Midterms BIOCHEMISTRY

Proteins

The chief constituents of all cells of the body

CHON

All proteins contain

Proteins

Most abundant and functionally diverse molecules in living systems

Proteins can yield _______ upon hydrolysis

proteios

Protein is derived from the Greek word _______, which means “of first important.”

Amino Acids

organic acid that has an amine (-NH2) group attached to a chain containing an acid group.

Carboxyl Group, Amino Group, R-Group

Each amino acid consists of:

Polypeptide Bond

the repeating sequence of the C and N atoms linked by peptide bond

Side Chain or R-Group

gives the amino acid it’s unique property and is not part of the backbone or the peptide bond.

Non-Polar Amino Acids

do not gain or lose protons or participate in hydrogen or ionic bonds

oily or lipid-like

side chains of these amino acids can be thought as _______ or ________, a property that promotes hydrophobic interaction

the surface of the proteins

For proteins found in the hydrophobic environment, the non-polar amino acids are found on

Polar Amino Acids

amino acids that have zero net charge at neutral pH

Acidic Amino Acids

the side chains of these amino acids are fully ionized, containing a negatively charged carboxylic group

basic amino acids

The side chains of the _______ _______ _______ accept proton

Non-Polar

less soluble in water

Polar

soluble in water

Amphoteric Compounds

can react with either acids or bases; act as buffers in the blood

Sequence

A protein has a completely defined order of amino acids, called its

Primary Structure

All the information necessary to make a protein is contained in the

Primary Structure

specified by the sequence of the piece of DNA containing a gene for that protein, and the sequence is unique to the individual protein

Secondary Structure

gives rise to regions of the polypeptide that form regular 3D structural patterns

a-helices, B-pleated sheet

Types of Secondary Structure

a-helices

Formed by a H-bond between every 4th peptide bond – C=O to N-H

a-helices

Usually in proteins that span a membrane

a-helices

can either coil to the right or the left

helical coiled coils

Two or more polypeptides can entwine to form very long, very stable, structures called

coiled coils

serve a mechanical role for the proteins mentioned above, which are all fibrous proteins

B-pleated sheet

Core of many proteins is the sheet

B-pleated sheet

Form rigid structures with the H-bond

Parallel, Anti-Parallel

2 Types of B-pleated sheet

Anti-Parallel

run in an opposite direction of its neighbor (A)

Tertiary Structure

results from the folding of α-helices, β-pleated sheets and other areas with other/no secondary structure

Parallel

run in the same direction with longer looping sections between them (B)

Tertiary Structure

Refers to the specific folding and bending of the coils into specific layers or fibers

Hydrophobic/Hydrophilic Interactions, Hydrogen Bonding, Disulfide Leakages, Chaperone Proteins Folding

Factors influencing tertiary structure include:

Quaternary Structure

results from the interaction of independent polypeptide chains

Quaternary Structure

occurs when two or more protein units combine to form a more complex unit.

Hydrophobic/Hydrophilic Interactions, Hydrogen Bonding, Shape and Charge Distribution on Associating Polypeptides

Factors influencing quaternary structure include:

Albumin, Globulin

Types of Proteins

Albumin

Soluble in water and salty solutions

Globulin

Slightly soluble in water; soluble in salt solutions

Nucleoproteins, Glycoproteins, Lipoproteins

Classification of Proteins

Nucleoproteins

Proteins combined with nucleic acids

Glycoproteins

containing carbohydrates in varying amounts

Glycoproteins

present in most organisms.

Lipoproteins

Proteins containing lipids

Protein Denaturation

the disruption and possible destruction of both the secondary and tertiary structures

Primary Structure

Since denaturation reactions are not strong enough to break the peptide bonds, the ________ _______ (sequence of amino acids) remains the same after a denaturation process

Denaturation

disrupts the normal alpha-helix and beta sheets in a protein and uncoils it into a random shape

Heat, pH, Organic Solvents, Detergents

Factors Affecting Denaturation

Heat

increases atomic vibrations, ruins interactions, need heat of >50⁰C to denature most proteins.

pH

breaks the salt bridges

Organic Solvents

disrupts hydrophobic interactions

Detergents

Hydrophobic part pushes into protein core

3D Shape

When a protein is denatured, it loses its

its biological activity

When a protein is denatured, it loses

Folding

Protein shape is determined by the sequence of the amino acids

Conformation

The final shape is called the __________ and has the lowest free energy possible

Denaturation

the process of unfolding the protein

Molecular Chaperones

small proteins that help guide the folding and keep the new protein from associating with the wrong partner

Protein Metabolism

denotes the various biochemical processes responsible for the synthesis of proteins and amino acids (anabolism), and the breakdown of proteins by catabolism

Transcription, Translation, and Post Transitional Modifications

steps of protein synthesis

Dietary Proteins

Are denatured on cooking

Parietal Cells

are responsible for gastric acid secretion, which aids in the digestion of food, absorption of minerals, and control of harmful bacteria.

Pepsinogens

are converted in the gastric lumen by gastric acid to pepsins, which contain two active-site aspartate residues

Absorption

Occurs in the small intestine of INFANTS immediately at birth

Absorption

In ADULTS, direct transfer of intact proteins or polypeptide in the body stimulates Ab formation

Hartnup’s Disease

a condition caused by the body's inability to absorb certain protein building blocks (amino acids) from the diet

Transamination

the transfer of an amine group from one molecule to another

Transaminases

Transamination is catalyzed by a family of enzymes called

Transamination Reaction

results in the exchange of an amine group on one acid with a ketone group on another acid. It is analogous to a double replacement reaction

Cytoplasm of: Heart, Kidney, Liver, Brain, Skeletal Muscle

Site of Transamination

Transaminases

Used in the diagnosis of a variety of disorders.

Serum Glutamic Oxaloacetic Transaminase

increased after myocardial infarction and with cirrhosis of the liver

Serum Glutamic Pyruvic Transaminase

increased during infectious hepatitis

Decreased Serum Transaminase Level

occurs during pregnancy and with Vit B6 deficiency.

Deamination

Removal of –NH2 group from an AA in the form of “free NH3” with simultaneous formation of its corresponding keto acid.

Oxidative Deamination

an amino acid is converted into the corresponding keto acid by the removal of the amine functional group as ammonia and the amine functional group is replaced by the ketone group

Mitochondria of: Heart, Kidney, Liver, Skeletal Muscle

Site of Deamination

Urea Cycle

This was the first metabolic cycle that was elucidated (while the idea of metabolic cycles had been around for some time already).

Hans Krebs, Kurt Henseleit

discovered the steps of urea synthesis in mammals

Ammonia

water insoluble/more toxic

Urea

water soluble/less toxic (excreted with urine through the kidney

Urea

Nitrogenous based products must be taken to the liver and converted into less toxic, soluble compounds called

Total Protein and A/G Ratio Test

often included as part of a comprehensive metabolic panel, a test that measures proteins and other substances in the blood

Total Protein and A/G Ratio Test

used to help diagnose kidney disease, liver disease, or nutritional problems.

Biuret Test

a chemical test that can be used to check for the presence of peptide bonds in a given analyte

Biuret Test

can be also be used to gauge the amount of protein present in the analyte

Millon’s Test

an analytical test used for the detection of the amino acid tyrosine, which is the only amino acid containing the phenol group.

Millon’s Test

specific test for tyrosine, but it is not a specific test for protein as it also detects the phenolic group present in other compounds as well.

Xanthoproteic Test

used to detect amino acids containing an aromatic nucleus (tyrosine, tryptophan and phenylalanine) in a protein solution which gives yellow color nitro derivatives on heating with conc. HNO3

Hopkin’s Cole Test

specific test used for the detection of indole ring and thus, tryptophan in proteins.

Ninhydrin Test

a chemical test which is used to check whether a given analyte contains amines or α-amino acids

Enzymes

protein catalysts utilized by essentially all mammalian cells in specific biochemical reactions in different organs of the body (different organelles and structures within a cell).

Enzymes

hastens catalysis without being consumed or altered during the process.

Catalytic RNA

All enzymes are proteins - except for a small group of

1700s

first recognition of biological catalysis in studies on the digestion of meat by stomach secretions

1800s

examination of the conversion of starch to sugar by saliva and various plant extracts could ferment sugar to alcohol, proving that fermentation was promoted by molecules that continued to function when removed from cells

1850

Louis Pasteur concluded that fermentation of sugar into alcohol by yeast is catalyzed by “fermenters”