Biochemistry Flashcards
define van der waals
interaction of electrons of non-polar substances
define electronegativity
ability to gain electrons- attraction of the nucleus
define catabolism
break down of molecules
define anabolism
synthesis of molecules
define exergonic
release of energy
define endogonic
requires energy
first law of thermodynamics
conservation of energy
second law of thermodynamics
energy transferral is not 100% efficient
reactions involve change in three things
- enthalpy
- entropy
- free energy
define exergonic reactions
products have less energy than reactants. energy change is negative. these reactions can be spontaneous.
define endogenic reactions
products have more energy than reactants. free energy change is positive. an input of energy is needed
amount of energy at the completion of equilibrium
more energy
hydrophilic electrostatic attractions
- ion-dipole interactions
2. dipole-dipole interactions
describe the primary structure of a protein
sequence of amino acid residues
describe the secondary structure of a protein
formation of a polypeptide backbone
describe the tertiary structure of a protein
3D structure
quaternary structure
spatial arrangement of polypeptide chains
where can polypeptides rotate
- alpha-carbon and amino group
2. alpha-carbon and carboxyl group
three types of secondary structures can be made
- alpha-helix: hydrogen bonds formed between -N-H and -C-O
- beta-sheets: anti-parallel strands, zig-zag structure
- triple helix: three helices with the same axises.
characteristics of fibrous proteins
long fibres, strong, insoluble e.g. keratin and collagen
characteristics of globular proteins
spherical shape, soluble,
forces that stabilise the tertiary structure
- electrostatic attractions
- hydrophobic interactions
- H-bonds
- disulphide bonds
define chaperones
proteins that aid folding of other proteins
factors that cause denaturation
- heat
- pH
- detergents
- thiol agents
examples of purines
A and G
examples of pyrimidines
U, C and T
which carbon does the OH group join to?
3’ carbon
which carbon does the phosphate group join to?
5’ carbon
which carbon is free to allow synthesis?
3’ carbon
name of DNA replication
semi-conservative
features to ensure DNA replication finishes quickly
- bidirectional
- free 3’ on the leading strand
- use of lagging strands and Okazaki fragments
define DNA ligase
enzyme that forms a phosphodiester bond
three classes of RNA
- rRNA
- tRNA
- mRNA
structure of tRNA
contains an anticodon, specific amino acid attaches to the 3’ end, cloverleaf shape.
five steps of transcription
- RNA polymerase binding
- DNA chain separation
- initiation
- elongation
- termination
describe the structure of promotor regions
contain a TATA box. the TATA box binding protein induces a kink in DNA which determines the start and direction.
which enzyme unwinds DNA?
DNA helicases
what does initiation require?
transcription factors
describe the process of elongation in transcription
DNA is unwound by RNA polymerase. It is synthesises in the 5’-to-3’ direction. Complementary to the template strand.
describe the process of termination in transcription
stem-loop structure is made followed by a line of U’s so a specific enzyme cleaves the RNA. Polymerase dissociates.
two functional domains of transcription factors are
- DNA binding domain
- transcriptional activation domain
define splicing
removal of introns
the end of the mRNA is processed by
- addition of poly(A) tail
- addition of a 5’ cap
these stabilise the mRNA
name the enzyme that binds amino acids to their corresponding tRNA molecules
aminoacyl-tRNA synthetases
three binding sites on ribosomes
- E (exit)
- P (peptidyl)
- A (aminoacyl)
stages of translation
- initiation
- elongation
- termination
describe initiation in translation
small subunit of the ribosome binds to the 5’ end of the mRNA and the large subunit joins once the tRNA is located in the P site
describe the process of elongation in translation
elongation factor brings the next aminoacyl-tRNA to the A site. GTP hydrolysis allows the EF to be released.
describe the process of the peptide bond formation
- peptidyl transferase catalyses the peptide bond formation between P and A.
- EF moves ribosome along mRNA
- empty tRNA moves to E site and is removed
describe the process of termination in translation
occurs when the A site encounters a stop codon
describe the types of base mutations
- point: change in a single base
- missense: change in amino acid sequence
- nonsense: creates a termination code
- silent: no change (degenerate)
- frameshift: changes reading frame
types of chromosomal mutations
- deletions
- duplication
- inversions
- translocations
three things that can happen to the finished protein
- targeted (moved to final destination)
- modification
- degradation
free ribosomes made proteins destined for?
- cytosol
- nucleus
- mitochondria
bound ribosomes make proteins destined for?
- membrane
- ER
- Golgi
function of an enzymes
speeds up the rate at which a reaction reaches equilibrium without being used up or affecting the position of equilibrium.
characteristics of enzymes
- protein
- catalysts
- efficient
- specific
- potent
define a coenzyme
organic molecules that only associate with enzymes transiently
define a cofactor
enzyme that has a metal coordination (metalloprotein)
an enzyme without a cofactor is called?
apoenzyme
apoenzyme + cofactor
holoenzyme
ways an enzyme can be regulated
- phosphorylation- active or inactive form carried out by kinases and phophatases
define a zymosen
inactive precursors of an enzyme
define Km
concentration in moles of the substrate when at 1/2 Vmax.
define Vmax
maximum velocity of a reaction
two types of reversible enzyme inhibition
- competitive (orthosteric site)
2. non-competitive (allosteric site)
irreversible enzyme inhibition
non-competitive causes bond breakage
effect on Vmax and Km during competitive inhibition
Vmax does not change, Km varies
effect on Vmax and Km during non-competitive inhibition
Vmax varies and Km does not change
define feedback inhibition
inhibition of rate limiting enzymes (mechanism of allosteric control
four pathways glucose can be used in
- aerobic glycolysis
- anaerobic glycolysis
- pentose phosphate pathway
- storage
how is glucose transported into the cell?
co-transport using Na+/glucose symporters (GLUT-1)
describe the three stages of glycolysis
- glucose is trapped and destabilised by the addition of phosphates
- two 3-carbon molecules are formed
- generation of ATP
products of glycolysis are?
- 2 pyruvate
- 2 net ATP
- 2NADH + 2H+
enzymes involved in glycolysis
- hexokinase (glucose to glucose 6-phosphate)
- phosphofructokinase controls rate of flow
- pyruvate kinase (pyruvate formed)
inhibitors of phosphofructokinase (PFK)
ATP
citrate
H+
define energy charge
ATP/ AMP
define the Warburg effect
regulation of anaerobic glycolysis in cancer cells. produces high rate of glucose to lactate.
for glycolysis to continue what must happen to the product NADH
it must be deoxidised to NAD+
location of the TCA cycle
mitochondria
location of glycolysis
cytoplasm
how does pyruvate enter the mitochondrial matrix
H+ gradient from cytosol to matrix using pyruvate transporters (symporters)
which enzyme catalysed the decarboxylation of pyruvate
pyruvate dehydrogenase complex
products of the link reaction
- NADH + H+
2. acetylCoA
characteristics of the TCA cycle
- 8 reactions
- 1 GTP formed
- 3 NADH
- 1 FADH2
- 2 CO2
- the cycle turns twice for each mole of glucose
what is the 6-carbon molecule in the TCA cycle called
citric acid
what is the 4-carbon molecule in the TCA cycle called
oxaloacetic acid
what does one mole of glucose produce in the TCA cycle? (only electron transporters)
10NADH
10H+
2FADH2
final destination of electrons
reduces O2 to H2O
describe how NADH moves from the cytosol to the mitochondrial matrix
- NADH is used to generate malate from oxaloacetate
- malate transporters transfer malate to the matrix
- malate is converted back to oxaloacetate generating NADH
define phosphoryl transfer potential
free energy after the hydrolysis of ATP
define electron transfer potential
how readily a substance donates an electron
two stages of the chemiosmotic theory
- electron transport
2. ATP synthesis
characteristics of the electron transport respiratory chain
- four multisubunit complexes on the inner mitochondrial membrane
- electrons from NADH enter at complex 1
- electrons from FADH2 enter at complex 2 (TCA cycle)
- electrons are transferred to O2 to form H2O
subunits names
Q and cytochrome C
define cytochromes
proteins that contain a haem group. the Fe2+ can take up and release electrons
describe the H+ gradient
more protons in the inter membrane space so they flow back to the matrix via ATP synthase channels
structure of ATP synthase
- F1 protrudes into the matrix
- F0 is in the inner membrane (proton channel)
- stator
- rotor (turns during proton flow)
inhibitors of oxidative phosphorylation
- cyanide
- azide
- CO
