1. Proteins Flashcards by Farha Hamza

What are proteins?

Polypeptides made up of amino acids joined covalently together.

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Whar does the folding of proteins depend on?

the chemical and physical properties of the amino acids

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What determines the amino acid sequence?

The amino acid sequence of a protein is encoded by a gene and determined by the nucleotide sequence of that gene.

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How are amino acids classified?

They are classified according of the chemical properties of the R groups

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What determines the acid base behaviour of the amino acids?

R groups

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What is an amino acid residue?

An amino acid residue is what remains of an amino acid after it has been joined by a peptide bond to form a protein

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List 7 chemical properties of R group that help classify amino acids

Hydrophobic
Hydrophilic 
Polar
Non polar
Acidic
Basic
Neutral

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List 2 physical properties of r groups that help classify amino acids?

Aliphatic

Aromatic

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What does high pK indicate?

Positively charged groups

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What does low pK indicate?

Negatively charged groups

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What happens if the pH of the solution < the pK value?

the group will be protonated

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What happens if the pH of the solution > the pK value?

the group will be deprotonated

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Define primary structure

The linear amino acid sequence of the polypeptide chain

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Define secondary structure

Local spatial arrangement of polypeptide backbone - conformations like helixes

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Define tertiary structure

The overall 3 dimensional configuration of the protein

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Define quaternary structure

Association between different polypeptides to form a multi subunit protein

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Define peptide bond formation

The linking of two amino acids accompanied by the abstraction of a molecule of water

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List two feature of peptide bonds

Planar - Ca, C, O, N, H and Ca all lie in the same plane

Rigid - C-N peptide bond has partial double bond characteristics
- Unable to rotate – contributes to planarity

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What does a trans on formation of the peptide bond mean?

Alpha Carbons of the two amino acid residues on opposite sides of peptide bond

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What does a cis transformation of a peptide bond mean?

Alpha Carbons of the two amino acid residues on the same sides of peptide bond

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Are the Bonds on either side of the peptide bond are free to rotate?

Yes

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What does the amino acid sequence of a protein determine?

The way in which the polypeptide chain folds

* The physical characteristics of the protein

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What is the isoelectric point of proteins?

The isoelectric point, pI, of a protein is the pH at which there is no overall net charge

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What is the pI of basic proteins and why?

pI > 7

Contain many positively charged (basic) amino acids

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What is the pI of acidic proteins an why?

pI < 7 | Contain many negatively charged (acidic) amino acids

What does is meant if the pH < pI ?

protein is protonated

What does it mean if pH > pI

protein is deprotonated

Define Peptides/oligopeptides

few amino acids in length

Define Polypeptides/proteins

Many amino acids

What are conjugated proteins?

When proteins contain covalently linked chemical components in addition to amino acids

Give an example of a conjugated protein

Lipoproteins

What causes the formation of alpha helixes?

H-bonds between N-H and C=O

Which proteins are strong helix formers?

Small hydrophobic residues such as Ala and Leu

Why does Pro act as a helix breaker?

because the rotation around the N-C a bond is impossible

Why does Gly act as a helix breaker

because the tiny R- | group supports other conformations

Describe the beta pleated sheet

Antiparallel b-sheet: adjacent b-strands run in opposite directions, with multiple inter-strand H-bonds stabilizing the structure.

What is the role of fibrous proteins?

support, shape, protection

What is the role of globular proteins?

catalysis, regulation

Describe the shape of fibrous proteins

Long strands or sheets

Describe the shape of globular proteins

Compact shape

Describe the structure of fibrous proteins

Single type of repeating secondary structure

Describe the structure of globular proteins

Several types of secondary structure

Give an example of a fibrous protein

collagen

Give an example of a globular protein

Haemoglobin

What is a motif?

Folding patterns containing 1 or more elements of secondary structure

What are domains?

Part of a polypeptide chain that fold into a distinct shape. Often has a specific functional role

Describe the folding of water soluble proteins

Polypeptide chains fold to so that hydrophobic side chains are buried and polar, charged chains are on the surface

What are the forces present in primary structure?

Covalent(peptide)

What are the forces present in secondary structure?

Hydrogen bonds

What are the forces present in tertiary structure?

``` Covalent Hydrogen bonds Ionic bonds Disulphides bridges Van der Waals Hydrophobic forces ```

What a re the forces present in quaternary structure?

``` Covalent Ionic, Disulphides bridges H-bonds, Van der Waals, hydrophobic ```

Between which group are disulphides bridges formed?

Between 2 cysteine groups

What type of bond is a disulphide bridge?

Covalent bond

What can break disulphide bridges?

Reducing agents

What happens to most proteins with disulphide bridges and why?

Most proteins with disulphide bonds are secreted. Extracellular conditions are harsher for proteins so most secreted have strong disulphides bonds which helps to maintain structure

How are electrostatic interactions formed?

Formed between charged groups

How are hydrogen bonds formed?

Formed between electronegative atom and a hydrogen bound to another electronegative atom

What is the hydrophobic effect?

Interaction between hydrophobic side chains. Due to displacement of water

What is Van der Waals?

Dipole-dipole interactions formed because of transient location of electrons at any given moment . * Very weak forces. * Intrinsic to any bond type

When are van der Waals forces important?

Important when surfaces of 2 large molecules come together

What is native conformation?

A normally folded protein that is functional is said to in the native conformation

What is protein denaturation?

Disruption of protein structure is known as denaturation. Caused by breaking of forces that hold proteins together. Losing the native conformation.

What 3 things cause protein denaturation and how?

Heat - Increased vibrational energy pH - Alters ionization states of amino acids Changes ionic/H-bonds Detergents/organic solvents - Disrupt hydrophobic interactions

How do proteins fold?

The folding process must be ordered Each step involves localised folding and with stable conformations maintained Driven by the need to find the most stable conformation

What happens when there is protein misfolding?

Altered conformation of a normal human protein promotes converts existing protein into diseased state