Chapter 2 Flashcards
What are the different protein functions?
- Catalysts (Enzymes)
- Transport and store other molecules (i.e. hemoglobin)
- Control Growth (hormones) - (insulin, epinephrine)
- Provide mechanical support and immune protection (Antibodies)
- Generate movment (collagen, myosin/actin)
What are the properties of proteins?
Proteins consist of a large range of functional groups
They include:
- -OH
- NH2
- -SH
- -COOH
they also have weak interactions between side groups
- Hydrogen bonds
- Vander waals
- Electrostatic/ Ionic
Proteins are linear polymers built of monomer units called amino acids, which are linked end to end.
Descripe and amino acid structure
Has an alpha carbon which is bonded to an amine group a carboxyl group and a R group.
Protein function is directly dependent on this three dimensional strucutre
All amino acids have the same structure except for Proline
All have one chiral carbon except for glycine
What are Amino Acids?
Amino acids are the building blocks of proteins
There are 20 different amino acids
All proteins are composed of these 20 which have an alpha-amino acid consist of a central carbon linked to
- An amino group
- Carboxlyic acid group
- A hydrogen atom
- A distinctive R group
Amino acids are chiral and may exist in one of two forms (mirror iamges): L isomer or D isomer
Eurkaryotes produce /utilize Lamino acids which can be S or R configureation however they are ususally S
What are Zwitterions?
Zwitterions are oppositely charged speicies/dipolar ions
Amino acids in solution at neutral pH predominantly exist as dipolar ions where the amino group is protonated (-NH3+) and the carbozyl group is deprotonated (-COO-)
How does the pH affect?
In acidic solution the amino group is protonated and the carboxyl group is not dissociated. Therefore both groups are protonated.
As the pH is raised the carboxylic acid is deprotonated therefore it exists as a dipolar form
In a basic solution (pH ~9) the protonated amino group loses a proton therefore both groups are deprotonated
What are aliphatic Side chains?
Name the amino acids
Side chains that are composed soley of carbons and hydrogens
- Glycine
- Alanine
- Valine
- leucine
- Isoleucine
- Proline
What are aromatic side chains?
Name the amino acids associated
Aromatic = Hydrophobic
- Phenylalanine (Most hydrophobic)
- Tryptophan (contains an indole ring)
- Tyrosine (presence of OH group makes molecule more reactive less hydrophobic)
What are the sulfhydryl group?
They are very reactive and they include sulfide bonds between sulfydryl groups
Amino acids:
- Cysteine
- Methionine
What are the amino acid hydroxyl containing alipatic side chains?
The presence of the -OH groups makes them reactive and they can undergo phosphoryltation.
Amino acids include:
- Serine
- Threonine
What are the amino acid Basic Side Chains?
They include
- Lysine
- Arginine
- Histidine (imidzole ring and its pKa is neutral)
- The imidazole group can be uncharged or positively charged at neutral pH nand the local environment.
- Able to cahnge its charge under conditions relatively close to pH
Describe the formation of a peptide bind?
To make a peptide bond we want to put amino acids together the process of them is to a link betwee the alpha carvozyl group of one amino acid to the alpha amino group.
When forming a bond you lose an amino group adn a carbozyl group
You also lose a water molecule when forming a peptide bond.
Translation is making proteins and a peptide bond is really stable. A protease digests proteins down into individual amino acids
Amino acids are then absorbed by the GI tract
What is the Primary Structure on an amino acid?
Why?
The primary structure is the sequence of amino acids that make up a protein.
Insulin is L amino acids (AA)
It’s primary structure is used in identifying a protein
1) Protein folding
1. 5) Amino acid 3D stuructures for biological function
2) Active Stie (from where the enzyme lies in converting to substrate) essential for knowing the mechanism of action
3) Abnormal Function - disease
4) evolution
Talk about Disulfide Bonds for example cysteine
All the things you need to know about disulfide bonds
Cysteine is oxidized when you have two sulfides binding together. However when you break that bond you reduce the form to S-H bonds
When you oxidize cysteine and a disulfide bond forms the name changes to cystine
All disulfide bonds are the same length and a disulfid bond can be an extracellular protein
Disulfide bonds have a planar structure and there is no charge associated with the peptide bond.
When you have a single disulfide bond they are free to rotate and are structurally flexible.
In the case of insulin two chains of amino acids of insulin have intra- chains and inter-chain. These chains represent disulfide bonds within a chain and connecting two chains. In this case there are three disulfide bonds. When they form they form over a confined distance. There for this cuases the protein to have **to be folded for the sulfur bonds to bind together. **
They can also exist in a number of different forms
Carbon-nitrogen bond has partial double bond character
The Cis/Trans is 50/50 for a peptide however the exception is proline
Trans for two alpha carton atoms that are on opposite sides of the peptide bond
Cis is when two alpha carbon atoms are on the same side of the peptide bond
Describe the characteristics of Secondary Structure.
Secondary structure is based on bond lengths and angles.
There are two parts of the secondary structure they include alpha helix and the B sheet. Also beta turns. These are common repeated structures in the secondary structures.
What is an Alpha helix?
What is alpha Heical coiled coil?
An alpha-helix is a tightly coiled backbone that forms the inner part of the rod and teh side chains extend outward in a helical array.
They are stabilized by hydrogen bonds between the NH and CO groups of the main chain.
10 A = 1nm
The R groups are pointed away from the center of the helix and the distance between between two alpha carbonsis abou 1.5A..
As we have learned hydrogen bonds stabilize a alpha helix and carbons 1 and 4 are on the same side of the helix therefore hydrogen bonds occur between the bonded carbons.
The inner region of helix is tightly packed like D not C
The average is 45A long and 30AA length this is known as the **membrane spanning region (the center of the helix most nonpolar) **
Alpha-helical coiled coil has two alpha helices interact with each other through weak interactions. It might be up to 1000A long. This is seen in structural proteins Keratin, myosin and tropomysosin.
Proline disrupots formation of alpha helix b/c hydrogen bonding gets messed up –> this destabilized regions of the alpha helix.
Block of negatively/positively charged side chains b/c of all that similar charge –> repellence = difficult to form an alpha helix
When you alternate negative and positive charged side chains it stabilizes and likely region will form an alpha structure
Describe the B sheet and the characteristics of the B sheet
It is composed of two or more polypeptide chains called beta strands. They are formed by linking two or more beta strands lying next to one another through hydrogen bonds.
It is similar to alpha helix: It is stabilized by formation of H bonds.
It is different from alpha helix because it has a much more extended type structure.
They are 3-4 A apart therefore they are more spread out
B sheets also have membrane spanning
- Antiparallel which means it folds back on itself.
- This whole thing is a single polypeptide
It is also mixed
Describe B turn and its characteristics
B turn gives an idea of where the proteins are bent.
They are a polypeptide chain that can change direction by making reverse turns and loops
The CO group of residue i of the polypeptide chains is hydrogen bonded to the NH group of residue i+3 to stablize the turn
Describe Tertiary Structure and list its characteristics
Tertiary Structure: is the overall course of the polypeptide chain. Water soluble proteins fold into compact structures with nonpolar cores
Takes into account interactions that occur across the entire length of the protein.
Therefore in general…
- The interior portion of protein consists of amino acids with non-polar side chains
- Exterior (surface) portion consists of a mix of amino acids with polar and non-polar side chains
Describe myoglobin
It is involved in oxygen transport in muscle
The capacity of myoglobin to bind oxygen depends on the presence of heme. A purple molecule in the middle = IRON. It is an oxygen binding site and Heme is iron.
It is 153 amino acids in length and 70% alpha helix
Myoglobin is responsible for oxygen transport inside of muscle cells. Hemoglobin is responsible for oxygen transport in the blood.
Describe the Porin Protein
The Porin Protein is a membrane expanding protein which forms water filled channels. The amino acids on the exterior face need to be happy in a hydrophoib environment. There is a reverse distribution of hydrophobic and hydrophilic amino acids. therefore it is an “inside out” amino acid distribution.
Gram neative Bacteria is the porin protein.
Outside: hydrophobic residues that interact with neighboring alkane chains
Insides: charged and polar amino acids taht surround a water-filled channel.
Describe Quaternary Structrure and its characteristics
*Quaternary structure is the interaction between subunits that alter the structure (and therefore function) of each protein Polypeptide chains can assemble into multisubunit structures. *
They are allosteric proteins (alter their ability to bind with a substrate and how things interact: it is a special case and not all proteins can exhibit this structure. In order. In order to be this structure…
- Multiple subunits (polypeptides, that are similar in structure)
- Interactions between subunits will alter the way the enzyme interacts with the substrae and the interactions of subunits will change the affinity.
It has a requirement of more than one subunit
NOTE: this eliminates myoglobin (which only has 1 subunit
Example: Hemoglobin has four different subunits of two types. It has alpha-globin and beta globin. Each subunit has 1 heme and hemoglobin has 4 heme. They can carry four molecules of oxygen and noncovalent bonds hold the subunits together.
Describe Protein Denaturation and other characterisitcs
Protein denaturation is destroying secondary/tertiary struture so that is ends with primary structure. This will make it difficult for th eprotein to retain any sort of activity.
The ribonuclease degrades RNA. its a single protein that has 104 aa in ends. Also to note intrachain disulfide bonds and that the amino acid sequence of a protein determines its 3D strucutre.
What is B-mercaptoethanol?
B-mercaptoethanol is a reducing agent for it breaks down disulfide bonds!
It has a disulfide bond which becomes reduced and the b-mercaptothanol becomes oxidized.
When urea is added it disrupts disulfide bonds.
When you have anative ribonuclease its active then it can be reduced by M urea and B meraptoethanol and it denatures the protein and it becomes inactive.
Sometime it can go back to its native. Not every protein can go back to its native form.
Describe the process of denaturing a protein
When you look at the graph it increases. It goes from a 0% unfolded to 100% unfolded.
At 0% is is at its native form and its active
At 100% it is at its denatured form and it is inactive
As you increase concentration of urea you unfold more go from almost completely native to almost completely denatured very quickly (steep slope)
It has a sigmoidal shape curve –> “cooperativeity”
The process of denaturing protein = loss of cooperative interactions in that protein.
Think jenga…your pulling out blocks the whole game but is stays standing, then you pull out the wrong one and the whole tower comes crashing down.
The the midpoint, will find some fully folded and some fully unded its an all or none
Describe the Alpha-helix vs the B sheet structure
A protein can form alpha helix and beta sheet
Some have prevelance for one or the other but prevalence is not that dramatic. Other factors will designate wheter an alpha helix or beta sheet is formed.
Surrounding sewuence, order of amino acids charge
What is protein folding?
Protein folding is the nucleation - condentation model of randomed coiled protein and a stable portion of the origingal
An example of this is when a monkey is put ina room with a type writer it probably won’t be able to type the combinations to be able to write a book.
The diseases from folding include Alzheimer’s and Parkinson’s disease
Describe Post-translational Modifaction of Proteins
The Post-translatinoal modification of Proteins includes
Hydroxyproline, Y-carboxyglutamate, carbohydrate-asparagine adduct and Phosphoserine.
1) Hydroxyproline: collagen function, vitamin C defieciency results in inability to from hydroxyproline. (Scurvy)
2) y-Carboxyglutamate: Prothrombin to the blood clotting, vitamin K deficiency results in inability to form prothrombin.
3) Carbohydrate-asparagine adduct: Glycoprotein and the increase hydrophilicity by adding carbohydrates and also found outside the cell.
4) Phosphoserine: Can undergo phosphorylation and is Reversible.
Classify each 20 amino acids into there relative groups side chains:
- Aliphatic
- Hydroxyl Alipthatic
- Aromatic
- Sulfur Containing
- Acidic
- Basic
- Amine derivative
Aliphatic
- Glycine
- Alanine
- Proline
- Valine
- Leucine
- Isoleucine
Hydroxyl Containing:
- Serine
- Threonine
Aromatic:
- Phenylalanine
- Trypotophan
- Tyrosine
Sulfur Containing:
- Cysteine
- Methionine
Acidic:
- Glutamate
- Asparate
Basic:
- Arginine
- Histine
- Lysine
Amine Derivatives:
- Aparagine
- Glutamine
How might a change in the pH alter the structure of a protein and therefore change the functions?
A change in pH alters the protein strucutre and function because it will determine if the functional groups associated with the protein are protonated, deprotonated or neutral.
For example, Histidine has a typical pKa of 6.0 (close to neutral) which allows for proton transfer
What are the characteristics of a peptide bond and how do the characteristics influence the structrue of proteins?
Peptide bonds are linear polymers formed by linking the alpha-carboxyl group of one amino acid and the alphs-amino group of another amino acids.
Planar
Very kinectically stable and the rate of hydrolysis is extremely slow.
Peptide bonds are uncharged
They have partial double bond character
Give two examples of post-translationally modified amino acids in a protein. `
** 1. Hydroxyproline**- In collagen that participates in the maintenance of tissue. A vitamin C deficiency will cause scurvy because of the hydroxyproline defiecieny. This results in a loss of teeth and blood vessels that don’t work
2. Y-carboxyglutamate - Prothombin, can lead to vitamin K deficiency and cause problems with bleeding
- Carbohydrate-asparagine adduct - On the outer surface of the cell membrane its extracellular protein that facilitates the interaction with other molecules. By adding the carbohydrate, it increases the hydrophilicty of the protein
- Phosphoserine: REVERSIBLE and can phosphorylate
Compare and Contrast Alpha-helices and Beta-sheets with respect to H-bonding, shape, ability to form coiled coils, and ability to span a membrane.
Alpha helices: Rod-like structure, tightly coiled backbone which forms the inner part of the rod and side cahins that extend out in a helical array. They have hydrogen bonding between the carbon and the R side chain. They are stabilized by hydrogen bonds. 1.5A
Beta Sheets - composed of two or more polypeptide chains called beta strands. The structure is fully extended rather than tightly coiled. The distance between adjacent amino acids is 3.5A. It is formed by linking two or more beta strands lying next to each other through hydrogen bonds.
Antiparallel arrangement the amino and carboxyl group of each amino acid are respectively bonded to the CO adn the NH group
Why is histidine often found at the active sites of proteins?
Histidine is often found at the active sites of proteins because the imidazole ring can bind and release protons in the course of enzymatic reactions.
Describe how a folded protein differs from an unfolded protein. Describe the transition of a protein from a folded to unfolded state (native to denatured)
Proteins can be denatured by heat or by chemical denaturants such as urea or guanidinium chloride. Only two conformational states are present in any significant exent. It’s and “all or non” process. Conditions that lead to the disruption of any part of a protein structure are likely to unravel the protein completely. 8M urea and B-meracaptoethanol are good and breaking hydrogen bonds and when used together can denature a protein
How do proteins which exhibit quaternary structrue differ from proteins which do no?
In order to exhibit quaternary strucutre, the protein has to contain more than 1 polypeptide. So, if a protein does exhibit quaternary structure, you know it has at least two polypeptides. Hemoglobin, for example, consists of two subunits of one type (designated alpha) and two subunits of another type (designated beta)
Each protein has a beginning and an end. How would one tell the beginning of a protein from the end?
The beginning of a protein is called the amino terminus and has teh NH3. The end of teh protein is called the carboxyl terminus and has teh CO2.
What effect would treatment of a protein with beta-mercaptoethanol or urea have on the structure or function of the protein?
Treatment of a protein with Beta-meraptoethanol (reducing agent) or urea (good at breaking hydrogen bonds) would denature the protein by removing the hydrogen bonds and the disulfide bonds. But, if you take a denatured protein and put it with trace amounts of beta-meraptoethanol the native protein can form eventually. This shows that the primary sequence determines the 3D strucutre of a protein .
