Lecture 2 Flashcards
Most abundant macromolecule in the cell?
Proteins
What determines the structure/function of a given protein?
The amino acid sequence of a protein determines it structure which ultimately determines how it is folded (3D structure) and what its function will be
What are proteins?
Polymers which are made up of amino acids monomers
Describe the structure of amino acids?
- Amino group
- alpha-carbon (bound to 4 atoms)
- Carboxyl group
- Side chain
T/F: At pH 7 the carboxyl and amino group of the amino acids are ionized ?
True, the amino group is positive and the carboxyl group is negative
How do the amino acid side chains differ?
- Polar/ Charged/ Hydrophobic
- Small/Large
- Covalently linked to polypeptides
Name the 5 polar amino acids?
- Asparagine
- Glutamine
- Serine
- Threonine
- Tyrosine
Least polar of the five amino acids and why ?
Tyrosine , has a hydrophobic ring that is more difficult for H-bonding
Characteristics of Polar amino acids?
- No charge
- Form H-bonding(non-covalent)
-Found near the cytosol
Name the three basic amino acids?
- Lysine
- Arginine
- Histidine
Histidine?
Only partially positive at a neutral pH because its nitrogens do not have high affinity for hydrogen
Characteristics of acidic and basic amino aicds?
can form ionic interactions between each other
10 Hydrophobic amino acids?
- Alanine
- Valine
- Proline
- Phenylalanine
- Glycine
- Cysteine
- Leucine
- Isoleucine
- Methionine
- Tryptophan
Characteristics of non polar amino acids?
Interact through hydrophobic interactions (exclusion of water molecules)
Cysteines?
Form disulfide bonding but not in the cytosol because it is a reduced environment
Link between two amino acids?
Peptide bond
What type of bonds can peptide bonds engage in?
Can engage in h-bonding
T/F: Both the polypeptide backbone and side chains can engage in non-covalent bonding?
True, polypeptide back bonde can for H-bonds with peptide bonds and side chains can form non-covalent bonds via H-bodning with polar amino acids
Flexibility of peptide bond?
Does not allow for free rotation due to the bond being planar and it has double bond character
Can the polypeptide backbone rotate at all?
Yes it can rotate around the alpha-carbon
Non-covalent interactions ?
- Hydrogen Bonds
- Van der Waals interactions(transient dipoles between all atoms)
- Ionic bonds
- Hydrophobic Interactions
How do hydrophobic interactions increase the entropy of the environment?
Hydrophobic molecules aggregate together meaning they require less water molecules to surround them . The excess water molecules are released to the environment and increase the entropy of it
Disulfide bonding?
-Covalent bonding
-Between cysteines
-Occurs in the extracellular proteins/secretory organelles
-Does not occur in the cytoso, nucleus or mitochondria
Purpose of disulfide bonding?
Reinforces structure of proteins with other proteins
Primary Structure of proteins?
Polypeptide backbone(linear amino acid sequence)
Tertiary Structure?
3-dimensional conformation of protein (has the function)
Secondary Structure of protein folding?
-Occurs within the polypeptide backbone (no side chains included)
-Results from H-bonding between N-H and C=O groups in the backbone
-Forms two common structures (alpha-helices or beta pleated sheets)
Alpha helix in the secondary structure?
-C=O and N-H form H-bonds every 4 peptide bonds in each turn of the helix
-Side chains point outwards
Beta pleated sheets secondary structure?
-side chains alternate up and down
-Very rigid structure
-Can be parallel(all carboy/N-terminus face the same direction) or antiparallel(alternate direction)
Tertiary structure of the protein?
-Complete 3D strucutre of the protein
-Secondary strucutres are packed together
-Side chain interactions
What are loops of tertiary structures?
Portions of the tertiary structure that are not secodnary structures and are flexible
T/F: THe entire tertiary structure is secondary structures?
No the teritary structure also includes loops which do not have secondary structures
What is th equarternary strcuture in protein folding?
Assembly of multiple protein subunits into a final protein
-Depends on non-covalent interactions
-Dimer : two polypeptide subunits
-Tetramer, 5-mer, etc.
-Oligomer: many subunits
Ways to visualize proteins without side chains?
- Polypetide backbone
- Ribbon diagram (secondary structures shown)
Ways to visualize proteins and their side chains?
Stick diagram
Way to visualize proteins and their mass?
-Space filling model
What is a domain?
An independtly folded unti within a protein, it can fold by itself and has its own independent function
Can a protein have more than one domain?
Yes
Domains found in HSP70?
Domain 1: ATPase domain (stimulates ATP hydrolysis)
Domain 2: Protein binding domain
Average length of a polypeptide and weight?
100 - 800 amino acids in length
12 kDa to 90 kDa in molecular weight
What does a specific protein interaction mean?
Only certain molecular surfaces can bind to the protein
-“lock and key” the protein surfaces must match well in order for the two molecules two interact
Protein interactions are often transient?
This means the interactions are reversible
-Ineractions from and then break apart quickly
Identical vs similar amino acids?
Identical : same AA
Similar : amino acids with similar properties, structure(same family)
Sequence similarity vs sequence divergence?
Similarity: sequences are conserved evolutionary (probably an important protein)
Divergence: sequence is not conserved and less important protein
What is a family of proteins/domains?
Proteins/domains with very similar sequences and structures. They often have related functions
T/F: proteins from one family ca be found in different organisms?
True, HSP70 ATPase domain in humans is found also in E.coli
