4: Protein Fundamentals I

Question 1

How are amino acids different? How are they the same?

Answer 1

different: identity of R group
same: amino terminus and acid terminus

Question 2

Direction of protein synthesis

Answer 2

amino to carboxyl end (N to C)

Question 3

How are amino acids used to form proteins?

Answer 3

amino acids are linked together through the formation of peptide (amide) bonds between each N-C-C’ cluster.

Peptide bonds are formed from dehydration

Question 4

What direction are codons read in translation?

Answer 4

5’ to 3’

Question 5

How is protein synthesis initiated?

Answer 5

1. three initiation factors (eIF4F, eIF4A, and eIF4B bind to mRNA 5’ cap and create a substrate for binding other components of the initiation complex
2. initiation complex forms (ribosomal subunit, initiator tRNA, and eIF initiation factors)
3. the initiation complex scans along the mRNA until AUG
4. eIF5 causes the release of all initiation factors
5. translation begins with the AUG codon.

Question 6

What are the steps of the elongation cycle in protein synthesis?

Answer 6

1. small subunit shifts one codon
2. Next tRNA moves into the A site
3. Large subunit shifts and the tRNAs are moved to the E and P sites
4. small subunit shifts one codon
5. next tRNA moves into A site
6. growing chain is transferred to the carboxyl group of the newly added amino acid
7. large subunit moves and tRNA with NO amino acid is ejected
8. the remaining tRNAs are moved into the other E and P sites (out of the A site)

Question 7

How is protein synthesis terminated?

Answer 7

1. stop codon is encountered
2. release factor moves into A site and the polypeptide is released from the ribosome

Question 8

What are the different types of chirality of proteins? Where are each of them found?

Answer 8

L-form is found in native normal biologically-active proteins
D-form can be used in synthetic proteins and isn’t found in nature at all

Question 9

What are the two components of primary structure proteins?

Answer 9

1. the sequence of specific amino acids
2. the chemical identity of R groups on specific amino acids

Question 10

What are characteristics of secondary structure proteins?

Answer 10

• low energy conformations of the backbone
• peptide bond is planar, but the other bonds rotate to MINIMIZE energy
• forms two key structures (alpha helices and beta sheets)

Question 11

Describe secondary alpha helix structure

Answer 11

• every N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier
• side chains project out from helix

Question 12

Describe secondary structure beta sheet

Answer 12

• aromatic and branched amino acids are favored
• can be parallel or anti-parallel
• anti-parallel is more stable due to linearity/lengths of hydrogen bonds

Question 13

describe loops in secondary structure

Answer 13

• loops connect helices and strands
• often contain glycine bc of small size
• often contain proline bc of rigid, bent formation

Question 14

What are tertiary structures?

Answer 14

interactions between secondary structures fold into tertiary structures

Question 15

What is a protein motif?

Answer 15

a type of arrangement of secondary structure elements in a particular pattern

Question 16

What is a protein domain?

Answer 16

a distinct functional and/or structural unit (shape) within one long protein/peptide sequence
- capable of independent folding, function, evolutionary pressure, etc.
- have defined functions

Question 17

Where is the placement of hydrophobic and hydrophilic residues in tertiary proteins?

Answer 17

Folding pushes the water molecules out
- hydrophobic residues are inside the core
- hydrophilic residues form the outside of the surface of the protein

Question 18

What is quaternary structure?

Answer 18

• consists of individual subunits (each subunits consist of independent peptide chains)