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BIOCHEM 1 > 3 - AMINO ACIDS AND PEPTIDES > Flashcards

3 - AMINO ACIDS AND PEPTIDES Flashcards

1
Q

the -NH2 functional group

A

amino group

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2
Q

the -COOH functional group that dissociates to give the carboxylate anion, -COO-, and a hydrogen ion

A

Carboxyl group

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3
Q

the portion of an amino acid that determines its identity

A

side chain group

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4
Q

the branch of chemistry that deals with the three-dimensional shape of molecules

A

Stereochemistry

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5
Q

refers to an object that is not superimposable on its mirror image

A

Chiral

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6
Q

are organic molecules that serve as the building blocks of proteins which are crucial for various biological functions in the body

A

Amino acids

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7
Q

a compound that contains both an amino group and a carboxyl group

A

Amino acids

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8
Q

R gives the identity to amino acid

A
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9
Q

Two stereoisomers of amino acids are designated L- or D-

A
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10
Q

All protein-derived amino acids have at least 1 stereocenter and are chiral, with the exception of glycine

A
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11
Q

Amino acids can be referred to by three letter or one letter codes (KNOW THESE!!!)

A
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12
Q

Group A: NONPOLAR SIDE CHAINS

Mnemonic:
Giant aliens viciously launch intense phasers making plasma targets pop

A

Gly
Ala
Val
Leu
Ile
Pro
Phe
Trp
Met

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13
Q

Group A: NONPOLAR SIDE CHAINS

  1. contain aliphatic hydrocarbon group
  2. has an aliphatic cyclic structure; nitrogen is bonded to 2 carbon atoms (imino acid)
  3. hydrocarbon aromatic ring
  4. indole ring side chain, aromatic
  5. sulfur atom in the side chain
A
  1. Ala, Val, Leu, Ile, Pro
  2. Pro
  3. Phe
  4. Trp
  5. Met
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14
Q

Group B: NEUTRAL POLAR CHAINS

Mnemonic:
Cats see three aspiring geniuses trying science

A

Ser
Thr
Tyr
Cys
Gln
Asn

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15
Q

Group B: NEUTRAL POLAR CHAINS

  1. side chain is polar hydroxyl group
  2. hydroxyl group bonded to aromatic hydrocarbon group
  3. side chain contains thiol group
  4. contain amide bonds in the side chain
A
  1. Ser, Thr
  2. Tyr
  3. Cys
  4. Gln, Ans
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16
Q

Group C: ACIDIC CHAINS

A

Glu
Asp

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17
Q

Group C: ACIDIC CHAINS

  1. both have a carboxyl group in their side chain
  2. can lose a proton, forming a carboxylate ion (glutamate and aspartate)
  3. these amino acids are negatively charged at neutral pH
A

Glu
Asp

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18
Q

Group D: BASIC CHAINS

Mnemonic:
Lemonade always hits

A

Lys
Arg
His

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19
Q

Group D: BASIC CHAINS

  1. side chains are positively charged at pH 7
  2. side chain NH3 group is attached to an aliphatic hydrocarbon chain
  3. side chain is a guanidino group
  4. side chain is an imidazole group
A
  1. Lys
  2. Arg
  3. His
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20
Q

are found only in a few connective tissues such as collagen

A

Hydroxyproline and hydroxylysine

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21
Q

is also an uncommon amino acid found in the thyroid gland

A

Thyroxine

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22
Q

low levels of thyroxine lead to hypothyroidism, characterized by lethargy and obesity

A
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23
Q

Guanidine group:

the side chain of arginine is a considerably stronger base than aliphatic amine basicity of the guanido group is attributed to the large resonance stabilization of the protonated form relative to the neutral form

A
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24
Q

Imidazole group:

the side chain imidazole group of histidine is a heterocyclic aromatic amine

A
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25
Q

refers to an object that is superimposable on its mirror image `

A

Achiral

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26
Q

laevus = left
dexter = right

A
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27
Q

molecules that differ from each other only in their configuration (3D shape); optical isomers

A

Stereoisomers

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28
Q

amino acids whose stereochemistry is the same as the stereochemical standards L- and D-glyceraldehyde

A
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29
Q

portions of monomers units included in polymers after splitting out water between the linked monomers

A

Residues

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30
Q

an amide bond between amino acids in a protein

A

Peptide bond

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31
Q

molecules formed by linking two to several dozen amino acids by amide bonds

A

Peptides

32
Q

the backbone of a protein; it is formed by linking amino acids by peptide (amide) bonds

A

Polypeptide chain

33
Q

structural formulas that differ from each other only in the position of electrons

A

Resonance structures

34
Q

Geometry of peptide bond:

the four atoms of a peptide bond and the two carbons joined to it lie in a plane with bond angles of 120 degrees about C and N

A
35
Q

refers to the arrangement of the atoms around the peptide bond; more stable due to less steric hindrance compared to the cis configuration, where the oxygen and hydrogen would be on the same side, leading to crowding and destabilization

A

S-trans

36
Q

a terminal carbon atom is referred to as the w-carbon, from the name of the last letter of the Greek alphabet.

A
37
Q

refers to the absence of a benzene ring

A

Aliphatic

38
Q

The hydroxyl group in tyrosine is bonded to an aromatic hydrocarbon group, which eventually loses a proton at higher pH. (The hydroxyl group in tyrosine is a phenol, which is a stronger acid than an aliphatic alcohol. As a result, the side chain of tyrosine can lose a proton in a titration, whereas those of serine and threonine would require such a high pH that pKa values are not normally listed for these side chains.)

A
39
Q

They are derived from the common amino
acids and are produced by modification of the parent amino acid after the protein is synthesized by the organism in a process called?

A

Posttranslational modification

40
Q

Hydroxyproline and hydroxylysine differ from the parent amino acids in that they have hydroxyl groups on their side chains; they are found only in a few connective-tissue proteins, such as collagen

A
41
Q

differs from tyrosine in that it has an extra iodine-containing aromatic group on the side chain; it is produced only in the thyroid gland, formed by posttranslational modification of tyrosine residues in the protein thyroglobulin

released as a hormone by proteolysis of thyroglobulin

A

Thyroxine

42
Q

has equal positive and negative charges; in solution, it is electrically neutral.

A

Zwitterion

43
Q

What happens when we titrate an amino acid?

A

When an amino acid is titrated, its titration curve indicates the reaction of each functional group with hydrogen ion.

44
Q

The pKa values of a-carboxyl groups are fairly low, around 2.

The pKa values of amino groups are much higher, with values ranging from 9 to 10.5.

The pKa values of side-chain groups, including side-chain carboxyl and amino groups, depend on the groups’ chemical nature.

A
45
Q

Histidine, lysine, and arginine are considered basic amino acids because each of their side chains has a nitrogen-containing group that can exist in either a protonated or deprotonated form. However, histidine has a pKa in the acidic range.

A
46
Q

Aspartic acid and glutamic acid are considered acidic because each has a carboxylic acid side chain with a low pKa value. These groups can still be titrated after the amino acid is incorporated into a peptide or protein, but the pKa of the titratable group on the side chain is not necessarily the same in a protein as it is in a free amino acid.

A
47
Q

a method for separating molecules on the basis of the ratio of charge

extremely useful in determining the important properties of proteins and nucleic acids

A

Electrophoresis

48
Q

the pH at which a molecule has no net charge; isoelectric point

A

Isoelectric pH (pI)

49
Q

At the isoelectric point (pH where the molecule has no net charge), pKa1 corresponds to the functional group that has dissociated. If two groups are dissociated, pKa1 is the higher value. pKa2 applies to the group that hasn’t dissociated, and if two groups remain undissociated, the lower pKa is used.

A
50
Q

Which of the following amino acids has a net charge of +2 at low pH? Which has a net charge of -2 at high pH? Aspartic acid, alanine, arginine, glutamic acid, leucine, lysine

A

Arginine and lysine have net charges of +2 at low pH because of their basic side
chains; aspartic acid and glutamic acid have net charges of -2 at high pH because
of their carboxylic acid side chains.

Alanine and leucine do not fall into either category because they do not have titratable side chain. (both nonpolar)

51
Q

practice on how to make peptide bonds idiot

A
52
Q

Individual amino acids can be linked by forming covalent bonds. The bond is formed between the a-carboxyl group of one amino acid and the a-amino group of the next one. Water is eliminated in the process, and the linked amino acid residues remain after water is eliminated.

A
53
Q

Another name for a compound formed by the reaction between an amino group and a carboxyl group is an?

A

Amide

54
Q

The carbon–nitrogen bond formed when two amino acids are linked in a
peptide bond is usually written as a single bond, with one pair of electrons
shared between the two atoms.

A
55
Q

No single resonance structure actually represents the bonding in the compound; instead all resonance structures contribute to the bonding situation

A
56
Q

The peptide bond is also stronger than an ordinary single bond because of this resonance stabilization.

A
57
Q

However, proteins and peptides also play key roles as hormones, alongside other compounds like steroids. Steroids are often associated with sports doping scandals, but peptide hormones are also significant. Two well-known peptide hormones, oxytocin and vasopressin, have cyclic structures formed by disulfide bonds. Both peptides consist of nine amino acids, an amide group at the C-terminal end, and a disulfide bond between cysteine residues at positions 1 and 6. Their primary difference lies in the specific amino acids at positions 3 and 8, which gives each peptide its distinct physiological role.

A
58
Q

Basicity:

alpha-NH3+ groups: the average value of pKa for an alpha-NH3+ group is 9.47, compared with a value of 10.76 for a secondary alkylammonium ion

A
59
Q

Guanidine group:

The side chain of arginine is a considerably stronger base than an aliphatic amine basicity than an aliphatic amine basicity of the guanido group is attributed to the large resonance stabilization of the protonated form relative to the neutral form.

A
60
Q

Imidazole group (5-membered ring with 2 nitrogen)

The side chain imidazole group of histidine is a heterocyclic aromatic amine.

A
61
Q

Acidity: alpha-COOH groups

The average pKa of an alpha-carboxyl group is 2.19, which makes them considerably stronger acids than acetic acid (pKa= 4.76)

The greater acidity of the amino acid carboxyl group is due to the electron withdrawing inductive effect of the -NH3+ group

A
62
Q

pKa is inversely related to acidity

Lower pKa = stronger acid

Higher pKa = weaker acid

A
63
Q

Predicting the net charge of an amino acid at a given pH is on your notes idiot

A
64
Q

pH > pKa

pH < pKa

A

group will be deprotonated

group will be protonated

65
Q

Amino group:

Protonated (-NH3+)

Deprotonated (-NH2)

A

when pH < pKa (~+1 charge)

when pH > pKa (~0 charge)

66
Q

Carboxyl group:

Protonated (-COOH)

A

when pH < pKa (-1 charge)

67
Q

pH < pI

A

amino acid will have a net positive charge

68
Q

pH = pI

A

amino acid will have no net charge (zwitterion)

69
Q

pH > pI

A

amino acid will have a net negative charge

70
Q

direction of the peptide chain that is significant in the content of the protein structure

A

Polarity

71
Q

N-Terminus to C-Terminus Orientation:

Peptide chains have a defined direction, starting from the N-terminus (the end with a free amino group, -NH2) and ending at the C-terminus (the end with a free carboxyl group, -COOH)

A
72
Q

are prime examples of biologically active peptides

are both nonapeptides (composed of nine amino acid) and differ by only two amino acids

are naturally produced in the body, primarily in the hypothalamus, which is found at the base of the brain above the pituitary gland, near the center of the skull

their release is triggered by various physiological and psychological factors; can be stimulated , and by taking supplements can also be considered

A

Oxytocin and Vasopressin

73
Q

Oxytocin:
Pain modulation: with analgesic properties, thereby reducing the perception of pain

Anxiety reduction: has the ability to reduce anxiety and promote relaxation

Wound healing: oxytocin has been shown to promote wound healing by enhancing tissues repair processes and relevant after surgical procedures

A
74
Q

Vasopressin:

Salivary gland function: influences the regulation of water balance and has been implicated in modulating salivary gland function; proper salivary flow is essential for oral health, aiding in the the prevention of dental caries and leading to overall oral cavity health

Hemeostasis: vasopressin’s vasoconstrictive properties can help in controlling bleeding during surgical procedures

Stress response: a key player in the body’s stress response, has the potential to manage stress

A
75
Q

Natural triggers of Oxytocin:

Physical touch
Social bonding
Stress reduction

A
76
Q

Natural triggers of Vasopressin:

Dehydration: when body is dehydrated (blood osmolality increases), vasopressin is released to conserve water by reducing urine output

Low blood pressure: a drop in blood pressure can trigger vasopressin release, which constricts blood vessels and raises blood pressure

Physical exercise: intense physical exercise can stimulate the release of vasopressin, which helps manage the body’s fluid balance

Stress

A

BIOCHEM 1 (11 decks)

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