8B and 9A - Peptides and Tertiary Structures

Question 1

What is glutathione?

Answer 1

A tripeptide found in most all organisms and is involved in protein and DNA synthesis, toxic substance metabolism (antioxidant) and amino acid transport

Question 2

What is vasopressin?

Answer 2

An antidiuretic hormone that regulates water balance, appetite and body temperature

Question 3

What is oxytocin?

Answer 3

A peptide that aids in uterine contraction and lactation

Question 4

What are homologous Proteins?

Answer 4

Proteins that share a similar sequence and arose from the same ancestor gene

Question 5

What is an invariant Amino Acid Sequence?

Answer 5

Those that are identical and presumed to be essential for function

Question 6

What is a conservative Amino Acid Change in a polypeptide sequence?

Answer 6

A change to a chemically similar amino acid

Question 7

What is the Variable Sequence Position in an amino acid sequence?

Answer 7

A less stringent sequence position, because they perform nonspecific functions

Question 8

What are 7 Reasons to Sequence Proteins?

Answer 8

3D Structure Interpretation
Protein Engineering
Structure Prediction
To find the gene
Identify Post-Translational modification
Molecular evolution studies
Phylogeny (history or organismal lineages)

Question 9

What genetic ‘even’t causes sickle cell anemia? Explain

Answer 9

Substitution of valine for a glutamic acid in β-globin subunit of hemoglobin. Valine is hydrophobic, unlike the charged amino acid will aggregate to form sickle shaped cells, low oxygen binding capacity and susceptibility to hemolysis is a result

Question 10

What characterizes hydrogen Bonding in polypeptide α-helices? (eg. what bonds with what?)

Answer 10

N-H hydrogen bonding with a carbonyl four amino acids away

Question 11

Which two amino acids do not foster α-helical formation?

Answer 11

glycine and proline

Question 12

Which type of beta pleated sheet is most stable?

Answer 12

Antiparallel sheets are much more stable than parallel sheets

Question 13

What are 4 examples of domains found in a large number of proteins?

Answer 13

Leucine Zippers (two alpha helices)
β-barrel
ATP binding domain or hexokinase
The α/β zinc binding motif

Question 14

What do mosaic/modular Proteins consist of?

Answer 14

Repeated domains

Question 15

What are 5 Interactions that stabilize tertiary structures?

Answer 15

Hydrophobic Interactions
Electrostatic Interactions (salt bridges)
Hydrogen Bonds
Covalent Bonds
Hydration

Question 16

What are oligomers

Answer 16

(In Quaternary Structures) Identical subunits in multisubunit proteins. Composed of protomers.

Question 17

What are three reasons for multisubunit proteins?

Answer 17

Synthesis of subunits may be more efficient

In supramolecular complexes, replacement of worn-out components can be handled more effectively

Biological function may be regulated by complex interactions of multiple subunits

Question 18

What type of interactions hold together polypeptide subunits?

Answer 18

Noncovalent interactions, covalent interactions like disulfide bridges are less common. Desmosine and lysinonorleucine linkages are also covalent (but rare as well)

Question 19

What type of chemical bond is a disulfide bridge?

Answer 19

Covalent

Question 20

What is allostery?

Answer 20

Control of protein function by ligand binding. Ligands that do this are called effectors and modulators.

Question 21

What is an allosteric transition?

Answer 21

Change of protein conformation in response to ligand binding.

Question 22

What are two types of unstructured protein?

Answer 22

Intrinsically unstructured proteins (IUPs) or natively unfolded proteins

Question 23

Proteins are categorized into families based on ___ and ____?

Answer 23

Proteins are categorized into families based on sequence and three dimensional shape (globular and fibrous)

Question 24

What are conjugated proteins?

Answer 24

Proteins that have a protein and non-protein component (eg. lipoprotein or glycoprotein)

Question 25

What are simple proteins?

Answer 25

Contain only amino acids

Question 26

What are the four levels of protein structure?

Answer 26

Primary
Secondary
Tertiary
Quaternary

Question 27

Each beta strand (secondary structure of polypeptide) is stabilized by hydrogen bonding between what two groups?

Answer 27

Between N-H and carbonyl groups of adjacent strands. Parallel sheets ar much less stable than antiparallel sheets because of less hydrogen bonding.

Question 28

What are five supersecondary structures (motifs) of proteins? (All have patterns of alpha-helix and beta-sheet structures).

Answer 28

1. βαβ unit (two beta sheets on either side of a helix)
2. β-meander (beta sheets side by side attached, like a closely space sin line)
3. αα unit (two alpha helices attached, extending next to each other)
4. β-barrel (a barrel formed by beta sheets wrapped into a cylinder
5. Greek key (beta sheets going up and down side by side to form a hollow S sort of)

Question 29

Protein folding is defined as?

Answer 29

The process by which a nascent molecule acquires a highly organized structure. Information for folding is contained in the amino acid sequence

Question 30

What does tertiary protein structure refer to?

Answer 30

The unique 3D structures formed by globular proteins, sometimes with prosthetic groups.

• Many proteins fold in a way to bring distant amino acids into close proximity
• Globular proteins are compact because of efficient packing

Question 31

What is the core structural element of a domain called?

Answer 31

A fold

Question 32

Domain modules are coded for by what type of genetic sequences?

Answer 32

Genetic sequences created by gene duplications

Question 33

What is quaternary structure of proteins?

Answer 33

A protein that is composed of several polypeptide chains (subunits)
- Multisubunit proteins may be composed, at leas in part, of identical subunits and are referred to as oligomers (composed of protomers)

Question 34

What are three reasons for the common occurrence of multisubunit proteins?

Answer 34

1. Synthesis of subunits may be more efficient
2. In supramolecular complexes replacement of worn-out components can be handled more effectively
3. Biological function may be regulated by complex interactions of multiple subunits.

Question 35

Polypeptide subunits are mostly held together by what type of chemical interactions? What are some exceptions?

Answer 35

Noncovalent interactions

- Some exceptions are disulfide bridges (covalent) and desmosine and lysinonorleucine linkages (also covalent)