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Bio 130 > Week 2 Lecture > Flashcards

Week 2 Lecture Flashcards

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1
Q

What are the diffrent protein structures?

A
  1. Primary (Sequence) it is the AA sequence and it dictates the overall structure.
  2. Secondary (Local folding): alpha helix
  3. Teritary (Long range folding): 3D structure
  4. Quaternery (Multimeric organisation): More than one polypeptide chain
  5. Multiprotein complexes: **Multi protein complexes. **
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2
Q

True/ False:

All proteins have Quaternery and multiprotein complexes

A

False, and the definition of proteins varies.

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3
Q

What are the four catergories of amino acids?

A

1.Uncharged polar
2. Non polar
3. Acidic
4. Basic

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4
Q

What are proteins composed of?

A

Amino Acids

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5
Q

What are the classification for amino acids?

A

AA can be written as 3 letters (Asp) or as a single letter

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6
Q

How is genetic code or amino acids groups together?

A

They are grouped together based on similar properties. (All the non-polar ones are to the left while all the acidic ones are in the bottom. (third column, third row)

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7
Q

What is the formula for Cystein?

A

CH2—SH

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8
Q

Why are the covalent disulphide bonds important in the cystein?

A

They act as braces, causing holding and stabilising the protien structure.

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8
Q

Why is cystein important?

A

It behaves differently in oxidative conditions and reduction conditions

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8
Q

What happens to cystein in Oxidative conditions?

A

It forms a covalent disilphide bond with another cystein (interspecific disulphide bonds) or within its own (Intrachain disulphide bonds)

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9
Q

What happens to disulphide bonds in cystein in reduction conditions (both interchain disulphide bonds and intrachain disulphide bonds)?

A

The bonds break in the reduction rxn, this usually happens in the cytosol ,

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10
Q

think of the location under oxidative conditions

Where are the cystein with disulphide bonds found?

A

In the ER leumen or the outside of the cell.

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11
Q

Where are the peptide bonds made?

A

Peptide bonds are made in the ribosome.

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12
Q

What molecule is formed when a ribosome synthesises a peptide bond?

A

Condensation reaction takes place to form a water molecule.

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12
Q

True/False: H or OH from R groups can also participate in a condensation reaction

A

False, the ribosome only takes OH from carboxyl group and H from an animo group

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12
Q

What is the carbon that is attached to both amino group and double bonded to O called?

A

Carbonyl carbon

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12
Q

Think of what is attaced to a carbon with peptide bond…

How do you find a peptide bond?

A

The carbonyl carbon is attached to amino group and is double bonded to an O

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13
Q

What is the nitrogen called once the condensation takes place and a peptide bond is formed?

A

Amide Nitrogen

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14
Q

What are residues?

A

Residues are the individual amino acids that are linked together by peptide bonds to form a polypeptide chain.

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15
Q

What are the two ends of a primary protein?

A

N-terminal (NH2) and C-terminal (Carboxyl termial)

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16
Q

Does differences in primary AA sequence matter?

A

Yes!

17
Q

How do you identify the backbone of a primary protein?

A

It is everthing except the branches (R group)

18
Q

What was Liam treated with?

A

Vasoprissin substitute called Oxytocin.

19
Q

What are the diffrences and Similarties in Vasopressin and Oxytocin?

A
  1. Both are 9 AA neuropeptide hormones
  2. Their AA sequence is identical, except in 2 positions.
  3. Vasoprissin controls urine production, while oxytocin helps in birth, lactation and pair bonding.
20
Q

Which terminus do you start from?

How do you start numbering the AA sequnce

A

Start numbering from N-terminus.

21
Q

True/ False: Alpha Helix can be a small part of the chain or can also be the entire chain

A

True

22
Q

How does aplha helix gets its stability from?

A

From the H-bonding between the O from carboxyl group of C1 and hydrogen from C5 of the C5 alpha carbon.

Note: This bond is formed every four carbons away, O from n and H from n + 4

23
Q

Do the R groups form the H bond or stabilixe the alpha helix?

A

No, they do not stabalise, infact they are not even drawn on the alpha helix.

24
Q

What are the differences between a Dna and alpha helix?

A
  1. Dna has 5’ and 3’ ends while aplha helix has N-terminal and a C-terminal end
  2. Dna is double helix while alpha helix is single stranded
  3. Dna has base-pairs holding it together while alpha helix does not need the residues to hold it together
  4. Dna has basepairs facing inwards while the alpha helix has R groups facing outwards.
25
Q
  1. Which of the following is NOT correct regarding amino acid side chains?
    a. They can play a significant role in polypeptide folding.
    b. They are the most important for helping to stabilize α-helix and β-sheet secondary
    structures.
    c. They can play a significant role in the function of the polypeptide.
    d. They are what gives each amino acid its unique biochemical properties.
A

B

26
Q

How many beta sheets, polypeptide chains and strands are present in this picture?

A

1 polypeptide chain, 1 betasheet and 3 strands

27
Q

Where does H-bonding occur in Betasheet?

A

Carbonyl oxygen of 1aa, and H of a peptide backbone (neighbouring strand). (R groups are not invloved in H bonding, but they project up and down)

28
Q

What do arrows represnt in beta sheets?

A

Strands

29
Q

How is H-bonding different in betasheets compared to alpha helix?

A

In alpha helix the bonding occurs in the carbonyl oxygen in first carbon and the H from amino group of fourth carbon (n, n+1) of the SAME STRAND

While in the betasheets, the hydrogen bonding takes place between carboxyl oxygen and hydrogen from DIFFERENT STRANDS

30
Q

Is this parallel or anti-parallel betasheet?

A

Antiparallel as arrows are pointing different directions

31
Q

is this parallel or antiparallel betasheet?

A

Parallel betasheets as arrows are pointing the same direction.

32
Q

What are the two types of betasheets?

A

Parallel (arrows fare in the same direction) and Antiparallel(arrows pointing different directions)

33
Q

True/False:
Helices always form Coiled coils

A

False, they sometimes do not always.

34
Q

What are helix with coiled coil form called?

A

Amphipathic

35
Q

Why do some alpha-helices form amphipathic proteins?

A

If an alpha helix has two R groups, one hydrophobic and the other hydrophillic they tend to form a coil with another aplha helix so the hydrophobic ends can face the inside where there is no water and the outside can be the hydrophillic groups.

36
Q

Where are coiled-coils found?

A

In alpha-Keratin of hair and skin, and also myosin motor proteins.

37
Q

What is an example of super-secondary structure?

A

Coiled-coils

38
Q

What are the forces involved to give the polypeptide chain its 3D shape?

A
  1. Hydrogen Bonds (remember between carbonyl oxygen, amino H)
  2. Non colvalent disulphide bonds (Like in cystein)
  3. Hydrophillic interactions (like in the amphipathic - coiled coils)
  4. And other interactions between the residue and the R groups.
39
Q

What do the forces determine in tertiary structure?

A

They determine how the entire peptide chain folds.

40
Q

Give 3 examples of tertiary structure interactions which have H-bonding.

A
  1. Backbone to backbone: H-bonding between atoms of two peptide bonds.
  2. Backbone to sidechain: H-bonding between atoms of a peptide bond and an amino acid side chain
  3. Sidechain to sidechain: Hydrogen bonds between atoms of two amino acid side chains.
41
Q

Name the proteins that help make the folding of aa chain efficient

A

Chaperon proteins, though the aa determines the folds, chaperon proteins help make this process more efficient.

42
Q

Think in terms of stability

Which conformation do proteins usually fold into?

A

Energitically favoured conformation.

43
Q

What are domains in proteins?

A

They are bascially one polypeptide chain, with differnet tertiary structures that work semi-independently with each other. Domains are specilized for different functions.

The different domains are connected by **intrincially disordered sequences. **

Eukaryotes have about 2 domains. Domains are important in evolution of proteins.

44
Q

How many domains does this protein have?

A

3

45
Q

What are protein families?

A

Have similar primary, secondary and teritory structures, but the members evolved different funtions and ,most proteins belong to families with similar structural domains.

46
Q

How do you study a single protein?

A
  1. Purify proteins of intrest (use various types of chromotography
  2. Then determine aa sequence
  3. Discover 3D structure using technology
47
Q
A

Bio 130 (9 decks)

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