Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Biochemistry > Amino Acids, Peptides, Proteins and Enzymes (Lec 2) > Flashcards

Amino Acids, Peptides, Proteins and Enzymes (Lec 2) Flashcards

1
Q

AA Characteristics

A 
All amino acids (except Proline) have:
−	acidic carboxyl group
−	basic amino group
−	α hydrogen
−	R substituent (side chain, makes AA unique)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Chirality of AA’s

A

All amino acids are chiral (except glycine) meaning that they are non-superimposable on their mirror images (enantiomers).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

AA Classification

A

Nonpolar, aliphatic (7), Aromatic (3), Polar, uncharged (5), Positively charged (3), Negatively charged (2)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Ionization of AA’s

A

At low pH, the amino acid exists in a positively charged form (cation)
− Carboxyl and amino groups are protonated

At high pH, the amino acid exists in a negatively charged form (anion)
− Carboxyl and amino groups are deprotonated

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Zwitterion Form

A

The condition in which an Amino Acid exists as both a positively and negative chargely charged molecule

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

AA with Uncharged Sidechains

A

Amino Acids with uncarged side chains (E.g. Glycine)
• The pKa of the α-carboxyl group is 2.34.
• The pKa of the α-amino group is 9.6.
Glycine can therefore act as a buffer in 2 pH ranges

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Isoelectric Point

A

Specific pH point where AA carry a ‘net charge’ of 0

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Peptide Ends

A

Are NOT the same
1st side: Amino-terminal end (amino terminus = N-terminal)
2nd side: Carboxyl-terminal end

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Naming Peptides

A
  1. Using full amino acid names (serylglycaltyrosylalanylleucine)
  2. 3-letter code abbreviation (Ser-Gly-Tyr-Ala-Leu)
  3. 1-letter code for longer peptides/proteins (SGYAL)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Protein Composition

A

Polypetides and possibly; Cofactors, Coenzymes, Prosthetic groups, Covalently attached cofactors, etc.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Protein Structure

A

Protein molecules adopt a specific 3D conformation (native fold) that is able to fullfil a specific biological function

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Native Fold

A

The 3-dimensional structure that proteins adopt when folding

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Four Levels of Protein Structure

A
  1. Primary Structure (amino acid sequence joined by peptide bonds)
  2. Secondary Structure (multiple primary structures arranged into units of secondary structure e.g. Helix or Sheets)
  3. Tertiary Structure (built up of secondary structures)
  4. Quaternary Structure (built up of tertiary structures)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Primary Strucutre: Peptide Bonds

A

Sequence of amino acids bonded covalently in a line by peptide bonds. Each bond has some double-bond character due to resonance and CANNOT ROTATE

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Peptide Bond Resonance

A

Resonance causes the peptide bonds to:

  • be less reactive (very strong)
  • be rigid and nearly planar (not free to rotate)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Secondary Structures

A

Refers to the local spatial arrangement of the polypeptide backbone. Produces 2 common arrangements:

  1. Alpha Helixes
  2. Beta Sheets
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Random Coil

A

Irregular arrangement of the polypeptide backbone

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

The Alpha Helix

A

Stabilised by Hydrogen Bonds between nearby residues producing a helix structure. Right (clockwise) or Left (anti-clockwise) handed with 3.6 residues (5.4 Å) per turn.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

The Alpha Helix: Bonding

A

Stabilised by H Bonds between the backbone amides of n and n+4 amino acids (H bonds between every 4 amino acids)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

The Beta Sheet

A

The planarity of the peptide bond and tetrahedral geometry of the alpha carbon create a pleated sheet-like structure.

21
Q

The Beta Sheet: Bonding

A

H Bonds between the backbone amides in different strands hold backbone together

22
Q

Parallel Beta Sheet

A

H-Bonded strands run in the same direction

  • H bonds between strands are bent (weaker)
  • More resistant to temp.
23
Q

Antiparallel Beta Sheet

A

H-Bonded strands run in opposite directions

  • H bonds between strands are linear (strong)
  • Less resistant to temp.
24
Q

Tertiary Structures

A

Refers to the overall spatial arrangement of atoms (sheets or helixes) in a protein

25
Q

Tertiary Structures: Bonding

A

Stabilized by numerous weak interactions between amino acid side chains. Largely hydrophobic and polar interactions, can be stabilized by disulfide bonds

26
Q

Tertiary Structures: 2 Major Classes

A
  1. Fibrous (water soluble)

2. Globular (lipid soluble)

27
Q

Quaternary Structures

A

Formed by the assembly of individual polypeptides into a larger functional cluster (Primary -> Secondary -> Tertiary -> Quaternary)

28
Q

Protein Stability and Folding

A

A protein’s function determined by its 3D structure

29
Q

Protein Folding Speed

A

Proteins fold to lowest-energy fold in μsecs. Search for minimum is not random as direction to lowest energy native structure is thermodynamically favourable

30
Q

Chaperones

A

Prevent misfolding and aggregation of onfolded peptides

31
Q

Globular Protein Functions

A

Reverse binding of ligands, transport/storage of ions and molecules, defense against pathogens, muscular contraction, biological catalysis

32
Q

Protein Interaction with other Molecules: Ligand

A

A molecule that binds to a protein is a Ligand. Ligands bind via same non-covalent interactions that dictate protein structure. Reversible, transient process of chemical equilibrium (A + B ↔AB).

33
Q

Binding Specificity

A
  1. Lock and Key Model

2. Induced Fit Model

34
Q

Specificity: Lock and Key Model

A

Assumes that proteins and ligands have complementary binding site which allows for high specificity. Complementary in: size, shape, charge, hydrophobic /hydrophilic properties

35
Q

Specificity: Induced Fit

A

Assumes that both the protein and ligand exhibit conformational changes upon ligand binding. Allows for tighter binding of ligand and higher affinity for different ligand.

36
Q

Enzymatic Catalysis

A

Enzymes increase reaction rate (k) by decreasing activation barriers (ΔG‡)

37
Q

How to Lower ΔG‡

A

Enzymes use binding energy of substrates to organise reactants into a rigid ES complex. Allows reaction to become thermodynamically favourable

38
Q

Catalytic Mechanisms

A
  1. Acid-base catalysis: give or take protons
  2. Covalent catalysis: change reaction paths
  3. Metal Ion catalysis: use redox cofactors (pKa shifters)
39
Q

Covalent Catalysis

A

A transient covalent bond between the enzyme and the substrate that changes the reaction pathway

40
Q

Metal Ion Catalysis

A

Involves a metal ion bound to the enzyme that interacts with substrate to facilitate binding

41
Q

Enzyme Inhibition

A

Compounds that decrease an enzyme’s activity

42
Q

Competitive Inhibition

A

Competes with substrate for binding

  • binds active site
  • does not affect catalysis
43
Q

Competitive Inhibition: Lineweaver-Burk

A
  • No change in Vmax; apparent increase in KM

* Lineweaver-Burk: lines intersect at the y-axis (1/Vmax).

44
Q

Uncompetitive Inhibition

A

Only binds to ES complex

  • does not affect substrate binding
  • inhibits catalytic function
45
Q

Uncompetitive Inhibition: Lineweaver-Burk

A
  • Decrease in Vmax; apparent decrease in KM
  • No change in KM/Vmax
  • Lineweaver-Burk: lines are parallel.
46
Q

Mixed Inhibition

A

Binds enzyme with or without substrate

  • binds to regulatory site
  • inhibits both substrate binding and catalysis
47
Q

Mixed Inhibition: Lineweaver-Burk

A
  • Decrease in Vmax; apparent change in KM
  • Lineweaver-Burk: lines intersect left from the y-axis.
  • Noncompetitive inhibitors are mixed inhibitors such that there is no change in KM.
48
Q

Non-Covalent Modification (Allosteric)

A

Allosteric regulators are:

  • generally small chemicals
  • can be positive (improve enzymatic catalysis)
  • can be negative (reduce enzymatic catalysis)
49
Q

Covalent Modification

A

Irreversible or reversible, positive or negative

Biochemistry (12 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions