PSMA (Biochemistry) pt. 2

Proteins

• complex, organic nitrogenous substances with very high molecular weights, found in all plant and animal cells, and consisting largely or entirely of alpha-amino acids united in peptide linkage

Enzymatic catalyst

• speed up chemical or biochemical reaction

• ex. amylase breakdown starches into sugar

Transport and storage

• it facilitates the transport of molecule across cell membrane and store essential substances

• ex. hemoglobin, ferritin

Coordinated motion

• protein are crucial for muscle contraction and movement

• ex. actin, myosin

actin and myosin

• protein that works together in muscle fibers

Immune protection

• antibodies

• proteins that identifies and neutralize pathogen

• ex. immunoglobulin

Generation and transmission of nerve

• proteins that play a key role in signaling pathways of neurons

• ex. neurotransmitter receptor

neurotransmitter receptor

• protein that facilitate communication between our nerve cells

control of growth and differentiation

• protein that regulates cellular processes including growth and differentiation

• ex. growth factors

Growth factors

• stimulates cell division and development

Cell signaling

• protein act as signaling molecules transmitting information within and between cells

• ex. receptor

Receptor

• protein on a cell surface that receives signals from hormone and other molecules

hormones

• protein that regulate physiological processes

• ex. insulin

insulin

• protein hormone that regulate glucose metabolism

protein

• one of the major components of biological membranes

• ex. membrane protein

membrane protein

• can facilitate transport, communication and cell recognition

1. Simple proteins

2. Conjugated proteins

3. Derived proteins

classification based on composition, physical and chemical properties of the protein

• Albumin (egg white)

• Globulin (immunoglobulin)

• Glutelin (wheat gluten)

• Prolamine (glyadine)

• Albuminoid or Scleroprotein (keratin in hair and nails

• Histone (gene regulation)

• Protamine (sperm cell of fish, protamine sulfate)

examples of simple proteins

• nucleoprotein

• glycoprotein

• phosphoprotein

• chromoprotein

• lipoproteins

• metalloproteins

examples of conjugated proteins

Nucleoprotein

• for genetic material storage and expression

• chromatin and ribosomes

Glycoprotein

• involved in cell recognition, signaling and immune response

• ex. antibodies and musine

Phosphoprotein

• important for cellular signaling and regulation

• ex. casein in milk

Chromoprotein

• function involving the light absorption and color in biological system

• hemoglobin

lipoprotein

• involved in transporting lipids through the bloodstream

• ex. LDL, HDL

Metalloprotein

• catalysts and electron transport

• ex. ferritin, cytochrome

• primary derived

• secondary derived

examples of derived proteins

primary derived

• for biological activity and nutritional purposes

• ex. peptides

secondary derived

• for biological function of original protein

• ex. amino acids

1. Fibrous proteins

2. Globular proteins

classification based on the shape and certain physical characteristics of the protein

Fibrous proteins

• provide structure support and strength to our cells and tissue

• ex. collagen, keratin, elastin

Globular proteins

• somewhat like structuring spherical or globular in shape, soluble in water

• ex. amylase, lactase

1. Enzymes

2. Storage proteins

3. Regulatory proteins

4. Structural proteins

5. Protective proteins

6. Transport proteins

7. Contractile or Motile prote

classification based on biologic functions

Enzymes

• acts as biological catalyst and speeding biochemical reaction without being consumed in the process

• ex. amylase, DNA polymerase

Storage protein

• ex. milk protein in young mammals, ferritin stores iron in soluble and non toxic form

Regulatory protein

• regulates and controls various biological processes including gene expression and cell signaling

• ex. insulin, transcription factors

Structural protein

• supports and shape to our cell and tissue

• ex. collagen and keratin

Protective proteins

• defense against pathogens and harmful agents

• ex. antibodies, fibrinogen

Transport proteins

• specific or certain molecule that facilitates their movement

• ex. hemoglobin, albumin

Contractile or motile protein

• often involved in muscle contraction and cellular movement

• ex. actin, myosin

1. Primary structure

2. Secondary structure

   1. a-helix

   2. b-sheets

3. Tertiary structure

4. Quaternary structure

What are the protein structures

Primary structure

• linear sequence of amino acids in a polypeptide chain

Secondary structure

• local folding of polypeptide chain into a specific shape due to the hydrogen bonding

alpha helix

• right handed coil of amino acids next to the hydrogen bond

• ex. fibrous protein/keratin

beta sheets

• formed between two or more segments of the polypeptide chain lying side by side and link hydrogen bond

• parallel and anti-parallel to give different properties

• ex. silk fibroin

Tertiary structure

• three dimensional shape of protein formed by the folding of polypeptide chain

• ex. globular shape of the enzyme

Quaternary structure

• arrangement of multiple polypeptide chain into a single function protein complex

• ex. hemoglobin with 4 polypeptide subunits 2 alpha and 2 beta chains

Prions

• midfolded protein

• ex. neurodegenerative diseases/alzheimers can lead to death

Denaturation of proteins

• destroy the higher structural levels of protein

Renaturation of proteins

• the recovery of the protein from its denatured state

Amino acids

• building blocks of proteins

Alanine

Ala, A

Arginine

Arg, R

Asparagine

Asn, N

Aspartic acid

Asp, D

Cysteine

Cys, C

Glutamic acid

Glu, E

Glutamine

Gln, Q

Glycine

Gly, G

Histidine

His, H

Isoleucine

Ile, I

Leucine

Leu, L

Lysine

Lys, K

Methionine

Met, M

Phenylalanine

Phe, F

Proline

Pro, P

Serine

Ser, S

Threonine

Thr, T

Tryptophan

Trp, W

Tyrosine

Tyr, Y

Valine

Val, V

HILL-TT-PVM

• Histidine

• Isoleucine

• Leucine

• Lysine

• Threonine

• Tryptophan

• Phenylalanine

• Valine

• Methionine

What are the Essential amino acids

AAAA-C-GGG-PSST

• Alanine

• Arginine

• Asparagine

• Aspartic acid

• Cysteine

• Glutamic acid

• Glutamine

• Glycine

• Proline

• Selenocysteine

• Serine

• Tyrosine

What are the NON-essential amino acids

Asparagine

• first amino acid to be discovered

• found in asparagus in 1806

Glutamate

• first isolated from wheat gluten

Tyrosine

• first isolated from cheese

• name is derived from the Greek “tyros” meaning “cheese”

Glycine

• Greek “glykos” means “sweet”

• so named because of its sweet taste

Glycine

• precursor of heme, purine, creatine

Glutamic acid

• precursor of GABA

Phenylalanine & Tyrosine

• precursor of thyroxine, epinephrine, melanin

Tryptophan

• precursor of niacin, serotonin, melatonin, indole and skalote

Lysine and Methionine

• precursor of carnitine

Histidine

• precursor of histamine

4 calories

1 gram of carbohydrates

9 calories

1 gram of fats

4 calories

1 gram of protein

hydroxyproline & hydroxylysine

• found in collagen

• make collagen strong and stable

N-Methyllysine

• found in myosin

• helps muscles contract properly

Gamma-carboxyglutamic acid

• found in prothrombin

• helps prothrombin bind calcium

Desmosine (derivative of lysine)

• found in elastin

• gives elastin its elasticity

N-acetyllysine

• found in histones that are associated with chromosomes

• helps control genes, how tightly DNA is wrapped around histones

Serine, Threonine, Tyrosine

• Phosphorylation and dephosphorylation of these play a major role in activation and inactivation of enzymes

GABA, serotonin

• amino acids or their derivatives act as chemical messengers

Argenine, Citruline, Ornithine

• several amino acids act as metabolic intermediates

hormones

• can be derived from amino acids

D- and L-amino acids

• both of these are present in polypeptide antibiotics elaborated by microorganisms

• amino acids with nonpolar or hydrophobic R groups

• amino acids with UNCHARGED POLAR R Groups

• Amino Acids with POSITIVELY CHARGED POLAR R Groups (Basic Amino Acids)

• Amino Acids with NEGATIVELY CHARGED POLAR R Groups (Acidic Amino Acids)

Classification of amino acids based on polarity

amino acids with Non-polar or Hydrophobic R groups

• referred to as neutral amino acids containing hydrocarbon R groups

• interact poorly with water

• play an important role maintaining the 3-dimensional structure of proteins

1. Aromatic

2. Aliphatic

two types of hydrocarbon side chains

• Phenylalanine (Benzene ring)

• Tryptophan (Indole Ring)

Aromatic examples

• Glycine

• Alanine

• Valine

• Leucine

• Isoleucine

• Methionine

• Proline

Aliphatic examples