Proteins PPT Flashcards by Franchez Cassandra Escander

during denaturation, proteins will not lose their structure, with regard to

primary structure

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the characteristic features of the peptide bond include all the following, except

a. does not allow freedom of rotation
it is a partial double bond
always has cis configuration
absorbs UV light at 280 nm

always has cis configuration

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the force maintaining the primary structure of a protein:

peptide bond

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The forces maintaining the secondary, tertiary and quaternary structures of a protein are the follow-ing, except:

A. Electrostatic (ionic) bonds
B. Hydrophobic forces
C. Van der Waals forces
D. Peptide bond

peptide bond

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The amino acid which did not allow formation of alpha-helix is

Proline

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Tertiary structure of a protein describes

A. The sequence of amino acids B. Location of disulphide bonds
C. Amino terminal end amino acid D. The nature of protein folding

nature of protein foldng

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One of the following proteins does not have a qua-ternary structure:

A. Albumin
B. Hemoglobin
C. Lactate dehydrogenase
D. Immunoglobulin G

albumin

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All the following reagents are used for identifying the rst amino acid in a protein, except:

A. Cyanogen bromide
B. Fluorodinitrobenzene
C. Dansyl chloride
D. Phenyl isothiocyanate

cyanogen bromide

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Proteins can be precipitated by the following meth-ods, except:

A. Adding alcohol and acetone
B. Saturating with ammonium sulphate
C. Using salts of heavy metals
D. Shifting the pH away from the iso electric point

D. Shifting the pH away from the iso electric point

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Denatured proteins:

A. Are soluble
B. Are difcult to digest
C. Are biologically inactive
D. Peptide bonds are broken

C. Are biologically inactive

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Which of the following is a simple protein?

A. Casein
B. Insulin
C. Hemoglobin
D. Tyrosinase

Insulin

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In glycoproteins, the carbohydrate chains are com-bined through glycosidic linkages with:

A. Hydroxyl groups of serine or threonine residues of proteins
B. Epsilon amino nitrogen of lysine residues of pro-teins
C. Guanidium group of arginine residues of proteins
D. Phenol group of tyrosine residues of proteins

A. Hydroxyl groups of serine or threonine residues of proteins

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The protein which does not answer the aldehyde test is

Gelatin

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Proteins may be estimated by the following meth-ods, except

A. Biuret method
B. Heat coagulation
C. Kjeldahl’s digestion
D. Nephelometry

B. Heat coagulation

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All the following are examples of tertiary structure of proteins, except:

A. Alpha helix
B. Beta pleated sheet
C. Triple stranded helix
D. Peptide bonds

Peptide bonds

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Tertiary structure of a protein describes

D. The nature of protein folding

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4-17. Proteins may be denatured irreversibly by:

A. Adding urea
B. Bringing to iso electric pH
C. Heat coagulation
D. Reduction with mercaptoethano

C. Heat coagulation

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Lectins are:

A. Animal proteins having specic amino acid binding site
B. Antibody molecules acting against cells
C. Plant proteins having specic carbohydrate bind-ing site
D. Blood proteins having a lecithin group

D. Blood proteins having a lecithin group

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Ultraviolet light at 280 nm is absorbed by which component of proteins?

A. Peptide bonds
B. Sulfhydryl group of cysteine
C. Indole ring of tryptophan
D. Imidazole ring of proline

Indole ring of tryptophan

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The nature of the bond linking amino acids to each other is

A. Covalent
B. Co-ordinate
C. Ionic
D. Hydrophobic

covalent

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How many peptide bonds are present in gluta th-ione?

A. 1 B. 2 C. 3 D. 4

c. 3

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Basic difference between two polypeptides is in the —

A. Structural conformation
B. Primary sequence of amino acids C. Number of side chains
D. Number of hydrophobic bonds

B. Primary sequence of amino acids

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Human insulin differs from bovine insulin in:

A. Biological activity
B. Number of amino acids
C. Position of disulde bonds
D. Sequence of amino acids

D. Sequence of amino acids

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A covalent bond between the alpha carboxyl group of one amino acid and alpha amino group of the neighboring amino acid is called

A. Cis double bond
B. Isopeptide bond
C. Pseudopeptide bond
D. Peptide bond

peptide bond

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Study of linear sequence of amino acids is done by all techniques listed except: A. End group analysis B. Hydrolysis by proteolytic enzymes C. Analyzing the content of each amino acid D. Denaturing the protein

D. Denaturing the protein

Different polypeptide chains are held together by: A. Peptide bonds B. Disulphide bonds C. Glycosidic bonds D. Ester bonds

B. Disulphide bonds

Primary structure decides: A. Rate of synthesis of protein B. Biological activity of the protein C. Rate of degradation of the protein D. Effect of proteolytic enzymes on protein

B. Biological activity of the protein

Secondary and tertiary levels of protein structure are dependent on a. Presence of disulde bonds b. Primary structure c. PH of the medium d. PK value of component amino acids

b. Primary structure

The protein having predominantly alpha heli cal structure is collagen keratin fibroin myoglobin

collagen

Which of the following is NOT true regarding the tertiary structure of proteins A. It is a random coil structure B. Disulde bonds are formed between any two cys-teine residues C. Position of disulde bonds are predetermined and xed D. Denaturation using reducing agents does not aff-ect the disulde bonds

D. Denaturation using reducing agents does not aff-ect the disulde bonds

Protein having a large number of disulde bonds is A. collagen B. keratin C. hemoglobin D. albumin

keratin

Which of the following proteins does not possess a quaternary structure? A. Myoglobin B. Lactate dehydrogenase C. Hemoglobin D. Immunoglobulin M

A. Myoglobin

Which of the following is NOT true regarding hem-oglobin? A. Has 4 independent subunits B. Each subunit has one heme residue C. Each subunit can bind one molecule of oxygen D. All four subunits are similar

D. All four subunits are similar

draw glycine structure

draw Alanine structure

glycine letter code

Gly/G

glycine is polar nonpolar + charge - charge

non-polar

Alanine is? polar nonpolar + charge - charge

non-polar

alanine letter code

Ala/A

draw valine structure

valine is ? polar nonpolar + charge - charge

non polar

draw cysteine structure +1

cysteine is polar nonpolar + charge - charge

non polar

cysteine letter code

Cys/C

valine letter code

Val/V

Proline letter code

Pro/P

draw proline structure

proline is polar nonpolar + charge - charge

nonpolar

draw leucine structure

leucine is polar nonpolar + charge - charge

non polar

leucine letter code

Leu L

draw isoleucine structure

isoleucine is polar nonpolar + charge - charge

nonpolar

isoleucine letter code

Ile / I

methionine structure

methionine is polar nonpolar + charge - charge

nonpolar

methionine letter code

Met/M

Tryptophan structure

Tryptophan is polar nonpolar + charge - charge

nonpolar

Tryptophan letter code

Trp/W

Phenylalanine structure

Phenylalanine is polar nonpolar + charge - charge

nonpolar

Phenylalanine letter code

Phe/F

Lysine structure

Lysine is polar nonpolar + charge - charge

+ charge

Lysine letter code

Lys/K

Arginine structure

Arginine is polar nonpolar + charge - charge

+ charge

Arginine letter code

Arg/R

Histidine structure

Histidine is polar nonpolar + charge - charge

+ charge

Histidine letter code

His/H

serine structure

serine is polar nonpolar + charge - charge

polar

serine letter word

Ser/S

Threonine structure

Threonine is polar nonpolar + charge - charge

polar

Tyrosine structure

Threonine letter code

Thr/T

Tyrosine letter code

Tyr/Y

Tyrosine structure

Tyrosine is polar nonpolar + charge - charge

polar

Asparagine structuer

Asparagine polar nonpolar + charge - charge

polar

Asparagine letter code

Asn/N

Glutamine structure

Glutamine is polar nonpolar + charge - charge

polar

glutamine letter code

Gln/Q

Aspartic acid structure

Aspartic acid is polar nonpolar + charge - charge

- charge

aspartic acid letter code

Asp/D

Glutamic acid structure

Glutamic acid is polar nonpolar + charge - charge

- charge

Glutamic acid letter code

Glu/ E

Amino acids with aliphatic side chains (5)

Glycine (G), Alanine (A), Valine (V), Leucine (L) and Isoleucine (I)

amino acids that have branched amino acid chains

Valine Leucine Isoleucine

Hydroxyl group containing amino acids (3)

Serine (S) Threonine (T) Tyrosine (Y)

3. Sulphur containing amino acids (2)

Cysteine Methionine

is formed by the condensation of two cysteine molecules.

Cystine

4. Acidic amino acids and their amides (4)

Glutamic acid (E) and Aspartic acid (D) Glutamine (Q) and Asparagine (N) are their respective amide derivatives.

Basic amino acids:

Lysine (K), Arginine (R) (with guanidine group) and Histidine (H)(with imidazole ring

6. Aromatic amino acids (3)

Phenylalanine (F), Tyrosine (Y) and Tryptophan (w) (with indole ring)

Imino acids

Proline

ionic forms of the amino acid (neutral = net charge 0)

zwitterion

amino acids that show optical and stereochemical properties

asymmetric/chiral carbon

only achiral carbon

glycine

same chemical composition, different spatial organization

stereoisomers

type of stereoisomers where nonsuperimposable mirror-image (L and D)

enantiomers

L means

Levorotatory behaviour

D means

Dextrorotatory

types of amino acids that predominate in nature

L-amino acids

are amino acids weak/strong polyprotic acids

weak

An acid that contains more than one ionizable proton

polyprotic acid

pH where amino acids have a net charge of 0

isoeletric point (pI)

pI formula

1/2 (pK1+pK2)

at neutral pH, acidic amino acids have a what net charge

negative

acidic amino acids pI formula

pI = 1/2 (Pk1+PKr)

have net positive charge at neutral pH

basic amino acids

pI for basic amino acids

pI = 1/2 (Pkr+PK2)

produced by modifications of one of the 20 amino acids already incorporated into a protein

uncommon amino acids

example of uncommon amino acids

carboxyglutamate hydroxyproline hydroxylysine selenocysteine phosphoserine

example uncommon amino acids with biological functions (occur rarely in proteins)

dopamine histamine citrulline GABA Tiroxine L-ornithine

neurotransmitter

dopamine

allergy reactions

histamine

urea cycle intermediate (2)

Citrulline L-ornithine

covalent amide bond established between a-COOH and a-NH3+ groups of two amino acids

peptide bond

allow the polymerisation of amino acids to form peptides and proteins

polymerisation

usually found in trans conformation

peptide bond

about 0.133nm long (shorter than single bond butl onger than a double bond))

peptide bond

peptides according to number of amino acids

dipeptide tripeptide oligopeptide polypeptide

more than 12 but less than 20 amino acids

oligopeptide

liberates the amino acids of a protein

acid hydrolysis

chromatographic methods used to separate amino acids:

ion exhcange chromatography thin layer chromatography reverse-phase high performance liquid chromatography (HPLC)

the charged molecule of interest are exchanged for another ion (salt ion) on a charged solid support (resins)

ion exchange chromatography

amino acids absorbed on a thin layer of silica gel

thin layer chromatography

amino acids separated on the based of their polarity by the use of a column having a nonpolar liquid immobilised on an inert matrix

HPLC

reagent that combines with free amino terminus of protein

Phenylisothiocynate

not only identifies the N-terminal residue of protein, successive reaction cycles can reveal the amino acid sequence of a peptide

flourescence

proteins for catalysis

enzymes

proteins for structural role

collagen fibroin elastn

proteins against mechanical or chemical damage

keratin

proteins to avoid blood loss

fibrinogen and thrombin

proteins for immunosystem proteins

immuoglobins

proteins for storage

ovalbumin casein ferritin

protein without prosthetic group

apoprotein

protein with prostetic group

holoprotein

overall three dimesional architecture of aprotein (the radicals can be modified their spatial position by rotation, bonds are not cleavage during this process)

conformation

geometric possibilities from a particular set of atoms. In going from one configuration from another, covalent bonds must be broken and rearranged

configuration

strands run in opposite directions

antiparallel

usually located in the protein surface stabilized by hydrogen bonds they allow the protein strands to change direction glycine and proline are predominant amino acids

beta-turns

combinations of few secondary strtuctures giving characteristic geometric shape

supersecondary strctures

globular proteins containing a combination of different super secondary structures

domains or modules

location of amino acids side chain in globular proteins are based on polarities nonpolar are (inside/outside)

inside

location of amino acids side chain in globular proteins are based on polarities charged are usually located at what

surface of protein

location of amino acids side chain in globular proteins are based on polarities polar and uncharged are located

inside the protein/in the surface (usually)

interactions allowing tertiary structure stabilization

charge-charge van der Waals repulsion hydrogen bonds hydrophobic interactions disulfide bridges

loss of protein structure and function

denaturation

restoration of native structure and biological role

renaturation

proteins that may assist the protein folding process

chaperones

condensed intermediate on the folding pathway that contains much of the secondary structure elements on the native conformation but many incorrect tertiary structure interactions

molten-globule

protein containing several identical subunits

oligomer

structural unit of an oligomeric protein

protomer

contains two protomers

tetramers

found in epidermal layer, nails, hair, feathers

fibrous proteins (a-keratins)

different grade of hardness of a-keratin is on the basis of what residue

%CYs disulfide bridges

most abundant protein in vertebrates

colalgen

provides framework that gives the tissues their form and strength

collagens

simple helical structure (left handed)

collagen

inorganic form of collagen

hydroxyapatite

method that is titration based, measure nitrogen then protein are detected

Kjeldahl method

high temperature is required for this

Enhanced dumas method

when high conc. of protein is present

Biureate test

low conc. of protein present unable to detect through Biureate

lowery methods

biurate reagent + phosphomolybdate and phosphotungstate

lowery method

solubility testare tests performed to determine the ability of compounds to dissolve in a solvent, which is usually a liquid. These tests are essential to determine the size and polarity of unknown compounds and the presence of acidic and basic functional groups.

solubility test

protein is not soluble in solvent looks like

cloudy solution

a chemical test useful to identify ammonia, primary/secondary amines, or amino acid

ninhydrin test

positive for ninhydrin test

purple-colored complex

proline in ninhydrin test

yellow

is a chemical test which is used to check whether a given analyte contains amines or α-amino acids.

ninhydrin test

positive in ninhydrin test indicates

presence of ammonia, primary/secondary amines, or amino acids

a chemical test that can be used to check for the presence of peptide bonds in a given analyte.

biuret test

biuret reagent

hydrated copper sulfate sodium hydroxide sodium-potassium tartate

pink in biuret test indicates

presence of peptides

is used to detect amino acids containing an aromatic nucleus (tyrosine, tryptophan and phenylalanine) in a protein solution which gives yellow color nitro derivatives on heating with conc. HNO3.

xanthoproteic test

reagent for xanthoproteic test

conc. nitric acid 40% NaOH

xanthoproteic test positive indicates

tyrosine and tryptophan present

color of positive xanthoproteic test

yellow orange

is an analytical test used for the detection of the amino acid tyrosine, which is the only amino acid containing the phenol group.

Millon's test

millon's reagent

mercuric nitrate mercurous nitrate in nitric acid and distilled water.

Millon's reagent positive is indicated by

red or pink precipitate present

is a time-tested colorimetric assay.

Bradford assay

is a widely used colorimetric method for determining protein concentration in a solution

bradford assay

reagent in Bradford assaywhich is prepared in phosphoric acid. When the dye binds to proteins, it undergoes a color change that shifts the absorbance maximum from 465 nm to 595 nm

Coomassie Brilliant Blue G-250

the intensity of the color change is directly/indirectly proportional to the protein concentration,

directly

is a biochemical test consisting of colorimetric reaction for the detection and quantification of guanidinium groups, used as a qualitative test for arginine that is either free or in protein

sakaguchi test

sakaguchi reagent

1% 1-naphthol in alcohol with a few drops of 10% sodium hypobromite solution of bromine water.

sakaguchi positive test indicates

presence of arginine or guanidium compound

color of positive sakaguchi test

red

is a specific test used for the detection of indole ring and thus, tryptophan in proteins.

hopkin's cole test

hopkin's cole reagent

Glyoxylic acid

positive hopkin's cole is indicated by

purple ring

positive hopkin's cole test means

tryptophan is present

looks for the presence of cystine in the urine through a semi-quantitative test

nitroprusside test

s a biochemical test used for the detection of the free –SH groups in amino acids or the cysteine amino acid in a protein.

nitroprusside test

reagent for nitruprusside test

2 freshly prepared sodium nitroprusside Concentrated Sodium hydroxide

positive nitroprusside test indicator

red colored complex

positive nitroprusside test means

cysteine is present

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