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MMBIO 240 > Chapter 4 > Flashcards

Chapter 4 Flashcards

1
Q

How are amino acids categorized?

A

By chemical properties

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2
Q

How many common amino acids are there?

A

20

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3
Q

What is a primary structure?

A

A Polypeptide: Chain-like sequence of amino acids bound with peptide bonds

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4
Q

What forms the peptide bond? What is released as a byproduct?

A

Peptide (covalent) bond forms between C of one amino acid and N of another. H2O is released as a biproduct

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5
Q

What elements is the Amino Group composed of?

A

NH2

(H3N+ on left side)

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6
Q

What elements is the Carboxyl Group composed of?

A

COOH

(COO- on right side)

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7
Q

Why is the Methionine R Group important?

A

AUG is start codon that codes for Methionine Amino Acid!

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8
Q

What are the Nonpolar, Aliphatic R Groups? What distinguishes them?

A

ALIPHATIC: lots of single bonds with Carbon and Hydrogen -> HYDROPHOBIC

  • Glycine
  • Alanine
  • Proline* (extra cov. bond)
  • Valine
  • Leucine
  • Isoleucine
  • Methionine (AUG -> Met!)
  • NO PLACE FOR AGGREGATION OF ELECTRONS
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9
Q

What are the Highly Polar, Negatively Charged R Groups? What distinguishes them?

A

HYDROPHILIC

  • Aspartate
  • Glutamate
  • ACIDIC (-) SIDE CHAINS WITH COO- CARBOXYL ATTATCHED
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10
Q

What are the Highly Polar, Positively Charged R Groups? What distinguishes them?

A

HYDROPHILIC

  • Histidine
  • Lysine
  • Arginine
  • BASIC (+) SIDE CHAINS
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11
Q

What are the Polar, Uncharged R Groups? What distinguishes them?

A

HYDROPHILIC

  • Serine
  • Threonine
  • Cysteine
  • Asparagine
  • Glutamine
  • CAN HYDROGEN BOND BECAUSE OF -OH AND -NH2 GROUPS
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12
Q

What are the Nonpolar, Aromatic R Groups? What distinguishes them?

A

AROMATIC: Rings with alternating Carbon double bonds -> HYDROPHOBIC

  • Phenylalanine
  • Tyrosine
  • Tryptophan
  • NO PLACE FOR AGGREGATION OF ELECTRONS
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13
Q

How are amino acids connected?

A

In a polypeptide chain

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14
Q

What does the linear sequence of a polypeptide chain have?

A
  1. amino terminus
    (or N-terminus)
  2. carboxyl terminus
    (or C-terminus)
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15
Q

How do you read an amino acid sequence? Which is designated as the “starting point” of a protein sequence?

A

From N-terminus (left)
To C-terminus (right)

  • N-terminus is starting point
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16
Q

In which directions are DNA transcribed, RNA translated and Amino Acid Chains created?

A

5’->3’ (only add to 3’ end)
N->C (only add to C terminus)

FIVE TO THREE,
“N” TO “C”

17
Q

How can evolutionary relationships be determined?

A

By comparing primary sequences

18
Q

What are secondary structures?

A

Regularly repeating elements within a protein in which H-bonds form between polar atoms in the backbone chain

19
Q

What allows secondary structures to fold?

A

Reverse Turns

20
Q

What are Reverse Turns?

A

Loops where secondary structural elements reverse themselves

21
Q

What is a Dimer?

A

A protein consisting of two polypeptide subunits

(quaternary structure composed of two tertiary structures)

22
Q

What is a Polymer?

A

A huge molecule made by the bonding of a series of macromolecules, which are composed of many repeating subunits

(a protein (quaternary structure) composed of more than two tertiary structures)

23
Q

What are Domains?

A

Independent folding units within a protein

24
Q

What are the building blocks of Domains?

A

Supersecondary Structural Elements

25
Q

What does the word “residue” refer to?

A

Residue = Amino Acid

26
Q

How do cis and trans play a role in protein folding?

A

cis and trans isomerases (same molecule, different orientation) affect the directions in which the growing amino acid chain will fold, creating alpha helices and beta sheets

27
Q

Where is the Phi Angle?

A

Between Nitrogen (amino group) and Central Carbon

28
Q

Where is the Psi Angle?

A

Between Central Carbon and End Carbon (carboxyl group)

29
Q

What makes a peptide bond stronger than the phi bond?

A

Resonance

30
Q

What are the R groups associated with glycine, methionine, and histidine?

A

Glycine (Gly/G):
R Group: Hydrogen (H)

Methionine (Met/M)
R Group: Methyl (a long hydrocarbon chain with a SULFUR in the middle)

Histidine (His, H)
R Group: Imidazole ring

31
Q

How can you recognize polar vs. nonpolar R groups (or any molecule)?

A
  • PAY ATTENTION TO ELECTRONEGATIVITY AND WHERE ELECTRONS ARE LOCATED!
    If the electronegativity difference between two atoms is significant, a polar covalent bond is formed, resulting in an uneven distribution of electron density.
32
Q

How is it that tyrosine is nonpolar even though it contains an OH group?

A

Although tyrosine carries a single hydroxyl (OH) group, it still contains a very non-polar benzene ring.

33
Q

Can you identify a protein sequence based on a genetic sequence using the table provided in lecture?

A

I think so!

34
Q

Where would hydrophobic amino acids be found in a protein?

A

Hydrophobic amino acids are found in the interior of the protein (because they’re scared of the water on the outside)

35
Q

Around what bonds do a polypeptide rotate? What is the difference between its trans and cis versions? Can it rotate around the peptide bond? Why or why not?

A

The single bonds connecting adjacent amino acids. Trans results from Phi angles and Cis results from Psi angles. Rotation is limited around the peptide bond in comparison to the single bond because peptide bonds are partial double bonds.

36
Q

What does the free-energy funnel tell us about proteins?

A

A protein wants to fold until it gets to the lowest free energy (until entropy is minimal)

37
Q

How do prion diseases occur?

A

Incorrect protein folding causes a cascade of misfolds

38
Q

What is the role of chaperone proteins?

A

Chaperone proteins prevent inappropriate folding (like a mom at a stake dance). They have an inner chamber that takes in folding proteins

39
Q

Do all proteins require a chaperone?

A

No, some proteins fold spontaneously by themselves.

MMBIO 240 (15 decks)

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