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Cell Basics > Proteins 1+2 > Flashcards

Proteins 1+2 Flashcards

1
Q

What is organization like in primary secondary tertiary and quaternary proteins

A

Primary- disulfide bonds
Secondary- Local arrangements
Tertiary- 3D packing
Quaternary- Number and position of polypeptide subunits

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2
Q

How many amino acids do humans synthesise

A

11

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3
Q

What side chain do proteins always start with

A

Methionine

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4
Q

What side chain is relatively unreactive

A

Methionine

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5
Q

Which side chain can form complexes with various metal ions

A

Cysteine

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6
Q

What does a disulfide bond form between

A

Cysteine molecules. 2 form CYSTINE

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7
Q

When do disulfide bonds not form

A

In cytosol

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8
Q

What is the peptide bond like

A

Has double bond character. There is delocalization of pie electrons over the entire peptide bond rather than just over the c=o bond. The partial double character of N-C bond means restricted rotation and the bond is planar.

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9
Q

Is a cis or trans formation favored in a peptide bond?

A

Trans, because of steric clashes

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10
Q

Where do hydrogen bonds form in secondary structures?

A

Carboxyl group of one amino acid and an amino group of another

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11
Q

What is the secondary structure?

A

Doesn’t include side chains

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12
Q

What is the alpha helix like compared to the beta pleated Sheet?

A

Alpha helix side chains-
Beta side chains- up and down

In beta side chains, parallel goes from N to C terminal, antiparallel goes from C to N

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13
Q

Whats a tertiary structure?

A

Refers to the exact 3D structure, and the packing of the secondary structural elements within it

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14
Q

What do polypeptides greater than 200 amino acids display?

A

Domains (which often serve as independent units of function)

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15
Q

What are structural motifs? And what are made of structural motifs?

A

Secondary structures linked by loops in specific 3D arrangements

Domains

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16
Q

When are structural motifs and domains achieved?

A

After biosynthesis

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17
Q

What does the conformation attained in a structural motif dependent on? And what is folding caused by?

A

Amino acids present

Caused by position and extent of secondary structure

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18
Q

what are the major stabilizing forces of conformation?

A

Hydrophobic interactions
Electrostatic attraction
Covalent linkages

19
Q

What’s a hydrophobic interaction caused by?

A

Nonpolar residues are buried on the inside of a polypeptide’s interior

20
Q

How are IM forces different in thermophiles and psychrophiles?

A

Thermophiles- increased IM interactions

Psychrophiles- decreased IM interactions

21
Q

How many common amino acids are there?

A

20

22
Q

What’s an oligomer

A

A multi-subunit complex

  • identical polypeptides (homo-oligomer)
  • non-identical polypeptides (hetero-oligomer)
23
Q

What’s a protomer?

A

The identical subunits of a complex

24
Q

HOW do chains associate with each other permanently

A

Disulfide bonds

25
Q

How do chains associate with each other transiently (non permanently)

A

electrostatic interaction (e.g. hydrophobic interactions)

26
Q

What is a quaternary structure

A

Arrangement in 3D space

27
Q

How do subunits usually interact

A

Non- covalently

can have disulfide bonds

28
Q

What do transcient oligomers show?

A

Decreases hydrophobicity at the interface

29
Q

Advantages of subunits

A

Allow for;
-expansion
-easier repair (can remove and repair each subunit instead of repairing the whole thing)
alternate site of assembly
-reduced genetic coding so less chance of mutation
-Small subunits made so can easily move protein

30
Q

Why might oligomers make better enzymes

A
  • Size increase supports the 3D structure better
  • IN a homo-oligomer, each subunit will have an active site
  • Subunits permit regulation
31
Q

Characteristics of fibrous proteins

A

Display one type of secondary structure

-only have structural jobs

32
Q

Example of fibrous protein

A

alpha keratin

33
Q

Characteristic of globular protein

A

Secondary structures interspersed by flexible loops with hydrophilic residues that interact with water

34
Q

example of globular protein

A

Haemoglobin

35
Q

What is the structure of haemoglobin

A

Perforin ran with Fe2+ coordinated to it in the middle

36
Q

Names of states of hemoglobin when oxygen is bound to it, and not bound to it

A

Taut- not bound

Relaxed- bound

37
Q

What state of haemoglobin means a higher affinity for oxygen?

A

Relaxed

38
Q

Advantage of having more than one subunit in haemoglobin

A

Means that you can take up and release oxygen easily because of cooperativity

39
Q

When can modifications of proteins take place?

A

Co translational or post translational

40
Q

Examples of post translational modifications

A

introduced by enzyme

  • phosphorylation/methylation/acetylation
  • can be reversible or not
  • Proteolysis (irreversible) is used to activate enzymes
41
Q

What’s glycosylation?

A

Attachment of carbs to extracellular and cell-surface proteins- (stabilizes and protects against digestion, or for recognition)

42
Q

Whats the difference between glycoprotein and proteoglycan

A

glycoprotein- carb is the major component

proteoglycan- protein is the major component

43
Q

What’s N-linked glycosylation

A

attachment of sugar to asparagine

44
Q

What’s O-linked glycosylation

A

Attachment of sugar to hydroxyl group of sereine or thymine

Cell Basics (8 decks)

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