mercaptoethanol, and dithiotreitol) can disrupt specific stabilizing bonds or forces in the protein which leads to alteration in its structure as manifested by the precipitation of the protein from the solution

Chemical agents

stabilizing bonds and force in proteins (4)

H-bon salt bridge (ionic bond) hydrophobic interaction disulfide bond/linkage/bridge

denaturation causes the ___ in proteins

loss in biological function

detects peptide bonds Cu2+ forms coordination complex with the N of the peptide bond

Biuret test (copper II ion)

presence of tryptophan and tyrosine

Xanthoproteic test

confirm the presence of tyrosine

Millons test

detection of tryptophan

Hpkins-Cole Test

tests for the presence of ammonia results in the production of deep blue colour (Ruhemann's purple), in the presence of an amino groupp

Ninhydrin test

reagent in Xanthoproteic test

nitric acid

reagent in Hopkins-Cole test

glyoxylic acid and cocentrated sulfuric acid