Amino Acids, Peptides, And Proteins

Front 1

Describe basic structure of amino acids.

Back 1

- four groups attached to central (alpha) carbon:

• amino group

• carboxylic acid group

• hydrogen atom

• R group

Hint 1

Mnemonic: "CHAR"

Front 2

What is the significance of R groups in amino acids?

Back 2

R groups determine both the chemistry and function of a given amino acid.

Front 3

How many amino acids appear in eukaryotic organisms? How are they termed in comparison to other amino acids?

Back 3

There are a total of twenty amino acids that appear in eukaryotic organisms; termed proteinogenic amino acids.

Front 4

What is the stereochemistry of the alpha carbon in all amino acids?

Back 4

the stereochemistry is L .

However...

• D-amino acids can exist in prokaryotes and eukaryotes (sometimes)

Hint 4

Mnemonic: L ove all aminos...

Front 5

What are some characteristics of proteinogenic amino acids? What are the exceptions?

Back 5

Most all amino acids are chiral, and thus have optical activity (ability to polarize light). Glycine is the only amino acid that is not chiral because it has two H atoms attached.

All amino acids have an (S) absolute configuration, except for cysteine which is still an L - amino acid but an R configuration. This is due to the presence of the thiol group having priority over the carboxylic group.

Front 6

What are the amino acids with nonpolar, nonaromatic side chains?

Back 6

Glycine, Alanine, Leucine, Isoleucine, Methionine, Valine and Proline

Hint 6

Go Ask Loghten to Make some Vivacious Pastries.

Front 7

What are the aromatic amino acids?

Back 7

Tryptophan (largest), Tyrosine and Phenylalanine (smallest)

Hint 7

TTP : Time To Party!

Front 8

What are the polar amino acids?

Back 8

Serine, Cysteine, Glutamine, Asparagine and Threonine

Hint 8

Save Carrie from Getting A bad Talk.

Front 9

What are the positively charged amino acids (basic/alkaline)?

Back 9

Arginine, Lysine and Histidine

Hint 9

Act Like Her: Positive (+)

Front 10

What are the negatively charged (acidic) amino acids?

Back 10

Glutamate (Glutamic Acid) and Aspartate (Aspartic Acid)

Hint 10

Go Away! (-)

Front 11

Name the amino acids that are hydrophobic.

Back 11

Alanine, Isoleucine, Leucine ,Valine and Phenylalanine

Hint 11

Mnemonic: Alex Is Like Very Petrified

Front 12

Name the hydrophilic amino acids.

Back 12

Histidine, Arginine, Lysine, Glutamate and Aspartate

Hint 12

• all charged amino acids

• Mnemonic: Haley's Amazing (K)ids Give Adventure

Front 13

Amino acids are _______; can accept and donate protons.

Back 13

Amphoteric

Front 14

pH at which half of the species is deprotonated; [HA] = [A-]

Back 14

pKa

Front 15

True/False: Amino acids exist in different forms at different pH values.

Back 15

True

Front 16

When an amino acids pH is near its pI (isoelectric point), it is...

Back 16

a neutral zwitterion

Front 17

At high (alkaline) pH, the amino acid is fully...

Back 17

deprotonated

Hint 17

Basic people 😒...always takin' my " ".

Front 18

At low (acidic) pH, the amino acid is fully...

Back 18

protonated

Hint 18

I need all my " " for protection...

Front 19

the pH at which the molecule is electrically neutral

Back 19

isoelectric point (pI)

Front 20

the pI of uncharged amino acids can be calculated by...

Back 20

averaging the pKa values

Front 21

the pI for negatively charged amino acids can be calculated by...

Back 21

averaging the pK a values of the R group and the carboxyl group.

Front 22

the pI for positively charged amino acids can be calculated by...

Back 22

averaging the pK a values of the R group and the amino group

Front 23

Amine acids without charged side chains have a pI...

Back 23

around 6

Front 24

Acidic amino acids have pI...

Back 24

well below 6

Front 25

Basic amino acids have a pI...

Back 25

well above 6

Front 26

What are peptides (bonds)? Dipeptides, Tripeptides, Oligo- and Poly-?

Back 26

Peptides are chains of amino acid sequences. A dipeptides is a peptide chain that contains 2 amino acid residues; tripeptides have 3, oligopeptides have "few" (<20), and polypeptide have "many" (>20).

Front 27

What type of reaction(s) occur during the formation of peptide bonds?

Back 27

Condensation or Dehydration: the release of one water molecule

Process: the nucleophillic amino group of one amino acid will attack the electrophillic carbonyl group of another amino acid.

Front 28

Peptide bonds...

Back 28

Special aside bond and help hold peptides together; are rigid because of resonance.

Front 29

What type of reaction breaks peptide bonds?

Back 29

Hydrolysis: a reaction involving the addition if water.

Front 30

What is a primary structure?

Back 30

The linear sequence of amino acids in a peptide, that is stabilized by peptide bonds.

Hint 30

"Ala-Glu-Thr..."

Front 31

What is the secondary structure?

Back 31

local structure of neighboring amino acids; stabilized by hydrogen bonds between amino groups and adjacent carbons. Most common are a-helices and B-pleated sheets.

Hint 31

Front 32

alpha-helix(ces)

Back 32

clockwise coils around a central axis.

Front 33

B-pleated sheets

Back 33

rippled strands that can be parallel or antiparallel.

Front 34

Why is proline important in a protein's secondary structure?

Back 34

Proline is a 5-member ringed amino acid. It's presence is rare in the middle of both alpha helices and beta pleated sheets due to its rigid cyclic structure; it introduces a kink in peptide chain.

Proline can be found in helices that cross the cell membrane & the start of an alpha helix, and the turns between chains of beta pleated sheets.

Front 35

What is the tertiary structure?

Back 35

the three-dimensional shape of a single polypeptide chain; is stabilized by hydrophobic interactions , acid-base interactions (salt-bridges), hydrogen bonding, and disulfide bonds.

Hint 35

Front 36

What is the quatenary structure?

Back 36

the interaction between peptides in proteins that contain multiple subunits.

Hint 36

Ex: Hemoglobin

Front 37

Hydrophobic Interactions

Back 37

push hydrophobic R groups to the interior of protein, which increase entropy of surrounding water molecules and creates -dG (Gibbs free energy).

Front 38

Disulfide Bonds

Back 38

when two cysteine molecules are oxidized and create a covalent bond to form cystine. Increases stability.

Done with the help of electron accepting enzyme or acceptor molecule (like water 💧)

Front 39

Conjugated Proteins

Back 39

Proteins with covalently attached molecules.

molecules.

molecules.

Front 40

Prosthetic Group

Back 40

the attached molecule in a conjugated protein

Can be a metal ion, vitamin, lipid, carbohydrate, or nucleic acid.

Front 41

Denaturation

Back 41

loss of three-dimensional protein structure

Front 42

What causes denaturation?

Back 42

Heat and increased concentration of solutes:

• Heat: when temp. increase the average kinetic energy increases; the extra energy can overcome hydrophobic interactions

• Solutes: directly interfere with forces that hold protein together; disrupt 3° and 4° structures by breaking disulfide bridges ; can overcome hydrogen bonds and other side chains interactions

• Detergents can solubilize proteins and disrupt covalent bonds