Chapter 2

Question 1

What are the different protein functions?

Answer 1

1. Catalysts (Enzymes)
2. Transport and store other molecules (i.e. hemoglobin)
3. Control Growth (hormones) - (insulin, epinephrine)
4. Provide mechanical support and immune protection (Antibodies)
5. Generate movment (collagen, myosin/actin)

Question 2

What are the properties of proteins?

Answer 2

Proteins consist of a large range of functional groups

They include:

• -OH
• • NH2
• -SH
• -COOH

they also have weak interactions between side groups

1. Hydrogen bonds
2. Vander waals
3. Electrostatic/ Ionic

Proteins are linear polymers built of monomer units called amino acids, which are linked end to end.

Question 3

Descripe and amino acid structure

Answer 3

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

Question 4

What are Amino Acids?

Answer 4

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

Question 5

What are Zwitterions?

Answer 5

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-)

Question 6

How does the pH affect?

Answer 6

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

Question 7

What are aliphatic Side chains?

Name the amino acids

Answer 7

Side chains that are composed soley of carbons and hydrogens

1. Glycine
2. Alanine
3. Valine
4. leucine
5. Isoleucine
6. Proline

Question 8

What are aromatic side chains?

Name the amino acids associated

Answer 8

Aromatic = Hydrophobic

1. Phenylalanine (Most hydrophobic)
2. Tryptophan (contains an indole ring)
3. Tyrosine (presence of OH group makes molecule more reactive less hydrophobic)

Question 9

What are the sulfhydryl group?

Answer 9

They are very reactive and they include sulfide bonds between sulfydryl groups

Amino acids:

1. Cysteine
2. Methionine

Question 10

What are the amino acid hydroxyl containing alipatic side chains?

Answer 10

The presence of the -OH groups makes them reactive and they can undergo phosphoryltation.

Amino acids include:

1. Serine
2. Threonine

Question 11

What are the amino acid Basic Side Chains?

Answer 11

They include

1. Lysine
2. Arginine
3. 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

Question 12

Describe the formation of a peptide bind?

Answer 12

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

Question 13

What is the Primary Structure on an amino acid?

Why?

Answer 13

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

Question 14

Talk about Disulfide Bonds for example cysteine

All the things you need to know about disulfide bonds

Answer 14

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

Question 15

Describe the characteristics of Secondary Structure.

Answer 15

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.

Question 16

What is an Alpha helix?

What is alpha Heical coiled coil?

Answer 16

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

Question 17

Describe the B sheet and the characteristics of the B sheet

Answer 17

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

Question 18

Describe B turn and its characteristics

Answer 18

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

Question 19

Describe Tertiary Structure and list its characteristics

Answer 19

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

Question 20

Describe myoglobin

Answer 20

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.

Question 21

Describe the Porin Protein

Answer 21

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.

Question 22

Describe Quaternary Structrure and its characteristics

Answer 22

*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.

Question 23

Describe Protein Denaturation and other characterisitcs

Answer 23

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.

Question 24

What is B-mercaptoethanol?

Answer 24

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.

Question 25

Describe the process of denaturing a protein

Answer 25

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

Question 26

Describe the Alpha-helix vs the B sheet structure

Answer 26

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

Question 27

What is protein folding?

Answer 27

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

Question 28

Describe Post-translational Modifaction of Proteins

Answer 28

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.

Question 29

Classify each 20 amino acids into there relative groups side chains:

• Aliphatic
• Hydroxyl Alipthatic
• Aromatic
• Sulfur Containing
• Acidic
• Basic
• Amine derivative

Answer 29

Aliphatic

1. Glycine
2. Alanine
3. Proline
4. Valine
5. Leucine
6. Isoleucine

Hydroxyl Containing:

1. Serine
2. Threonine

Aromatic:

1. Phenylalanine
2. Trypotophan
3. Tyrosine

Sulfur Containing:

1. Cysteine
2. Methionine

Acidic:

1. Glutamate
2. Asparate

Basic:

1. Arginine
2. Histine
3. Lysine

Amine Derivatives:

1. Aparagine
2. Glutamine

Question 30

How might a change in the pH alter the structure of a protein and therefore change the functions?

Answer 30

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

Question 31

What are the characteristics of a peptide bond and how do the characteristics influence the structrue of proteins?

Answer 31

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

Question 32

Give two examples of post-translationally modified amino acids in a protein. `

Answer 32

** 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

3. 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
4. Phosphoserine: REVERSIBLE and can phosphorylate

Question 33

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.

Answer 33

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

Question 34

Why is histidine often found at the active sites of proteins?

Answer 34

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.

Question 35

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)

Answer 35

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

Question 36

How do proteins which exhibit quaternary structrue differ from proteins which do no?

Answer 36

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)

Question 37

Each protein has a beginning and an end. How would one tell the beginning of a protein from the end?

Answer 37

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.

Question 38

What effect would treatment of a protein with beta-mercaptoethanol or urea have on the structure or function of the protein?

Answer 38

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 .