Week 2 Lecture Flashcards by Alisha Jameer Shaik

What are the diffrent protein structures?

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

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True/ False:

All proteins have Quaternery and multiprotein complexes

False, and the definition of proteins varies.

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What are the four catergories of amino acids?

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

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What are proteins composed of?

Amino Acids

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What are the classification for amino acids?

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

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How is genetic code or amino acids groups together?

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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What is the formula for Cystein?

CH2—SH

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Why are the covalent disulphide bonds important in the cystein?

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

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Why is cystein important?

It behaves differently in oxidative conditions and reduction conditions

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What happens to cystein in Oxidative conditions?

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

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

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

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think of the location under oxidative conditions

Where are the cystein with disulphide bonds found?

In the ER leumen or the outside of the cell.

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Where are the peptide bonds made?

Peptide bonds are made in the ribosome.

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

Condensation reaction takes place to form a water molecule.

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

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

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

Carbonyl carbon

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

How do you find a peptide bond?

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

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

Amide Nitrogen

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What are residues?

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

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What are the two ends of a primary protein?

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

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Does differences in primary AA sequence matter?

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Yes!

How do you identify the backbone of a primary protein?

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It is everthing except the branches (R group)

What was Liam treated with?

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Vasoprissin substitute called Oxytocin.

What are the diffrences and Similarties in Vasopressin and Oxytocin?

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

# Which terminus do you start from? How do you start numbering the AA sequnce

Start numbering from N-terminus.

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

True

How does aplha helix gets its stability from?

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

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

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

What are the differences between a Dna and alpha helix?

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.

2. 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.

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

1 polypeptide chain, 1 betasheet and 3 strands

Where does H-bonding occur in Betasheet?

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)

What do arrows represnt in beta sheets?

Strands

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

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

Is this parallel or anti-parallel betasheet?

Antiparallel as arrows are pointing different directions

is this parallel or antiparallel betasheet?

Parallel betasheets as arrows are pointing the same direction.

What are the two types of betasheets?

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

True/False: Helices always form Coiled coils

False, they sometimes do not always.

What are helix with coiled coil form called?

Amphipathic

Why do some alpha-helices form amphipathic proteins?

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.

Where are coiled-coils found?

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

What is an example of super-secondary structure?

Coiled-coils

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

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.

What do the forces determine in tertiary structure?

They determine how the entire peptide chain folds.

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

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.

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

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

# Think in terms of stability Which conformation do proteins usually fold into?

Energitically favoured conformation.

What are domains in proteins?

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.

How many domains does this protein have?

What are protein families?

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

How do you study a single protein?

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

Week 2 Lecture Flashcards

(52 cards)