Biochemistry- All key words and Theory

The three fundamental groups of organisms

• Eukaryotes (humans, mammals etc)
  Well defined nucleus within each cell.
  (multiple celled)

• Bacteria
  (single celled)

• Archea (single celled)

DNA

• Stores genetic information

• Constructed from four building blocks (bases)
  - Adenine (A)
  - Cytosine (C)
  - Guanine (G)
  - Thymine (T)

• DesoxyNucleacAcid

• Double helix where the bases bond through hydrogen bonds

Covalent bonds

The sharing of electrons between two atoms creating a bond

Non-covalent bonds

• Ionic interactions

• hydrogen bonds

• Van der waals interactions

  • Hydrophobicinteractions

Properties of water

• polar molecule

  • Highly cohesive(strong interactions with itself)

Hydrophobic effect

The tendency of nonpolar molecules to asscociate with eachother and unlikelyness to associate with the polar solvent.

Ionic interaction energy

• K = is a proportionality constant (k = 1389, for energies in units of kilojoules per mole, or 332 for energies in kilocalories per mole).

• q1 and q2 are the charges on the two atoms (in units of the electronic charge)

• r is the distance between the two atoms (in angstroms)

• D is the dielectric constant

Homologs

Molecules that have been derived from the same ancestor

• Paralogs ( differ in function)

  • Orhtologs ( similar in function)

Conservative substitution

Replaces one amino acid with another that is similar in size and chemical properties

Nonconservative substitution

An amino acid is replaced by one that is structurally dissimilar

Divergent evolution

Proteins that are derived from common ancestors

Convergent evolution

Different evolutionairy pathways leading to the same solution

RNA

Ribonucleic Acid

• Single stranded molecule

  • Used to transfer information from dna

3D structure vs Sequence identity

3D structure is more conserved

Enzymes

proteins that catalyze specific chemical reactions in biological systems

Side chain (R group)

The variable group attached to the central carbon in an amino acid

L amino acid

Naturally occuring form of amino acids

Zwitterion

A dipolar ion , both negative and positive

Peptide bond

A covalent bond between the carboxyl group of a amnino acid and the amino group of another. Forms proteins

Disulfide bonds

provides stability for secondary proteins

Primary structure

The linear sequence of amino acids in a protein

Torsion angle

Angles that describe rotation around bonds in the protein backline

Phi (ϕ) angle

The torsion angle around the bond between the nitrogen and alpha carbon (N–Cα) of an amino acid.

Psi (ψ) angle

The torsion angle around the bond between the alpha carbon and the carbonyl carbon (Cα–C) of an amino acid.

Secondary structure

Local folding patterns of the polypeptide chain

alpha helix

A right handed helical structure stabalized by hydrogen bonds psi and phi below 100

β pleated sheet

A sheet-like secondary structure formed by hydrogen bonds between β strands.

β strand

A single sgment of a polypeptide chain

Tertiary structure

The overall 3D structure of a single polypeptide chain

Globular protein

A compact spherical protein

All Hydrophilic Proteinogenic Amino Acids

• Serine (Ser,S)

• Threonine (Thr,T)

• Asparagine (Asn,N)

• Glutamine (Glu,Q)

• Tyrosine (Tyr,Y)

• Aspartic acid (Asp,D)

• Glutamate (Glu, E)

• Lysine (Lys,K)

• Arginine (Arg,R)

• Histidine (His, H)

All hydrophobic Proteinogenic Amino Acids

• Glycine (Gly,G)

• Alanine (Ala, A)

• Valine (Val,V)

• Leucine (leu,L)

• Isoleucine (Ile,I)

• Methionine (Met,M)

  • Proline (Pro,P)

All aromatic proteinogenic aminoacids

• Phenylalanine (Phe,F)

• Tyrosine (Tyr,Y)

  • Tryptophen (Trp,W)

All acidic proteinogenic amino acids

• Aspartic acid(aspartate) (Asp, D)

  • Glutamic acid( Glu, E)

All Basic proteingenic amino acids

• Lysine (Lys,K)

• Arginine (Arg,R)

  • Histidine (His,H)

Proteome

The functional representation of a genome

Assay development

A Sspecific test that detects the unique activity or property of the target protein.

Specific Activity

The ratio of enzyme activity to the amount of protein in the mixture

Homogenate

A homogenate is a mixture resulting from breaking open cells to release their contents, creating a uniform solution of cellular components for further analysis or purification. Can be achieved by centrifusion.

Protein purification techniques

Proteins can be purified based of:
- Solubility
- Size
- Charge
- Binding affinity

Techniques:

• Salting out (solubility)

• Dialysis (size)

• Gel-Filtration (size)

• Ion-Exchange chromatograpy (charge)

• Affinity chromatography

  • HPLC

Gel electrophoresis

A molecule with a net charge will move in an electric field. This phenomenon, termed electrophoresis.

The velocity of migration (v) of a protein (or any molecule) in an electric field depends on the electric field strength (E), the net charge on the protein (z), and the frictional coefficient (f ).
v = Ez/f
f = 6πηr

Isoelectric focusing

Electrophoretical separation of proteins based ontheir relative acidic and basic residue contents

The isoelectric point (pI) of a protein

The pH at which its net charge is zero

Two-dimensional electrophoresis

Isoelectric focusing can be combined with SDS-PAGE to obtain very high resolution separations by two-dimensional electrophoresis

Ultracentrifugation

Used to separate biomolecules and determine their masses

Sedimentation coefficient (s)

Rate of movement of a particle when experiencing centrifugal force.
s = m*(1-vρ)/f

• m= mass particle

  • v = partial specific volume

• ρ = density of the medium

  • f= frictional coefficient

Antibody ( immunoglobulin)

responds to an antigen

polyclonal antibodies

Polyclonal antibodies are a mixture of antibodies produced by different B cells that recognize and bind to multiple sites (epitopes) on the same antigen.

Monoclonal antibodies

Monoclonal antibodies are identical antibodies produced by a single B cell clone that recognize and bind to one specific epitope on an antigen.

The enzyme-linked immunosorbent assay

Assay that makes use of an enzyme that can produce a coloured product. Helps detecting and quantifying proteins

Western blotting

Western blotting is a technique used to detect specific proteins in a sample by separating them by size using gel electrophoresis, transferring them to a membrane, and probing with antibodies.

co- immunoprecipitation

A technique used to detect and study protein-protein interactions by using an antibody to capture a target protein and any interacting partners from a sample, allowing for their identification and analysis.

Fluorescence microscopy

makes the target protein fluorescent

Matrix-assisted laser desorption/ionization (MALDI)

A technique used to ionize large biomolecules for spectral analysis

Electrospray ionization

A method of ionizing molecules by applying voltage to a liquid

Time-Of-Flight analyzer

A mass spectrometer that measures the time it takes ions to reach a detector

Edman degradation

A method for sequencing proteins by sequentially removing one amino acid at a time from the N-terminus.

Phenyl isothiocyanate

A reagent used in Edman degradation for labeling the amino acid being removed.

Tandem mass spectrometry

A technique that involves multiple stages of mass spectrometry to identify and analyze peptides or proteins.

Overlap peptide

Peptides that overlap in sequence and are used to confirm protein identification through mass spectrometry.

Peptide mass fingerprinting

A method of identifying proteins by analyzing the masses of peptide fragments generated by digestion.

Fourier transform

A mathematical technique used to analyze signals, commonly used in NMR and mass spectrometry.

Chemical shift

A change in the resonance frequency of nuclei in NMR spectroscopy, providing information about their environment.

Enzyme

A biological catalist, usually of the protein classq

Substrate

The reactant that a enzyme binds upon during a enzyme substrate reaction

Cofactor

A non protein compound required for an enzymes activity.
(Can be a metal ion or organic compound)

Apoenzyme

The protein portion of an enzyme

Haloenzyme

The complete protein incl cofactor

Free energy (ΔG)

The energy available to do work in a chemical reaction

Active site

The region on the enzyme where the subtrate binding and catalysis occurs

Michaelis–Menten Equation

An equation describing the relation between enzymatic rate and substrate concentration

Kₘ (Michaelis constant)

The substrate concentration at which the reaction rate is half of V_max
Shows the enzymes affinity for the substrate( lower K_m = higher affinity)

V_max

The maximum rate of enzymatic reactions

Lineweaver–Burk Equation

A linear transformation of the michaelis -menten equation, used to graphically determine Km and Vmax
(the reciprocal of the mm equation)

Turnover effect K_cat

The number of substrate molecules converted into product when the enzyme is saturated with substrate

k_cat/Km ratio

a measure of catalytic efficiency

Competitive inhibition

Inhibitor competes with substrate for binding at active site

Uncompetitive inhibition

Inhibitor only binds to enzyme-substrate complex

Noncompetitive inhibition

Inhibitor binds to a non active site

Substrate analog

a molecule that mimics the substrate, binds to enzyme and deactivates it

Suicide inhibition

Irreversible reaction where an enzyme converts the inhibtor into a reactive form that covalently binds and deactivates

Binding energy

The energy released when an enzyme binds to its substrate

Induced fit

A model where enzymes change shapoe upon binding with the substrate in order to improve reactivity

Covalent catalyis

A mechanism where an enzyme forms a temporary covalent bond with the substrate

General acid base catalysis

Enzyme catalysis that involves donation or acceptance of a proton to stabalize reactin intermediates

Metal ion catalysis

The use of metal ions in enzyme catalysis to stabalize charges or start reactions

Catalytic triad

A group of three coordinated amino acids in an enzymes active site that work together to catalyze reactions

Oxyanion hole

A pocket in an enzymes active site that stabalizes the negatively charge intermediate

Protease inhibitor

A molecule that binds to and blocks the activity of a protease enzyme

Proton shuttle

A series of residues or molecules that facilitate the movement of protons during enzymatic reactions

Methylases

Enzymes that add methyl groups to DNA or proteins

P-loop

a protein motif that binds the phosphate groups of nucleotides like atp

Nucleotide

the building block of nucleic acids, consisting of a sugar , phosphate and nucleic base

Deoxyribose

the sugar found in DNA

Ribose

The sugar found in RNA

Nucleoside

A molecule that contains a sugar and nucleic base without a phosphate group

DNA polymerase

An enzyme that polymerises DNA by adding nucleotides to a growing strand

Template

The strand of DNA or RNA that guides the synthesis of the complementary strand

Primer

A short DNA or RNa piece that provides the starting point of polymerization

mRNA

messenger RNA, molecule that carries genetic information from DNA to the ribosome