分子与细胞生物学 4 - L3abc Proteins (1)

3 Proteins

本章的内容是蛋白质，一共分为五小节：本节a部分主要讲述蛋白质的基本构成以及氨基酸，bc部分则开始描述蛋白质的高级结构。下一节将继续讨论蛋白质的高级结构以及蛋白质折叠。本章的第三节将讨论蛋白质的调节与控制。第四五节将以不同的蛋白质实验室方法作为第三章的结尾。如果有不太明白的或者有错误的地方随时来找UP主喔~ 文集本部分的参考文献Essential Cell Biology, 5th ed. Alberts, et al. 2019. 部分内容来自khanacademy与维基百科.

封面图：https://cdn1.byjus.com/biology/2017/08/30063857/Proteins-Structure.jpg

3a Proteins Overview & Amino acids

Some protein functions

    Enzyme (catalysts) - Eg digestive enzymes, DNA polymerase

    Structural proteins - shape & protection - Eg keratin in skin and hair, actin in cells

    Signals - Eg hormones, Neurotransmitters

    Binding proteins - Eg receptors, hemoglobin

Specific structures are required for function! (eg to bind substrate!)

        Structures need to be stable but also dynamic (change when necessary)

Structures:

        Amino acids - polymerize into polypeptide chain (covalent bonds)

        Polypeptide chain assembles into a folded protein

        Several proteins associate into a protein complex

Individual polypeptide chain alone is called the monomer

        Or a subunit in the protein complex (di-/tri-/tetra- mer)

Amino Acids

    Central α carbon attached to 4 groups:

        - Amino group [at pH 7 gain proton]

        - Carboxylic acid [at pH 7 lose proton]

        - H

        - Side chain (R)

Four classes of side chains

    Positively charged - ionic

    Negatively charged - ionic

    Polar - H-bond

    Non-polar - hydrophobic

    20 amino acids in total, each one has a 3-letter code

Four interesting amino acids

        - Histidine (His, H)

            pKa is about 7 (about half protonated at pH=7)

            Can be both a H+ donor and acceptor

            Useful in acid-base catalysis - Histidine can be both the source and sink for protons in acid-base catalysis reactions - the substrate becomes protonated and deprotonated during the reaction.

         - Proline (Pro, P)

            Side chain is covalently bound backbone in two places

                Connected to both the alpha carbon and the N atom.

                Other amino acids - side chain only connected to Cα

                Proline backbone position is constrained. It is fixed into a rigid bend. (Bend angle)

        - Glycine (Gly, G)

                Glycine’s side chain is only an H, smallest amino acid

                Glycine fits in places in proteins where other amino acids could not fit

        - Cysteine (Cys, C)

                Has a sulfhydral group (end of the chain) that can undergo redox reactions

                -SH + HS- →oxidation→ -S-S- (disulfide bond, covalent)

                Methionine (Met, M): S in the middle of the side chain, not chemically interesting.

                Two Cysteines can be oxidized to form a covalent disulfide bond (within or between polypeptides).

                Disulfides - only extracellular proteins - stabilize protein structures outside the cell (no molecular oxygen inside of the cell).

                Hair - has S - smiles so bad when burn.

3b Peptide Backbone

Levels of protein structure:

    Primary structure - linear sequence - amino acid residues

    Secondary structure - local folding - α helix / β sheet

    Tertiary structure - global folding - polypeptide chain

    Quaternary structure - protein complex - assembled subunits

Bonds:

    Primary: covalent, peptide bonds

    Secondary/Tertiary/Quaternary: non-covalent

    Tertiary/Quaternary: also disulfide bonds which is covalent

Amino acids have full charges (+/-)

Peptide bond is uncharged but polar

        Bottom O partial negative

        Top H partial positive

An amino acid peptide:

        Has an amino-terminal end & a carboxyl-terminal end

        Peptide backbone is polar, with full charges on at N- and C- terminus

        N-terminus is always shown to the left!

        One peptide bond will give a polar group

3c Secondary structure

        Protein folding is automatic, amino acid sequence determines 3-D structure!

Secondary structures

        Local interactions - only backbone atoms are shown

        H-bonds between backbone groups: carboxyl group O --- H amino acid group

α helix: H bonds form to an amino acid that is 1 turn ahead within the helix

    Amino & Carboxyl - 4 positions away

    eg keratin protein in hair is α helical

β sheet: H bonds form between β strands

    Usually twisted, not completely flat

    Parallel: with same C-N terminal directions

    Antiparallel: with alternative C-N terminal directions

    eg Skill protein consist of stacks of β-sheet

Side chains

    α helix: outside the helix

    β sheet: both above / below the sheet

Loops

    Surface of the protein

    L oops are different and irregular

α helix and β sheet (and loop) can together appear in one protein [most are these!]. These structure are stable - maintain structure through H-bonds. Side chains group can vary, only backbone groups fold.

Ribbon diagram

    Traces backbone, highlight secondary structures

    Deceptively open

Space-filling model

    Realistic atom sizes, illustrates tight packing

    Hard to see details, but more accurate

Tightly pack proteins structured more stable than loosely packed ones.

        Thight packing - no space between atoms - allows dispersion forces have there maximum effect.