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Lecture 8

BIL 255 Lecture 8: BIL 255 Topic 6B 2-9

Course Code
BIL 255
Diresta Dan

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BIL 255- Topic 6B: Proteins (2/9/17)
I. Proteins (Work Horses of Cell Metabolism)
A. Proteome
1. Entire set of proteins expressed by a genome either a cell’s or a whole
a. E. coli = 4250 proteins
b. Yeats = 6000 proteins
c. Human = 100000 proteins
B. Proteins Classified by Function
1. Enzymes: catalytic activity and function
a. Tryptophan synthase: makes amino acid tryptophan
b. DNA Polymerase: copies DNA
2. Transport proteins: bind and carry ligands
a. Hemoglobin: carries oxygen
b. Transferrin: carries Iron
3. Storage proteins: stores small molecules or iron
a. Casein: in milk is a source of amino acids for baby mammals
4. Contractile (Motor Proteins): contract, change shape and compose the
elements of the cytoskeleton
a. Actin, Myosin, and Tubulin
5. Structural (Support Proteins): collagen of tendons and cartilage, elastin of
ligaments, keratin of hair, feathers and nails, and fibroin of silk and webs
6. Defensive (Protector Proteins): antibodies, fibrinogen and thrombin, snake
venoms and bacterial toxins
a. IgF in humans
7. Regulatory (Signal Proteins): regulate metabolic processes, hormones,
transcription factors and enhancers, and growth factor proteins
a. Lactose repressor: in bacteria silences the gene for the enzymes that
degrade the sugar lactose
8. Receptors (Detect Stimuli): detects signals and transmits them to the cell’s
response machinery
a. Rhodopsin: in the retina detects light
C. Nomenclature
1. Proteins are named based upon their solubility because of the early chemical
analysis of isolated proteins
2. Simple Proteins: on acid hydrolysis yields only amino acids
a. Albumins: soluble in pure water; are globular in shape and include
many different enzymes
b. Globulins: soluble in dilute aqueous solutions; insoluble in pure water
c. Prolamins: insoluble in water, but are soluble in 50-90% simple
alcoholic solutions

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d. Histones: have a unique structure and are highly numbered basic
amino acids
1) Lys, Arg, His: form a complex with DNA
e. Glutelins: insoluble in most solvents; but soluble in dilute acids/ bases
f. Protamines: not based upon solubility; they have a small molecular
weight with around 80% Arginine and have no Cysteine
g. Scleroproteins: insoluble in most solvents
1) Have a fibrous structure which make them architectural
proteins of cartilage and connective tissue
2) Collagen: high in Glycine, Proline and no Cysteine; when its
boiled gelatin is formed
3) Keratins: proteins of skin and hair; they are highly basic
amino acids (Lys, Arg, His) but have some Cysteine
3. Complex Proteins: on hydrolysis yields amino acids and other molecules
a. Lipoproteins (+ lipids): blood, membrane and transport proteins
b. Glycoproteins (+ carbohydrates): antibodies and cell surface proteins
c. Nucleoproteins (+ nucleic acids): ribosomes and organelles
4. Common Terminology
a. Dipeptide: 2 amino acids
b. Tripeptide: 3 amino acids
c. Oligopeptide: short chain of amino acids (2-20 amino acids)
d. Peptide: Less than 50 amino acids
e. Polypeptide: A few to a lot of amino acids (up to 100 amino acids) with
a molecular weight of around 10,000
f. Protein: Polypeptide with well-defined 3D structure
II. Structure of Proteins
A. Infinite Possibilities
1. The Average Protein: has 300-500 amino acids and has a molecular weight of
around 35kD to 55kD; a protein of 300 amino acids made with 20 different
amino acids can have 20300 linear arrays of amino acids
2. Beef Insulin (1st sequenced protein) was done by Fred Sanger
a. This is commonly referred to as bovine insulin
1) The A chain contains 21 amino acids
2) The B chain contains 30 amino acids
3. We suspect about 100,000 human proteins, yet ewe have only seen about
10,000 through x-ray crystallography
B. 4 Protein Levels
1. Primary: linear sequence of amino acids
2. Secondary: Regular, recurring orientation of amino acids in a peptide chain
due to a hydrogen bond
3. Tertiary: Complete 3D shape of a peptide (weak electrostatic forces)

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4. Quaternary: Spatial relationships between two or more different polypeptides
or subunits
C. Primary Sequence
1. Linear Sequence
a. Repeated peptide bonds form the backbone of the polypeptide chain
b. R side groups project outward on alternate sides along a zig-zag
2. Chain
a. One end of the polypeptide chains has a free amine group
1) N-terminus
b. Other end has a free carboxylic group
1) C-terminus
3. Size
a. Determined by mass ( MW in Daltons = 1 amu)
1) Average MW of all amino acids is about 113 Da
i. Protein has a mass of 5763 Da = 51 amino Acids
4. Protein Primary Sequence is determined by reading the genome sequence
5. Protein function is derived from the 3D structure (conformation) which is
specified by the primary amino acid sequence and its local environs
a. Lysozymes: a family of enzymes which damage bacterial cell walls by
hydrolyzing the glycosidic bonds between N-acetylmuramic acid and
N-acetyl-D-glucosamine residues in peptidoglycans
1) Found in egg whites and human tears with 129 amino acids
with a MW= 14,600
6. Consequences of Primary Sequencing
a. Polymorphisms: Some proteins have different primary amino acid
sequences, yet exhibit the same activity
1) Peroxidase Family: Substrates hydrogen peroxide, organic
hydroperoxides or lipid peroxides
i. Horseradish Peroxidase, Catalase, Cytochrome-c
Peroxidase, Hemoprotein, Gutathione Peroxidase,
Thyroid Peroxidase
b. Invariants: Do not vary by a lot in amino acid sequence
1) Ubiquitin: Signals degradation of a protein via a proteasome
i. 96% eukaryotic sequence universality
2) Histones: (H2A, H2B, H3 and H4) wraps 147 base pairs of
DNA around 1.65 times
i. Few sequence differences among species
c. Site Specificity: Unique sequences determine intra-cellular location
and function
1) Signal Sequence: for protein targeting
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