Proteins

proteins - have 7 main functions  

• enzyme catalysis - faciliates/speeds up certain chemical reactions; ex. enzymes
• defense - recognizes foreign microbes; forms the center of the immune system; ex. immunoglobulins, toxins, antibodies
• transport - moves certain small molecules/ions; ex. hemoglobin, proton pump
• support - structural role; ex. fibers, collagen (most abundant protein in vertebrates), keratin, fibrin
• motion - contracting muscles; ex. actin, myosin
• regulation - receives/sends information to regulate body functions; ex. hormones
• storage - holds molecules such as calcium and iron; ex. ferritin

amino acid - 20 different kinds used in specific orders to form proteins  

• molecule consists of an amino group, carboxyl group, hydrogen atom, and side group (determines the molecule's characteristics) connected to a central carbon atom
• nonpolar amino acids have CH2 or CH3 as side group
• polar amino acids have oxygen or hydrogen as side group
• charged amino acids have acids/bases as side group
• aromatic amino acids have organic rings w/ alternating single/double bonds as side group
• special-function amino acids have unique individual characteristics
• peptide bond - bonds between amino acids; forms between the hydrogen and carboxyl groups
• polypeptide - protein composed of 1+ long chains

protein structure - shape determines function  

• shape found through x-ray diffraction
• internal amino acids are generally nonpolar
• most polar/charged amino acids are found on the surface
• 6 levels of structure - primary, secondary, motifs, tertiary, domains, quaternary
• factors of protein shape - hydrogen bonds between amino acids, disulfide bridges between side chains, ionic bonds, Van der Waals attractions (weak attractions due to electron clouds), hydrophobic exclusion (polar portions gather on the outside, nonpolar portions go towards the interior)

primary protein structure - specific amino acid sequence  

• determined by nucleotide sequence that codes for the protein
• any of the 20 different amino acids can appear at any position in a protein
• side groups play no role in peptide structure, but important in primary structure

secondary protein structure - determined by hydrogen bonds  

• folds the amino acid chain
• alpha helix - forms when hydrogen bonds form in a chain
• beta helix - when parallel chains are linked into a pleated shape

motif - aka "supersecondary structure"  

• combining parts of the secondary structure into folds and creases
• beta alpha beta motif - creates a fold
• Rossmann fold - beta alpha beta alpha beta motif
• beta barrel - beta helix folded to form a tube
• alpha turn alpha - used by proteins to bind DNA double helix

tertiary structure - positions the motifs/folds into the interior  

• final folded shape of the globular protein
• protein goes into the tertiary form due to hydrophobic exclusion
• can be unfolded (denatured) and still return to original shape
• no holes in the protein interior
• close nonpolar chains are attracted together by van der Waal's forces
• change in any amino acid can affect how they stay together in a protein

domain - structurally independent functional unit; ex. exons in genes  

• independent of all other domains
• if severed from the protein, would still maintain the same shape
• connected to other domains by single polypeptide chains

quaternary structure - 2+ polypeptide chains connecting to form a functional protein  

• arrangement of the subunits
• subunits connect to each other in nonpolar areas
• altering a single amino acid can affect the entire structure

chaperone protein - helps new proteins fold correctly  

• w/o, proteins would fail to fold/function correctly
• over 17 types, mostly heat shock proteins (high heat causes proteins to unfold)
• gives wrongly folded proteins a chance to fix itself and fold correctly
• deficiency in this protein may cause various diseases like Cystic Fibrosis or Alzheimer

denaturation - unfolding of proteins  

• can occur if pH, temperature, or ionic concentration is changed
• leads to biologically inactive proteins (venoms, made of proteins, stop working in high temperature or in presence of acids/bases)
• salt-curing/pickling used high concentrations of salt/vinegar to stop the enzymes of microorganisms from working
• most enzymes can only function well in very specific conditions
• usually, only smaller proteins can fully refold themselves after being denatured
• dissociation - different from denaturation; subunits can dissociate and still go back to their quaternary structure