BIOCHEM Exam 2

Practice these terms and definitions to do a good job on the nursing biochem class for exam 2!

What is biochemistry?

Study of the chemistry of life; all chemical reactions in a living organism

Ammonium Ion ; amine group

-NH3+ ; -NH2

Hydroxyl group

-OH

Carboxyl group ; carboxylate ion (carboxylic acid)

O=C—OH ; O=C—O-

Carbonyl group

O=C

Amide

O=C—N—H

Thiols ; sulfides ; disulfides

—SH ; —S— ; —S—S—

4 Biomacromolecules

Proteins, Lipids, Carbohydrates, Nucleic acids

Lipids

Membranes, fatty acids, cholesterol, eicosanoids

Carbohydrates

Table sugar, cellulose, starch, glycogen

Nucleic Acids

RNA, DNA

Protein Class & Function: Enzymes

Catalyze biochemical reactions (biochemical catalysts)

Protein Class & Function: Hormones

Messengers that regulate bodily fluids

Types of hormones

Glucagon - slows down gastric emptying, stimulates insulin production

Insulin - regulates glucose metabolism

Growth Hormone - stimulates growth & cell reproduction

Protein Class & Function: Storage Proteins

store essential substances for immediate availability

Examples of storage proteins

Ovalbumin - main protein nutrient in egg whites 

Casein - major protein in milk for baby mammal development

Ferritin - protein that stores iron in a nontoxic form, diagnostic test for iron deficiency 

Protein Class & Function: Transport proteins

Carry substances through blood & through the cell membranes

Types of transport proteins

Hemoglobin - transport oxygen in the blood

Serum albumin - transports fatty acids in blood

Glucose transporter - forms pore in cell membranes for glucose to pass through

Protein Class & Function: Structural proteins

Support and maintain shape of cell

Examples of structural proteins

collagen - support bone and teeth

elastin - ligaments

keratin - fingernails, hair

Protein Class & Function: Protective proteins

provide defense against invaders & protect from injurty

Example of protection proteins

Antibodies - recognize foreign substances

Protein Class & Function: Contractile proteins

Do mechanical work (actin & myosin in muscle, kinesin in vesicle transport)

Isomers

compounds with the same chemical formulas, but different structures

Constitutional isomers

isomers that differ in the bonding order of atoms

Stereoisomers

isomers that have atoms bonded in the same order but with different arrangements in space

Enantiomers

mirror images of stereoisomers that cannot be superimposed

Diastereoisomers

stereoisomers that are not mirror images

Hydrophobic

substance will not dissolve in water; cannot H-bond with water

Hydrophilic

Substance that can dissolve in water; H-bonds with water

Nonpolar amino acids (no charge)

Alkanes (single-bonds) & Arenes (rings) 

Neutral polar (no charge)

Hydroxyl, thiol, or amide groups

Acidic amino acid

carboxylic acid (negative charge)

Basic amino acid

Amine group (positive charge)

Zwitterions

both positive and negative charges (dipolar)

Zwitterion rule

All amino acids are zwitterionic at pH 7 because their backbone carboxylic acid carries a negative charge & backbone amine carries a positive charge at pH 7

Formation of a peptide bond

Two amino acids covalently linked together by an amide bond (peptide bond) form a dipeptide

Special structural amino acids

Glycine - no organic side chain, —H

Proline - secondary amine, forms tertiary amide upon formation of peptide bond, ridged structure, found at end of helix

Cysteine - thiol group forms disulfide bonds in extracellular proteins

Primary structure

Covalent bonds; intramolecular bonds occurring between atoms of amino acids, in peptide bonds & disulfide bonds

Secondary structure

Noncovalent interactions; hydrogen bonds between backbone amide groups

Tertiary structure

Hydrophobic effect (does not stabilize, the folding stabilizes)

Van der Waals

Salt Bridge

Hydrogen bonding

Quaternary structure

disulfide bonds & noncovalent forces, new covalent bonds

a-Helix

Stabilized by amide groups which 1) form peptide bonds between adjacent resides & 2) hydrogen bond between amide groups 4 residues away

B-strands

B-pleated sheets stabilized by amide groups which 1) form peptide bonds between adjacent residues & 2) hydrogen bond between amide groups on adjacent strands

Globular protein structure classification

Forms a globe-like structure, typically water soluble as hydrophilic residues are on the surface (water loving)

Fibrous protein structure classification

Forms fibers & sheets, typically insoluble containing small hydrophobic residues tightly packed together in layers 

Conjugated proteins

require non-protein components for function

Glycoproteins

covalently bound carbohydrates (form receptors on cell surface)

Lipoproteins

covalently bound to lipids (transport cholesterol through blood)

Metalloproteins

metal ions (trace minerals) for structure stabilization or catalytic function

Phosphoproteins

covalently bound phosphate groups used to activate or deactivate a protein or provide binding sites for protein attachment

Hemoproteins

contain heme groups/porphyrin rings (oxygen transporters, energy producing enzymes)

Nucleoproteins

contain ribonucleic acids (ribosomes used in protein synthesis)

Globular conjugated proteins

Oxygen transporters:

Myoglobin (found in muscles) tertiary structure — 8 chains

Hemoglobin (found in red blood cells) quaternary structure — 8 chains, only 4 to function

Oxygen transfer occurs in the capillary

Myoglobin has higher affinity for oxygen than hemoglobin does

Sickle Cell Anemia 

Acidic residue is changed to a hydrophobic residue — #6 is changed from glutamate to Val (a mutated form), which causes the disease

New hydrophobic residue finds a hydrophobic pocket on an adjacent molecule, causing aggregation

Globular protein becomes fibrous protein

Electrophoresis: analytical and diagnostic tool

Based on charge and size 

Positive goes to anode, negative goes to cathode

Fibrous proteins: collagen

Tough, insoluble proteins with quaternary structure

Tropocollagen — quaternary structure stabilized by hydrogen bonds

Every third residue is glycine, proline & derivative of proline called hydroxylated proline

Connective tissue - covalent bonds occur between strands (disulfide)

Scurvy

Vitamin C deficiency

Vitamin C needed to create hydroxylated proline

Symptoms: skin lesions, bruising, joint pain, swollen, bleeding gums with tooth loss, spontaneous nasal bleed

Curable with proper diet: fruits & vegetables

Brittle Bone Disease (osteogenesis imperfecta) 

Dominant inheritance - from only one parent

Type 1: normal collagen, insufficient amounts

Primarily before puberty, uncommon bone fractures, brittle teeth, greying sclera, loose joints, weak muscles

Type 2 : poor amounts and quality of collagen

Fracture occur before birth, severe respiratory problems

Chaperones

protein and protein complexes that assist in the folding of other proteins; keep proteins from aggregating in nonfunctional units

Prions

Proteins located in central nervous system, convert a-helices and loop region to B-sheets, infectious agents that reduce normally folded prions to change shape

Transmissible spongiform encephalopathies

result of prion malformation, rare degenerative brain disorders from tiny holes that give brain a spongy appearance, rapidly progressive and fatal

Protein Degradation

breaking peptide bonds with hydrolysis

Autophagy

Eating of self; self-degradative process that is important for balancing sources of energy at critical times in development and in response to nutrient stress

Lysosomes

Organelle in cell that acts as garbage disposal to degrade any unwanted/unneeded material within the cell and release nutrients

Proteasomes

degrade unfolded or unneeded protein by proteolysis

Protein denaturation

unfold, break non-covalent

Heat

disrupts the non-covalent interactions (cooking an egg)

Mechanical agitation

foaming/air bubbles cause lack of water

Detergents

can interact with hydrophobic sidechains and unfold the protein

Organic compounds

polar solvents can disrupt H-bonds

pH change

basic and acid side chains change charge disrupting salt bridges

Inorganic salts

at high concentrations and disrupt salt bridges

Enzyme

a biological catalyst (ends in -ase)

Substrate

reactant of an enzyme catalyzed reaction

Turnover number

number of substrate molecules that are converted to product over a given time period

Cofactor

nonprotein substance that binds to the protein and is required for catalysis

coenzyme

organic cofactors typically found in redox enzymes

apoenyzme

protein minus its cofactor/coenzyme

holoenzyme

catalytically active enzyme (apoenzyme with its cofactor/coenzyme)

Active site

pocket in enzyme where catalysis takes place

Purpose of an enzyme

to be the catalyst of a biochemical reaction

Proximity effect

bring reactants together

Orientation effect

hold reactions at the required distance and orientation for the reaction

Energy effect

lower activation energy by inducing a strain on the bonds of the substance

catalytic effect

provide acidic, basic, and other types of functional groups that are required for catalysis

Oxidoreductase

catalyze oxidation-reduction reactions

requires a coenzyme for catalysis

Dehydrogenases

removes 2 hydrogen atoms from a substrate to form a double bond (requires FAD or NAD+ as coenzyme)

Transferases

transfer of a functional group (amino or phosphoryl) between substrates

Kinases

transfer a phosphoryl group (—PO3 2-) between substrates

Transaminase

transfers an amino group (—NH3 +) between substrates

Hydrolases

catalyze hydrolysis of substrates (water lysis)

water splitting - substrate bonds break by adding an H to the product

Lipases

hydrolyze ester bonds in lipids

Proteases

hydrolyze peptide bonds (backbone amides)

Nucleases

hydrolyze the phosphate ester bonds in DNA/RNA

Amylases

hydrolyzes the 1,4 glycosidic bonds in amylose (starch)

Isomerases

catalyze the isomerization of substrate (rearrange bonds of substrate)

lyases

catalyze the elimination of a functional group by forming a double bond or breaking a double bond

Ligases

catalyze bond formation couple with ATP hydrolysis