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Biochem > Lesson 5-8 > Flashcards

Lesson 5-8 Flashcards

1
Q

All peptides, polypeptides and proteins in the mammalian are polymers of…?

A

alpha-L-amino acids

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2
Q

The alpha-amino acids in peptides and proteins consists of:

A

a carboxylic (-COOH) and an amino (-NH4) functional group attached to the same carbon atom. this carbon is the alpha-carbon.

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3
Q

The one amino acid not exhibiting chirality is:

A

Glycine. Since its “R-group” is a hydrogen atom.

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4
Q

All of the amino acids in proteins exhibit the same absolute…?

A

steric configuration (based on the arbitrry): proteinogenic L-amino acids are related to the L (levarotatory)-glyceraldehyde.

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5
Q

Where can you find D-amino acids?

A

Polypeptide antibiotics, microbes, plants and insects. (not in proteins)

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6
Q

What is the Isoelectric point?

A

= pH value at which the amino acid has no net charge

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7
Q

Glubular proteins:

A
  • have tightly folded peptide chains that are rougly spherical in shape.
  • Albumins: such as ovalbumin in eg white, lactalbumin in milk, serum albumin in the blood.
  • globulins
  • enzymes, hormones
  • water soluble
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8
Q

Gluboular enzyme protein:

A

catalase

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9
Q

Fibrous proteins:

A
  • contains polypeptidechains arranged in extended, parallel layers, or shet-like structures
  • collagen in CT
  • elastins in ligaments and arteries
  • keratins in hair, wool, nails and hoofs.
  • water soluble
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10
Q

“other type” intermediate proteins:

A
  • long rod-like structure
  • myosin in muscle, fibrinogen
  • water soluble
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11
Q

Classification of proteins by shape or solubility:

A
  • Globular proteins
  • Fibrous proteins
  • “other type” intermediate proteins
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12
Q

Classification of proteins by composition

A
  • Simple proteins

- Conjugated proteins

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13
Q

Simple proteins:

A
  • yield only amino acids (or derivates of amino acids) on hydrolysis
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14
Q

Conjugated proteins:

A
  • consist of a simple protein combined with a nonprotein compound
  • Glycoproteins, Nucleoproteins, Phosphoproteins, Chromoproteins, Hemoproteins, Lipoproteins, Flavoproteins, Metalloproteins
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15
Q

What is the nonprotein part of a conjugated protein?

A

The prosthetic group

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16
Q

Classification of proteins by function:

A
  • contractile proteins
  • transport proteins
  • enzymes
  • protein hormones
  • protection proteins
  • storage proteins
  • regulation proteins
  • receptor proteins
  • toxic proteins
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17
Q

Secondary structure of proteins:

A

the arrangement of a polypeptide into regularly repeating units (alpha helix, beta structure = beta plated sheet, collagen), random coil or beta-turn configuration by the formation of intramolecular hydrogen bonds along the length of the chain

18
Q

Primary structure:

A

Sequence of amino acids

19
Q

Tertiary structure of proteins:

A
  • Regularly repeating units, irregular parts, orientation of side chains and stabilizing bonds.
  • The proteins thrre-dimensional (spatial) structure by complete folding of the sheets and helicec of a secondary structure held in position by apolar (inside) and polar (outside) bonds between the chains.
20
Q

What is the Native conformation?

A

Each protein has at least one tree-dimensional conformation in which it is stable and active under biological conditions of temperature and pH

21
Q

What is the Chain-conformation?

A

The tree-dimensional arrangement (secondary and tertiary structure together) of atoms in a structure.

22
Q

What is protein folding?

A

The process by which a protein structure assumes its functional shape, active, native conformation.

23
Q

What is protein unfolding?

A

Denaturation resulting in loss of function.
- happens when proteins are heated, or exposed to acids or bases, or high salt concentrations.

denaturation can be revirsible and irreversible.

24
Q

What is renaturation?

A
  • Denaturation is sometimes reversible; an unfolded protein can be restored to correct folding and regain biological activity. This is called renaturation.
25
Q

Denaturation by heat:

A

Heat coagulates almost all protein. The increased motion within the molecules breakes the hydrophobic interactions and hydrogen bonds.

26
Q

Denaturation by Acid and Bases:

A

Denature proteins by changing the pH of the solution of the protein, and thus changing carboxyl groups to carboxylate ions, amino acid groups to ammonium ions, or vice versa.
Ionic bonds in the proteins are broken.

27
Q

Denaturation by Reducing-oxidizing agents:

A

Convert disulfide bonds to free sulfhydryl groups. Oxidizing agents can convert sulhydryl groups back to disulfide bonds, but the structure of the protein may be significantly different from the native protein.

28
Q

Denaturation by Hydrogen-bonding solvents:

A

Denature proteins by disrupting the hydrogen bonds within the molecule.

29
Q

Denaturation by Heavy metal ions:

A

Such as Ag+, Hg2+ and Pb2+, denature proteins by reacting with sulfhydryl bonds to form stable metal-sulfur bonds or the carboxylate ions in the side chains of acidic amino acids.

30
Q

Denaturation by salting out:

A

removal of hydrate hull

31
Q

Denaturation of duodecylsulphate, mercaptoethanol

A

at fel electrophoresis.

32
Q

Bonds in the Primary structure:

A

Peptide bond (primary, covalent bond) –> between amino acids

33
Q

Bonds in the secondary and tertiary structure:

A
  • disulfide bond (primary, covalent bond) –> between SH-containing side chains (Cys).
  • Ionic bonds (primary bond) –> between polar, charged side chains (acidic/basic amino acids: Arg, Lys, His, Glu, Asp)
  • Dipol-dipol interactions (Secondary bond) –> between polar, non-charged side chains (Ser, Thr, Asn, Gln).
  • Van der Waals dispersion force (secondary, hydrophobic bond) –> between non-polar side chains (Leu, Val, Ile etc).
  • H-bonds –> between CO and NH groups of peptide bonds.
34
Q

Bonds in the Quaternary structure:

A

Between polypeptide subunits-chains

  • dispersion, dipol, H-bond
  • sometimes disulfide bond (insulin)
35
Q

Forces stabilizing proteins

Covalent bond

A
  • Peptide bond

- Disulfide bonds

36
Q

Forces stabilizing proteins

Non- Covalent bond

A
  • van der Waals forces
  • dipole-dipole interactions
  • H-bonding
  • Ionic Bonds
37
Q

What is condensation?

A

The peptide bond that connect two amino acids in a polymer, is formed between the alpha-amino group of one amino acid and the alpha-carboxyl group of another. This reaction is called condensation, and it liberates a water molecule.

38
Q

What is a Disulfide bond?

A
  • it is a covalent bond between two sulfur atoms. It results from the oxidation of the -SH (sulfhydryl) groups of two cysteine molecules, forming cystine
  • The disulfide bond determines conformation of protein molecules and restricts the flexibility of the polupeptide chain.
39
Q

What is can der Waals forces?

A
  • Dispersion force, hydrophobic.
  • they exist between non-polar molecules or atoms.
  • they are the weakest of all intermolecular forces.
40
Q

What are Dipole-dipole interactions?

A
  • it result when two polar molecules approach each other in space.
  • when this occurs the partially negative portion of one of the polar molecules is attracted to the partially positive portion of the second polar molecule.
41
Q

What is H-bonds?

A

It results from the attractive force between a hydrogen atom covalentely bonded to a very electronegative atom such as N, O or F.

42
Q

What is Ionic bonds?

A

It can be formed at physiological pH between the negatively-charged carboxylate group and the positively-charged ammonium group.
- or between the carboxyl group of an acidic amino acid (Glu, Asp) an the amino group of a basic amino acid (Lys, Arg, His), and help to oull portions of a chain together.

Biochem (14 decks)

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