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MCAT Biochemistry > Amino Acids and Enzymes > Flashcards

Amino Acids and Enzymes Flashcards

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MCAT flashcards
1
Q

Amino Acids

A

Building blocks of proteins
Contain side groups with varying physical and chemical properties

Multitude of functions of protein formed by the different properties amino acids have due to their side groups

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2
Q

Polypeptide

A

Chain of amino acids linked together by peptide bonds; a protein
Primary, Secondary, Tertiary and sometimes Quaternary structure

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3
Q

Amide

A

Amine connected to a carbonyl Carbon

Amine formed by peptide bonds between two amino acids

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4
Q

Hydrolysis of a Peptide Bond

A

Peptide reacts with water (and usually an enzyme) to form two separate amino acid chains

Separates the peptide bond on a peptide

Reverse reaction is dehydration reaction of amino acid chains

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5
Q

What are some factors in causing the partial double bond character of the peptide bond?

A
  • Nitrogen is most stable with four bonds
  • Oxygen attracts electron density (partial negative charge of O in carboxylic acid on amino acid)
    These two factors mean that electrons delocalize to give the peptide bond a partial double bond character (more rigid bond which does not rotate freely)
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6
Q

What are alpha amino acids?

A

20 amino acids in which most proteins in all species are made from

Amine is attached to the carbon in the alpha position to the carbonyl

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7
Q

Essential amino acids

A

Amino acids that cannot be manufactured and must be ingested directly

For humans 9/20 amino acids are essential

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8
Q

Side Chain of Amino Acid

A

AKA R group, attached to alpha Carbon

R group makes amino acid distinct

Divided into four categories based on distinct chemical properties: (1) acidic, (2) basic, (3) polar, and (4) nonpolar

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9
Q

What is Sickle Cell Disease caused by?

A

An acidic glutamate is replaced with a nonpolar valine
- Changes structure of hemoglobin chain and causes it to polymerize, bending the cell into a sickle shape under low oxygen conditions

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10
Q

Chirality of amino acids

A

Alpha carbon of alpha amino acids has four chemically distinct groups attached to it except in the case of Glycine, whose R group is a H

Therefore, 19/20 of alpha amino acids are chiral at alpha C

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11
Q

Nonpolar Amino acids

A

Glycine (Gly, G), Alanine (Ala, A), Valine (Val, V), Leucine (Leu, L), Isoleucine (Ile, I), Phenylalanine (Phe, F), Tryptophan (Trp, W), Methionine (Met, M), Proline (Pro, P)

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12
Q

Polar Amino Acids

A

Serine (Ser, S), Threonine (Thr, T), Cystein (Cys, C), Asparagine (Asn, N), Tyrosine (Tyr, Y), Glutamine (Gln, Q)

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13
Q

Acidic Amino Acids

A

Aspartic acid (Asp, D), Glutamic acid (Glu, E)

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14
Q

Basic Amino Acids

A

Histidine (His, H), Lysine (Lys, K), Arginine (Arg, R)

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15
Q

Primary structure of protein

A

Number and sequence of amino acids in a polypeptide

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16
Q

Secondary structure of protein

A

Single chain of protein forms into distinct shapes such as twisting into an alpha helix or lying along itself in a beta-pleated sheet

Beta-pleated sheet segments can lie in parallel or antiparallel directions
Secondary structure reinforced by H-bonds between carbonyl O of AA and Hydrogen on N group of another

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17
Q

Tertiary structure of protein

A

Large proteins with three-dimensional shape formed by curls and folds of peptide chain

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18
Q

Five forces of Tertiary structure

A

Five forces:

  1. Covalent disulfide bonds btwn 2 cysteine AAs
  2. Electrostatic interactions between acidic and basic chains
  3. H-bond
  4. Van der Waals forces
  5. Hydrophobic/nonpolar side chains aggregating away from water
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19
Q

How does proline shape protein structure

A

Proline has a more rigid structure due to it’s side group bonding with the amine, causing kinks in alpha or beta sheets (turns)

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20
Q

Quaternary structure of a protein

A

Very large proteins have quaternary structure when two or more polypeptide chains bind together

21
Q

Solvation Layer

A

Organized structures that force hydrophobic groups towards center of proteins and hydrophilic groups towards outside

Hydrophobic groups organizing towards the center allows decrease in size of highly ordered solvation layer, increasing entropy of the system

22
Q

Denatured Protein

A

Native conformation of a protein is disrupted, causing a loss of functionality
Caused by a denaturing agent, sometimes removal of the agent will cause spontaneous reformation of the protein’s native conformation

23
Q

Denaturing Agents

A

Urea disrupts H-bonds
Salt or change in pH disrupts Electrostatic bonds
Mercaptoethanol disrupts Disulfide bonds
Organic solvents disrupt Hydrophobic forces
Heat disrupts All forces

24
Q

Two types of proteins

A

Globular: function as enzymes (e.g. pepsin), hormones (e.g. insulin), membrane pumps and channels (e.g. Na+/K+ pump), membrane receptors, intercellular and intracellular transport and storage, osmotic regulators, immune reponse
Structural: Made from long polymers, maintain and add strength to cellular and matrix structure

25
Q

Structural Protein Example

A

Collagen: Structural protein made from unique type of helix

Most abundant protein in the body

Add great strength to the skin, tendons, ligaments, and bone

26
Q

What’s an example of a Globular protein that can be a structural protein under certain conditions?

A

Tubulin can make up eukaryotic flagella and cilia, because can polymerize under right conditions

27
Q

Glycoproteins

A

Proteins with carbohydrates attached
E.g. AB antigens on red blood cells

Generally more than 50% protein

28
Q

Proteoglycans

A

Major component of extracellular matrix

Generally more than 50% carbohydrates

29
Q

Cytochrome

A

Proteins which require a prosthetic heme group in order to function

They usually add color to the cell
E.g. hemoglobin and cytochromes of ETC in inner membrane of mitochondria

30
Q

Conjugated proteins

A

Proteins which require nonproteinaceous components to function

31
Q

Minerals

A

Dissolved inorganic ions inside and outside the cell

Create electrochemical gradients across membranes- assist in transport of substances entering and exiting the cell
Solidify: hydroxyapatite in bone
Cofactors: assisting enzymes

32
Q

Enzyme

A

Globular protein or nucleic acid that acts as a catalyst for a chemical reaction, in other words by lowering the activation energy, thus increasing the rate of the reaction
Increase reaction rate by 1000-1 trillion times initial rate
Regulatory role: Cause necessary chemical reactions to occur and prevent unnecessary ones

33
Q

How does an enzyme effect quantity of products and reactants at equilibirum

A

Enzyme does not alter this quantity and does not change the Gibbs Free Energy change of a reaction

34
Q

Substrate

A

Reactant(s) upon which an enzyme works. Generally smaller than the enzyme

Substrate binds to enzyme at active site, forming enzyme-substrate complex

35
Q

Enzyme specificity

A

Enzymes are designed to work on a specific group of substrate or substrates

Lock-and-key model: example of substrate locking into active site on enzyme and enzyme active site only fits specific substrate

36
Q

Induced Fit Model

A

Model of enzyme-substrate complex in which after binding of the substrate, the enzyme and the substrate change shape to tighten the bond and increase the specificity. This can destabilize the substrate and allow reaction to proceed faster.

37
Q

Saturation Kinetics

A

As concentration of substrate increases, relative rate of reaction increases until maximal rate (V_max) is reached

Substrates must eventually wait in line for a free enzyme to be ready to convert the substrate to the product
V_max is proportional to enzyme concentration

38
Q

Turnover Number (k_cat)

A

Number of substrates that can be converted to products in a given unit of time given the concentration of substrate is saturated

Rough measure of catalytic efficiency of an enzyme
K_cat = V_max / [E]_t where [E] is conc of enzyme at time t

39
Q

Michaelis Constant (K_m)

A

Substrate concentration in which rate of reaction is equal to 1/2 V_max

Indicates how highly concentrated the substrate must be to speed up the reaction
Inversely proportional to enzyme-substrate affinity
Is not affected by enzyme concentration

40
Q

Michaelis-Menten curves

A

Plot reaction velocity as a function of substrate concentration

Show enzyme’s V_max and K_m

41
Q

Explain Glucokinase and hexokinase in terms of K_m and glucose concentrations

A

Glucokinase and hexokinase phosphorylate glucose, converting it to glucose-6-phosphate, however Glucokinase has a higher K_m and requires higher concentrations of glucose to start working. Glucokinase is in the liver and only responds once glucose is very high to convert glucose to glycogen and fatty acids, while other cells can phosphorylate glucose at lower conc.

42
Q

What is the effect of temperature and pH on reaction rate of an enzyme?

A

As temperature and pH increase, enzyme reaction rate increases until denaturing begins and then the rate drops off

43
Q

Cofactor

A

Many enzymes require a non-protein cofactor to reach optimal activity
Coenzymes or Metal Ions

44
Q

Coenzymes

A

Organic molecules that are cofactors
- Need to be present in excess quantities to catalyze reaction
- Water-soluble vitamins
Two types: Cosubstrates and Prosthetic groups

45
Q

Cosubstrates

A

A Coenzyme that reversibly binds to a specific enzyme, and transfers some chemical group to another substrate

- reverts to original form via another enzymatic reaction
- ATP is an example

46
Q

Prosthetic Groups

A

Remain covalently bound to enzyme throughout the reaction

- emerge from reaction unchanged
- e.g. heme which binds with catalase in peroxisomes to degrade hydrogen peroxide

47
Q

Metal Ions

A

Second type of cofactor; inorganic small molecules required for some enzyme activities

  • Can act alone or with a prosthetic group
  • present in stoichiometric amounts, not consumed in the processes
  • e.g. iron, copper, manganese, magnesium, calcium, zinc
48
Q

What is an enzyme without its cofactor called?

A

Apoenzyme

49
Q

What is an enzyme with its cofactor called?

A

Holoenzyme

MCAT Biochemistry (11 decks)

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