Proteins Flashcards
Amylase, lipase ad pepsin are all kinds of which type of protein?
They are all digestive enzymes which play a role in breaking down food into smaller pieces which can be readily absorbed by the body.
Which protein is responsible for carrying substances throughout the body in blood or lymph?
Hemoglobin
Which group of proteins are responsible for protecting the body from foreign pathogens?
Antibodies
What is the smallest building block of a protein?
What are the characteristic functional groups this molecule must contain?
An amino acid, which is made up of 1 amino group, one carboxyl group (acid) and 1 nitrogen atom (and an R group)
What is the name given to the group of molecules that consist of:
- more than 1 amino acid bonded together
- 2 amino acids bonded together
- 3 or more amino acids bonded together
Which type of chemical reaction is required to form the bonds between the amino acids?
- Peptide
- Dipeptide
- Polypeptide
They bond via dehydration synthesis (carboxyl grp from growing end of the chain will react with the amino grp of the incoming chain) and form peptide bonds
Most amino acids are drawn as neutral molecules, however, this is not usually how they appear at biological pHs. Why is this? What is the name (of German origin) for this type of molecule?
At physiological pHs, the nitrogen bonded to the alpha will usually be protonated, giving it a positive charge, and the carboxyl grp will usually be deprotonated giving it a negative charge. This means the molecule has equal and opposite charges on each side making it net neutral.
This is called a zwitterion (hybrid ion)
Polypeptides have directionality. Which free functional group is found at the:
- N terminus of a peptide chain?
- C terminus of a peptide chain?
- Amino group is at the N terminus
- Carboxyl group is at the C terminus
At physiological pHs, amino acids have an equal and opposite charge on either side, giving them a net neutral charge. Which part of the amino acid is usually found protonated and which part is deprotonated?
The carboxyl group is acidic so will readily donate a proton to the solution giving it a negative charge.
The Amino group is basic and will readily accept a proton giving it a positive charge.
How many different amino acids are there?
Bonus points for naming them all.
There are 20 different amino acids which bond to form proteins.
They are:
- Glycine
- Alanine
- Valine
- Leucine
- Isoleucine
- Proline
- Methionine
- Phenylalanine
- Tyrosine
- Tryptophan
- Serine
- Cystine
- Lysine
- Threonine
- Histidine
- Arginine
- Asparagine
- Glutamine
- Aspartic Acid
- Glutamic Acid
In the context of protein structure, what is involved in the following setpe:
- Primary structure
- Secondary structure
- Tertiary structure
- Quatinary structure
- Primary structure: Refers to the sequence the amino acids which make up a protein and the peptide bonds that keep them together. Primary structure is like the alphabetic code for a protein.
- Secondary structure: Refers to the bonds formed between the atoms in the backbone of the molecule - that is not involving any atoms in the R groups. This is where alpha helices and beta sheets will occur.
- Tertiary structure: Refers to the overall three-dimensional structure of a polypeptide. The tertiary structure is primarily a result of interactions in the R group atoms. The interactions can include: hydrogen bonding, ionic bonding, dipole-dipole interactions, London dispersion forces, and disulfide bonds – basically, everything except covalent bonds.
- Quaternary structure: If a protein consists of more than 1 amino acid chain, the interactions between these chains (usually London dispersion forces and hydrogen bonding) will give the protein its quaternary structure
How does an alpha helix form in a protein?
In an α helix, the carbonyl (C=O) of one amino acid is hydrogen bonded to the amino H (N-H) of an amino acid that is four down the chain. (E.g., the carbonyl of amino acid 1 would form a hydrogen bond to the N-H of amino acid 5.) This pattern of bonding pulls the polypeptide chain into a helical structure that resembles a curled ribbon, with each turn of the helix containing 3.6 amino acids. The R groups of the amino acids stick outward from the α helix, where they are free to interact.
How does a beta sheet form in a protein?
In a β pleated sheet, two or more segments of a polypeptide chain line up next to each other, forming a sheet-like structure held together by hydrogen bonds. The hydrogen bonds form between carbonyl and amino groups of backbone, while the R groups extend above and below the plane of the sheet.
The strands of a β pleated sheet may be parallel, pointing in the same direction (meaning that their N- and C-termini match up), or antiparallel, pointing in opposite directions (meaning that the N-terminus of one strand is positioned next to the C-terminus of the other).
Why is the amino acid proline sometimes known as the helix breaker?
Because its unusual R group (which bonds to the amino group to form a ring) creates a bend in the chain and is not compatible with helix formation.
Proline is typically found in bends, unstructured regions between secondary structures.
What is the strongest type of bond found in the tertiary structure of proteins?
Disulfide bonds.
they are covalent linkages between the sulfur-containing side chains of cysteines and act as molecular “safety pins,” keeping parts of the polypeptide firmly attached to one another.
What type of bonding is present in the secondary structure of protein?
Hydrogen bonds occur between the amino acid backbone causing the protein to bend and fold in repeating patterns. (alpha helices and beta pleated sheets)
When is a protein said to be denatured?
When a protein loses its higher-order structure (shape, bends, folds), but not its primary sequence i.e. due to a change in temperature or pH.
What is the name of the process under which a protein may unfold, lose it’s structure or even completely die due to things like changes in temperature or pH?
Denaturisation
What is the role of a chaperone protein in a cell?
They assist in the folding process of proteins as they emerge from the ribosomes.
What does a cell’s surface area have to do with its likelihood of survival?
The larger the cells surface area to volume (SA:V) ratio is, the more efficiently it is in diffusion an removal of waste products.
As a cell gets larger, it’s volume will increase faster than it’s surface area and therefore eventually will not be able to diffuse/ remove wast products quick enough to survive.
