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Intro to Biochem and Cell Biology > Proteins > Flashcards

Proteins Flashcards

1
Q

What do amino acids consist of ?

A
  • Carbon
  • Amino group (H2N)
  • Carboxyl group (OCOH)
  • Hydrogen
  • Side chain (R)
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2
Q

What does an atom consist of ?

A

Nucleus & electrons

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3
Q

How is a covalent bond formed between 2 atoms?

A

Share electrons

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4
Q

What is bond polarity ?

A

Uneven electrons share

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5
Q

What atoms in an amino acid are involved in polarity ?

A

Nδ- , Oδ- Cδ+ , Hδ+

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6
Q

What happens when rather than sharing electrons, atoms gain or lose them ?

A
  • Ions: positive , lost electrons
  • Ions: negative, gain electrons
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7
Q

Which atoms in an amino acid are often positively and which negativeley chraged?

A

N+ O-

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8
Q

They’re 5

What groups are amino acids divided in based on properties of their side chains ?

A
  • Polar/ Non-polar
  • Hydrophillic/Hydrophobic
  • Acidic/Basic
  • Ionisable/charged
  • Special amino acids
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9
Q

What is the polar and non polar group about ?

A

Polar
* Uneven share of electrons in bond
* Electronegative stoms “pull” electrons of a bond towards them
Non-polar
* Even electroons share

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10
Q

What is hydrophilic / Hydrophobic?

A
  • Polar side chains are Hyrophillic: they like water
  • Nonpolar side chains are hydrophobic: they don’t like water
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11
Q

What is acidic and base?

A
  • Acidic groups yield H+ to solution
  • Base groups remove H+ from solution
  • pH = -log H+concentration
  • Higher H+, lower the pH, hence acids have low pH and bases high pH
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12
Q

What does ionisable and charged mean?

A
  • Ionisation = to add or remove electrons
  • charged = positive or negative
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13
Q

What are the chraged amino acids?

A

Negatively charged amino acids:
*aspartic acid
* Glutamic acid
Positively charged amino acids :
*Lysine
*Arginine
*Histidine

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14
Q

What are special amino acids ?

A
  • Cysterine has sulfhydryl (SH) that can for s-s bonds
  • Glycine has H (very small)
  • Proline is cyclic
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15
Q

What type of bonds are formed between amino acids?

A

Peptide bonds

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15
Q

What type of bonds are formed between amino acids?

A

Peptide bonds

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16
Q

What are dipole-dipole interactions?

A

When opposite poles attract

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17
Q

What is hydrogen bonding?

A
  • It’s a type of dipole-dipole interaction involving hydrogen
  • Amino acids can be hydrogen bond **donors ** or acceptors
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18
Q

When can hydrogen bonding occur ?

A

It can occur between pepetide bonds in the same region chain

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19
Q

Secondary structure involves hydrogen bonding between atoms associated with….

A
  • R groups
  • C-termini
  • N-termini
  • Cysteines
  • Peptide bonds (pole attraction)
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20
Q

What is Van der Waals interactions ? (non-covalent bonding)

A

non polar
* even electron share
* But temporaray dipole
* only involves non polar chains

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21
Q

What is hydrophibicity ?

A
  • Polar side chains are hydrophillic (like water)
  • Nonpolar side chains are hydrophobic (don’t like water)
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22
Q

Why are some chains hydrophillic (like water)?

A

Because and polar side chains can hydrogen bond , they’re attracted to each other

22
Q

Why polar side chains hydrophillic (like water)?

A

Because side chains can hydrogen bond , they’re attracted to each other

23
Q

Why are non polar side chains hydrophobic?

A

Because non polar side chains and water can’t hydrogen bond, non polar side don’t attrccated to water

24
Q

What are hydrophobic interactions ?

A
  • Relationship between polar water and hydrophobes (low water soluble) non polar, high hydrocrabon chain amino acids
25
Q

What are ionic interaction ?

A

Opposites sttract strongly

25
Q

What are ionic interaction ?

A

Opposites attract strongly

26
Q

What are the levels of protein structure ?

A
  • Primary structure
  • Secondary structure
  • Tertiary structure
  • Quaternary structure
27
Q

What does the primary structure consist of ?

A

sequence of amino acids linked to form chains

28
Q

What does the secondary structure consist of ?

A

Region where chains fold and where peptide interactions occur

29
Q

what does the teritiary structure consist of ?

A

Folded regions come together to form 3D shape, this is where R groups interactions

30
Q

what does the quatenary structure consist of?

A

Association of several polypeptide chains (e.g. protein subunits)

30
Q

what does the quatenary structure consist of?

A

Association of several polypeptide chains (e.g. protein subunits)

31
Q

Is water polar or non polar?

A

Polar

32
Q

What does the term polar bond mean?

A

Uneven electron share across the bond

33
Q

What mantains tertiary structure of alpha helicases as globular protein ?

A

The internal hydrophobic interactions

34
Q

What is the arrangements of amino acids in helicases?

A
  • Hydrophobic amino acids face inwards
  • Hydrophillic face outwards
35
Q

what is a hydrophobic pocket ?

A

A binding site that contains mostly hydrophobic amino acids

36
Q

What is a myoglobin ?

A

Something thst contains a heme prosthetic group that can reversibly bind to oxygen

37
Q

What does oxygen binding look like with myoglobin?

A
  • High affinity for oxygen
  • Binds when very little
  • Captures & stores oxygen in muscle (20-30torr)
  • Exercise = reduces oxygen so myoglobin rapidly releases into the tissues as all oxygen is tranposrted in the lungs
38
Q

What does oxygen binding to hemoglobin look like ?

A
  • Low affinity for axygen
  • Capture oxygen in lungs where lots
  • Relese in tissue where needed
39
Q

What is an ezyme ?

A

A biological catalyst

40
Q

What is a catalyst ?

A

Something that speeds up chemical reactions without themselves being changed

41
Q

Why do we need enzymes ?

A

Accelerate reactions by up to 1 million+:without them reactions are too slow !!!!

42
Q

What is an active site ?

A

Position on protein where substrate bind and are converted to products

42
Q

What is an active site ?

A

Position on protein where substrate bind and are converted to products

43
Q

What are 3D active sites called ?

A

Cleft / Crevice

43
Q

What are 3D active sites called ?

A

Cleft / Crevice

44
Q

What is the lock and key mechanism of enzyme action ?

A

Enzyme breaks a large molecule into smaller ones. The same enzyme will aslo catalyse the reverse rection - it will join the smaller molecules together again

45
Q

What is the induced fit hypothesis of enzyme action ?

A

When the substrate binds to the enzymes’s active site, it induces a change of shape so that the substrate and enzyme become fully complementary

46
Q

What are enzymes deactivated by ?

A
  • Heavy Metal Salts (Hg+2, Pb+2, Ag+1, Cd+2)
    because they disrupt electrostatic interactions
  • Reducing agents

They both distrupt S-S bonds

47
Q

What is added to amino acid when they’re not enough?

A

Add a cofactor
* Metals
* Small organics (some vitamin derivatives)
* Prosthetic group (tightly bound)
* Cosubstrate (loosely bound)
* Coenzymes

48
Q

What is a competitive inhibitor ?

A

When an inhibitor temporarily bind to an active site so that its substrate can’t bind

49
Q

What is a non-competitive inhibitors ?

A

Inhibitor will bind to an allosteric which changes the shape of the active site so that the substrate can’t bind.

50
Q

examples on non polar amino acids

A

leucine
valine
phenylaline

51
Q

examples of polar amino acids

A

aspartic acid
glutamic acids
glutamine

Intro to Biochem and Cell Biology (14 decks)

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