KH 03 Flashcards
What are proteins?
Linear polymers of amino acids joined by peptide bonds. For this reason, proteins are sometimes referred to as
polypeptides.
Proteins are made by translation of _____ transcribed from
genomic ___.
mRNAs, DNA
What is the basic biological point of DNA and RNA?
To allow the synthesis of proteins, which carry out the physical and chemical function of cells.
How long are the smallest proteins?
About 40 amino acids long
How long is the average protein?
About 300 to 400 amino acids in length
What is the longest known protein and how long is it?
Titin and it’s about 30 000 amino acids long
What is the primary structure?
The specific sequence of amino acids in a protein
Proteins fold into definite 3D structures depending on the _____ of
amino acids.
sequence
What are the functions of a protein determined by?
It’s overall shape (i.e., specific folding pattern driven by amino acid sequence) and the distribution throughout that overall shape of the
amino acid side chains with their distinctive chemical properties.
What are the 2 major classes of amino acid side chains?
Hydrophilic and hydrophobic
What is a hydrophilic amino acid side chain?
A side chain that has a polar electronic charge distribution and therefore interacts with the polar water (can also be neutral)
What is a hydrophobic amino acid side chain?
A side chain that has a non-polar electronic charge distribution and therefore does not interact with the polar water
What is the hydrophobic effect?
Water molecules surrounding hydrophobic molecules dispersed in water adopt a constrained, cage-like organization (low entropy). If hydrophobic molecules combine, 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. Combination of hydrophobic molecules also favored by weak non-covalent van der Waals intermolecular interactions. Furthermore, there is a tendency for hydrophobic molecules to stay together because it’s more efficient to make a cage of 2 things that are together than to make 2 cages individually.
Hydrophilic side chains like to be _____ the protein and be near water.
outside
Hydrophobic side chains like to be _____ the protein and be far from water.
inside
What is a conformation?
The three-dimensional arrangement of side groups on a molecule which can freely rotate into different positions without breaking any bonds.
Secondary and tertiary structures determine the path of the _____ _____ through space and hence, the overall shape of the molecule.
peptide backbone
Does DNA determine the protein function?
Kind of. DNA determines only the amino acid sequence of the protein but it is indirectly linked to the 3D structure and the function of the protein.
What is dictated by the amino acid sequence?
Protein structure and function
What is a domain?
Domains are rather stable partial structures that are connected to the rest of the protein but are structurally more or less independent
What does the 5’ end in DNA/RNA correspond to in a polypeptide?
The N-terminus
What does the 3’ end in DNA/RNA correspond to in a polypeptide?
The C-terminus
What are the 2 major peptide chain backbone conformation in the secondary structure?
Alpha-helix and Beta-sheet
What does the secondary structure refer to?
Local conformations of the peptide chain backbone
If 60% of the length of the average polypeptide chain consists of segments of alpha-helix and beta-sheet, what does the remaining 40% correspond to?
It consists of the polypeptide chain linking those alpha-helix and beta-sheet
What is the periodicity of the bonds in the alpha-helix?
Amino acids form H-bonds with amino acids n + 4 (4 residues down the side chain). Tilted axis of H-bonds drives periodicity of 3.6 residues per turn.
What do surface properties of a polypeptide exclusively depend on?
Side chains. These will determine the
propensity for alpha-helixes/beta-sheets to form, and also their interactions with other parts of the protein (and thus its stability).
_____ link 2 adjacent Beta-strands
H-bonds
Where do amino acid side chains protrude from in the beta-sheet?
Above and below the plane of the Beta-sheet
Are the strands in the beta-sheet parallel or anti-parallel?
Both! They may be parallel or antiparallel
Secondary structure is local. Most polypeptides have _____ secondary structure elements.
multiple.
What does the tertiary structure refer to?
The overall conformation of the polypeptide, i.e., the spatial organization of the multiple secondary structure elements
Most of the structure-driving interactions among the amino acids
in a protein are _____ bonds.
Non-covalent
What are the bonds among peptide backbone carbonyl and amino groups that support alpha-helix and
beta-sheet secondary structure?
H-bonds
What are the bonds between amino acid side chains with polar side chains?
H-bonds
What are the bonds between positively charged (basic) and negatively
charged (acidic) side chains?
Ionic bonds
What are the bonds for the interactions among hydrophobic side chains?
Van der Waals interactions
What is the important covalent bond interaction?
The side chain of the amino acid cysteine contains a sulfhydryl group
that can form covalent S-S (disulfide) bonds with other cysteine side chains.
In proteins, disulfide
bonds can be _____,
contributing to tertiary
structure, or _____,
contributing to
quaternary structure
intrachain, interchain
What is a “motif” of a protein structure?
Combinations of secondary structures forming distinct local 3D structure.
What are 3 motifs?
The coiled-coil motif, the EFhand/helix-loop-helix motif and the Zinc-finger motif
Are motifs structurally independant entities?
No. Motifs lose their characteristic 3D-shape if cut away from the rest of the protein. The rest of the protein contributes to the stability of the local motif.
Are domains structurally independant entities?
Yes. Domains do not lose their characteristic 3D-shape if cut away from the rest of the protein because they contain a sufficient number of bonds to hold the domain in its characteristic chain. The rest of the protein contributes little to the stability of a domain. They are covalently-joined to the rest of the protein
What is bigger, a domain or a motif?
A domain
