biomolecules 1

DNA vs RNA

DNA - deoxyribonucleic acid

RNA - Ribonucleic acid

composed of chains of nucleotides

a sugar phosphate backbone

nucleotide

3 parts:

• phosphate (PO₄^-) group that is negatively charged

• 5 carbon sugar (deoxyribose in DNA or ribose in RNA)

• nitrogen containing base

DNA bases

pyrimidines: single ring base

purines: double ring base

complimentary binding patterns: cytosine and guanine (3 hydrogen bonds), adenine and thymine (2 hydrogen bonds)

RNA bases

bases: adenine, guanine, cytosine and uracil instead of thymine

transcription (DNA to mRNA)

initiation: RNA polymerase binds to DNA and unwinds a 17-18bp (base pair) segment of the promoter region (open complex)

elongation: RNA polymerase moves along the DNA template synthesizing message mRNA until it reaches the terminator region

termination: transcribed terminator sequence causes RNA polymerase to pause and dissociate

translation (mRNA to protein)

in the cytoplasm, a ribosome attaches to the mRNA and translates its message into a polypeptide

the process is aided by transfer RNAs (tRNAs)

each tRNA molecule has a triplet anticodon on one end and amino acid attachment site on the other

triplet anticodon: 3 bases = 1 codon = 1 amino acid

amino acid

building unit of a protein

carboxyl group (COOH) + R group + amino group (NH₂)

characteristics of amino acid R group

non-polar hydrophobic

• aliphatic (hydrocarbon chain) → glycine, alanine, valine, leucine

• aromatic (ring structure) → phenylalanine, tryptophan

polar hydrophilic

• neutral → serine, threonine, tyrosine, glutamine, cysteine

• basic (positive charge) → lysine, arginine, histidine

• acidic (negative charge) → aspartic acid (aspartate), glutamic acid (glutamate)

groups of amino acid R groups

small amino acids: glycine and alanine

branched amino acid: valine, leucine, isoleucine

Sulphur containing amino acid: cysteine and methionine

amino acid found at a bend in a protein: proline

amino acids that can by phosphorylated: serine, threonine and tyrosine

amino acids that can be glycosylated: asparagine, serine and threonine

amino acid that can be nitrosylated: cysteine

primary structure of proteins

amino acids formed in a polypeptide chain

amino acids linked together with peptide bonds

this bond is formed between the carboxyl group of one amino acid and the amino group of next amino acid

the peptide bond is C(O)NH

chain has direction

• start = amino terminus = N terminus

• end = carboxyl terminus = C terminus

secondary structure of proteins

this is the spatial arrangement of the primary structure

it is determining by hydrogen bonding

the amino acid sequence controls folding

these structures have a regular repetitive folding pattern

most important are the alpha helix and beta pleated sheet

tertiary structure of proteins

this is further folding of the polypeptide chain

folding into a globular form

compact folded structure (hydrophobic AAs on the inside, hydrophilic AAs on the outside)

it stabilized by a wide range of bonds and interactions between the side chains of amino acids: disulphide bonds, hydrophobic interactions, ionic bonds, hydrogen bonds

quaternary structure of proteins

it is the arrangement of protein subunits in a multimeric protein

the 3D arrangement of more than one tertiary polypeptide

consist of 2 or more polypeptide chains

polypeptide may be the same or different

held together by non covalent interactions and inter-chain disulphide bonds

process of protein strucure

typical bonds in a protein

covalent bonds

• peptide bonds

• disulphide bonds

non covalent bonds

• hydrogen bonds

• hydrophobic interactions

• ionic bonds

native conformation of proteins

it is the functional fully folded protein structure

it is a unique 3 dimensional structure that determines the biological function of the protein

• enzymatic

• protection

• regulation

• signal transduction

• storage

• transport

post translational modifications (PTM)

chemical modification of a protein after translation

a functional group is attached to an amino acid

results in a change in protein function

increases the diversity of the proteome

some common PTMs

• phosphorylation: + phosphate = phosphoprotein

• glycosylation: + sugar group = glycoprotein

• ubiquitination: + ubiquitin = death signal

• nitrosylation: + NO (nitric oxide)