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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.
U4. Protein Structure
• 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
U5. Protein Structure
• Four levels of Structure Primary Secondary Tertiary Quaternary
U5. Protein Structure
• 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
U5. Protein Structure
• 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
U5. Protein Structure
• Secondary Structure Types of structures
Alpha Helix: delicate coil held by H bonds between every fourth amino acid
U5. Protein Structure
• 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
U5. Protein Structure
• Tertiary Structure: polypeptide bends and folds over itself. Irregular
contortions resulting in interactions between R groups of amino acids
U5. Protein Structure
• Tertiary Structure: polypeptide bends and folds over itself. Forms a definite 3D
structure important in determining the specificity of the protein
U5. Protein Structure
Tertiary Structure Types of bonds:
Disulfide bridges: strong covalent bond between sulfur atoms
H bonds between Polar side chains
U5. Protein Structure
Tertiary Structure Types of bonds:
Van der Waals: strong interactions between Hydrophobic side chains
Ionic bonds between + and – charged side chains
U5. Protein Structure
• Quaternary Structure = 3-D overall protein structure can involve two or
more polypeptide chains combined bonded together to form a single protein structure
U5. 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
U7. Functions of Proteins
• 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
U5. Types of Proteins
Fibrous: composed of many polypeptide chains in long narrow strand-like shape, usually insoluble in water
U5. Types of Proteins
Fibrous Ex:• Collagen: connective
tissue of humans• Actin: component of
human muscle, involved in contractions
U5. Types of Proteins
Globular: two or more polypeptides that form a 3D glob-like shape, mostly water soluble
U5. Types of Proteins
Globular: Ex: Hemoglobin:
delivers oxygen to body tissue
Insulin: involved in regulating blood glucose levels
U5. Types of Proteins
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
U5. Types of Proteins
Number Example Background
2 Integrin
Membrane protein used to make connections between structures inside and outside cells
U5. Types of Proteins
Number Example Background
3 Collagen
Structural protein in tendons, ligaments, skin and blood vessel walls; provides high tensile strength, with limited stretching
U5. Types of Proteins
Number Example Background
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
A1. Examples of Proteins
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
A1. Examples of Proteins
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
A1. Examples of Proteins
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
A1. Examples of Proteins
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
A1. Examples of Proteins
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
A1. Examples of Proteins
Collagen•Bundles give ligaments and blood vessel walls immense strength•Form part of teeth and bone structure to prevent cracks and fractures
A1. Examples of Proteins
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
A1. Examples of Proteins
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
A2. Denaturation of Proteins
• Denaturation (break down) of proteins is caused by: Change in pH (extreme) Heat
A2. Denaturation of Proteins
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
A2. Denaturation of Proteins
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
U7. Functions of Proteins
• Functions: Catalysis: Muscle contraction: Cytoskeletons: Tensile strength: Blood clotting: Transport of nutrients and
gases: Cell adhesion: Membrane transport: Hormones: Receptors: Packing of DNA Immunity: