Download Topic 2.4 Proteins Notes 2.4 Proteins 14-15

2.4 Proteins
IB Biology HL 1
Mrs. Peters
Fall 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 Acid
Hydrophobic: 9 groups
• 3 R groups contain rings
• 6 R groups do not contain
rings
U2. Amino Acids
Types of Amino Acids
Hydrophilic: 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 together
Examples:
Number
1
Example
Background
Lysozyme
Enzyme in secretions such
as nasal mucus and tears,
kills some bacteria by
digesting cell walls
U5. Types of Proteins
Number
2
Example
Background
Integrin
Membrane protein used to
make connections between
structures inside and
outside cells
U5. Types of Proteins
Number
3
Example
Collagen
Background
Structural protein in
tendons, ligaments, skin
and blood vessel walls;
provides high tensile
strength, with limited
stretching
U5. Types of Proteins
•
Number
4
Example
hemoglobin
Background
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: