biochemistry - protein structure

bacterial cell composition, water to chemical ratio

70% water, 30% chemicals (mostly proteins - more than DNA)

fraction of a cells energy used to make proteins

2/3 of a cells energy is used on protein synthesis

types, functions and characteristics of proteins in cells

• proteins are the most abundant, complex and versatile molecule that life creates

• produce or break down enzymes

• transmit information via ligands and receptors

• generate force and movement using pumps and motor proteins

hierarchical organisation of nucleic acids

nucleotides → codons → genes

hierarchical organisation of proteins

amino acids → a-helix and b- pleated sheets → protein

basic bond types present in the hierarchical organisation of proteins

primary: covalent structure

secondary: local non-covalent structure

tertiary: overall conformation of a chain

quaternary: interactions of multiple chains

what are proteins

proteins are linear polymers of amino acids with common: central alpha carbon, one hydrogen, one carboyxl group and a variable R-group part

draw the generic amino acid structure

what property of amino acid structure allows for stereoisomerism

the alpha-carbon is assymetric allowing for 2 mirror images (stereoisomers) L and D

• the mirror images are chemically distinct

• all amino acids in nature are L amino acids

by which mechanism does bonding of amino acids occur

peptide bond formation through condensation

• cells form peptide bonds in a directional sequence

• new amino acids elongate the polymer at the carboxyl group

• subsequent amino acids are added from the N-terminus (free amino group start) to the C-terminus (free-carboxy group end)

why do cells make polypeptides in a directional manner

• because they are translated from a direction template of mRNA

• this is transcribed from a direction source (DNA)

distinguish between covalent and ionic bond energies

covalent: electron sharing between atoms of similar electro negativity

peptide bonds (very strong) and disulfide bridges are used

ionic: electron transfer between molecules of opposite charges

(called salt bridges in proteins)

define a dipole moment

occurs in partially charged molecules with uneven electron distribution

• happens due to polarity and difference in electro negativity

• electrons are attacted to the negative atom leading to a partial charge

define a hydrogen bond

a partially positive hydrogen, covalently bonded to an electronegative atom (F,O,N) interacting with a lone electron pair of electronegative atoms

• involved H in the middle bonded to 2 electronegative atoms (1 on each side). 1 electronegative atom acts as a donor atom forming a covalent bond (very strong and immovable) with the middle H while the acceptor atom forms a non-covalent bond with the H by moving its lone electron pair

when is a hydrogen bond most energetically favorable

if all three atoms are in a straight line

(when the 180 degree angle deviates, there is a significant loss in bond energy)

name and briefly explain the three different types of van der waal forces

1. permanent dipoles

→ has dipole moments due to partial charge

→ permanent dipole formes when molecules are aligned

2. dipole-induced-dipole

→ occurs when molecules of equal electronegative charge are in close proximity

3. london dispersion

→ occurs when electron distribution of two non dipole molecules fluctuates and spontaneously causses an unequal electron distribution

define a van der waal force and order them from strongest to weakest

attractions arising from temporary or permanent dipoles

permanent dipole (strongest) → dipole-induced → london dispersion (weakest)

state all the types of non covalent bonds

ionic interactions (salt bridges)

hydrogen bonds

van der waal interactions

explain why is H2O regarded as the universal solvent

it can alter non-covalent structures and therefore weaken bonds due to its polarity

• it can shield and compensate charge

• good solvent for other polar substances

• can donate or accent electrons

• molcules attempting to form H bonds in solution will compete with H2O

• to maximise H bonds, liquid water assumes disorganised networks while crystalising at freezing point

properties of ionic and polar molecules in water

always hydrophilic

interact with water using H bonds and electrostatic attaction

properties of nonpolar molecules in water

hydrophobic due to equal electron distribution

instead H2O reacts with it self to avoid fats

includes saturated hydrocarbons such as fats

define the hydrophobic effect

when water molecules form cages around fats to reduce its entropy

arises from the property of liquid water

not a type of interaction as it is solvent mediated

driven only by entropy

state the 4 categories of the amino acids

charged, polar & uncharged, special, hydrophobic

(all determined by side group)

list the charged amino acid examples

arginine, histidine, lysine (positive)

aspartic acid, glutamic acid (negative)

list the polar uncharged amino acids

serine, threonine, asparagine, glutamine

list the special cases of amino acids

cysteine, selenocysteine, glycine, proline

explain by glycine and proline are special cases in amino acids

glycine has a H as side chain and thus not an L amino acid

proline is cyclic

list the hydrophobic amino acid types

alanine, valine, isoleucine, leucine, methionine, phenylalanine, tryosine, tryptophan

features of a double bond

shorter than expected C-N bond length

partial negative charge on O atom

partial + charge on N atom

features of a peptide bond

• planar

• can only exist as cis or trans

• trans is favored as atoms are less cacked

• has a resonsance structure with no double bonds but rather delocalised electrons

concequence for protein folding due to the inability of rotation around the peptide bond

• proteins fold through rotation around the phi and psi bonds of the polypeptide chain

• rotation creates phi and psi torsion angles

• some values cause steric clash if the N and H are in close proximity but there is no hydrogen bond present

what does the ramachandran plot show

energies reflect steric constraints

clusters of low energy map to common secondary structures

residue type matters: gly is permissive, pro is restricted, bulky amino acids are more restricted

structural features of the alpha helix

• formed by regular H-bond pattern of the backbone

• carbonyl R1 acceptor to amino of R4 donor

• backbone follows a chiral right-handed path

• side chains point outward

• often amphipathic with one hydrophilic face and another hydrophopbic

favorable in Ala, Leu, Met, Arg, Lys

broken by Gly and Pro

Glycine - entropic penality for contraining angles/ no C beta meaning no backbone shielding

Proline - disrupts H bond pattern, kinks the helix

how to alpha helixes form hetpad repeats

• due to 3.6 residues/ turn repeat, two helices with hydrophobic residues in positions x and x+7 can align to form stable dimers

• every 7th amino acid theres a hydrophobic amino acid therefore the most hydrophobic amino acid group is found in the middle

• favorable in leucine of leucine zippers

• utilised for homodimerisation or heterodimerisation

• forms a left-handed supercoil

explain the presence of N and C caps on alpha helixes

• termini of helices break the regular H-bond pattern

• at the N terminus: H bonds between S/T or D/N bonding with the backbone amino group form the N cap

• often Gly enables main chain inversion at the N-terminus to maximise backbone H-bonding forming the C cap

explain the structure of the beta sheet

OPTION 1:

• adjacent strands run in opposite N→C directions

• alternating side chains project to opposite faces

• nearly linear, well aligned inter-strand H bonds

• complementary alignment of peptide dipoles

• strands are commonly connected by short turns

OPTION 2:

• parralel with adjacent strands running in the same N→C direction

• alternating side chains project to opposite faces

• inter-strand H bonds are skewed typically weaker than in antiparralel sheets

• parralel alignment of peptide dipoles

• strands usually linked by longer loops or helical segments

• not favorable due to kinks which reduce energy

→ beta sheets can be mixed with parallel and anti parallel strands in the same sheet

→ arises from complex chain connectivity making pure parallel/ pure anti parallel layouts imposible

functions of turns and loops in secondary protein structures

• binding ligands

• protein-protein interactions

• allostery ( conformational switching )

explain motif folding of proteins

• alpha helices and beta sheets organizing locally to form small motifs (2-4 elements)

• motifs do not fold stably on their own and need surrounding structure to do so

• multiple motifs can combine to make 1 fomain

• the same motif can be found in many different domains

explain what a domain is in terms of proteins

• domains are discrene units of tertiary structure

• they form and maintain their structure indepedently

• some proteins have only 1 domain, others can have many

• the same domain can be found in many different proteins

• when proteins have the same domain, they are often funtionally related

what drives the formation of secondary and tertiary structure

1. attractive interactions (enthalpy decrease in the protein)

2. the hydrophobic effect (entropy increase in the solvent)

3. loss of flexibility (entropy decrease in protein)

adaptations of membrane proteins

• some proteins have evolved to populate the interior of lipid bilayers

• these proteins have adapted their structural properties for hydrophobic residues to face the membrane interior

• this sheilds the polar backbone

• more common in alpha helix, but present in some beta sheets too

explain the method of techniques used to deduce protein structures

1. x-ray crystallography

• necessitates the generation of protein crystals in an irregular lattice which gives diffraction patterns

• diffraction patterns are regular once hit with an x-ray beam and regular aligning of atoms

• they compute an electron density map

2. nuclear magnetic resonance

• spin active nuclei align in a strong pulsed magnetic field

• their relaxation emits a signal with characteristic spectra depending on their microchemical environment

• multidimentational NMR maps resonances to atoms and yields restrains such as distances and couplings

• combination of restrains in computational refinement to produce a conformer ensemble consistent with data

• great for solution structures and dynamics but size limited

3. cryogenic electron microscopy

• vitrified particles are imaged using electron beams in a microscrope

• noisy 2D projectections are recorded in random orientation

• computational classification and D3 reconstruction yield electron-density map