Midterms BIOCHEMISTRY

The chief constituents of all cells of the body

All proteins contain

Most abundant and functionally diverse molecules in living systems

Proteins can yield _______ upon hydrolysis

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

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

Each amino acid consists of:

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

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

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

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

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

amino acids that have zero net charge at neutral pH

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

The side chains of the _______ _______ _______ accept proton

less soluble in water

soluble in water

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

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

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

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

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

Types of Secondary Structure

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

Usually in proteins that span a membrane

can either coil to the right or the left

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

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

Core of many proteins is the sheet

Form rigid structures with the H-bond

2 Types of B-pleated sheet

run in an opposite direction of its neighbor (A)

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

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

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

Factors influencing tertiary structure include:

results from the interaction of independent polypeptide chains

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

Factors influencing quaternary structure include:

Types of Proteins

Soluble in water and salty solutions

Slightly soluble in water; soluble in salt solutions

Classification of Proteins

Proteins combined with nucleic acids

containing carbohydrates in varying amounts

present in most organisms.

Proteins containing lipids

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

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

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

Factors Affecting Denaturation

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

breaks the salt bridges

disrupts hydrophobic interactions

Hydrophobic part pushes into protein core

When a protein is denatured, it loses its

When a protein is denatured, it loses

Protein shape is determined by the sequence of the amino acids

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

the process of unfolding the protein

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

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

steps of protein synthesis

Are denatured on cooking

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

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

Occurs in the small intestine of INFANTS immediately at birth

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

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

the transfer of an amine group from one molecule to another

Transamination is catalyzed by a family of enzymes called

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

Site of Transamination

Used in the diagnosis of a variety of disorders.

increased after myocardial infarction and with cirrhosis of the liver

increased during infectious hepatitis

occurs during pregnancy and with Vit B6 deficiency.

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

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

Site of Deamination

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

discovered the steps of urea synthesis in mammals

water insoluble/more toxic

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

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

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

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

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

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

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

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.

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

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

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

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).

hastens catalysis without being consumed or altered during the process.

All enzymes are proteins - except for a small group of

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

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

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