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Protein and AA: Structure

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Amino Acids

General Structure of an amino acid

  • R group is the side chain that makes an amino acid different from one another

  • amino acids have an α-carbon

    • the one next to the carboxyl group​

    • has 4 different attachments

      • ​α-NH2

      • α-H

      • α-COOH

      • R group of side chain (key functional group)

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  • amino acids have asymmetry due to the 4 attachments

    • 2 possible configurations​

      • L (amino group of the left) - levo​

      • D (amino group on the right) - dextro

    • only L amino acids occur in mammals

  • all 20 amino acids are important

  • body can make ~10 of the 20 (non essential)

  • cannot make ~10 of the 20 (essential)

    • must obtain from eating​

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Protein Structure

four levels of structure

  • primary 1°

    • linear sequence of amino acids joined by peptide bonds​

    • dictated by gene

    • DNA --> RNA --> AA sequence

  • secondary 2°

    • coils, pleats within each chain​

    • hydrogen bonding

  • tertiary 3°

    • how the chain folds up in a 3D structure​

    • bonds through side chains (R group)

  • quaternary

    • 2 or more chains linked together​

    • usually by disulfide bridges

peptide vs protein

  • peptide nomenclature

    • di or tripeptide - 2 or 3 amino acids​

    • peptide - polymer of short chain length

    • polypeptide - up to 50 amino acids

    • protein - >50 amino acids

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1° structure

  • how amino acids are joined

  • chain peptide bonds

  • dipeptide

    • 2 AA​

    • 1 peptide bond

  • the sequence of the primary chain can be affected by gene mutations

    • could have malfunctioning protein​

    • mutations due to UV radiation

    • metabolism errors

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2° structure

  • still a linear sequence

  • needs to "reorganize through role of bonding through side chains (R group)

  • leads to two types of 2° structure

    • ​α helix

    • β pleated sheets

  • H bonds are attraction between H and O in different parts of the chain

  • H bonds in 2° leads to production of 3° or 3D structure

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2° structure --> 3° structure

  • bending and folding

  • 3D structure

    • each protein has a preferred arrangement

    • due to side chain (R group) interactions

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4° structure

  • due to the presence of 2 or more proteins

  • held together by similar forces as 3°

  • not all proteins have a 4° structure

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Forces and Bonds

Van der Waals

  • very weak attractions or repulsions between R groups

  • based on distance

H bonds

  • weak attractions between H and O on different R groups

Hydrophobic interactions

  • associations of non-polar R groups or molecules

  • since water molecules cling together through strong H bonds, non-polar regions of proteins are excluded from interaction with water

  • non-polar regions are forced together in "hydrophobic" regions

    • weakly "bonded" this way​

  • the AAs in hydrophobic regions are usually the ones that have hydrocarbons as their R group

Salt bridges

  • weak ionic linkages between NH2 and COO

  • amino groups are present as their NH3 ions in neutral solution and COO are present as carboxylate ions

  • the positive charge of an NH3 ion on one chain is attracted to the negative charge of a carboxylate ion on another

  • a salt bridge is an ionic bond between between ions that are part of a larger covalently bonded unit

Disulfide bonds

  • between two sulfhydral (SH) groups on opposing cystines

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Denaturation

  • unfolding and disorganization of protein structure without hydrolysis of peptide bonds

    • organic solvents​

    • heat

      • ie. egg whites​

    • change in pH

  • may be reversible, although not usually

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Protein Function

Structure

  • protein and skeleton in animals

    • collagen, keratin​

Storage

  • specific proteins (source of AA) for nourishment

    • milk and wheat protein​

    • we don't store excess protein to have reserves, our reserves are functional protein

Protection

  • antibodies

    • globulins​

  • blood clotting

    • thrombin​

    • fibrinogen

Regulation

  • protein hormones

    • insulin, glucagon​

Nerve impulses

  • specialized proteins act as receptors in nerve and eye

    • opsin​

Motion

  • muscle fibers

    • actin, myosin​

Transport in blood

  • albumin

    • transports minerals, fat soluble vitamins, FAs​

  • apolipoproteins

    • transports TGs and CHL​

  • hemoglobin

    • transports O2​

Secondary Functions

Buffers

  • due to COOH and NH2 as R groups

Osmotic pressure

  • plasma proteins cannot cross out of capillaries 

  • because they remain in blood vessels, they help maintain the right number of particles to maintain proper fluid balance in blood vessels. 

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©2023 by Syracuse University Dr.Margaret Voss

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