Protein and AA: Structure

Amino Acids
General Structure of an amino acid
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R group is the side chain that makes an amino acid different from one another
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amino acids have an α-carbon
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the one next to the carboxyl group​
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has 4 different attachments
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​α-NH2
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α-H
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α-COOH
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R group of side chain (key functional group)
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amino acids have asymmetry due to the 4 attachments
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2 possible configurations​
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L (amino group of the left) - levo​
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D (amino group on the right) - dextro
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only L amino acids occur in mammals
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all 20 amino acids are important
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body can make ~10 of the 20 (non essential)
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cannot make ~10 of the 20 (essential)
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must obtain from eating​
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Protein Structure
four levels of structure
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primary 1°
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linear sequence of amino acids joined by peptide bonds​
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dictated by gene
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DNA --> RNA --> AA sequence
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secondary 2°
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coils, pleats within each chain​
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hydrogen bonding
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tertiary 3°
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how the chain folds up in a 3D structure​
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bonds through side chains (R group)
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quaternary
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2 or more chains linked together​
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usually by disulfide bridges
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peptide vs protein
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peptide nomenclature
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di or tripeptide - 2 or 3 amino acids​
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peptide - polymer of short chain length
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polypeptide - up to 50 amino acids
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protein - >50 amino acids
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1° structure
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how amino acids are joined
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chain peptide bonds
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dipeptide
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2 AA​
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1 peptide bond
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the sequence of the primary chain can be affected by gene mutations
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could have malfunctioning protein​
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mutations due to UV radiation
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metabolism errors
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2° structure
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still a linear sequence
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needs to "reorganize through role of bonding through side chains (R group)
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leads to two types of 2° structure
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​α helix
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β pleated sheets
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H bonds are attraction between H and O in different parts of the chain
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H bonds in 2° leads to production of 3° or 3D structure

2° structure --> 3° structure
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bending and folding
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3D structure
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each protein has a preferred arrangement
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due to side chain (R group) interactions
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4° structure
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due to the presence of 2 or more proteins
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held together by similar forces as 3°
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not all proteins have a 4° structure

Forces and Bonds
Van der Waals
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very weak attractions or repulsions between R groups
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based on distance
H bonds
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weak attractions between H and O on different R groups
Hydrophobic interactions
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associations of non-polar R groups or molecules
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since water molecules cling together through strong H bonds, non-polar regions of proteins are excluded from interaction with water
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non-polar regions are forced together in "hydrophobic" regions
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weakly "bonded" this way​
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the AAs in hydrophobic regions are usually the ones that have hydrocarbons as their R group
Salt bridges
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weak ionic linkages between NH2 and COO
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amino groups are present as their NH3 ions in neutral solution and COO are present as carboxylate ions
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the positive charge of an NH3 ion on one chain is attracted to the negative charge of a carboxylate ion on another
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a salt bridge is an ionic bond between between ions that are part of a larger covalently bonded unit
Disulfide bonds
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between two sulfhydral (SH) groups on opposing cystines






Denaturation
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unfolding and disorganization of protein structure without hydrolysis of peptide bonds
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organic solvents​
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heat
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ie. egg whites​
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change in pH
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may be reversible, although not usually

Protein Function
Structure
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protein and skeleton in animals
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collagen, keratin​
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Storage
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specific proteins (source of AA) for nourishment
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milk and wheat protein​
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we don't store excess protein to have reserves, our reserves are functional protein
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Protection
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antibodies
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globulins​
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blood clotting
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thrombin​
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fibrinogen
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Regulation
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protein hormones
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insulin, glucagon​
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Nerve impulses
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specialized proteins act as receptors in nerve and eye
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opsin​
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Motion
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muscle fibers
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actin, myosin​
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Transport in blood
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albumin
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transports minerals, fat soluble vitamins, FAs​
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apolipoproteins
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transports TGs and CHL​
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hemoglobin
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transports O2​
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Secondary Functions
Buffers
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due to COOH and NH2 as R groups
Osmotic pressure
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plasma proteins cannot cross out of capillaries
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because they remain in blood vessels, they help maintain the right number of particles to maintain proper fluid balance in blood vessels.

