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Amino acids > Lecture 2 > Flashcards

Lecture 2 Flashcards

1
Q 
Classification of proteins by: 
1)
2)
3)
4)
A

1) Location in an organism - intra/ extracellular.
2) By function - structural/ biological active
3) By shape - fibrous/ globular
4) By chemical composition - simple/ complex

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2
Q

Classification of proteins according to their 3D structure

A

1) Globular proteins: spheroidal shape, both secondary structures are abundant.
2) Fibrous proteins: rod-like shape, one secondary structure predominates.

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3
Q

Conjugated protein

3 examples

A

It is a protein that functions in interaction with other chemical groups, attached by covalent bond or weak interactions.

  • Lipoproteins + lipids
  • Glycoproteins + carbohydrates
  • Phosphoproteins + phosphate groups
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4
Q

Peptide bond formation

A
  • Dehydration synthesis.
  • Required the input of energy.

-Carboxyl group of one amino acids, reacts with the amino group of another amino acid, releasing a water molecule.

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5
Q

Peptide bond characteristics (4)

-KNOW THE STRUCTURE OF A PEPTIDE BOND

A
  • Partial double bond character.
  • Trans configuration (more stable)
  • Uncharged, but polar.
  • Planar
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6
Q

Structure of a simple peptide

A

Amino- end: left side (usually, look where is it)
Carboxyl end: right side.
Peptide bonds (o=c-n-h) in between amino acids.

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7
Q

Primary structure of proteins (3)

A
  • Order of amino acids.
  • Stabilized by peptide bonds.
  • Reads from N- to C- end.
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8
Q

Secondary structure of proteins (3)

A
  • Spatial arrangement of the polypeptide chain by rotation of the planar peptide bonds around the alpha carbon.
  • Stabilized by hydrogen bonds.
  • It can be a-helix or B- helix.
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9
Q

α – helix structure (6)

A
  • Backbone is formed by hydrogen bonds.
  • Bond between the carbonyl oxygen and the amide hydrogen of an amino acid residue located 4 residues further down the chain.
  • Right- handed helix.
  • Peptide bond planes are parallel to the axis of the helix.
  • Stabilized by hydrogen bonds.
  • R-groups are perpendicular.
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10
Q

β-sheet (3)

A
  • Hydrogen bonds occurs between regions of separate neighboring polypeptide strands aligned parallel to each other.
  • It can be parallel or anti parallel.
  • R- are placed above or below the plane of the sheet.
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11
Q

β-bend (reverse or β-turn) (5)

A
  • Reverse the direction of the polypeptide chain.
  • Helps it to form a compact, globular shape.
  • Often connect successive strands of anti parallel sheets.
  • Hydrogen bond stabilizes it.
  • Are found on the surface of the polypeptide.
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12
Q

Non-repetitive secondary structure (3)

A
  • Loop or coil formation.
  • Less regular than α- or β-.
  • 1/2 of a protein molecule exist in it.
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13
Q

Motifs (3)

A
  • Structural characteristics.
  • Super-secondary structure.
  • Do not allow us to predict the biological functions.
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14
Q

Tertiary structure of proteins

A

-Spatial arrangement of the secondary structures.
-Stabilized by interaction between side chains, it can be:
1- Hydrogen bonds (polar and hydrophilic side chains).
2- Hydrophobic (predominant).
3-Disulfide bonds (oxidizing conditions).
4- Ionic (two oppositely charged side chains).

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15
Q

Domain

A
  • Functional and 3- dimensional structural units.
  • Different domains have different functions.
  • Can be independently stable and folded.
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16
Q

Quaternary structure of proteins (3)

A
  • Oligomeric structure of a protein.
  • Composed of 2 OR MORE SUBUNITS.
  • Stabilized by non- covalent interactions and disulfide bonds.
17
Q

Folding - a stepwise process

A
  • Interactions between AA side chains determine how long a polypeptide chain folds.
  • Secondary structures form first.
  • Ionic interactions play an important role.
  • Process continues until complete domains form and the entire polypeptide is folded.
  • Fully folded (native) form = low energy state.
18
Q

Assisted folding

  • Information needed for correct protein folding is contained in…
  • A protein begins to fold in stages during….
  • Definition of Chaperones
A
  • the primary structure of the polypeptide.
  • its synthesis.
  • A specialized group of proteins required for the proper folding of many proteins.
19
Q

Example of molecular chaperones

A
  1. Hsp70: present in cell with elevated temperature, it binds to regions rich in hydrophobic residues. Prevent inappropriate aggregation.
  2. Chaperonins: serve as a template for the folding process.
20
Q

Examples of diseases caused by protein misfolding

A
  • Alzheimer’s disease.
  • Type 2 diabetes.
  • Parkinson’s disease.
21
Q

Systemic amyloidosis

  1. Primary systemic amyloidosis.
  2. Secondary systemic amyloidosis.
A

Soluble proteins that are secreted from the cell in a misfolded state and converted to amyloid fiber (insoluble)

  1. Misfolded immunoglobin.
  2. Increase in secretion of amyloid A protein.
22
Q

Prion disease

A
  • Transmissible spongiform encephalopathies.
  • Fatal neurodegenerative.
  • Result from the deposition of insoluble protein aggregates in neural cells.
23
Q

Prion disease

  • Infectious protein form.
  • Non- infectious protein form.
A
  • PrPSc - form insoluble aggregates of fibrils, greater amount of B- sheets, highly resistant to proteolytic degradation.
  • PrP - normal proteins, greater amount of alpha helices.
24
Q

Prion disease

-Key to becoming infectious lies in…

A

Changes in the 3-dimensional conformation.

25
Q

Why do they say a peptide bond has a partial double bond character

A

Because even though the bond between the Carbon (of the carboxyl group) and the Nitrogen (of the amino group) is a single bond, rotation is not allowed. Acting like a double bond.
However, rotation is allowed between the other bonds.

26
Q

B- sheet

  1. Antiparallel
  2. Parallel

CHARACTERISTICS

A
  1. N and C terminals alternate.
    N –> C
    C –> N
  2. All the N terminals are together.
    N –> C
    N –> C
27
Q

Interchain vs. Intrachain bonds

A

Interchain - H bonds are formed between the polypeptide backbone of separate polypeptide chains.

Intrachain - H bonds are formed by a single polypeptide chain folding back on itself.

28
Q

Two major categories of Quaternary proteins

A

Fibrous proteins - two sub-units held together by ionic and disulfide bonds

Globular proteins - spherical shape, ex hemoglobin (4 sub-units).

29
Q

Protein disulfide isomerase

A

interchange of disulfide bonds

Amino acids (6 decks)

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