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Biochemistry > Week 2 > Flashcards

Week 2 Flashcards

1
Q

What is the difference between nonessential and essential aa’s in humans?

A

Non essential are made in the body; essential must be supplied by the diet

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2
Q

What is a peptide bond?

A

Formed by condensation (taking water out of it) between amine and carboxylic acid

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3
Q

What assists hydrolysis of peptide bonds?

A

Proteases

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4
Q

What is polypeptide cross linking for?

A

Formed by cysteine disulfide bonds that stabilizes tertiary and quaternary structures

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5
Q

What is a protein that folds into its specific 3-D structure in order to become a functional protein?

A

Native fold

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6
Q

What are the favorable interactions in proteins?

A
  1. Hydrophobic effect
  2. Hydrogen bonds
  3. Londen dispersion
  4. Electrostatic interactions
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7
Q

Explain the hydrophobic effect.

A

It minimizes interactions of water by driving the proteins to fold into a 3-D shape resulting to the increase in entropy

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8
Q

What is the importance for hydrogen bonds for protein formation?

A

Binds a-helices and b-sheets in a protein

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9
Q

What is the importance for London dispersion for protein formation?

A

Stabilizes the interior of the protein

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10
Q

What is the importance for electrostatic interactions for protein formation?

A

Stabilizes the protein by salt bridges

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11
Q

Describe the primary structure of a protein

A

AAs are attached by peptide bounds. Once attached an single aa unit is a residue.

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12
Q

What are the 3 forms of secondary structures of proteins?

A
  1. a-helix
  2. B-sheets
  3. B-turn
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13
Q

Describe the formation of an alpha helix

A

Held by H-bonds with a turn of 3.6 residues

Side chains point outward

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14
Q

What are the problems of proline in a-helicases?

A

The rotation around N-C bond is impossible could create more steric hinderance

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15
Q

What are the problems of glycine in a-helicases?

A

The tiny R-group supports other conformations

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16
Q

Describe the formation of a B-sheet

A

Arrangement is held together by inter- and intra-chain H-bonds between backbone amides

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17
Q

What is the difference between parallel and antiparallel sheets?

A

Parallel sheets’ strands are oriented in the same side while anti- are in opposite directions
Parallel have weaker H-bonds, anti- has stronger

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18
Q

Describe the formation of a B-turn

A

Gly and Pro are found

H-bond stabilizes from a carbonyl to an amide three residues down the sequence

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19
Q

Describe the tertiary structure of a protein

A

Stabilized by weak interactions and disulfide bonds

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20
Q

Describe the quaternary structure of a protein

A

Proteins that consist of more than one polypeptide chain

Chains interact with one another non-covalently via electrostatic attractions, H-bonds, and hydrophobic interactions

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21
Q

What is s molecule that is made of a number of smaller subunits?

A

Oligomers

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22
Q

What is the difference between homodimers and heterodimers?

A

Homodimer: simplest, contains identical protein subunits

Heterodimer: contains subunits from different gene products

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23
Q

How does quaternary structure of proteins increase functionality?

A
  1. Provide structural properties not present in individual subunits
  2. Provide a mechanism for regulation of protein function through conformational change
  3. Bring linked functional components into close proximity
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24
Q

What are the two multi-subunit complexes of proteins?

A
  1. Fibrous

2. Globular

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25
Q

What is the difference between fibrous and globular proteins?

A

Fibrous: provide mechanical support and flexibility in tissues. Less water soluble than globular proteins.
Globular: backbones folds on itself to produce a more or less spherical shape. Soluble in water and salt solutions.

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26
Q

What is the purpose for chaperone proteins?

A
  1. Help newly synthesized proteins fold properly
  2. Rescue misfiled proteins
  3. Disrupt protein aggregates
27
Q

What are the 5 functional classes of proteins?

A
  1. Structural
  2. Transport
  3. Metabolic
  4. Genomic caretaker
  5. Cell signaling
28
Q

What is the importance for enzymes?

A

Catalyze and speed up biochemical reactions without being consumed

29
Q

What are co-factors for?

A

Assists catalysts when amino acid side chains aren’t enough

30
Q

What are examples of cofactors?

A

K+: pyruvate kinase

Mg2+: Hexokinase, G6P, Pyruvate kinase

31
Q

What is an enzyme without a cofactor called?

A

Apoenzyme

32
Q

What is a completely catalyzes enzyme called?

A

Holoenzyme

33
Q

What is a prosthetic group?

A

Coenzyme/factor bound tightly or covalently to the enzyme

34
Q

What is a coenzyme?

A

Complex organic or metalloorganic molecules that act as transient carriers of specific functional groups
Derived from vitamins and not covalently bound to enzymes

35
Q

What is the typical enzyme nomenclature?

A

Substrate + reaction performed + -ase

36
Q

What are the classes of enzymes?

A
  1. Oxidoreductase
  2. Transferases
  3. Hydrolases
  4. Lysases
  5. Isomerases
  6. Ligases
37
Q

How do enzymes work?

A

Speed up reactions by acting as a catalyst and increase the rate of chemical reactions

38
Q

What happens at an enzyme’s active site?

A

Substrates and cofactors bind

39
Q

What are catalytic groups?

A

Amino acid residues lined in the active site that help make or break bonds

40
Q

What is enzyme specificity?

A

When active sites have the ability to discriminate among possible substrate molecules

41
Q

What are the features of an active site?

A
  1. 3-D cleft or crevice containing polar residues for stabilization
  2. Takes a small portion of enzyme
  3. Specificity of binding
  4. Microenvironement
  5. Substrate binds by weak interactions
42
Q

What is an induced-fit model?

A

Enzymes undergo conformational change upon binding to substrate

43
Q

Describe the active site of lyase

A
  1. Binding of the substrate induces a conformational change in the enzyme
  2. Residues within the active sites reposition increasing the number of binding interactions
  3. Repositioning causes a strain between bonds A and B
  4. Strain facilitates cleavage of bond
44
Q

Why are enzymes considered catalysts?

A

Alters the rates of reaction without changing the ratio of substrate and products at equilibrium

45
Q

What is the condition where the substrate is strained and unstable?

A

Transition state

46
Q

What is the difference between the energy of the substrate and the trasition state complex (ES)?

A

Activation energy

47
Q

Describe E + S → ES → EP → E + P

A
  1. Enzyme binds to substrate to ES
  2. Substrate reaches the transition state and bonds are rearranged
  3. Product releases
  4. Enzyme resets
48
Q

What is a spontaneous reaction where delta G is negative?

A

Exergonic

49
Q

What is a reaction where delta G is positive?

A

Endergonic

50
Q

What is the relationship between the reaction rate and the concentration of the reactants called?

A

Rate law

51
Q

What is k?

A

Proportionality constant relating the concentration of substrate to the rate of the reaction

52
Q

What is zero order?

A

Rate of reaction is independent of the concentration of the reactants k[S]^0

When [S] is so high that the enzyme is completely saturated

53
Q

What is 1st order?

A

Rate of the reaction is directly proportional to the concentration of reactants k[S]^1

The rate doubles, when [S] doubles


54
Q

What is 2nd order?

A

Reaction depends on the either the square of the concentration of the reactant or the product of the concentration of the two reactants k[S]^2

Rate quadruples when [S] doubles

55
Q

Why doesn’t enzymes affect reaction equilibrium?

A

The reaction reaches equilibrium more quickly and same amount of product is produced

56
Q

What catalysis occurs where molecules other than water acts as a proton donor and acceptor?

A

Acid-Base Catalysis

57
Q

What catalysis where active site contains a reactive group forms a temporary covalent bond?

A

Covalent catalysis

58
Q

What catalysis where ions act as a nucleophile or electrophile or serve as a bridge between E and S?

A

Metal-ion catalysis

59
Q

What AA’s are involved with catalysis?

A
  1. All polar amino acids

2. Ser, Cys, Lys, and His

60
Q

Why does chymotrypsin possess a highly reactive serine residue?

A

Serine proteases covalently catalysis

It would cleave peptide bonds on the carboxyl terminal of the large hydrophobic aromatic AAs

Uses a Ser residue to carry out a nucleophillic attack of the carbonyl carbon of the substrate

61
Q

What amino acids are involved in a triad?

A

Asp, His, and Ser

62
Q

What is the importance of serine proteases?

A
  1. Abound and many are drug targets
  2. Thrombin is an important enzyme for blood clots
  3. Many anticoagulants aim to inhibit the serine protease, thrombin
63
Q

What are the conditions for proper enzyme function?

A
  1. 37C, higher temperatures will denature proteins
  2. Reaction rates of enzyme increases as pH moves from acidic to physiologic range
  3. Functional groups in active sites are ionized, and more H-bonds are formed
  4. Affected by salt concentration, substrate concentration, and inhibitors

Biochemistry (16 decks)

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