Biochemistry- Amino acids and proteins

Question 1

Label the structure of Amino Acid

Answer 1

look at yellow flashcard

Question 2

What is the significance of the R side chain?

Answer 2

• The other groups (amine, hydrogen, carboxylic acid) are fixed
• Unique side chain (R) determine the properties of the individual amino acid
  1. Size
  2. Shape (structure)
  3. Charge (negative, positive or neutral)
  4. Hydrophobicity (how well it dissolves)
  5. Reactivity (what will bind to it)

Question 3

What are the (9) Essential Amino Acids?

Answer 3

1. Threonine (Thr, T)
2. Valine (Val, V)-hydrophobic
3. Leucine (Leu, L)
4. Isoleucine (Ile, I)
5. Methionine (Met, M)
6. Phenylalanine (Phe, F)-aromatic
7. Tryptophan (Tyr, W)
8. Histidine (His, H)-basic
9. Lysine (Lys, K)

Question 4

All amino acids have mirror images (true/false)

Answer 4

False, Amino acids have mirror images except glycine

Question 5

Chirality of Amino Acids, Why do they have mirror images?

Answer 5

-because of the 4 groups linked to the Alpha Carbon have different molecular weights

Question 6

How to classify amino acids using D/L Nomenclature?

Answer 6

All natural amino acids have the L-configuration based on the L-glyceraldehyde

-if the polarized light bends after shining on the amino acid to the left (L) if it bends to the right (D)

Question 7

Groups added to the R side chain:

Answer 7

-Chemical groups such as phosphate, carboxylic acid, methyl can be added or removed from the R side chains

Question 8

Why do we modify the side chains of amino acids?

Answer 8

To make active products such as hormones like histamine and dopamine.
-translation

Question 9

What are the active products we can make from modifying the protein side chains?

Answer 9

Hormones:
1. Histamine- chemical released when you have an allergic response, making you sneeze and have skin rash.
It is made from the amino acid histidine after removing carboxylic acid

2. Dopamine- chemical is released in your brain and you have a feeling of pleasure; this can occur after exercise.
   It is made from the amino acid tyrosine after adding hydroxyl group and removing carboxylic acid.

Question 10

What hormone is made after modifying the amino acid side chain by removing COO- carboxylic acid?

Answer 10

Histamine from histidine

Question 11

What hormone is made after removing carboxylic acid and adding hydroxyl group ?

Answer 11

Dopamine from tyrosine

Question 12

What is the central dogma in biology?

Answer 12

DNA-> transcription -> RNA -> translation -> Protein-> Replication-> DNA

Question 13

What does the translation machinery in cell ribosomes do?

Answer 13

Synthesize proteins from individual amino acids

Question 14

Explain Peptide bond formation:

Answer 14

1. Peptide bond forms through the process of condensation
2. One amino acid joins with another while eliminating 1 water molecule H2O (water)
3. Carboxylic acid links to the nitrogen in the structure

Question 15

What is the importance of protein structure?

Answer 15

• Due to the fact that proteins are made up of 20 different building blocks or amino acids. Much more complicated than other biomolecules.
• diverse structure and function
• proteins do alot of “work” in living organisms because their structures allow them to fit all job descriptions

Question 16

Define Primary structure:

Answer 16

Order of the amino acids or the amino acid SEQUENCE

Question 17

Define Secondary structure:

Answer 17

The Shapes (motifs) within a single protein or polypeptide

Question 18

Define Tertiary structure:

Answer 18

The 3-D structure of the entire protein or polypeptide

Question 19

Define Quarternary structure:

Answer 19

Overall structure of 2 or more proteins associated together (protein complex)

Question 20

What are the most common secondary structures?

Answer 20

1. Alpha helix (coiled)
2. Beta sheet (flat/unwrapped)
3. Extended loop (unwrapped, no shape)

Question 21

Proteins are hormones:

Answer 21

Can bind to receptors on the cell membrane surface and tell the cell what to do

Question 22

Function of proteins:

Answer 22

1. Enzymes
2. Muscles
3. Hormones
4. Immunity
5. Chromosome packing
6. Source of energy
7. Cell membrane structure
8. Fluid balance

Question 23

Proteins in the cell membrane structure:

Answer 23

1. Integral membrane protein (channels, let substances in and out)
2. Lipid anchored protein
3. Peripheral membrane protein

Question 24

What are the 5 methods of purifying proteins?

Answer 24

1. Solubility (salt precipitation, protein solubility in increasing salt)
2. Ion charge ( protein binding to ion exchange beads)
3. Hydrophobicity (Hydrophobic interaction chromatography)
4. Size (Gel filtration chromatography)
5. Affinity (Affinity chromatography)

Question 25

Explain the Protein binding to ion exchange beads method:

Ion charge

Answer 25

1. Want to separate negatively charged proteins
2. Positively charged gel beads will attract the negatively charged beads
3. Unwanted proteins will flow out
4. Add NaCl, the Cl- has a strong negative charge and will bind to the positive bead “knocking out” the negative proteins and displacing it.
5. Have separated your protein
   Elution: flow out

Question 26

Explain the hydrophobic interaction chromatography:

Answer 26

[] Proteins have a globular shape , have hydrophobic amino acids in the core (no water, where all the hydrophobic residues go)

1. High salt causes the protein to change shape and force the hydrophobic residues to come out to the surface
2. Apply the mixture to the column, the hydrophobic amino acids of the protein will attach themselves to the column
   [in the column there are hydrophobic groups so the hydrophobic amino acids bind to each other]
3. Unwanted will flow out
4. To remove the protein binded to the column add “elution buffer” (no salt). They will return to normal shape become hydrophilic again and will not bind to column and leave

Question 27

Explain the gel filtration chromatography:

Answer 27

Column with different sized holes drilled into the beads
1. Apply the protein mixture with different sized proteins
2. Small proteins go into the beads and the big proteins will pass through
3. The bigger proteins move faster and smaller ones will move slow
4. Collect different time points. Early time points= bigger proteins
later time points= smaller proteins

Question 28

Explain purifying proteins using salt precipitation:

Answer 28

Different proteins have different solubility limits when increasing levels of salt are present

Question 29

Explain purifying proteins using Affinity Chromatography:

Answer 29

1. Beads connected to ligand
2. Add the sample protein
3. Impurities are removed from the complex
4. Lastly add salt (NaCl) change the structure of protein or boil to denature the shape

Question 30

What is the disease associated with protein structure:

Answer 30

Sickle cell anemia
-Sickle-shaped red blood cells cannot pass through capillaries due to the fact that the sharp edges may get catch the side of the capillary

Question 31

Haemoglobin group

Answer 31

4 heme groups

Question 32

What is 2,3-diphosphoglycerate? What is its function?

Answer 32

2,3-DPG is the byproduct of glycolytic pathway (glycolysis) when ATPs are produce in RBCs
-regulates the structure and function of haemoglobin

Question 33

Explain the affinity of 2,3-DPG:

Answer 33

2,3-DPG has higher affinity to deoxyhaemoglobin than oxyhaemoglobin

Question 34

Explain how the structure of haemoglobin changes with oxygen and without oxygen (along with 2,3-DPG):

Answer 34

In oxyhaemoglobin the B-chain moves closer when haemoglobin is oxygenated

In deoxyhaemoglobin the B-chain is pulled apart when O2 is unloaded, permitting entry of 2,3-DPG, resulting lower affinity of O2

Question 35

Describe the cooperative binding of oxygen:

Answer 35

• uptake of oxygen by a heme subunit results in a SHIFT in the deoxyhaemoglobin structure and 2,3-DPG expelled . This change facilitates the binding of oxygen by the other 3 heme sub-units
• Binding of oxygen at one site in the haemoglobin tetramer (4) influence the oxygen binding properties at the other sites
• binds faster as it moves to the 2nd and 3rd units

Question 36

Define the term oxygen affinity:

Answer 36

measures how readily the haemoglobin binds or releases oxygen
-The amount of oxygen bound to the haemoglobin at anytime is related to the partial pressure of oxygen (measurement of oxygen level)

Question 37

Describe oxygen when the partial pressure is high (in the lungs):

Answer 37

The partial pressure of oxygen is typically high, and therefore the oxygen binds readily to haemoglobin.
-When the partial pressure is high, oxygen readily loads, high affinity for good binding

Question 38

Describe oxygen when the partial pressure is low (in the blood):

Answer 38

As the blood circulates to other body tissue. Partial pressure of oxygen is less, haemoglobin releases the oxygen into the tissue. Low affinity for good release of oxygen