Brainscape's Knowledge GenomeTM


Top Flashcards (Certified)
All Flashcards

MCAT Amino Acids > Basic Amino Acid Structure > Flashcards

Basic Amino Acid Structure Flashcards

understand basic structure for further amino acid understanding

1
Q

Amino acids are building blocks for what macromolecule

A

Proteins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What are some functions of proteins

A

enzymes, hormones, receptors, channels, antibodies, support structures

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What is the basic/ generic amino acid structure

A

carboxylic acid =O- OH, amino group NH2, and an R group attached to the same carbon as the amino group

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

How many different R groups

A

20 found in cells

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What are the acidic amino acids and why are they important

A
  1. Aspartic Acid- Asp- R group CH2COOH pKa 3.9
  2. Glutamic Acid- Glu- R group CH2CH2COOH pKa 4.1 (lower pKa= stronger acid and higher Ka= stronger acid)
    They are important because acidic amino acids can ionize metals and can facilitate the transfer of protons and stabilize reaction intermediates in enzymes

ACIDIC ANTS ARE GROSS- acidic- aspartic acid and glutamic acid

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What are the basic amino acids and why are they important

A
  1. Lysine- Lys- R group (CH2)4 NH2- pKa 10
  2. Arginine- Arg- R group (CH2)3 NH2 (one double bonded) NH2 pKa 12
  3. Histidine- His- R group CH2 and a 5 membered cyclic with a double bonded N and topped with a N-H pka
    They are important because their side chains are acidic at physiological pH and can aid in binding to negative DNA or folding protein

BASIC LIARS ARE HORRIBLE- basic- lysine, arginine, and histidine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What are the nonpolar (hydrophobic) amino acids and why are they important

A
  1. Glycine- Gly- single Hydrogen as the side chain
  2. Alanine- Ala- single CH3 as the side chain
  3. Valine- Val- side chain CH-< (CH3)2
  4. Leucine- Leu- side chain CH2-CH-<(CH3)2
    5.Isoleucine- Ile- CH-< CH3 and CH2-CH3
    END OF ALKYL
  5. Phenylalanine- Phe- like alanine with - then a benzene ring
  6. Tryptophan- Trp- a 5 member then 6 member ring with a NH on the top of the 5 member ring
    END OF AROMATIC SIDE
    In aqueous environments (like inside cells), nonpolar amino acids tend to cluster together, minimizing their contact with water. This leads to the formation of a hydrophobic core within proteins. This hydrophobic core is a major driving force in protein folding, as it stabilizes the three-dimensional structure of the protein

NO PERSON GOES ALL VIOLENT LOVE, I PERSONALLY TRY- nonpolar- glycine alanine, valine, leucine, isoleucine, phenylaline, tryptophan

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What are the polar (hydrophilic) amino acids and why are they important

A
  1. Serine- Ser- R group CH2- OH
  2. Threonine- Thr- R group CH-<CH3 and OH
  3. Tyrosine- Tyr- R group -/ then benzene with ortho OH
    DONE WITH ALCOHOL CONTAINING
  4. Asparagine- Asn- R group CH2C=ONH2
  5. Glutamine- Gln- R group CH2CH2C=ONH2
    DONE WITH CARBONYL CONTAINING
    Polar amino acids have many important qualities including their ability to be soluble in water and like water, leading to them usually congregating on the outer layer of polypeptides to hide hydrophobic amino acids inside, their polarizability also leads to Hydrogen bonding abilities (Secondary, Tertiary, and Quaternary structure) , as well as the alcohol containing groups being able to act as nucleophiles or act in phosphorylation (the addition of a phosphate group).

PLEASE SIS THAT TROLL AINT GOT IT CRAZY- Polar- Serine, Threonine, Tyrosine, Asparagine, Glutamine, Cysteine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What are the sulfur containing amino acids and why are they important

A
  1. Cysteine- Cys- R group CH2SH
  2. Methionine- Met- R group CH2CH2SCH3

SORRY CANT MATH- sulfur- cysteine and methionine

Important for bisulfide bridges which aid in the folding of many enzymes and antibodies

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What are the acidic and basic sites of an amino acid? What is the function of being able to be both an acid or base called?

A

the acidic group is the carboxylic aciid
the basic group is the amine
Amino acids are amphoteric- acid or base

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What is the Henderson Hasselbach equation and why is it important?

A

pH= pKa+log ([A-]/[HA])

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What happens when pH of solution is less than pKa of acidic group

A

the acidic group will be in its protonated form (NH3+ or COOH)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What happens when pH of solution is greater than pKa of acidic group

A

the acidic group will be in its deprotonated form (NH2 or COO-)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

At pH 5 what form are both the amino and carboxylate group in?

A

pH 5 greater than carboxylate group pKa - carboxylate group will be deprotonated- COO-

pH 5 less than amino group pKa- amino group will be in its protonated form- NH3+

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What does the term Zwitterion mean

A

A zwitterion is an ion that is dipolar, or has sites of both positive and negative charge, but they balance out into a zero net charge

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What does it mean for a molecule to be at its Isoelectric point (pI)

A

The pH in which a molecule is uncharged (where it is zwitterionic)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

How would one calculate a molecule’s pI?
Use Glycine as an example

A

PI= the average of each pKa
example= average of both amino group (9.5) and carboxylate group (2)= a pH of 6

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What amino acid has the highest pI

A

Arginine (due to all the amine groups)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What amino acid has the lowest pI

A

Aspartic acid (due to the additional carboxylic acid)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What are the common covalent bonds between amino acids in proteins

A

peptide bonds and disulfide bridges

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

How is a peptide bond formed

A

loss of water at the amine group of one amino acid and the alcohol (part of carboxylic acid) at the other amino acid forming a NH to bridge them together

22
Q

What is a unit of an amino acid called when it is a part of a polypeptide

23
Q

What is the amino terminus

A

the first amino in the chain of peptide bonding

24
Q

What is the carboxy terminus

A

the last amino in the chain of peptide bonding

25
Are polypeptide chains thermodynamically favorable?
Polypeptide chains are less favorable than individual amino acids because they leave more free energy when formed
26
So then how are polypeptides/ proteins formed in cells?
During protein synthesis (though it is endergonic and requires energy) stored energy is used to force the peptide bonds
27
Why do the bonds hold together if their destruction is more favorable?
The peptide bonds are held in place because their hydrolysis (degradation using the addition of water) has a high activation energy and is kinetically unfavorable
28
What is proteolysis?
Hydrolysis of a protein by another protein or proteolytic enzyme, and they split the peptide bond adjacent ( to the right) of the target protein
29
What amino acid does trypsin cleave
Trypsin cleaves at the positively charged, basic, carboxyl side of basic amino acids lysine and arginine and histidine
30
What amino acid does chymotrypsin cleave?
Chymotrypsin cleaves at large hydrophobic (nonpolar) phenylalanine and tryptophan
31
What is a thiol?
sulfhydryl (SH)
32
What is the process of creating a disulfide bond?
Two thiols of two separate thiols lose their hydrogens to form S-S bonds
33
What is the difference between cysteine and cystine
Cysteine is the amino acid containing the hydrogen Cystine is the amino's bonded together via disulfide bridge without hydrogen
34
Why are disulfide bonds important?
important for the strong covalent bonding in 3D structure, especially in extracellular proteins within oxidizing conditions connected
35
What type of bonds are found in primary structures
peptide bonding it is the order of amino acids bonded together
36
What type of bonds are found in secondary structures
hydrogen bonding bonds between backbone groups N-H and C=O into alpha helix or beta pleats
37
What type of bonds are found in tertiary structures
Hydrophobic interactions aka Van der Waals interactions in nonpolar aminos only: The clumping together of nonpolar parts in the core. Hydrogen bonds: Weaker attractions between polar parts. Ionic bonds: Strong attractions between charged parts. Disulfide bonds: Strong covalent links between cysteine residues. The 3D stucture that creates the site specific pocket for transportation, enzymes, etc
38
What type of bonds are found in quaternary structure
The same forces as tertiary, but instead of linking pieces of a chain to each other, this structure combines many polypeptides like hemoglobin (4) or RNA polymerase II (12)
39
What are things affected by enzymes
enzymes lower reaction activation energy make a reaction kinetically favorable
40
What is not affected by an enzyme
does not effect the overall free energy (delta G) not thermodynamically favorable
41
hydrolase
hydrolyzes (add or subtact water) chemical bonds example ATPases, proteases
42
isomerase
rearranges bonds within a molecule to form an isomer (same formula different structure)
43
ligase
forms a chemical bond example DNA ligase
44
lyase
breaks chemical bonds by means other than oxidation or hydrolysis example pyruvate decarboxylate (removes CO2 from pyruvate to form actealdehyde)
45
kinase
transfers a phosphate group to a molecule from a high energy carrier such as ATP (add or remove phosphate group) example phosphofructokinase
46
oxidoreductase
runs redox reactions examples oxidases, reductases, dehydrogenases
47
polymerase
polymerization (addition of nucleotides to the leading strand of DNA by DNA polymerase II)
48
phosphatase
removes a phosphate group from a molecule
49
phosphorylase
transfers a phosphate group to a molecule from inorganic phosphate example glycogen phosphorylase
50
protease
hydrolyzes peptide bonds protein breaking apart peptide bonds examples trypsin, chymotrypsin, pepsin
51
What is reaction coupling and why is it important
enzymes can only proceed on reactions that would occur in nature (spontaneous) but they speed the reaction up (kinettically favorable) for reactions that are not thermodynamically favored (nonspontaneous) like protein and DNA synthesis sometimes reactions happen in chains to get the energy started a great example is ATP hydrolysis!!! Delta G= ~ negative 7-12 kcal/mol
52

MCAT Amino Acids (2 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions