Chapter 2- Proteins Part 1 Flashcards
Proteins have many __________ roles
biological
What are proteins roles?
enzymes, structure, transport and binding
proteins are built from _____ amino acids which are the amino acids ____________.
the 20 common or standard, coded by genes into protein synthesis
Amino Acid structure is
Amine (NH3) + Carboxylic Acid (COO-) + H + R group
What type of isomer makes proteins and amino acids?
L isomer
What are the 4 classifications for the 20 standard amino acids?
non polar, polar, basic and acidic
Draw alanine.
CH3 sticking North, nonpolar, not strongly hydrophobic
Describe Glycine.
H sticking North, It is achiral, non polar, not strongly hydrophobic
Which amino acids are non polar?
Valine, Leucine, Isoleucine, Methionine (has a sulfur)
Which amino acid reacts with its backbone?
Proline (its backbone is a CH2 plus CH2 plus CH2 connected to the N+H2)
Which are the aromatic amino acid?
phenylalanine, tyrosine (non polar, has hydroxides) , tryptophan (biggest amino acid)
What are the 3 hydroxide amino acids?
Tyrosine, Serine, Threonine
Which amino acids are polar non ionizable Amino Acids?
Serine, Threonine, Asparagine, Glutamine
What is special about glutamine?
That it has a polar amide (a double bonded O to a C attached to a N) in the side chain
What is the most chemically reactive amino acid? And what does it look like?
Cysteine (amino acid structure plus CH2 attached to a S attached to a H)
Which amino acid has a 5 membered ring?
Hisitidine
Which are the acidic amino acids?
Aspartate and Glutamate
What is a characteristic of all acid base reactions?
Protonation
Low pH= net + or - charge?
+
High pH= net + or - charge?
-
Which pKa are approximately 3-4?
- terminal alpha carboxyl group
- aspartic acid
- glutamic acid
Which pKa are approximately 6-8?
Histidine (closer to biological pH which is 7.5)
Which pKa is approximately “fairly” high above 7?
terminal amino group
Which pKa is approximately “high” above 7?
- lysine
- arginine
What is the most reactive amino acid and why?
Cysteine because it can form a disulfide bonded cystine (two cysteines attach at the cystine). It has a thiol in its side chain
Amino acids can be held together by what?
amide bonds called peptide bonds
The peptide bond is most famous for…
breaking down pepsin (peptobismo, pepsi)
Biological polypeptides are divided into what?
peptides and proteins (depending on length)
Biological polypeptides are classified how?
Peptides (small, 30ish or smaller monomers long, short enough where it can’t have 3D structure)
Proteins (large, 30ish or longer monomers long, long enough to have 3D structure)
Protein structure is the basis of what?
protein function and its divided into levels because of its complexity.
Structure determines what?
function (just like a protein that bind to DNA can determine function because of its specificity)
A protein found in mammalian milk needs to have what in order to bind to what?
Needs to have high affinity and high specificity so that iron can bind
What are the levels of protein structure?
Primary structure
Secondary structure
Tertiary structure
Quaternary structure
What is proteins primary structure?
sequence of amino acids
What is the longest, shortest and average amino acids?
longest 30,000 amino acids long
shortest 30 amino acids long
average 450 amino acids long
What is protein secondary structure?
local or adjacent amino acids with a regular arrangement of the backbone
What is a Ramachandran plot used for?
They show the constraints to the backbone and what it can rotate and what it cannot until it clashes.
The two common types of protein secondary structure are what?
alpha helix and the beta sheet or beta strand
What is a helix breaker?
Proline
Alpha and beta secondary structure have what kind of bonds? Between where?
hydrogen bonds between backbone moieties.
Which Amino Acid is a helix breaker?
Proline
Do side chains matter when we talk about alpha secondary structure?
No they are not relevant. The bonds also are not relevant.
Is a random coil a secondary structure?
No.
Protein tertiary structure is the 3D what?
arrangement of the molecule in space
What kind of beta sheets is a Fatty Acid binding protein?
beta barrell
What is a prosthetic? What is it made of? What is a good example of a prosthetic?
a tool that extends what a protein can do. It is not made of Amino Acids. A great example of this is the heme in an iron binding protein (like hemoglobin) so it can bind to O2.
What type of interactions hold together tertiary structure?
Non-local interactions which are distant places in the chain.
Name the types of non local interactions.
- Covalent
- ionic bond
- hydrogen bond
- hydrophobic interactions
What is the strongest non local interaction?
covalent (but it is the least important and least abundant)
Two covalent bonds create what?
a disulfide bridge
Two ionic bonds create what?
a salt bridge between full charges
Non-local interactions: most important to least important.
- hydrophobic interactions
- hydrogen bond
- ionic bond
- covalent bond
Non-local interactions: most abundant to least abundant.
- hydrophobic interactions
- hydrogen bond
- ionic bond
- covalent bond
Non-local interactions: strongest to weakest
- covalent bond
- ionic bond
- hydrogen bond
- hydrophobic interactions
What is an example of a two covalent bond creating a disulfide bridge?
The two non local cysteines creating a cystine.
What is an example of two ionic bonds creating a salt bridge between full charges?
An aspartate and a lysine coming together with the O (aspartate) and NH3+ (lysine). This interaction is not as strong in an aqueous solution.
What is an example of two hydrogen bonds coming together between and donor and a acceptor?
A glutamine and a serine coming together with the O (glutamine, H donor) and the H (serine, H acceptor)
What is an example of two hydrophobic interactions coming together?
It is between two non polar side chains. Like pheynlalanine (aromatic ring) and leucine (qt 2 ch3) it gives the most energy to the structure and it is not soluble in H2O
Protein quaternary structure involves the association of what?
more than one tertiary structure into the functional protein
What is a good example of quaternary structure?
- Hemoglobin doesn’t function as a single chain but 4 chains put together.
- Rhinovirus protein is very large it has 4 different chains with over 240 proteins and 240 quaternary structures together
What creates fibrous proteins or structural proteins?
large quaternary structure complexes with is most abundant in humans.
What is a good example of a large quaternary structure complex that creates fibrous proteins or structural proteins?
Collagen and keratin. The soluble protein and the comes together in quaternary structure
What destroys protein function or its native structure?
Denaturation and aggregation
What does protein denaturation do?
It unfolds the protein. And because of the unfolded structure it lacks 3D structure so it has no function.
How do you denature a protein?
Temperature (ex. cooking a raw egg and the egg whites turn white)
Chemically (ex. Ceviche cooks in an acidic solution and denatures the proteins of the fish to be edible and cook)
How does a protein unfold in chemical denaturation?
competes with non local bonds
How do proteins fold? (think the example in class with the model)
process initiated by hydrophobic collapse
How did us as humans almost understand and solve the protein folding issue?
Through AI they were able to predict a structure but not how it chemically comes together
Can you have the same amino acid sequence and it be different structures?
Yes, this is why protein folding is so difficult.
What does the term hydrophobic collapse entail?
parts of the protein runs away from water and then starts to fold into the protein
What kind of environment is created inside a hydrophobic collapse?
A water poor environment
What kind of process is protein folding?
cooperative kinetic process determined by primary structure
What dictates the proteins fold?
The amino acid sequence which has the info to create the primary structure
What do chaperons do for protein folding?
Keep proteins from misfolding not assist in folding
The most favorable structure for a protein to fold to is….?
The native structure
low energy in protein folding means…
more stability
All proteins _____________ but some proteins are very _____________ __________________.
breathe
conformationally flexible
What is confirmational change for a protein?
A protein changing shape due to outside factors. A protein in one environment can change into a different shape in another environment
Why is post translational modification (PTM) important in the structure and function of mature proteins?
Because it is why
What is most important for the structure and function of mature proteins?
Post-Translational modification or PTM
Name an example of PTM.
disulfide bridges, green fluoroscent proteins found in jellyfish that PTM into a beta barrel
What percentage of proteins are PTM?
60-80%
What does PTM mean?
changes covalent structure of 3 or more AA
What can extend what a protein can do chemically?
prosthetics and PTM
