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Biochemistry > Amino Acids and Proteins (exam 2 start) > Flashcards

Amino Acids and Proteins (exam 2 start) Flashcards

1
Q

What is a codon?

A
  • base triplets that correspond to a specific amino acid in mRNA
  • allows 4^3 or 64 diff combos
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2
Q

What direction do codons go in?

A
  • 5’->3’
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3
Q

What are the stop signals to end translation?

A
  1. UAA
  2. UAG
  3. UGA
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4
Q

What is the start/Met signal for translation?

A
  1. AUG
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5
Q

Triplet Code

A
  • three bases specify an amino acid
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6
Q

Degenerate

A
  • multiple codons can specify a single amino acid.
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7
Q

Specific/Unambiguous

A
  • each codon specifies only one amino acid.
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8
Q

Non-Overlapping

A
  • once a start codon is recognized, there is only one correct “reading frame” of triplets.
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9
Q

No Punctuation

A
  • once initiated, bases are “read” continuously (without pausing) until a stop codon is reached.
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10
Q

Universal

A
  • the translation process and codingin all species (investigated) is always the same.
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11
Q

How many standard amino acids are there?

A
  • 20
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12
Q

What is the standard structure of each amino acid?

A
  • has an amino and carboxyl group joined by a -CH- group the (a carbon)
  • the R group is the unique feature to each amino acid
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13
Q

Stereoisomers

A
  • Molecules that have the same structural formulas and bonding patterns, but with a different arrangement of atoms or groups in space.
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14
Q

Enantiomers

A
  • Stereoisomers that are “mirror images” of each other.

- referred to as D(clockwise) and L(ccw) enantiomers/mirror images

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15
Q

Chiral atoms

A
  • When 4 different groups are attached to a carbon atom,

- also called a stereocenter, or an asymmetric carbon

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16
Q

All amino acids except _____ can exist in D and L forms because in each case the a-carbon is asymmetric. It is the sole exception because two of the four groups bonded to the a carbon are both H atoms, thus eliminating asymmetry and making it achiral.

A
  • glycine
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17
Q

How to distinguish D and L isomers?

A
  • if one chiral center R=D and S=L

- nearly all form S formation/L isomer

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18
Q

Amphoteric

A
  • can act as both an acid and a base
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19
Q

What is the zwitterion form on an amino acid and why does it occur?

A
  • when an amino acid is around a neutral pH the a-carboxylic acid group is deprotonated (COO- charge) and the a-amino group is protonated (NH3+ charge)
  • this is the primary form amino acids are written in
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20
Q

Does the zwitterion form have a net charge?

A
  • no it is normally in equal numbers one + and one - charge
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21
Q

What is the isoelectric point?

A
  • the pH when there is no net charge
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22
Q

What does it mean that the a-carbon is “asymmetric”

A
  • there are four different groups attatched
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23
Q

What is classification of amino acids primarily based on?

A
  • R group properties
  • Potential interactions with water**
  • Presence / absence of dissociable groups
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24
Q

6 main groups of amino acids

A
  1. nonpolar aliphatic amino acids ( 5, GAVLI)
  2. nonpolar amino acids (2, PM)
  3. nonpolar aromatic amino acids (3, FYW)
  4. polar amino acids (5, SCTNQ)
  5. Positively charged amino acids (3, HKR)
  6. Negatively charged amino acids (2, DE)
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25
Q

Nonpolar Aliphatic amino acids

from left to right R group is more extended and hydrophobic

A
  • glycine, alanine, valine, leucine and isoleucine
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26
Q

Nonpolar aromatic amino acids

A
  • phenylanlanine, tyrosine and tryptophan
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27
Q

Nonpolar amino acids

A
  • proline, methionine
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28
Q

What is the exception in the nonpolar aromatic amino acids that is polar?

A
  • tyrosine
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29
Q

Polar amino acids

A
  • serine, cysteine, threonine, asparagine, glutamine
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30
Q

_______ contain hydrocarbon groups with no charge

A
  • nonpolar amino acids
31
Q

________ have functional groups that can easily interact with water through hydrogen bonding

A
  • Polar amino acids
32
Q

Cysteine oxidation leads to:

A
  • a reversible disulfide bond
33
Q

When does a disulfide bridge form and what is its purpose?

A
  • when two cysteine residues form this bond

- Helps stabilize polypeptides and proteins

34
Q

Which aromatic amino acids account for most of the UV absorbance by proteins in the absorption spectra around 280nm and which is higher.

A
  • tryptophan (red 278nm > tyrosine(blue 274nm)

- absorptivity scale is logarithmic, amino acids absorb weakly in the UV compared to nucleic acids

35
Q

Positively Charged Polar(basic) amino acids

A
  • histidine, lysine and arginine
36
Q

Negatively Charged Polar(acidic) amino acids

A
  • aspartic acid and glutamic acid
37
Q

_________ have side chains with a carboxylate group that ionizes at physiological pH

A
  • Acidic amino acids
38
Q

_________ bear a positive charge at physiological pH

A
  • Basic amino acids
39
Q

Essential amino acids

A
  • Must be obtained in the diet (from foods).
40
Q

Non Essential amino acids

A
  • Can be made by the human body (biosynthesis).
41
Q

Essential Amino acids include:

A
  • “(ILL) (Me)n (Ph)ail (The) (Tryp) of (Valine)”

- isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan and valine

42
Q

What is the function of Post-translational modifications of amino acids?

A
  • modified after being incorporated into a protein
  • may function in signaling pathways, calcium binding, stabilizing structures such as collagen, or play roles in gene expression or suppression
43
Q

Non-standard amino acids

A
  1. y-Carboxyglutamate
  2. 4-hydroxyproline
  3. 5-hydroxylysine
  4. o-phosphoserine
44
Q

y-Carboxyglutamate characteristics

A
  • Found in proteins that bind Ca2+ ions, including pro-thrombin for blood clotting & Osteocalcin in bone
45
Q

4-hydroxyproline characteristics

A
  • Found in plant cell walls and collagen of connective tissues.
46
Q

5-hydroxylysine characteristics

A
  • Also found in collagen of connective tissues.
47
Q

o-phosphoserine characteristics

A
  • Phosphorylated derivative of –OH containing AA’s

- involved in signaling & gene expression.

48
Q

Are non standard amino acids found in nonprotein amino acids or protein amino acids?

A
  • nonprotein amino acids
49
Q

Non standard amino acid Neurotransmitters

A
  1. GABA
  2. Serotonin
  3. Glycine
50
Q

Function of GABA, or gamma-aminobutyric acid

A
  • inhibitory NT of the brain, involved in muscle relaxation, sleep, diminished emotional reaction and sedation.
51
Q

Function of Serotonin

A
  • NT of the brain; modulates mood, appetite, sexual activity, aggression, body temperature, sleep, smooth muscle constriction.
52
Q

Function of glycine

A
  • an inhibitory neurotransmitter, suppresses neural transmission.
53
Q

How does Strychnine affect glycine

A
  • counteracts role of glycine, causing hyperstimulation, convulsions, death due to “exhaustion”.
54
Q

Non standard amino acid Hormones

A
  1. melatonin
  2. Thyroxine
  3. Indole-3-Acetic Acid (IAA)
55
Q

Function of melatonin

A
  • secreted by the pineal gland during darkness; linked to circadian rhythms and sleep-wake cycles.
56
Q

Function of thyroxine

A
  • secreted by the thyroid; increases rates of chemical reactions and metabolism in almost all cells of the body.
57
Q

Function of Indole-3-Acetic Acid (IAA)

A
  • major plant hormone, stimulates cell growth & elongation, rooting; inhibits axillary bud development.
58
Q

Nonstandard amino acid peptides

A
  1. Glutathione
  2. Vasopressin
  3. Oxytocin
59
Q

Function of glutathione

A
  • is a tripeptide found in most all organisms and is involved in protein and DNA synthesis, toxic substance metabolism, and amino acid transport
60
Q

Function of Vasopressin

A
  • is an antidiuretic hormone that regulates water balance, appetite, and body temperature
61
Q

Function of oxytocin

A
  • is a peptide that aids in uterine contraction and lactation
62
Q

what does the condensation of two amino acids do?

A
  • forms a peptide bond and releases water

- This reaction is not thermodynamically favorable and is coupled to ATP hydrolysis during protein biosynthesis

63
Q

Cricks Wobble hypothesis

A
  • That the first base of an anticodon (5’-3’) can sometimes recognize more than one base on the third position of the codon
64
Q

Base pairing capabilities in wobble pairs

A
  1. G pairs with C or U
  2. C pairs with G
  3. A pairs with U
  4. U pairs with A or G
  5. I pairs with A, U or C
65
Q

How are tRNAs and amino acids paired?

A
  • aminoacyl-tRNA synthetases (aaRS)
66
Q

What are the two steps performed by aminoacyl-tRNA synthetases?

A
  1. Adenylation- first the amino acid which is bound to the aaRS is activated by ATP to form aminoacyl adenylate
  2. Acceptance of tRNA- while still bound to the enzyme, the intermediate reacts with one of the correct tRNAs to form the covalent bond and release AMP
67
Q

What is formed by aminoacyl-tRNA synthetases?

A
  • aminoacyl-tRNAs
68
Q

Three stages of Protein synthesis

A
  1. DNA serves as a template for RNA production
  2. messenger RNA attaches to a ribosome
  3. transfer RNA bonds to a specific codon
69
Q

What subunits can a ribosome be dissociated into?

A
  • a large subunit (50S)

- a small subunit (30S)

70
Q

Large subunit(50S) ribosome components

A
  • contains two rRNA molecules (5S and 23S) and 34 different proteins
71
Q

Small subunit (30S) ribosome components

A
  • contains one rRNA (16S) and 21 proteins
72
Q

Ph and pI values of titrations as OH is added in Glycine, glutamic acid and lysine

A
  1. Neutral pH- 2.3, pI-6, pH- 9.6
  2. Acidic pH-2.2, pI-3.2, pH-4.3 pH-9.7
  3. Basic pH-2.2, pH-9.0 pI-9.7, pH-10.5
73
Q

Titration curve of histidine

pH vs moles -OH added per mole histidine

A
  • pKA= 1.8, pKa=6.0, pI=7.6, pKa=9.2

Biochemistry (15 decks)

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