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Cell and Molecular Bio > Biochemistry- Amino acids and proteins > Flashcards

Biochemistry- Amino acids and proteins Flashcards

1
Q

Label the structure of Amino Acid

A

look at yellow flashcard

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2
Q

What is the significance of the R side chain?

A
  • 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)
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3
Q

What are the (9) Essential Amino Acids?

A
  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)
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4
Q

All amino acids have mirror images (true/false)

A

False, Amino acids have mirror images except glycine

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5
Q

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

A

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

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6
Q

How to classify amino acids using D/L Nomenclature?

A

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)

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7
Q

Groups added to the R side chain:

A

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

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8
Q

Why do we modify the side chains of amino acids?

A

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

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9
Q

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

A

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

  1. 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.
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10
Q

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

A

Histamine from histidine

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11
Q

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

A

Dopamine from tyrosine

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12
Q

What is the central dogma in biology?

A

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

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13
Q

What does the translation machinery in cell ribosomes do?

A

Synthesize proteins from individual amino acids

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14
Q

Explain Peptide bond formation:

A
  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
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15
Q

What is the importance of protein structure?

A
  • 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
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16
Q

Define Primary structure:

A

Order of the amino acids or the amino acid SEQUENCE

17
Q

Define Secondary structure:

A

The Shapes (motifs) within a single protein or polypeptide

18
Q

Define Tertiary structure:

A

The 3-D structure of the entire protein or polypeptide

19
Q

Define Quarternary structure:

A

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

20
Q

What are the most common secondary structures?

A
  1. Alpha helix (coiled)
  2. Beta sheet (flat/unwrapped)
  3. Extended loop (unwrapped, no shape)
21
Q

Proteins are hormones:

A

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

22
Q

Function of proteins:

A
  1. Enzymes
  2. Muscles
  3. Hormones
  4. Immunity
  5. Chromosome packing
  6. Source of energy
  7. Cell membrane structure
  8. Fluid balance
23
Q

Proteins in the cell membrane structure:

A
  1. Integral membrane protein (channels, let substances in and out)
  2. Lipid anchored protein
  3. Peripheral membrane protein
24
Q

What are the 5 methods of purifying proteins?

A
  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)
25
Q

Explain the Protein binding to ion exchange beads method:

Ion charge

A
  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
26
Q

Explain the hydrophobic interaction chromatography:

A

[] 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
27
Q

Explain the gel filtration chromatography:

A

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

28
Q

Explain purifying proteins using salt precipitation:

A

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

29
Q

Explain purifying proteins using Affinity Chromatography:

A
  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
30
Q

What is the disease associated with protein structure:

A

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

31
Q

Haemoglobin group

A

4 heme groups

32
Q

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

A

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

33
Q

Explain the affinity of 2,3-DPG:

A

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

34
Q

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

A

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

35
Q

Describe the cooperative binding of oxygen:

A
  • 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
36
Q

Define the term oxygen affinity:

A

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)

37
Q

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

A

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

38
Q

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

A

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

Cell and Molecular Bio (13 decks)

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