Protein Synthesis and Structure

Question 1

What are the monomers that make up proteins?

Answer 1

Amino acids are the monomers that make up proteins

Question 2

What are the key characterisitcs of the amino acids that make up proteins?

Answer 2

There are 20 different amino acids that are found in proteins, and they can be hydrophilic or hydrophobic

Question 3

Amino acids are linked together by […]

Answer 3

Amino acids are linked together by peptide bonds

Question 4

A protein is made of […] linked together into a […]

Answer 4

A protein is made of amino acids linked together into a polypeptide chain

Question 5

What drives the synthesis of proteins?

Answer 5

Genetic information directs the synthesis of proteins

Question 6

The nucleotide sequence of RNA is translated into the […] of a protein via the […]

Answer 6

The nucleotide sequence of RNA is translated into the amino acid sequence of a protein via the genetic code

Question 7

How many possible reading frames does an RNA molecule have?

Answer 7

An RNA molecule has three possible reading frames

Question 8

The genetic code contains codons for […] and […]

Answer 8

The genetic code contains codons for START and STOP

Question 9

The start codon is always […] and therefore defines the reading frame

Answer 9

The start codon is always AUG and therefore defines the reading frame

Question 10

In eukaryotic cells translation begins at the first […] and ends at the first […] stop codon

Answer 10

In eukaryotic cells translation begins at the first AUG and ends at the first in-frame stop codon

Question 11

Polypeptides are synthesized in the […] direction

Answer 11

Popypeptides are synthesized in the NH2- to -COOH direction

Question 12

How is the base sequence in mRNA translated into
the amino acid sequence of a protein?

Answer 12

1. Adaptors ‘translate’ the RNA code and bring in approrpriate amino acids (t-RNA: transfer-RNA)
2. A machine aligns the mRNA sequence with the adaptors and then link the amino acids together to form the polypeptide chain

Question 13

What do tRNAs do?

Answer 13

tRNAs link amino acids to codons

Question 14

What is tRNA synthesases?

Answer 14

An anzyme that attach amino acids to tRNA
- There is at least one tRNA synthestase for each amino acid
- Each tRNA synthetase is specific for one amino aced and the appropriate tRNA(s)

Question 15

mRNA is decoded on […] and this process is known as […]

Answer 15

mRNA is decoded on ribosomes and this process is known as translation

Question 16

Translation begins when […] binds to the start codon

Answer 16

Translation begins when Methionine-iniator tRNA (MET) binds to the start codon

Question 17

Translation ends when […] binds to stop codon

Answer 17

Translation ends when Release Factor binds to stop codon

Question 18

Proteins come in a variety of […] and […]

Answer 18

Proteins come in a variety of shapes and sizes

Question 19

What is the primary level of protein structure?

Answer 19

The primary level of structure is the amino acid sequence

Question 20

What is the secondary level of protein structure?

Answer 20

The secondary level of protein structure is the path of the polymer backbone (ignoring side-chains) aka the alpha-carbon chain backbone

Question 21

What is the tertiary level of protein structure?

Answer 21

The tertiary level of protein structure is the overall structure of one polypeptide including all side chains (the positions of all atoms in the polypeptide, aka the “3D structure”)

Question 22

What is the quarternary level or protein structure?

Answer 22

The quarternary level or protein structure is the overall (“3D”) structure of a multi-subunit protein (some proteins are made of more than 1 polypetide bound tightly together)

Question 23

What determines the 3D structure of an amino acid sequence?

Answer 23

The 3D structure of a protein is determined solely by its amino acid sequence

Question 24

The folding of many proteins is assisted by […]

Answer 24

The folding of many proteins is assisted by chaperone proteins

Question 25

What are the four types of noncavalent interactions that help determine the 3D structure of a protein?

Answer 25

• van der Waals interactions
• electrostatic interactions
• hydrogen bonds
• hydrophobic interactions

Question 26

A “folded” protein has a specific structure determined by its […], in which all of these interactions are optimized

Answer 26

A “folded” protein has a specific structure determined by its minimum energy state, in which all of these interactions are optimized

Question 27

What makes something hydrophilic or hydrophobic?

Answer 27

• polar molecules are hydrophilic
• nonpolar molecules are hydrophobic

Question 28

Hydrophobic interactions drive proteins to fold into […]

Answer 28

Hydrophobic interactions drive proteins to fold into compact conformations

Question 29

Specific conformations of the […] commonly found in proteins are refered to as secondary structures

Answer 29

Specific conformations of the polypeptide commonly found in proteins are refered to as secondary structures

Question 30

What are the two most common secondary structures?

Answer 30

alpha-helices and beta-sheets

Question 31

What are the different ways that protein structures are depicted?

Answer 31

• Backbone
• Ribbon or “Cartoon”
• Wire
• Space-filling

Question 32

What are the steps in DNA translation?

Answer 32

1. With the growing peptide in the P-site the appropraite aminoacyl-tRNA finds the A site
2. A peptide bond is formed by elimination of H20
3. The large ribosomal subunit translocates down the mRNA
4. the small ribosomal subunit translocates, moving the free tRNA into the E-site and the tRNA with the newly attached amino acid into the P site
   - the unattached protein can now leave and the cycle starts over