biochemistry Flashcards
What is a nucleoside?
- a base
- a sugar
What is a nucleotide?
- a nucleoside
- a phosphate group
What are the purines?
- guanine
- adenine
What are the pyrimidines?
- cytosine
- thymine
- uracil
Where are phosphodiester bonds formed?
Between a free 3’ OH group and a 5’ triphosphate group
Where a new nucleotides are added?
To the free 3’ end
What unwinds DNA?
Helicase
What removes wrong nucleotides during replication?
3’ to 5’ exonuclease
What type of RNA polymerase synthesises all mRNA?
Pol 2
What are the 5 stages of transcription?
- RNA polymerase binding
- DNA chain separation
- transcription initiation
- elongation
- termination
What binds promotors?
RNA polymerases
Describe steroid receptors
- family of transcription factors
- dna binding and ligand binding domains highly conserved
- bind at SREs, steroid response elements
Where would you find a poly A tail or 5’ cap?
At the end of mRNAs
What binds amino acids to their corresponding tRNA molecules?
amino-acyl tRNA synthetases
What are the three binding sites of ribosomes?
- E (exit site)
- P (peptidyl site)
- A (acceptor site)
Name the types of gene mutation
- point mutation
- missense mutation
- nonsense mutation
- silent mutation
- frameshift mutation
Name the types of chromosomal mutations
- deletions
- duplications
- inversions
- translocations
What is targeting (a finished protein)?
Moving protein to its final cellular destination
Free ribosomes in the cytosol make proteins for where?
- cytosol
- nucleus
- mitochondria
Bound ribosomes in the endoplasmic reticulum make proteins for where?
- plasma membrane
- secretion
- Golgi apparatus
- er
Describe enzymes
- efficient
- potent
- specific
- does not affect equilibrium
Describe glycogen storage disease
Enzyme deficiency that results in failure of glycogen to enter transition ‘phosphorylated’ state
Describe co-factors
- metal ions
- inorganic
- involved in redox reactions
- stabilise transition states
Describe co-enzymes
- organic molecules
- associated with the enzyme only transiently
- can change charge or structure during the course of the reaction but are regenerated
- many are derived from vitamins
What are prosthetic groups?
Tightly bound coenzymes
What is an apoenzyme?
An enzyme without a cofactor
What is a haloenzyme?
An enzyme with a cofactor
Describe isozymes
Isoforms of enzymes, they catalyse the same reaction but have different properties, structure and sequence
Describe creatine kinase (CK)
- a dimeric protein
- binds to the muscle sarcomere
The presence of creatine kinase can indicate what?
- the appearance of the brain form in the blood suggests a stroke
- the appearance of the heart type suggests a heart attack
What molecule carries out phosphorylation reactions?
Protein kinases
Describe zymogens
Inactive precursors of an enzyme, irreversibly transformed into active enzymes by cleavage of a covalent bond eg. digestive enzymes, blood clotting enzymes
What is Vmax?
The maximum velocity of a reaction, no active sites are left
What is Km?
The concentration in moles of S which gives 1/2 Vmax
What does the michaelis-menden equation describe?
Describes the rate of catalysis as a function of substrate concentration. Describes a hyperbola
What are the units of Km?
- molar
- moles/l
- moles/dm3
What does low and high Km mean?
Low- efficient enzyme
High- rate is slower, less efficient enzyme
What does the y-intercept indicate?
Vmax
What does the x-intercept indicate?
Km
Define electronegativity
The attractive force that an atomic nucleus exerts on electrons within a bond
What is acylation?
The addition of an acyl group
What is carboxylation?
addition of a carboxyl group
What is condensation and hydrolysis?
Condensation- water is removed
Hydrolysis- water is added
What is the most oxidised and most reduced forms of carbon?
Most reduced is CH2 (alkane group) and the most oxidised is CO2 (carbon dioxide)
Name functions of biomolecules
- information storage
- structural
- energy generation
- energy currency/ storage
- recognition / communication / specificity
What are the three types of carbohydrates?
- monosaccharides
- polysaccharides
- disaccharides
What is the first law of thermodynamics?
Energy is neither created or destroyed
What is the second law of thermodynamics?
When energy is converted from one form to another, some of that energy becomes unavailable to do work (not 100% efficient)
What is the free energy equation (ΔG)?
ΔG= ΔH- TΔS
What is an exergonic reaction?
A reaction in which the total free energy of the products is less than the total free energy of the reactants ΔG is negative. It can occur spontaneously
What is an endergonic reaction?
A reaction in which the total free energy of the products is more than the total free energy of the reactants. ΔG is positive. Reactions don’t occur spontaneously, they need an input of energy to proceed
Describe standard conditions
- T= 298k
- 1 atmosphere pressure
- 1M (mol/l) concentration of reactants
- pH= 7
Define metabolism
All the reactions taking place in the body divided into anabolism and catabolism
Define catabolism
Breaking down complex molecules into smaller molecules and releasing energy
Define anabolism
Synthesising complex molecules out of smaller molecules through energy-consuming reactions
Describe glycolysis (catabolic reaction)
Initial breakdown of glucose for the generation of ATP. Net gain of 2 ATP molecules per glucose molecule
Describe gluconeogenesis (anabolic reaction)
Making new glucose from non-carbohydrate precursors eg. pyruvate. Costs energy
Describe the shape of water
It is a bent molecule, it is polar and forms a dipole
Describe amphipathic molecules
They have regions (domains) which are either hydrophilic or hydrophobic. They form micelles in water. Example, phospholipids on the cell membrane
What do all amino acids contain?
- an amine group (NH2)
- a carboxyl group (COOH)
- a hydrogen
- a side chain
All bonded to an alpha carbon atom
What are D and L forms of amino acids?
Non superimposable mirror images. Stereoisomers
Describe non-polar amino acids
- no charge difference between amino and carboxyl ends of the molecule
- don’t dissolve in water
- will interact with lipid or non-polar molecules
- common in membrane spanning parts of proteins
Describe polar, uncharged amino acids
- no charge difference between amine and carboxyl groups
- hydrogen bonding interaction with water
- dissolves in water
- variable solubility
- amphiphilic nature
Describe peptide bonds
Have a partial double bond character, planar, strong and rigid, important for folding of proteins
What molecules are proton donors and proton acceptors?
Acids are proton donors
Bases are proton acceptors
What does pH measure?
The amount of protons in a solution
Describe the pH formula
pH= -log10 [h+]
What are zwitterons?
Amino acids without charged side groups (in neutral solution) They have two pKa values
What is the isoelectric point?
The pH at which a molecule has no net charge
What is the primary structure of a protein?
The sequence of amino acid residues
What is the secondary structure of a protein?
The localised conformation of the polypeptide backbone
What is the tertiary structure of a protein?
The 3d structure of the entire polypeptide, including all side chains, consists of local regions with distinct secondary structures
What is the quaternary structure of a protein?
The spatial arrangement of polypeptide chains in a protein with multiple subunits
Describe alpha helices
- rod like
- one polypeptide chain
Describe beta sheets
- hydrogen bonds between neighbouring peptides
- two directions (parallel, antiparallel)
- turns between strands
- zig zag structure
Describe the collagen triple helix
- component of bone and connective tissue
- very strong
- water insoluble fibres
- covalent inter and intra molecular bonds
Describe fibrous proteins
- contain polypeptide chains organised parallel along a single axis
- long fibres or sheets
- insoluble in water
- eg. keratin in hair
Describe globular proteins
- folded into a spherical shape
- soluble in water
- eg. myoglobin, haemoglobin
What forces stabilise tertiary structure?
- covalent disulphide bonds
- electro static interactions
- hydrophobic interactions
- hydrogen bonds
- complex formation with metal ions
Describe haemoglobin
- four subunits
- two alpha and 2 beta chains
- each contains a haem group
- allosteric (binding of one oxygen changes affinity for other subunits)
Describe competitive inhibition
- Orthosteric inhibition (at same site)
- inhibitor binds to the active (catalytic) site and blocks substrate access
Describe non-competitive inhibition
- allosteric inhibition
- Inhibition binds to a site other than the catalytic centre, inhibits enzyme by changing conformation
Describe the effects of competitive inhibition on vmax and km
Enzymes reach the Km later, Vmax is not affected
Describe the effects of non-competitive inhibition on vmax and km
Km doesn’t change but Vmax varies. A non-productive complex is formed
Describe feedback inhibition
Inhibition of rate limiting enzymes by end product (allosteric control)
What graph shape is created when the substrate concentration of allosteric enzymes is increased?
A sigmoidal curve
