PROTEINS



2.4 PROTEINS

• Proteins are an extremely important molecule

• About 50% of a cell’s dry weight is protein

• Proteins are polymers composed of repeating monomer units called amino acids

• All proteins are manufactured from 20 different amino acids

• Every amino acid contains the same parts:

-an amino/amine group (NH2)

-a carboxyl group (COOH)

-a hydrogen

-a specific R group (side chain)

• Each of these parts is attached to a central carbon atom.

• Generalized amino acid:

• Each amino acid has a different side chain (R group) ( this is what makes each amino acid distinct

• The properties of amino acids reflect the properties of the individual R groups

• Example: R groups can be polar (hydrophilic) or non-polar (hydrophobic), act as an acid (giving up electrons to become negatively charged), act as a base (accepting electrons to become positively charged)

The Formation of Proteins

• Proteins are formed by the linking of amino acids through a dehydration synthesis reaction.

• This happens on ribosomes through a process called translation.

• The carboxyl group of one amino acid reacts with the amino group of the next amino acid

• Specifically, the –OH of the carboxyl combines with one an H of the amino group:

• The bond between the amino acids is called a peptide bond

• The joining of two amino acids yields a dipeptide

• Three or more amino acids form a polypeptide

• Proteins always have an amino group on one end and a carboxyl group on the other end.

• Linking several amino acids together produces a repeating sequence of atoms along the chain (N-C-C-N-C-C-)

Ex: alanine + serine + glycine

Protein Conformation

• Protein conformation – shape of the protein molecule

• When a cell makes polypeptides the structure of the polypeptide will determine its function (structure determines function)

• The shape therefore is very important for the function

• There are 4 levels of protein structure:

1) Primary

2) Secondary

3) Tertiary

4) Quaternary

1) Primary Structure

❖ sequence of amino acids

❖ each protein has a unique sequence of amino acids

❖ amino acids can be linked together in any sequence giving a huge range of possible polypeptides

❖ The number of amino acids in a polypeptide can be anything from 20 to tens of thousands.

❖ Ex: Insulin contains 51 amino acids; Human titin (a protein in muscle tissue) contains 34, 350 amino acids; Mouse titin contains 34,350 amino acids.

❖ if the sequence of a polypeptide molecule is incorrect the protein will

not function (example: If even ONE of those 51 amino acids in insulin is

substituted for a different one, the protein shape may be altered and

the protein will not work!!)

❖ the amino acid sequence is determined by genes in DNA

2) Secondary Structure

❖ Formed when a primary structure folds upon itself

❖ There are two basic shapes ( a) alpha helix ( α-helix)

b) beta pleated sheet ( β -pleated sheet)

( you can also have a random coil

❖ the twisting and bending occurs because of interactions within the chain itself (ex. H-bonding)

[pic]

a) ALPHA HELIX – found in the proteins of hair, wool, horns, feathers

[pic]

b) BETA PLEATED SHEET – found in silk

[pic]

3) Tertiary Structure

❖ Involves the folding of secondary structures to form a globular (round, compact, 3-D) protein shape

❖ Held together by many bonds between interacting R groups

❖ H-bonds

❖ dipole-dipole

❖ Ionic

❖ Covalent

❖ London forces

❖ Hydrophobic Forces

❖ disulfide brides ( covalent bond that forms between S of one side chain and S of another side chain) as wells as hydrophobic interactions (hydrophobic amino acids orienting themselves away from polar water)

❖ Therefore, the amino acid sequence determines the 3-D conformation of a protein

❖ Example: myoglobin (O2 carrier in muscle cells)

4) Quaternary Structure

❖ Occurs when two or more tertiary structures interact to form a globular protein structure

❖ A protein may consist of a single polypeptide (ex: myoglobin) or more than one polypeptide

❖ Example: hemoglobin (O2 carrier in blood)

[pic]

[pic]

Proteins and Polypeptides

|Number of Polypeptides |Example |Function |

|1 |Lysozyme |Found in nasal mucus and tears |

| | |Kills bacteria |

|2 |Integrin |Membrane protein used to make connections between structures inside and |

| | |outside a cell |

|3 |Collagen |Structural protein in tendons, ligaments, skin, blood vessels |

|4 |Hemoglobin |Transports oxygen |

| | |Found in red blood cells |

Fibrous vs Globular Proteins

• Proteins can be fibrous or globular

| |FIBROUS PROTEINS |GLOBULAR PROTEINS |

|Shape |long |Tightly folded; compact |

|Solubility |Insoluble in water |*Soluble in water |

|Organization |Secondary Structure most significant |Tertiary Structure most significant |

|Function |Structural |Functional (they do something |

|Examples |Collagen, keratin, myosin |Hemoglobin enzymes, antibodies, hormones |

* Protein Solubility

• 8 of the 20 amino acids are nonpolar (hydrophobic)

• The remaining 12 are polar (hydrophilic)

• For globular proteins leaving the polar ones on the exterior (see tertiary structure)

• This allows the protein to dissolve in water

• If a protein contains less non-polar amino acids, the less soluble it will be

Denaturation

• A protein’s shape is also determined by the environmental conditions in which the protein is found

• The structure of a protein is sensitive to pH, temperature, salt concentration, chemicals

• If any of these conditions falls outside a favorable range, a protein’s conformation is altered and therefore its function is altered

• When a protein loses its shape, we say it is denatured

• These conditions do not alter the primary structure (amino acid sequence) therefore if put back into normal conditions, the protein could regain its original shape (however if a sequence is disrupted (ex. with denaturing agent) then the protein will not regain its shape)

• A denatured protein does not usually return to its former structure

• Example: curling your hair

• adds heat to the keratin (protein) of your hair.

• The heat alters the 3-D shape of the hair and allows the curl to stay.

• Once the hair is washed, the crimp is gone and keratin returns to normal

• Example: perming your hair

• adds agents which break bonds and then another chemical which causes bonds to reform in different places so that your hair can hold the curl (specifically the formation of disulfide bridges)

Functions of proteins

• Proteins have many diverse structures and therefore many functions (structure determines function)

|Protein Function |Description |

|Enzyme |Catalyze chemical reactions in an organism |

| |Ex: Amylase catalyzes the breakdown of starch |

|Muscle Contraction |Proteins actin and myosin together cause the muscle contractions |

| |that make you move |

|Cytoskeletons |Give shape to cells and form spindle fibres during mitosis |

| |Ex: tubulin |

|Tensile Strengthening |Give strength to skins, tendons, ligaments, blood vessels |

| |Ex: Collagen |

|Blood Clotting |Plasma proteins that stop bleeding and repair damaged blood |

| |vessels |

| |Ex: fibrin |

|Transport of nutrients and gases |Proteins in the blood transport oxygen, carbon dioxide, iron, |

| |lipids |

| |Ex: hemoglobin transports O2 |

|Cell Adhesion |Membrane proteins that cause adjacent cell membranes to stick to |

| |each other |

|Membrane Transport |Used for facilitated diffusion and active transport (Protein |

| |channels and protein pumps) |

|Hormones |Chemical messengers |

| |Ex: insulin |

|Receptors |Binding sites in membranes and cytoplasm for hormones, |

| |neurotransmitters, tastes, smells, light |

|Protein Function |Description |

|Packing of DNA |Histones are proteins that associate with eukaryotic DNA and keep|

| |it organized |

|Immunity |Antibodies are proteins that recognize foreign invaders |

|Storage |Casein is the protein of milk which stores amino acids used for |

| |developing baby mammals |

|Pigments |Chemicals that absorb and reflect light. |

| |Ex: melanin |

|Packing of DNA |Histones are proteins that associate with eukaryotic DNA and keep|

| |it organized |

|Immunity |Antibodies are proteins that recognize foreign invaders |

Examples of Proteins

Rubisco (Ribulose bisphosphate carboxylase)

- Found in plant cells

- An important enzymes in photosynthesis

- Rubisco fixes inorganic carbon in the form of CO2 into organic carbon in the form of simple sugars

- It is the most abundant protein on Earth and possibly the most important

Immunoglobulin

- Also known as antibodies

- They recognize specific pathogens and bond to them, flagging them to be destroyed

Collagen

- ¼ of the proteins in the human body are collagen

- Give strength to ligaments, blood vessels

- Structure to teeth and bones

Insulin

- Hormone made by the pancreas that promotes cells to absorb glucose and the liver to produce glycogen, thereby lowering blood glucose levels

Rhodopsin

- A vision pigment that absorbs light and sends a nerve impulse to the brain about the light received

Spider Silk

- Different types and functions

- Extremely strong for its density

Proteomes

- A proteome is all of the proteins produced by a cell, tissue or an organism

- Every individual has a unique proteome

- The genome of an organism is fixed but the proteome is variable because different cells in an organism make different proteins, even at different times.

- With the exception of identical twins, none of us have identical proteins, so each of us has a unique proteome.

- Even the proteomes of identical twins can become different with time and different experiences.

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