2.4 Proteins IB Biology HL 1 Mrs. Peters Fall 2014

2.4 Proteins

IB Biology HL 1Mrs. PetersFall 2014

U1. Amino Acid Review

• Amino Acid Structure:• An amino group

bonded to a central carbon bonded to a carboxyl group, an “R” group (some other functional group) bonded to the central carbon

U1. Amino Acid Structure

• Amino Acid: Draw an amino acid

• You must be able to ID it from others.

U2. Amino Acids

• Types of Amino Acids 20 different (don’t

memorize) Grouped by the

properties of side chain Non-polar side chains =

hydrophobic Polar side chains =

hydrophillic

U2. Amino Acids

Types of Amino AcidHydrophobic: 9 groups•3 R groups contain rings•6 R groups do not contain rings

U2. Amino Acids

Types of Amino AcidsHydrophilic: 11 groups•4 R groups are polar but not charged•4 R groups act as an acid, negatively charged•3 R groups act as a base, positively charged

U1. Protein Structure

• Made up of amino acids• Amino acids are linked together by condensation

to form polypeptides• Ribosomes conduct the reaction

S1. Draw peptide bond

Bond forms between the OH on the carboxyl group of one amino acid and the lower H on the amino group of the other.


• Polypeptides are based on a specific sequence coded by genes (DNA)

• size vary in length from a few amino acids to thousands

• Proteins consist of one or more polypeptides folded and coiled into specific formations


• Four levels of Structure Primary Secondary Tertiary Quaternary


• Primary Structure: polypeptide chain Unique sequence of amino

acids, based on the gene sequence, held together by a peptide bond

Primary structure determines the next three levels, a slight change in one amino acid can affect the protein’s form and function


• Secondary Structure: Coiling and folding of the polypeptide Created by H bonds

between the oxygen in one carboxyl group and the hydrogen of an amino group


• Secondary Structure Types of structures

Alpha Helix: delicate coil held by H bonds between every fourth amino acid


• Secondary Structure Types of structures

Beta Pleated Sheet: two or more regions of polypeptide chains lie parallel to each other with H bonds holding structure together


• Tertiary Structure: polypeptide bends and folds over itself. Irregular

contortions resulting in interactions between R groups of amino acids


• Tertiary Structure: polypeptide bends and folds over itself. Forms a definite 3D

structure important in determining the specificity of the protein


Tertiary Structure Types of bonds:

Disulfide bridges: strong covalent bond between sulfur atoms

H bonds between Polar side chains


Tertiary Structure Types of bonds:

Van der Waals: strong interactions between Hydrophobic side chains

Ionic bonds between + and – charged side chains


• Quaternary Structure = 3-D overall protein structure can involve two or

more polypeptide chains combined bonded together to form a single protein structure


• Quaternary Structure = 3-D overall protein structure All types of bonds in

other levels involved in this level also

U7. Functions of Proteins

• Organisms synthesize proteins for a wide range of functions

• Function depends on structure and interactions of amino acids of the polymer


• Functions: Catalysis: Muscle contraction: Cytoskeletons: Tensile strength: Blood clotting: Transport of nutrients and

gases: Cell adhesion: Membrane transport: Hormones: Receptors: Packing of DNA Immunity:

U5. Types of Proteins

• Two types of proteins Fibrous Globular


Fibrous: composed of many polypeptide chains in long narrow strand-like shape, usually insoluble in water


Fibrous Ex:• Collagen: connective

tissue of humans• Actin: component of

human muscle, involved in contractions


Globular: two or more polypeptides that form a 3D glob-like shape, mostly water soluble


Globular: Ex: Hemoglobin:

delivers oxygen to body tissue

Insulin: involved in regulating blood glucose levels


Proteins may consist of one polypeptide or more than one linked togetherExamples:

Number Example Background

1 Lysozyme

Enzyme in secretions such as nasal mucus and tears, kills some bacteria by digesting cell walls



2 Integrin

Membrane protein used to make connections between structures inside and outside cells



3 Collagen

Structural protein in tendons, ligaments, skin and blood vessel walls; provides high tensile strength, with limited stretching



4 hemoglobin

Transport protein in red blood cells, binds O2 in lungs and releases in tissues

•

A1. Examples of Proteins

Rubisco: (Ribulose bisphosphate carboxylase)•Most important enzyme (catalyst) in the world• catalyze reactions that fix CO2 from atmosphere

•provides the source of carbon for all carbon compounds living organisms need

Chemwiki.ucdavis.edu


Insulin•Hormone produced to signal cells to absorb glucose and help reduce blood glucose levels•secreted by B cells in pancreas•transported by blood

Beautifulproteinsblogspot.com


Immunoglobulins•Antibodies•sites on the two arms bind to the antigen on pathogens (bacteria), the other parts act as a marker for phagocytes to engulf the pathogen•Body produces a range with different types of binding sites•Basis for specific immunity to disease

En.wikipedia.org


Rhodopsin•Vision pigment that absorbs light •membrane protein in rod cells of the retina•Contains a light sensitive molecule (not made of amino acids) surrounded by an opsin polypeptide

Common.wikimedia.org


Rhodopsin (continued)•When molecule absorbs light photon, it changes shape, causing the opsin to change sending a nerve impulse to the brain•Very low light intensities can be detected

Common.wikimedia.org


Collagen•Rope-like proteins•More abundant than any other protein•Forms a mesh of fibers in skin and in blood vessel walls that resist tearing


Collagen•Bundles give ligaments and blood vessel walls immense strength•Form part of teeth and bone structure to prevent cracks and fractures


Spider Silk•Several different types are produced for different functions•Dragline silk is stronger than KevlarTM

•Used to make webs and lifelines for suspension

Web.mit.ecu


Spider Silk•Parallel arrays are formed in regions when first made, other regions are disordered tangles•When stretched, regions gradually extend, making the silk extensible and very resistant to breakage.

Web.mit.ecu

A2. Denaturation of Proteins

Denaturation •Break down of the original structure•Bonds and interactions are broken or disrupted•Permanent, can not return to original structure


• Denaturation (break down) of proteins is caused by: Change in pH (extreme) Heat


Extreme pH•Both acidic and alkaline will cause denaturation•Changes to the R groups, breaking ionic bonds or causing new ionic bonds•Structure is altered•All proteins have an optimal pH to work best


Heat•Causes vibrations within molecule breaking intermolecular bonds and interactions•Structure is altered•Work at an optimum temperature•Heat tolerance varies in proteins

U8. Proteome

Proteome: all proteins produced by a cell, tissue or organism•Reveals what is actually happening in every cell•Each individual has a unique proteome (even identical twins!)

Nature.com


• Functions: Catalysis: Muscle contraction: Cytoskeletons: Tensile strength: Blood clotting: Transport of nutrients and

gases: Cell adhesion: Membrane transport: Hormones: Receptors: Packing of DNA Immunity:

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2.4 Proteins IB Biology HL 1 Mrs. Peters Fall 2014