KH3 Flashcards by Talia Labute

What is a protein’s primary structure?

The specific sequence of amino acids in a protein

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What is the structure of linear polymers

Folded into definite 3D structures depending on the sequence of amino acids

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What is the function of a protein determined by

Overall shape and the distribution throughout that overall shape of the amino acid side chains with their distinctive chemical properties

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What are the two major classes of amino acid side chains

Hydrophilic (polar electronic charge distribution and interact well with the polar solvent water)

Hydrophobic (non-polar charge distribution and therefore do not interact well with the polar solvent water)

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What is the hydrophobic effect

water molecules surrounding hydrophobic molecules dispersed in water adopt a constrained, cage-like organization (low entropy)

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What happens if hydrophobic molecules coalesce in the hydrophobic effect

The total number of low entropy, constrained water molecules is reduced, and this net increase in entropy ultimately drives the formation of separate hydrophobic and aqueous phases (higher entropy when there are less water molecules after aggregation)

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What does DNA indirectly determine in terms of proteins

DNA determines amino acid sequence of the protein but ultimately dictates the 3D structure and ultimately function of the protein

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What does secondary structure refer to

The local conformations of the peptide chain backbone

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What are the two major peptide chain backbone conformations

Alpha helix and beta sheet

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What are the two major peptide chain backbone conformations based on

H-bonding between peptide bond carbonyl O atoms on one amino acid residue, and amino group hydrogens on a different amino acid residue

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How does the bonding work in alpha helix structures

Amino acid n H-bonds with amino acid n+4

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What is the periodicity of alpha helix structures

Titled axis of U-bonds drives periodicity of 3.6 residues per turn

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What is the gross structure of alpha helices

Straight rod

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What are surface properties of alpha helix structures dependent on

Side chains

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What are surface properties of alpha helices that can be determined

Propensity for alpha helix to form
Interactions of the alpha helix with other parts of the protein (stability)

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How does bonding work in beta sheets and what does it create

H-bonds link two adjacent beta strands, can create large surfaces

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What property of beta sheets determines the interactions of the beta sheet with other parts of the protein and also the propensity for the beta sheet to form

Amino acid side chains protruding above and below the plane of the beta sheet

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What kind of relationships can the strands of beta sheets have

Strands may be parallel or antiparallel (and could be from different polypeptides)

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What are secondary structures described as and how many secondary structure elements do polypeptides have

Local and multiple

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What is tertiary structure

Overall conformation of the polypeptide (spatial organization of the multiple secondary structure elements)

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What is the function of amino acid side chains in tertiary structures

Mediate interactions between different parts of the protein and between the protein and its ligand GDP

What are most of the structure-driving interactions among the amino acids in a protein

Non-covalent bonds

What is an important covalent bond interaction that can be important

Side chain of the amino acid cysteine contains a sulfhydryl group that can form covalent S-S (disulfide) bonds with other cysteine side chains

What are examples of non-covalent bonds in proteins

H-bonds among peptide backbone carbonyl and amino groups that support alpha helix and beta sheet secondary structure
H-bonds between amino acid side chains with polar side chains
Ionic bonds between positively charged (basic) and negatively charged (acidic) side chains
Van der Waals interactions among hydrophobic side chains

What can disulfide bonds be and what kind of structures do the contribute to

Intrachain (tertiary structure) Interchain (quaternary structure)

What side of the polypeptide are new amino acids added to

C-terminus

What kinds of representations are there of tertiary structures and which ones are generally used and not used and why

1. Backbone trace (used, no distinct shape just tubes) 2. ball and stick model (not used, shows every atom) 3. Ribbon diagram (used, shows tubes and helix and sheet) 4. Water accessible surface (not used, different colours) 5. Hybrid model (used, ribbon diagram with white outer coating)

What are motifs of protein structures

Combinations of secondary structures forming distinct local 3D structure

What are the types of motifs of protein structure

1. Coiled-coil motif 2. EFhand/helix-loop-helix motif 3. Zinc-finger motif

What are the qualities of the coiled-coil motif

made up of two polypeptides, have a heptachlor repeat (every fourth molecule is a hydrophobic amino acid and every molecule in between in hydrophyllic amino acid) involved in protein:protein interactions

What are the qualities of the EFhand/helix loop-helix motif

Right angle, allows the binding of Ca2+

What are the qualities of the Zinc-finger motif

Common in transcription factors (binds to DNA/RNA)

What are the qualities of motifs

Recognizable structure, often characteristic amino acid sequence features, generally small, local, do not contain sufficient amount of structure maintaining bonds to hold the motif in its characteristic 3D shaper if cut away from the rest of the protein

Why are motifs not structurally independent entities

The rest of the protein contributes to the stability of the local motif, if cut away motif would fall apart

What are domains

3D structures with proteins that are larger than motifs and contain a sufficient number of bonds to hold the domain in its characteristic shape if it is cut away from the rest of the protein

Why are domains structurally independent entities

The rest of the protein contributes little to the stability of a domain (although covalently joined to the rest of the protein)

What are the four major structural classes of proteins

Fibrous proteins, integral membrane proteins, globular proteins, intrinsically disordered proteins

What are characteristics of intrinsically disordered proteins

Proteins that exist as random coils under physiological conditions, may adopt a specific secondary/tertiary structure upon binding to a well-structured partner protein

What is the structural definition of tertiary structure domains

40 aa-long region, compactly folded, can be made of various motifs

What is the structure of tertiary structure domains

Two different domains: globular domain (distal) and fibrous domain (proximal with a long protruding protein interacting with a smaller one) Heterodimer: two different polypeptides (HA1 and HA2)

What is the modular nature of protein domains

Similar domains can be found in diverse proteins, and also as multiple similar copies within any given protein

What are the characteristics of a quaternary structure (multimeric proteins)

Trimmer of identical subunits each composed of an HA1 and HA2 chain held together by non-covalent bonds, subunits also held together by non-covalent bonds

Can multimeric proteins contain any number of identical t or different polypeptides

Yes

What are supramolecular complexes

Large molecular machines made up of multiple distinct proteins each of which may itself contain multiple subunits

Are supramolecular complexes stable

No, they fall apart when job is done

What is a characteristic of the evolution of proteins

Evolution was not to maintain the structure of proteins but the functions, 3D structure almost more important than amino acid sequences

What is the hydrophobic effect

Tendency of hydrophobic molecules to find each other and to bond to each other in water

What do side chain interaction affect

Overall stability of protein

How does a beta sheet arrange amino acid side chains

Up and down

What does the water accessible surface model show us

Distribution of positive and negative charges

What can a disulfide bond between two cysteine side chains in a protein do

Cause change in structure and it can help hold together tertiary and quaternary structures

Why do all hydrophobic molecules line up on pitch (3.6) of an alpha helix thus putting them all in the middle in a heptad

Every second hydrophobic amino acid means that 7/2 is 3.5