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Biochemistry > Proteins > Flashcards

Proteins Flashcards

1
Q

What are the classification of standard amino acids

A

1) Non-polar amino acids

2) polar amino acids

3) acidic amino acids

4) basic amino acids

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2
Q

What are the non-polar amino acids

A

1) glycine

2) alanine

3) valine

4) leucine

5) isoleucine

6) phenylalanine

7) Tryptophan

8) methionine

9) proline

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3
Q

What are the polar amino acids

A

1) serine

2) cysteine

3) glutamine

4) asparagine

5) Tyrosine

6) Threonine

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4
Q

What are the acidic amino acids

A

1) Aspartate

2) glutamate

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5
Q

What are the basic amino acids

A

1) Lysine

2) Arginine

3) Histidine

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6
Q

What is the name of an amino acid polypeptide of 50 or less amino acids

A

Peptides

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7
Q

Polymers of more than 50 amino acids are called

A

Proteins/polypeptide

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8
Q

What is the meaning of amphoteric

A

That at physiological pH the carboxyl (-) and amino group (+) meaning that it is both acidic and basic

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9
Q

What are zwitterions

A

They are molecules that have both positive and negative charges on different atoms

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10
Q

What is the pKa of the carboxyl group

A

3

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11
Q

What is the pKa of the amino group

A

11

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12
Q

What determines the unique properties of amino acids and poly-peptides

A

The R-group

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13
Q

Amino acids are classified according to?

A

According to their R-group interaction with water molecules

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14
Q

What is the structure of glycine

A

As three of the groups connected to the a-carbon are the same I will only be mentioning the R-group in (paranthaces):

Gly-(H)

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15
Q

What is the structure of alanine?

A

Ala-(CH3)

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16
Q

What is the structure of valine?

A

Val-(CH)-(CH3)2

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17
Q

What is the structure of phenylalanine?

A

Phe-(CH2)-benzene

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18
Q

What is the structure of serine?

A

Ser-(CH2OH)

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19
Q

What is the structure of tyrosine?

A

Tyr-(CH2)-(benzene)-(OH)

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20
Q

What is the structure of Aspartate?

A

Asp-(CH2)-(C(=O)(-O(-))

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21
Q

What is the structure of glutamate?

A

Glu-(CH2)-(CH2)-(C(=O)(-O(-))

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22
Q

What is the structure of lysine

A

Lys-(CH2)4-(+NH3)

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23
Q

What are the type of interaction between two non-polar groups

A

Hydrophobic interactions

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24
Q

What type of interaction polar amino acids form

A

Hydrogen bonding

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25
Q

What is the pKa of histidine R-group?

A

6

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26
Q

What are the biological roles of amino acids?

A

1) Chemical messengers such as hormones and neurotransmitters

2) precursor for other molecules (nucleotides and heme)

3) metabolic intermediates

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27
Q

What is thyroxine?

A

Thyroxine is a hormone, produced by the thyroid gland, which regulates metabolism

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28
Q

What is melatonin?

A

A hormone that regulates night/day cycle

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29
Q

What is GABA?

A

It is a neurotransmitter, which inhibits the secretion of glucagon

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30
Q

What is serotonin?

A

It is a neurotransmitter which stabilizes the mood and feelings

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31
Q

Where can we find 4-hydroxyproline and 5-hydroxylysine

A

In collagen, as they are modified amino acids

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32
Q

What is the isoelectricpoint (pI)

A

the ph where the net charge of both groups are ionized having zero net charge (pI=pK1+pK2/2)

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33
Q

Which amino acid is non-chiral

A

Glycine

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34
Q

Most amino acids are what type of stereoisomers

A

In the L form

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35
Q

What are the chemical reactions amino acids can do?

A

1) dehydration (amide linkage, formation of a peptide bond)

2) dehydrogenation (oxidation, formation of disulfide bridge)

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36
Q

How does a peptide bond form?

A

It is the reaction between a-carboxyl group of an amino acid with an a-amino group of another amino acids removing a water molecule starting from the N-terminus to the C-terminus

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37
Q

How does a disulfide bond form?

A

Via the oxidation of non-adjacent cysteine amino acid forming cytine

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38
Q

What is the function of a disulfide bond?

A

It is a strong covalent bond which stabilizes polypeptides/proteins

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39
Q

What is the function of glutathione?

A

A tripeptide found in most organisms, involved in:

1) protein and DNA synthesis

2) toxic substance metabolism

3) amino acid transport

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40
Q

What is the function of vasopressin?

A

A nonapeptide, antidiuretic hormone that:

1) regulates water balance, appetite, and body temperature

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41
Q

What is oxytocin?

A

A nonapeptide that aids in uterine contraction and lactation

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42
Q

What is the structure of glutathione?

A

Y-glutamate-cysteine-glycine

43
Q

What is the structure of oxytocin?

A

Cysteine-tyrosine-isoleucine-glutamine-asparagine-cysteine-proline-leucine-glycine-NH2

44
Q

What is the structure of vasopressin?

A

Cysteine-tyrosine-phenylalanine-glutamine-asparagine-cysteine-proline-arginine-glycine-NH2

45
Q

What are the functions of proteins?

A

1) catalysis
2) structure
3) movement
4) defense
5) transport
6) regulation
7) storage
8) stress response

46
Q

How are proteins categorized?

A

1) sequence

2) 3D shape (globular, fibrous)

3) conjugation

47
Q

How many levels of protein structure are there?

A

1) primary (content of amino acid sequence held by peptide bond)

2) secondary

3) tertiary

4) quaternary

48
Q

In which level of protein structure a mutation can occur?

A

Primary structure

49
Q

What is a conservative mutation?

A

A mutation that changes an amino acid to a chemically similar amino changes without affecting the function

50
Q

What is a non-conservative mutation and an example of it

A

Non-conservative mutations, are mutations which changes the function of the protein, like sickle cell anemia which changes the glutamate to a valine in the B-subunit of the hemoglobin

51
Q

When does a protein becomes secondary?

A

When a primary structure is rearranged into either a-helix or b-sheets

52
Q

What stabilizes the secondary structure?

A

Hydrogen bond, between the a-carbonyl and the a-amine, found in the backbone between successive 5 amino acids

53
Q

How many forms of b-sheets are there and how are they formed?

A

2, parallel and anti parallel, when two or more polypeptide chain segments line up, side by side stabilized via hydrogen bonds

54
Q

What are motifs?

A

They are super secondary structures, with patterns of a-helix and b-sheets (bab)

55
Q

What is a tertiary structure?

A

It is a unique 3D folding structure, formed by globular proteins, and some have attached prosthetic group

56
Q

Which standard amino acids cannot foster a-helical structure?

A

Proline and glycine

57
Q

Which form of b-sheets are more stable

A

Antiparallel

58
Q

5 examples of super secondary structures

A

1) BAB unit

2) B-meander

3) b-barrel

4) aa unit

5) Greek key

59
Q

How is the tertiary structure stabilized?

A

By the interactions of the R-groups which stabilizes the structure via electrostatic forces

60
Q

What are domains?

A

Contained within Large globular proteins, they are segments of a polypeptide that have a specific function

61
Q

Where are domains found

A

On large globular proteins made of 200+ amino acids

62
Q

Examples of domains

A

1) EF HAND (BIND CALCIUM)

2) LEUCINE ZIPPER (DNA BINDING)

3) B-BARREL (FOR VISION)

4) ATP-BINDING DOMAIN OF HEXOKINASE

5) A/B ZINC BINDING MOTIF

63
Q

WHAT ARE THE INTERACTIONS THAT STABILIZES THE TERTIARY STRUCTURE (VIA THE R-GROUP INTERACTIONS)

A

1) COVALENT DISULFIDE BOND (BETWEEN TWO NON-ADJACENT CYSTEINE)

2) IONIC ELECTROSTATIC SALT BRIDGE INTERACTIONS (BETWEEN OPPOSITELY CHARGED R-GROUPS)

3) HYDROGEN BOND:

1) Ser-OH & HO-Tyr
2) carbonyl oxygen & hydroxyl groups
3) carbonyl oxygen & amine

4) HYDROPHOBIC INTERACTION (between non-polar amino acid R-groups)

5) HYDRATION

64
Q

WHY DOES COVALENT DISULFIDE BOND DOES NOT OCCUR INSIDE OUR CELLS?

A

DUE TO HIGH CYTOPLASMIC CONCENTRATION OF REDUCING AGENTS

65
Q

What are quaternary structures?

A

It is a protein that is composed of several polypeptide chains

66
Q

How are quaternary structure held together?

A

1) ionic

2) hydrogen

3) hydrophobic interactions

Non-common covalent interactions include:

1) disulfide bridges (immunoglobulins)
2) desmosine linkage
3) lysinonorleucine linkage

67
Q

What is allosteric transition?

A

The change on a protein by the binding of a ligand (effectors modulators) which can trigger its conformation which might alert its affinity for other ligand like in the case of the first oxygen binding to a hemoglobin

68
Q

What is oligomers?

A

When you have identical subunits form a multi subunit protein

69
Q

What are the advantages of oligomers

A
  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
70
Q

What is protein denaturation?

A

It is the disruption of protein structure but not the primary (it does not affect peptide bonds)

71
Q

What can cause denaturation?

A
  1. Strong acid or base
  2. Organic solvents
  3. Detergents
  4. Reducing agents
  5. Salt concentration
  6. Heavy metal ions
  7. Temperature
  8. Mechanical stress
72
Q

What are the molecular chaperones which helps in folding polypeptides with 100 or more amino acids

A

1) Ribosome associated chaperons

2) Hsp70 (bind and stabilize proteins during the early stages of development via ATP hydrolysis)

3) Hsp90

4) chaperonins (increase speed & efficiency of the folding process via ATP hydrolysis)

73
Q

How does molecular chaperones help in folding

A

By protecting them from inappropriate protein-protein interactions

74
Q

What happens if refolding cannot occur

A

Chaperons degenerate those proteins, as they can cause Alzheimer’s and Huntington’s diseases

75
Q

Where can we find fibrous proteins

A

They have a structural role with high proportions of a-helix & b-pleated sheets

1) collagen (triple a-helix, (gly-pro-4-hydroxyproline))

2) keratin (double a-helix)

3) fibroin (polymer of gly-ala)

76
Q

What is globular proteins?

A

Water soluble, with biological functions (precise binding of the ligand):

1) hemoglobin (its globin contains 2 alpha and 2 beta chains) & myoglobin (its login protein contains 8 a-helix)

2) enzyme

3) peptide hormone (insulin, glucagon, etc)

4) immunoglobulin (defense)

77
Q

What Type of hemoglobin contains gamma chains instead of beta

A

Embryonic and fetal hemoglobin which have a higher affinity for oxygen

78
Q

Oxygenation of hemoglobin causes the dimers to slide how many degrees?

A

15

79
Q

In what condition is the hemoglobin when it is in its taut form

A

Deoxygenated

80
Q

What is the Bohr effect?

A

Release of oxygen from the hemoglobin due to a decrease in the pH

81
Q

What is the smallest and only achiral amino acid

A

Glycine

82
Q

Which amino acids have a benzene ring

A

1) phenylalanine
2) tryptophan
3) Tyrosine

83
Q

Which amino acids contain sulfur

A

1) methionine
2) cysteine

84
Q

What is unique about polar amino acids

A

They contain either hydroxyl, or amide, or sulfur group

85
Q

Which amino acid is a imino (secondary amino) acid

A

Proline

86
Q

Which neurotransmitter is derived from tryptophan

A

Serotonin

87
Q

Which hormone is derived from tyrosine

A

Thyroxine

88
Q

What is the ph of glutamate

A

3.22

89
Q

How to calculate the pi of acids and base

A

Acid: Pk1+pkr/2

Base: Pk2+pkr/2

90
Q

Peptide & disulfide bonds are a type of which bonds?

A

Covalent

91
Q

What is schiff base formation reaction

A

Electron sharing with another orbit, like aldimines

92
Q

Why is glutathione unique

A

Because the peptide bond between the cysteine and glutamate is formed between the R-group of glutamate and the amine of cysteine

93
Q

Three examples of conjugated proteins

A

1) lipoprotein

2) glycoprotein

3) hemoprotein

94
Q

What is homologous amino acids, and what is meant by invariant

A

Polypeptides with similar “sequence”, and invariant means that some of the amino acids are kept the same

95
Q

What is meant by a variable amino acid

A

Amino acid in a less stringent sequence performing nonspecific function

96
Q

What can disturb the a-helix structure

A

1) lots of glycine (due to it being small, no r-group & rotates a lot)
2) proline (it doesn’t have free Amine group so it doesn’t allow the rotation)
3) large number of charged amine group (it will have repulsion reaction
3) to many bulk R-group (like tryptophan)

97
Q

Usually the turns that are made up of which amino acid

A

Proline & glycine

98
Q

What is mosaic/modular proteins?

A

Proteins with a number of repeated domains

99
Q

What is the difference between a domain and a subunit?

A

Domains are in the same polypeptide sequence while subunits are on different polypeptide

100
Q

What is a proteoform?

A

Multiple proteins arise from the same gene

101
Q

The break down of primary structure is called?

A

Hydrolysis

102
Q

How does the binding of histidine affect the function of the hemoglobin & myoglobin

A

It stabilizes the heme

103
Q

What is the structure of cysteine?

A

Cys-CH2-SH

Biochemistry (12 decks)

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