DRM Biology Y11 - proteins 1 PROTEINS The essence of life.

DRM Biology Y11 - proteins 1

PROTEINSPROTEINS

The essence of lifeThe essence of life

2DRM Biology Y11 - proteins

What What isis a protein? a protein?Proteins are very Proteins are very long chains oflong chains of thousands repeated thousands repeated monomers called monomers called amino acidsamino acids..

These chains of amino acids are These chains of amino acids are also known asalso known as polypeptidespolypeptides. .

Proteins are :• very big • structurally complex• have their shapes adapted to several different functions• functionally sophisticated• most abundant molecule in cells (15% of cell’s dry mass)


The building blocks: amino The building blocks: amino acidsacids

There are 20 aminoacids. Each amino acid There are 20 aminoacids. Each amino acid consists of consists of anan amino group (NH amino group (NH22)),, aa carboxyl or acid group (COOH),carboxyl or acid group (COOH), one atom one atom of Hof H andand one residue or radical (R) groupone residue or radical (R) group which varies in each amino acidwhich varies in each amino acid. .

The R group ranges from a single H atom to a set The R group ranges from a single H atom to a set of several different atoms forming a side chain.of several different atoms forming a side chain.

The The R group gives the amino acid its R group gives the amino acid its propertiesproperties and hence the protein and hence the protein characteristics. It is the one involved in characteristics. It is the one involved in molecule-molecule interactions in the folding of molecule-molecule interactions in the folding of the protein.the protein.


The structure of an amino acidThe structure of an amino acid

In solution, amino acids tend In solution, amino acids tend to ionise (the COOH loses to ionise (the COOH loses its H becoming COO-) and its H becoming COO-) and the NHthe NH22 turns to H turns to H33NN++; ; that is why they are that is why they are represented like this:represented like this:

polar

charged

ACIDIC... negatively charged ASP & GLU

R group with 2nd COOH that ionizes above pH 7.0

BASIC... positively charged LYS, ARG, HIS mcb 2.14*

R group with 2nd amide that protonates below pH 7.0

POLAR UNCHARGED... SER, THR, ASN, GLN, TYR,

are soluble in water, i.e., hydrophilic mcb 2.14*

NON-POLAR... (aliphatic) ALA, VAL, ILE, LEU, PHE, TRP

contain only hydrocarbons R groups = hydrophobicity mcb 2.14*

AROMATIC & SPECIAL PHE,TRP,TYR,GLY,PRO,CYS

contain R groups with ring structures & others mcb 2.14*

http://fig.cox.miami.edu/~cmallery/255/255amino/p2x5x5.jpg












According to According to

their R their R

groups, the groups, the

amino acids amino acids

can be: can be:

polar neutralpolar neutral

polar acidicpolar acidic

polar basicpolar basic (all hydrophylic)(all hydrophylic)

or or

non polarnon polar (hydrophobic)(hydrophobic)


Some examples of amino Some examples of amino acidsacids


The peptide bond


The peptide bond

showing the

condensationreaction


Forming the polypeptide chain: now 4 aa together


Protein structure Protein structure levels: levels: an overviewan overviewProteins are not just a long Proteins are not just a long chain of amino acids. In the chain of amino acids. In the cell, the sequence of cell, the sequence of aminoacids folds to adquire aminoacids folds to adquire a spherical shape. a spherical shape.

This happens thanks to the This happens thanks to the interactions between the R interactions between the R groups of the different groups of the different amino acids that form the amino acids that form the chain. chain.

As the R groups tend to As the R groups tend to group together, the protein group together, the protein folds in a folds in a seconday structureseconday structure and then a further folding and then a further folding will lead to a will lead to a tertiary tertiary structure. structure.


Protein Protein structure: structure: level Ilevel I

During protein During protein synthesis, amino synthesis, amino acids are joined in a acids are joined in a long sequence or long sequence or chain called the chain called the primary structureprimary structure..


Protein Protein structurstructure: e: level IIlevel IIThe primary The primary structure can structure can later fold in 3 later fold in 3 ways: ways: the the alfa helixalfa helix, , the beta the beta sheetsheet or or irregularlyirregularly. . This further This further folding is the folding is the secondary secondary structure.structure.


Further folding of the Further folding of the secondary structure secondary structure leads to a rounder leads to a rounder shape called the shape called the tertiary structuretertiary structure. .

This tertiary structure This tertiary structure isis held by different held by different types of types of interactionsinteractions between the R between the R groupsgroups of the amino of the amino acids: acids: the H bonds, the H bonds, the S-S bonds, the the S-S bonds, the ionic “bonds” and ionic “bonds” and the non polar or the non polar or hydrophobic hydrophobic interactions.interactions.

Protein Protein structurestructure: : level IIIlevel III

Notice these are NOT covalent bonds because they do not involve atoms of the same amino acid but of different amino acids that may be very far away in the primary structure.


The The quaternary quaternary structurestructure refers to the refers to the spatial relationships spatial relationships between individual between individual polypeptide chains in a polypeptide chains in a multi chain protein. multi chain protein.

The The quaternary quaternary structurestructure can be shown can be shown by the proteins by the proteins consisting of consisting of two or two or more polypeptidemore polypeptide chainschains, , which may be which may be same or different.same or different.

One of the best known One of the best known examples of a multi examples of a multi subunit protein is subunit protein is haemoglobinhaemoglobin, the , the oxygen-carrying protein oxygen-carrying protein of RBCs and of RBCs and collagencollagen, a , a protein found in the protein found in the connective tissue acting connective tissue acting as support.as support.

Protein structure: Protein structure: level IVlevel IV


Let’s check: protein structure


When folding goes When folding goes wrongwrong

Cells have a mechanism of checking and disposing of Cells have a mechanism of checking and disposing of misfolded proteins. misfolded proteins.

When this mechanism fails, cells accumulate misfolded When this mechanism fails, cells accumulate misfolded proteins causing brain degeneration (as in Alzheimer’s proteins causing brain degeneration (as in Alzheimer’s disease).disease).

Sometimes, certain “naughty” proteins called Sometimes, certain “naughty” proteins called prionsprions act as infectious agents causing severe brain damage, act as infectious agents causing severe brain damage, as in spongy encephalopathies such as Creutzeld-Jacob as in spongy encephalopathies such as Creutzeld-Jacob disease in humans, scrapie in sheep, or BSE (mad cow disease in humans, scrapie in sheep, or BSE (mad cow disease).disease).

So knowing how a protein folds is crucial to understand So knowing how a protein folds is crucial to understand its functions and discover drugs to cure or prevent its functions and discover drugs to cure or prevent diseases.diseases.


Prions: normal and abnormal

normalabnormal


Scientists have already determined the Scientists have already determined the functions of many proteins using a variety functions of many proteins using a variety of methods. of methods.

For example, they can determine:For example, they can determine: How big a protein isHow big a protein is Where it's located in an organism or even Where it's located in an organism or even

inside a cellinside a cell Whether it interacts with DNA, RNA, Whether it interacts with DNA, RNA,

nucleotides, membranes, or other proteinsnucleotides, membranes, or other proteins Whether it's changed by the cell after being Whether it's changed by the cell after being

mademade Whether it can change other proteins by Whether it can change other proteins by

modifying them or breaking them into modifying them or breaking them into piecespieces


What disrupts normal What disrupts normal structure?structure?

Proteins are sensitive to several environmental factors that Proteins are sensitive to several environmental factors that may destroy the interactions between the R groups of may destroy the interactions between the R groups of aminoacids, causing a change in shape as the tertiary aminoacids, causing a change in shape as the tertiary structure is now broken. This process is called DENATURATION.structure is now broken. This process is called DENATURATION.

The most important factors are:The most important factors are: pHpH TemperatureTemperature Presence of heavy metals or high concentrations of saltsPresence of heavy metals or high concentrations of salts


Structure is adapted to functionDifferent parts of our cells and our body require different types of Different parts of our cells and our body require different types of proteins, so the protein’s shape will determine its function. Basically, proteins, so the protein’s shape will determine its function. Basically,

proteins can be either GLOBULAR or FIBROUS.proteins can be either GLOBULAR or FIBROUS.

FIBROUS proteins are very strong and flexible, with polypeptide chains arranged in parallel helices, they form part of structures like cartilage, hair and nails, they are reactive with acids, they are insoluble in water, they are made by a few repeated amino acids, they show predominance of secondary structure, and they are not easily affected by temperature or pH. Examples are Examples are keratin, collagen and silk.keratin, collagen and silk.

GLOBULAR proteins are spherical in shape, are easily affected by pH or temperature, are made by several different kinds of amino acids, they are soluble in water, and show predominance of tertiary structure. Examples are Examples are enzymes, haemoglobin, blood plasma proteins, etc. enzymes, haemoglobin, blood plasma proteins, etc.


So what are proteins for?Proteins are essential macromolecules that have several functions in a cell and in a body. It’s not just “for growth and repair”!

Some are:• Antibodies (defense)• Contractile (muscle, cytoskeleton)• Enzymes• Hormones• Storage• Transport• Structural (hair, nails, silk, membrane proteins)• Cell signalling (cell-cell communication)• Cell self-recognition (cell’s ID)• Osmotic and pH balance • Receptors • Pathogen-host interaction (viruses infect cells through proteins on

cell membranes)


Protein deficiencyProtein deficiencyThere are two types of this illness, each with separate signs of There are two types of this illness, each with separate signs of protein deficiency to watch for. In both, the signs of protein protein deficiency to watch for. In both, the signs of protein deficiency are clear and recognizable.deficiency are clear and recognizable.

The first kind is called The first kind is called MarasmusMarasmus. This kind is a form of near . This kind is a form of near starvation and is less common in the western world. It occurs starvation and is less common in the western world. It occurs most frequently in the third world in infants who are given diluted most frequently in the third world in infants who are given diluted baby formula. baby formula. The indicators of this kind of malnutrition The indicators of this kind of malnutrition are: Weight loss, fatigue and exhaustion, loss of natural are: Weight loss, fatigue and exhaustion, loss of natural fat stores (like the flesh around the bottom), muscle fat stores (like the flesh around the bottom), muscle wastage, and susceptibility to illness and infection due to wastage, and susceptibility to illness and infection due to a poorly functioning immune system.a poorly functioning immune system.

The other kind of this type of malnutrition is called The other kind of this type of malnutrition is called KwashiorkorKwashiorkor.. It is common in cases where the affected person has a diet that is It is common in cases where the affected person has a diet that is very low in protein, but high in carbohydrates. very low in protein, but high in carbohydrates. The indicators The indicators include: muscle wastage, fluid retention, and the liver include: muscle wastage, fluid retention, and the liver becoming enlarged and fatty.becoming enlarged and fatty.

In the western world, people most at risk for this dangerous In the western world, people most at risk for this dangerous condition are strict vegans and people suffering from anorexia or condition are strict vegans and people suffering from anorexia or athletic anorexia. athletic anorexia.

DRM Biology Y11 - proteins 1 PROTEINS The essence of life.

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