3 - AMINO ACIDS AND PEPTIDES

Question 1

the -NH2 functional group

Answer 1

amino group

Question 2

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

Answer 2

Carboxyl group

Question 3

the portion of an amino acid that determines its identity

Answer 3

side chain group

Question 4

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

Answer 4

Stereochemistry

Question 5

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

Answer 5

Chiral

Question 6

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

Answer 6

Amino acids

Question 7

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

Answer 7

Amino acids

Question 8

R gives the identity to amino acid

Question 9

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

Question 10

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

Question 11

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

Question 12

Group A: NONPOLAR SIDE CHAINS

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

Answer 12

Gly
Ala
Val
Leu
Ile
Pro
Phe
Trp
Met

Question 13

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

Answer 13

1. Ala, Val, Leu, Ile, Pro
2. Pro
3. Phe
4. Trp
5. Met

Question 14

Group B: NEUTRAL POLAR CHAINS

Mnemonic:
Cats see three aspiring geniuses trying science

Answer 14

Ser
Thr
Tyr
Cys
Gln
Asn

Question 15

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

Answer 15

1. Ser, Thr
2. Tyr
3. Cys
4. Gln, Ans

Question 16

Group C: ACIDIC CHAINS

Answer 16

Glu
Asp

Question 17

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

Answer 17

Glu
Asp

Question 18

Group D: BASIC CHAINS

Mnemonic:
Lemonade always hits

Answer 18

Lys
Arg
His

Question 19

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

Answer 19

2. Lys
3. Arg
4. His

Question 20

are found only in a few connective tissues such as collagen

Answer 20

Hydroxyproline and hydroxylysine

Question 21

is also an uncommon amino acid found in the thyroid gland

Answer 21

Thyroxine

Question 22

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

Question 23

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

Question 24

Imidazole group:

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

Question 25

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

Answer 25

Achiral

Question 26

laevus = left dexter = right

Question 27

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

Answer 27

Stereoisomers

Question 28

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

Question 29

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

Answer 29

Residues

Question 30

an amide bond between amino acids in a protein

Answer 30

Peptide bond

Question 31

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

Answer 31

Peptides

Question 32

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

Answer 32

Polypeptide chain

Question 33

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

Answer 33

Resonance structures

Question 34

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

Question 35

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

Answer 35

S-trans

Question 36

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

Question 37

refers to the absence of a benzene ring

Answer 37

Aliphatic

Question 38

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.)

Question 39

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?

Answer 39

Posttranslational modification

Question 40

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

Question 41

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

Answer 41

Thyroxine

Question 42

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

Answer 42

Zwitterion

Question 43

What happens when we titrate an amino acid?

Answer 43

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

Question 44

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.

Question 45

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.

Question 46

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.

Question 47

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

Answer 47

Electrophoresis

Question 48

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

Answer 48

Isoelectric pH (pI)

Question 49

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.

Question 50

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

Answer 50

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)

Question 51

practice on how to make peptide bonds idiot

Question 52

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.

Question 53

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

Answer 53

Amide

Question 54

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.

Question 55

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

Question 56

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

Question 57

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.

Question 58

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

Question 59

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.

Question 60

Imidazole group (5-membered ring with 2 nitrogen) The side chain imidazole group of histidine is a heterocyclic aromatic amine.

Question 61

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

Question 62

pKa is inversely related to acidity Lower pKa = stronger acid Higher pKa = weaker acid

Question 63

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

Question 64

pH > pKa pH < pKa

Answer 64

group will be deprotonated group will be protonated

Question 65

Amino group: Protonated (-NH3+) Deprotonated (-NH2)

Answer 65

when pH < pKa (~+1 charge) when pH > pKa (~0 charge)

Question 66

Carboxyl group: Protonated (-COOH)

Answer 66

when pH < pKa (-1 charge)

Question 67

pH < pI

Answer 67

amino acid will have a net positive charge

Question 68

pH = pI

Answer 68

amino acid will have no net charge (zwitterion)

Question 69

pH > pI

Answer 69

amino acid will have a net negative charge

Question 70

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

Answer 70

Polarity

Question 71

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)

Question 72

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

Answer 72

Oxytocin and Vasopressin

Question 73

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

Question 74

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

Question 75

Natural triggers of Oxytocin: Physical touch Social bonding Stress reduction

Question 76

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