Proteins Flashcards
What are the classification of standard amino acids
1) Non-polar amino acids
2) polar amino acids
3) acidic amino acids
4) basic amino acids
What are the non-polar amino acids
1) glycine
2) alanine
3) valine
4) leucine
5) isoleucine
6) phenylalanine
7) Tryptophan
8) methionine
9) proline
What are the polar amino acids
1) serine
2) cysteine
3) glutamine
4) asparagine
5) Tyrosine
6) Threonine
What are the acidic amino acids
1) Aspartate
2) glutamate
What are the basic amino acids
1) Lysine
2) Arginine
3) Histidine
What is the name of an amino acid polypeptide of 50 or less amino acids
Peptides
Polymers of more than 50 amino acids are called
Proteins/polypeptide
What is the meaning of amphoteric
That at physiological pH the carboxyl (-) and amino group (+) meaning that it is both acidic and basic
What are zwitterions
They are molecules that have both positive and negative charges on different atoms
What is the pKa of the carboxyl group
3
What is the pKa of the amino group
11
What determines the unique properties of amino acids and poly-peptides
The R-group
Amino acids are classified according to?
According to their R-group interaction with water molecules
What is the structure of glycine
As three of the groups connected to the a-carbon are the same I will only be mentioning the R-group in (paranthaces):
Gly-(H)
What is the structure of alanine?
Ala-(CH3)
What is the structure of valine?
Val-(CH)-(CH3)2
What is the structure of phenylalanine?
Phe-(CH2)-benzene
What is the structure of serine?
Ser-(CH2OH)
What is the structure of tyrosine?
Tyr-(CH2)-(benzene)-(OH)
What is the structure of Aspartate?
Asp-(CH2)-(C(=O)(-O(-))
What is the structure of glutamate?
Glu-(CH2)-(CH2)-(C(=O)(-O(-))
What is the structure of lysine
Lys-(CH2)4-(+NH3)
What are the type of interaction between two non-polar groups
Hydrophobic interactions
What type of interaction polar amino acids form
Hydrogen bonding
What is the pKa of histidine R-group?
6
What are the biological roles of amino acids?
1) Chemical messengers such as hormones and neurotransmitters
2) precursor for other molecules (nucleotides and heme)
3) metabolic intermediates
What is thyroxine?
Thyroxine is a hormone, produced by the thyroid gland, which regulates metabolism
What is melatonin?
A hormone that regulates night/day cycle
What is GABA?
It is a neurotransmitter, which inhibits the secretion of glucagon
What is serotonin?
It is a neurotransmitter which stabilizes the mood and feelings
Where can we find 4-hydroxyproline and 5-hydroxylysine
In collagen, as they are modified amino acids
What is the isoelectricpoint (pI)
the ph where the net charge of both groups are ionized having zero net charge (pI=pK1+pK2/2)
Which amino acid is non-chiral
Glycine
Most amino acids are what type of stereoisomers
In the L form
What are the chemical reactions amino acids can do?
1) dehydration (amide linkage, formation of a peptide bond)
2) dehydrogenation (oxidation, formation of disulfide bridge)
How does a peptide bond form?
It is the reaction between a-carboxyl group of an amino acid with an a-amino group of another amino acids removing a water molecule starting from the N-terminus to the C-terminus
How does a disulfide bond form?
Via the oxidation of non-adjacent cysteine amino acid forming cytine
What is the function of a disulfide bond?
It is a strong covalent bond which stabilizes polypeptides/proteins
What is the function of glutathione?
A tripeptide found in most organisms, involved in:
1) protein and DNA synthesis
2) toxic substance metabolism
3) amino acid transport
What is the function of vasopressin?
A nonapeptide, antidiuretic hormone that:
1) regulates water balance, appetite, and body temperature
What is oxytocin?
A nonapeptide that aids in uterine contraction and lactation
What is the structure of glutathione?
Y-glutamate-cysteine-glycine
What is the structure of oxytocin?
Cysteine-tyrosine-isoleucine-glutamine-asparagine-cysteine-proline-leucine-glycine-NH2
What is the structure of vasopressin?
Cysteine-tyrosine-phenylalanine-glutamine-asparagine-cysteine-proline-arginine-glycine-NH2
What are the functions of proteins?
1) catalysis
2) structure
3) movement
4) defense
5) transport
6) regulation
7) storage
8) stress response
How are proteins categorized?
1) sequence
2) 3D shape (globular, fibrous)
3) conjugation
How many levels of protein structure are there?
1) primary (content of amino acid sequence held by peptide bond)
2) secondary
3) tertiary
4) quaternary
In which level of protein structure a mutation can occur?
Primary structure
What is a conservative mutation?
A mutation that changes an amino acid to a chemically similar amino changes without affecting the function
What is a non-conservative mutation and an example of it
Non-conservative mutations, are mutations which changes the function of the protein, like sickle cell anemia which changes the glutamate to a valine in the B-subunit of the hemoglobin
When does a protein becomes secondary?
When a primary structure is rearranged into either a-helix or b-sheets
What stabilizes the secondary structure?
Hydrogen bond, between the a-carbonyl and the a-amine, found in the backbone between successive 5 amino acids
How many forms of b-sheets are there and how are they formed?
2, parallel and anti parallel, when two or more polypeptide chain segments line up, side by side stabilized via hydrogen bonds
What are motifs?
They are super secondary structures, with patterns of a-helix and b-sheets (bab)
What is a tertiary structure?
It is a unique 3D folding structure, formed by globular proteins, and some have attached prosthetic group
Which standard amino acids cannot foster a-helical structure?
Proline and glycine
Which form of b-sheets are more stable
Antiparallel
5 examples of super secondary structures
1) BAB unit
2) B-meander
3) b-barrel
4) aa unit
5) Greek key
How is the tertiary structure stabilized?
By the interactions of the R-groups which stabilizes the structure via electrostatic forces
What are domains?
Contained within Large globular proteins, they are segments of a polypeptide that have a specific function
Where are domains found
On large globular proteins made of 200+ amino acids
Examples of domains
1) EF HAND (BIND CALCIUM)
2) LEUCINE ZIPPER (DNA BINDING)
3) B-BARREL (FOR VISION)
4) ATP-BINDING DOMAIN OF HEXOKINASE
5) A/B ZINC BINDING MOTIF
WHAT ARE THE INTERACTIONS THAT STABILIZES THE TERTIARY STRUCTURE (VIA THE R-GROUP INTERACTIONS)
1) COVALENT DISULFIDE BOND (BETWEEN TWO NON-ADJACENT CYSTEINE)
2) IONIC ELECTROSTATIC SALT BRIDGE INTERACTIONS (BETWEEN OPPOSITELY CHARGED R-GROUPS)
3) HYDROGEN BOND:
1) Ser-OH & HO-Tyr
2) carbonyl oxygen & hydroxyl groups
3) carbonyl oxygen & amine
4) HYDROPHOBIC INTERACTION (between non-polar amino acid R-groups)
5) HYDRATION
WHY DOES COVALENT DISULFIDE BOND DOES NOT OCCUR INSIDE OUR CELLS?
DUE TO HIGH CYTOPLASMIC CONCENTRATION OF REDUCING AGENTS
What are quaternary structures?
It is a protein that is composed of several polypeptide chains
How are quaternary structure held together?
1) ionic
2) hydrogen
3) hydrophobic interactions
Non-common covalent interactions include:
1) disulfide bridges (immunoglobulins)
2) desmosine linkage
3) lysinonorleucine linkage
What is allosteric transition?
The change on a protein by the binding of a ligand (effectors modulators) which can trigger its conformation which might alert its affinity for other ligand like in the case of the first oxygen binding to a hemoglobin
What is oligomers?
When you have identical subunits form a multi subunit protein
What are the advantages of oligomers
- Synthesis of subunits may be more efficient
- In supramolecular complexes replacement of worn-out components can be handled more effectively
- Biological function may be regulated by complex interactions of multiple subunits
What is protein denaturation?
It is the disruption of protein structure but not the primary (it does not affect peptide bonds)
What can cause denaturation?
- Strong acid or base
- Organic solvents
- Detergents
- Reducing agents
- Salt concentration
- Heavy metal ions
- Temperature
- Mechanical stress
What are the molecular chaperones which helps in folding polypeptides with 100 or more amino acids
1) Ribosome associated chaperons
2) Hsp70 (bind and stabilize proteins during the early stages of development via ATP hydrolysis)
3) Hsp90
4) chaperonins (increase speed & efficiency of the folding process via ATP hydrolysis)
How does molecular chaperones help in folding
By protecting them from inappropriate protein-protein interactions
What happens if refolding cannot occur
Chaperons degenerate those proteins, as they can cause Alzheimer’s and Huntington’s diseases
Where can we find fibrous proteins
They have a structural role with high proportions of a-helix & b-pleated sheets
1) collagen (triple a-helix, (gly-pro-4-hydroxyproline))
2) keratin (double a-helix)
3) fibroin (polymer of gly-ala)
What is globular proteins?
Water soluble, with biological functions (precise binding of the ligand):
1) hemoglobin (its globin contains 2 alpha and 2 beta chains) & myoglobin (its login protein contains 8 a-helix)
2) enzyme
3) peptide hormone (insulin, glucagon, etc)
4) immunoglobulin (defense)
What Type of hemoglobin contains gamma chains instead of beta
Embryonic and fetal hemoglobin which have a higher affinity for oxygen
Oxygenation of hemoglobin causes the dimers to slide how many degrees?
15
In what condition is the hemoglobin when it is in its taut form
Deoxygenated
What is the Bohr effect?
Release of oxygen from the hemoglobin due to a decrease in the pH
What is the smallest and only achiral amino acid
Glycine
Which amino acids have a benzene ring
1) phenylalanine
2) tryptophan
3) Tyrosine
Which amino acids contain sulfur
1) methionine
2) cysteine
What is unique about polar amino acids
They contain either hydroxyl, or amide, or sulfur group
Which amino acid is a imino (secondary amino) acid
Proline
Which neurotransmitter is derived from tryptophan
Serotonin
Which hormone is derived from tyrosine
Thyroxine
What is the ph of glutamate
3.22
How to calculate the pi of acids and base
Acid: Pk1+pkr/2
Base: Pk2+pkr/2
Peptide & disulfide bonds are a type of which bonds?
Covalent
What is schiff base formation reaction
Electron sharing with another orbit, like aldimines
Why is glutathione unique
Because the peptide bond between the cysteine and glutamate is formed between the R-group of glutamate and the amine of cysteine
Three examples of conjugated proteins
1) lipoprotein
2) glycoprotein
3) hemoprotein
What is homologous amino acids, and what is meant by invariant
Polypeptides with similar “sequence”, and invariant means that some of the amino acids are kept the same
What is meant by a variable amino acid
Amino acid in a less stringent sequence performing nonspecific function
What can disturb the a-helix structure
1) lots of glycine (due to it being small, no r-group & rotates a lot)
2) proline (it doesn’t have free Amine group so it doesn’t allow the rotation)
3) large number of charged amine group (it will have repulsion reaction
3) to many bulk R-group (like tryptophan)
Usually the turns that are made up of which amino acid
Proline & glycine
What is mosaic/modular proteins?
Proteins with a number of repeated domains
What is the difference between a domain and a subunit?
Domains are in the same polypeptide sequence while subunits are on different polypeptide
What is a proteoform?
Multiple proteins arise from the same gene
The break down of primary structure is called?
Hydrolysis
How does the binding of histidine affect the function of the hemoglobin & myoglobin
It stabilizes the heme
What is the structure of cysteine?
Cys-CH2-SH
