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Biochemistry & Molecular Biology > 3. Amino Acids: 20 Building Blocks of Life > Flashcards

3. Amino Acids: 20 Building Blocks of Life Flashcards

1
Q

What are the 2 most abundant molecules in all living things?

A
  1. Water
  2. Proteins
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2
Q

What is the most diverse class of biological molecules?

A
  1. Proteins
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3
Q

What percentage of our body weight is protein?

A
  1. About 17%
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4
Q

How many kinds of amino acids are there in the human body?

A
  1. 20
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5
Q

What cells need amino acids?

A
  1. All cells
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6
Q

What is the core structure of all amino acids?

A
  1. A central Carbon
  2. An amino group with NH2
  3. An acid group with COOH
  4. A lone Hydrogen opposite the amino group
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7
Q

What is an Alpha Carbon?

A
  1. The central carbon of an amino acid
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8
Q

What is an Alpha Amino Group?

A
  1. The amino group connected to the alpha carbon in an amino acid
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9
Q

What is an alpha carboxyl group?

A
  1. The carboxyl group connected to the alpha carbon in an amino acid
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10
Q

What is an R group?

A
  1. The fourth group that varies in structure in an amino acid
  2. It is the only part of an amino acid that varies in structure from one to another
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11
Q

When are R groups aliphatic?

A
  1. When they contain only Carbons and Hydrogens, which have nearly identical electonegativities, making them nonpolar and hydrophobic
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12
Q

What percentage of amino acids are nonpolar and hydrophobic?

A
  1. About 50%
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13
Q

What place do hydrophobic amino acids occupy in a folded protein molecule?

A
  1. Inside the folded protein molecule, to avoid the water
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14
Q

How many amino acids exist in nature vs. in our bodies?

A
  1. Over 300 exist in nature
  2. Only 20 are coded for in our DNA
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15
Q

What is a peptide bond?

A
  1. The bond holding proteins together
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16
Q

How do peptide bonds form?

A
  1. By joining the carboxyl (COOH) group of one amino acid to the amino group NH2 of the next
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17
Q

What is the only amino acid that cannot exist in 2 mirror image forms?

A
  1. Glycine
  2. It has an H accross from another H, so there’s only one form of Glycine
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18
Q

What are the 2 forms of stereoisomers?

A
  1. L form
  2. D form
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19
Q

What is a Chiral molecule?

A
  1. A molecule with handedness, like left or right handed.
  2. They can appear in mirror image form
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20
Q

What is the percentage of D and L forms in an amino acid made apart from cells?

A
  1. 50% each
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21
Q

How are amino acids made inside cells for protein synthesis different in structure from those made without?

A
  1. They are almost entirely made in the L form, not 50/50 like the others
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22
Q

Why are amino acids made inside cells for protein synthesis different in structure from those made without?

A
  1. Enzymes synthesizing these amino acids have specific 3D structures that arrange reactants such that only one form can be made
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23
Q

How can you tell if a mixture of molecules was made by an enzyme or by nonbiological chemistry

A
  1. By analyzing its chirality
  2. If nonenzyme chemistry produced the molecules, they’ll have equal amounts of D and L forms
  3. Molecules made by enzymes will have one or the other.
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24
Q

What are the 5 Hydrophobic Amino Acids found in the body?

A
  1. Glycine
  2. Alanine
  3. Valine
  4. Leucine
  5. Isoleucine
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25
Q

How does the Hydrophobicity change among Amino Acid R Groups?

A
  1. They increase steadily from glycine to isoleucine as they increase in size and complexity
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26
Q

What is the simplest Amino Acid?

A
  1. Glycine, with only one Hydrogen as an R group
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27
Q

What is the most abundant protein in the human body?

A
  1. Collagen
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28
Q

What role does Glycine have in the nervous system?

A
  1. It acts as a signalling molecule for transmitting nerve signals in the spinal cord, brainstem, and retina.
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29
Q

What is the second simplest amino acid?

A
  1. Alanine
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30
Q

What is in Alanine’s R Group?

A
  1. A CH3 Methyl group
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31
Q

In which form is Alanine usually found in cells?

A
  1. D form
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32
Q

What benefit does D-alanine provide for bacteria?

A
  1. It is found in the cell wall of bacteria, where it is linked to other amino acids to form the supports for the cell wall
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33
Q

What 3 Amino Acids are known as the Branch Chain Amino Acids? (BCAA’s)

A
  1. Valine
  2. Leucine
  3. Isoleucine
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34
Q

Where do BCAA’s get their name?

A
  1. They contain R groups with longer chains of Carbon and Hydrogens
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35
Q

Why are BCAA’s more hydrophobic than other amino acids?

A
  1. Hydrophobic properties are somewhat additive in nature, so the more Carbons and Hydrogens they have, the more hydrophobic they are
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36
Q

How can taking BCAA supplements be potentially harmful?

A
  1. BCAA’s are present in higher levels with people who have insulin resistance like in Type 2 Diabetes
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37
Q

What 2 amino acids sometimes get grouped in with BCAA’s because they share some properties?

A
  1. Proline
  2. Methionine
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38
Q

In what ways is Proline different from Valine?

A
  1. Instead of making a V, it’s R Group loops around from the alpha Carbon to bond to the alpha amino group
39
Q

How is Proline unique among all Amino Acids?

A
  1. It is the only amino acid with a ring structure cause by its R group bonding with it’s alpha amino group, instead of its alpha carbon
40
Q

How is Methionine unique among amino acids?

A
  1. It is one of the 2 amino acids that contain sulfur
41
Q

Why does Methionine contain sulfur?

A
  1. Sulfur shares a similar electronegativity with carbon, resulting in a fairly even sharing of electrons
  2. The sulfer bonded to 2 carbons is nonpolar and therefore hydrophobic
42
Q

Why is Methionine so important?

A
  1. The cellular machinery for making proteins uses it as the first amino acid for making almost every protein on earth
43
Q

What is an aromatic amino acid?

A
  1. A subgroup of hydrophobic amino acids named for the large and quite stable aromatic ring structures on their side chains
44
Q

What does the R group of Phenylalanine contain?

A
  1. A phenyl ring of 6 carbons attached to an alanine
45
Q

Is Phenylalanine Hydrophobic, Hydrophilic, or ambiphilic?

A
  1. Hydrophobic
46
Q

What happens when an OH Hydroxyl is attached to the far side of the phenyl ring of phenylalanine?

A
  1. It becomes Tyrosine, a hydroxyl-containing version of phenylalanine
47
Q

How does Tyrosine differ in behavior from a traditional Phenylalanine?

A
  1. It contains some properties of hydrophilic amino acids, but its ring makes it also hydrophobic
48
Q

What is the largest hydrophobic amino acid?

A
  1. Triptophan
49
Q

What is the structure of Triptophan’s R Group?

A
  1. 9 Carbons and 1 Nitrogen in a structure called an indole ring
50
Q

What important functions does Triptophan have?

A
  1. It is a starting point for the synthesis of many important biomolecules, like the vitamin niacin and the plant hormones known as auxins.
  2. It is a component of the neurotransmitter serotonin, which converts into the sleep-related hormone melatonin
51
Q

Is triptophan why we get sleepy after eating Turkey at Thanksgiving?

A
  1. No, this is a myth.
52
Q

What two amino acids contain sulfur?

A
  1. Methionine
  2. Cysteine
53
Q

What is the first polar amino acid?

A
  1. Cyseine
54
Q

In what form is Cysteine’s sulfur found?

A
  1. In the form of an SH group, known as sulfhydryl
55
Q

Why is Cysteine’s SH group reactive?

A
  1. Because the H+ proton can readily be lost near physiological pH of 7.4, and loss of a proton leaves the side chain with an S that is negatively charged.
  2. The electrons in the sulfurs are lost in the reaction that creates a disulfide bond between them
56
Q

Is it common for a protein to have multiple cysteines?

A

Yes

57
Q

What 3 Amino Acids have an OH group?

A
  1. Serine
  2. Threonine
  3. Tyrosine
58
Q

How are the OH groups in Serine, Threonine, and Tyrosine different than the SH group of Cysteine?

A
  1. The Hydrogen on the OH doesn’t come off readily at physiological pH
59
Q

How are the OH groups in Serine, Threonine, and Tyrosine different than the COOH carboxyl groups of other amino acids?

A
  1. The R groups of these three will not normally form ions, but will stay together, remain uncharged, and hydrogen bond easily with water
  2. This makes them water friendly
60
Q

What is the simplest of the water friendly Amino Acids?

A

Serine

61
Q

How is the R Group of Serine composed?

A
  1. A single carbon plus an OH at the end
62
Q

What role does D-serine play?

A
  1. It serves as a signalling molecule in the brain
63
Q

What role does L-serine play?

A
  1. It plays an important role in the synthesis of numerous cellular molecules, including proteins, membrane components, and nucleotides for making RNA and DNA
64
Q

What is the largest hydroxyl-containing amino acid?

A

Tyrosine

65
Q

What role does Tyrosine play?

A
  1. It serves as the starting point for the synthesis of many biologically important molecules, including
    - melanin pigments that color hair, skin, and eyes
    - Thyroid hormones
    - Adrenaline
    - The nerve signaling molecule dopamine
66
Q

What are kinases?

A
  1. Enzymes that catalyze the replacement of the hydrogen on hydroxyl groups with a phosphate
67
Q

Why are kinases important?

A
  1. They are hugely important for protein regulation
68
Q

What is Phosphorylation?

A
  1. The transfer of phosphate molecules to a protein
69
Q

What purpose does phosphorylation have?

A
  1. It acts as a switch by toggling between the phosphorylated and unphosphorylated state to determine whether a protein is active or not
70
Q

What are the most common targets for phosphorylation?

A
  1. The hydroxyls of serine and threonine
71
Q

What role does Tyrosine phosphorylation play?

A
  1. Signal relaying within cells
72
Q

What 2 amino acids are acidic at physiological pH?

A
  1. Aspartate
  2. Glutamate
73
Q

What 3 amino acids are basic at physiological pH?

A
  1. Lysine
  2. Arginine
  3. Histidine
74
Q

What is Glutamate most commonly known for?

A
  1. Affecting how we taste
  2. It is reponsible for the savory, or umami, taste of some cheeses and soy sauce
75
Q

How does glutamate affect our taste?

A
  1. Our tongues have receptors that are sensitive to free glutamate
76
Q

What is Monosodium Glutamate?

A
  1. MSG
  2. It is the sodium salt of glutamate and is often used for enhancing the savory favor
77
Q

What is the pKa value of the R-group carboxyls of acidic amino acids?

A
  1. Around 4, meaning they lose their protons at the physiological pH of 7.4, leaving a negatively charged carboxyl group
78
Q

What is the difference between the R groups of Aspartate and Glutamate?

A
  1. The aspartate chain is smaller
  2. The glutamate side chain has one extra CH2 group
79
Q

Where did Glutamic acid get its name?

A
  1. From being discovered in Gluten, the wheat protein
80
Q

Where did Aspartic acid get its name?

A
  1. It was first obtained from a related amino acid called asparagine, which was found in asparagus
81
Q

What roles do the 2 acidic amino acids have in the body?

A
  1. They help use protein as an energy source when supplies of sugar run low or when a person goes on a low-carbohydrate diet
  2. In cells, they are important in managing ammonia (NH3), a toxic by-product of metabolism
82
Q

What is unique about Lysine’s R group?

A
  1. It is a long, flexible chain with a single positively charged nitrogen in the amine at the end
83
Q

What is unique about Arginine’s R group?

A
  1. It is a long, flexible chain, slightly longer than that of Lysine, with 3 positively charged nitrogens in the amine at the end.
84
Q

What roles does Arginine play in the body?

A
  1. It is a source of urea in the urea cycle
  2. It is a source of a cellular signaling molecule called nitric acid, which stimulates the relaxing of blood vessel walls and improves blood flow
85
Q

What is unique about Histidine’s R group?

A
  1. It’s ring contains 2 nitrogen atoms that share a proton when the pH is sufficiently low, giving the group as a whole a positive charge
  2. It is the basic amino acid with the lowest pKa, at 6, meaning at a physiological pH of 7.4, the proton is gone.
  3. Because it loses a proton, its ring is mostly uncharged.
  4. Reductions in pH can drastically increase the percentage of histadine rings with the proton on
86
Q

In what parts of the body is Histadine valuable?

A
  1. Many enzymes
  2. In the blood proteins myoglobin and hemoglobin
87
Q

What is the US Recommended Daily Allowance for dietary protein?

A
  1. 50 to 60 grams for adults
88
Q

How many amino acids cannot be made by our cells?

A
  1. 9
89
Q

What sources can produce all the amino acids needed for the human body?

A
  1. Plants
  2. Bacteria
90
Q

What is the best way to ensure we get all the amino acids we need?

A
  1. Consume a variety of plants, and the animals that eat them.
91
Q

In what situations do amino acid deficiencies exist?

A
  1. Specific medical conditions
  2. Very restrictive diets
92
Q

How common is amino acid deficiency?

A
  1. Extremely rare
93
Q

What are the 20 amino acids found in the human body?

A
  1. Alanine
  2. Arginine
  3. Asparagine
  4. Aspartic Acid
  5. Cysteine
  6. Glutamine
  7. Glutamic acid
  8. Glycine
  9. Histadine
  10. Isoleucine
  11. Leucine
  12. Lysine
  13. Methionine
  14. Phenylalanine
  15. Proline
  16. Serine
  17. Threonine
  18. Tryptophan
  19. Tyrosin
  20. Valine

Biochemistry & Molecular Biology (4 decks)

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