Lecture 8 (Protein)

8/8/2019 Lecture 8 (Protein)

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PROTEINS


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ProteinsMake up 50% of cell mass, most structurally

sophisticated molecules known

Contain C, H, O, N & sometimes S & P

Form basic structural material & aid in cell function

Long chains of amino acids (from 50 to 10,000+)joined by peptide bonds

Sequence of amino acid chain dictates which proteinis made


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AMINO ACIDS


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AMINO ACIDS- D AND L FORMS


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CATEGORIES OF AMINO ACIDS

HYDROPHOBIC

HYDROPHILIC

ELECTRICALLY CHARGED


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Types of R-groups: Acidic

In neutral solutions, R-group can lose proton to becomenegatively-charged

If interaction with basic R-group, helps stabilize aprotein


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Types of R-groups: Basic

In neutral solutions, R-group can gain proton tobecome positively-charged

If interaction with acidic R-group, helps stabilize aprotein


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Types of R-group: Aromatic

R-group is an aromatic (benzene) ring

Generally hydrophobic & non-reactive


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Types of R-group: Sulfur

R-group contains SHelps stabilize globular protein structure


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Types of R-group:

Uncharged Hydrophilic

R-groups can form H-bonds


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Types of R-group:

Inactive Hydrophobic

R-groups do not form H-bonds

Rarely reactive

Usually buried deep within a protein


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Types of R-group:

WITH HYDROXYL GROUPS IN SIDE CHAINS


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Types of R-groups: Special

The R-group of proline & amino group are covalentlylinked. This limits the rotation of the side chain andas a result proline is very rigid. This creates a fixedkink in the protein chain, thus limiting how a protein

folds in the region of proline residues. Usually located at the turn of a polypeptide chain in 3Dprotein structure


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GLYCINE


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CATEGORIES OF AMINO ACIDS

HYDROPHOBIC

HYDROPHILIC

ELECTRICALLY CHARGED


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Essential & non-essential amino acids

Non-essential:y Can be synthesized from other substances in the body

Essential:y Can not be synthesized in the body

y Must come from food

y If not adequate intake, cant make proteinsy Unable to sustain body structurally & functionally

= illness & eventually death


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Histidine

Isoleucine

Leucine

LysineMethionine

(cysteine partially meets needs because has S)

Phenylalanine(tyrosine partially meets needs)

Threonine

Tryptophan

Valine

9 essential amino acids9 essential amino acids


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Most animal sources:

Complete protein: all of essential aas

Vegetables:

Missing or low in certain aas

If combine different vegetables, can get all essential aas

Lysine & tryptophan hard to get from plants so vegetariansneed to ensure adequate intake


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From Amino Acids to ProteinsAmino acids form proteins bydehydration reactions

Peptide bonds form between amino acids

2 amino acids bonded together= dipeptide

Many amino acids linked= polypeptide

Peptides generally contain fewer than 2030 amino acidresidues, whereas polypeptides contain as many as 4000residues. We generally reserve the term protein for

a polypeptide (or for a complex of polypeptides) that has awell-defined three-dimensional structure.


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As a consequence of the peptide linkage, the backbone exhibits directionality

because all the amino groups are located on the same side of the C atoms. Thus

one end of a protein has a free (unlinked) amino group (the N-terminus) and the

other end has a free carboxyl group (the C-terminus). The sequence of a protein

chain is conventionally written with its N-terminal amino acid on the left and its C-

terminal amino acid on the right.


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PROTEIN SIZEy The size of a protein or a polypeptide is reported as its

y mass in daltons (adalton is 1 atomic mass unit) or

as its molecularyweight (MW), which is a dimensionless number. For

y example, a 10,000-MW protein has a mass of 10,000daltons

y (Da), or 10 kilodaltons (kDa).


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PROTEIN STRUCTURE AND FUNCTIONA proteins function depends on its specific conformationthe order of amino acids determines proteins three-dimensional conformation


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FOUR LEVELS OF PROTEIN STRUCTURE


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PRIMARY STRUCTUREy Conformation:

Linear structure-sequence of

amino acids (Linear polypetide chain)

y Molecular Biology:each type of protein has a uniqueprimary structure of amino acids

y determined by inherited genetic

information


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SECONDARY STRUCTUREy Proteins tend to twist or bendy Coilsand folds of secondary

structure

y Results from H-bondsbetween repeatingconstituents of polypeptidebackbone (NH & CO groups)

y -helix (coiled)

or

y -pleated sheet (foldedstructure)

helices and sheets are the major internalsupportive elements in proteins.

y Turns (Glycine or proline)Turns allow large proteins to fold into highly

compact structures.


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Tertiary Structure


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WHAT STABILIZES TERTIARY STRUCTURE?


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Quaternary StructureTwo or more polypeptide chains bonding & folding together


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(c) Other Types of Protein Structure

Glycoprotein:Oligosaccharide + polypeptide

Lipoprotein:Lipid + protein

Both types important in cellular processes


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Fibrous Proteins

Insoluble in water

Structural functions:chief building materials of body

e.g. collagen, elastin, keratin


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Globular Proteins

Tertiary or quaternary structure

Water-soluble

Chemically active

Used in all biological processes

e.g. antibodies, enzymes, protein-based hormones


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ENZYMESBiological catalysts that keep metabolic & biochemical reactions happening


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May be pure protein or may have cofactor (e.g. vitamin,metal ion)

Chemically specific

y Named for type of reaction they catalyze

y Usually end in ase


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PROTEINS FORMA VARIETY OF

SHAPES AND SIZES


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QUARTERNARY STRUCTURE


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OVERVIEW OF PROTEIN STRUCTURE AND FUNCTION

Protein structure determines biologicalfunction

3D structure allows recognition & binding

with specific moleculartargets


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PROTEIN FUNCTIONS


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Why Is Protein Structure Important?

Structure dictates function

Proteins can only function if configuredin specific way


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SICKLE CELL DISEASEACHANGE IN PRIMARY STRUCTURE


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MAD COW DISEASE (IMPROPER PROTEIN FOLDING)

BSE (Bovine spongiform encephalopathy) or "mad cow disease" is thought to be

caused by misfolded proteins called prions. The body does not know what to do

with these misfolded proteins and they accumulate in lysosomes (organellescontaining enzymes which break down cell components). Eventually, the

lysosomes burst, killing the cell and allowing the abnormal prions to spread to

other cells. Large areas of cell death leave holes in the brain, hence the word

"spongiform" as the brain starts to look like a sponge.


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PROTEIN FOLDING


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Lecture 8 (Protein)