Biochemistry Flashcards
What is a glycosidic bond?
The bonds that form between monosaccharides to form a disaccharide
What type of reactions form and break glycosidic bonds?
Formed by condensation
Broken by hydrolysis
What are sugars broken down into?
Monosaccharides
What is entropy?
Free energy tends towards an unusable state after multiple transformations - entropy is the degree of this
What is free energy?
The energy available to do work
How is ∆G calculated?
Energy of products - energy reactants
What does exergonic mean?
Free energy of products is less than reactants, ∆G is negative, reaction occurs spontaneously
What does endergonic mean?
Free energy of products is greater than reactants, ∆G is positive, reaction therefore requires input of energy (e.g. from ATP breakdown)
What does amphipathic mean?
Can be polar or non-polar
Do acids and bases donate or accept protons?
Acids donate
Bases accept
What is meant by the strength of an acid or base?
How readily it donates or accepts electrons - the dissociation constant
What is pH?
The number of protons in a solution
What is the equation for pH?
pH = -log10[Ka]
What does the Henderson Hasselbach equation determine?
pH of weak acids in a solution
What is the Henderson Hasselbach equation?
pH = pKa + log(base]/[acid]
What is a buffer?
A substance that resists change in pH upon moderate addition of acid/base
What is primary protein structure?
The sequence of amino acids
What is secondary protein structure?
The shape of the backbone
What are examples of secondary protein structures?
Alpha helix
Beta pleated sheet
Triple helix
What is tertiary protein structure?
3D structure including side chains
What are examples of tertiary protein structure?
Covalent disulphide bridge
Hydrophobic interaction
Hydrogen bonds
What level of protein structure determines if a protein is fibrous or globular?
Tertiary
What is quaternary protein structure?
The spacial arrangement of a chain in a protein with multiple subunits
Why does vitamin C deficiency cause scurvy?
Vitamin C is needed to hydrate proline
Hydroxyproline is needed for hydrogen bond formation
Vit C deficiency therefore causes weakened collagen
What can disrupt protein structure, and how do they do it?
Heat - increases vibrations
pH -interrupt electrostatic interactions
Detergents/urea.guanine hydrochloride - disrupt hydrophobic interactions
Thiols/reducing agents -disrupt disulphide bonds
In which direction does DNA replicate?
5’ to 3’
What does the lagging strand of DNA use to replicate?
Okazaki fragments
Which enzyme unwinds DNA?
Helicase
What is the term for the backbone of DNA?
Phosphodiester
Which enzyme replicated DNA?
DNA polymerase
What is a nucleotide made of?
Nitrogenous base + sugar + phosphate
What is a nucleoside made of?
Nitrogenous base + sugar (without phosphate)
What is an anti-retroviral?
Thymidine analogue which incorporates into viral DNA with more affinity than human DNA
It lacks 3’OH so terminates elongation
What is the function of rRNA?
Combines with proteins to form ribosomes
What is the function of tRNA?
Carries amino acids to incorporate into protiens
What is the function mRNA?
Encodes genetic information
Identical to the coding DNA and complementary to template DNA
Where does transcription take place?
Nucleus
What is the function of a TATA box?
A TATA box is present 25 nucleotides behind, to introduce a kink into DNA to determine start and direction of transcription
How does premature mRNA become mature mRNA?
Splices out introns, keeps exons
Adds poly-adenosine tail
Adds 5’ cap to prevent the transcript from being broken down
Where does translation take place?
Cytoplasm
What is the start codon?
Methionide
What is an example of a stop codon?
AUG, AGU, UAG
Which enzyme binds amino acid to the corresponding tRNA, and with what type of bond?
Aminoacyl-tRNA
Covalent bond
What do free ribosomes produce and for what purpose?
Proteins that are translocated post-translationally for cytosol, nucleus and mitochondria
What do bound ribosomes produce and for what purpose?
Proteins that are translocated co-translationally for membrane, endoplasmic reticulum, Golgi and secretion
What is the function of enzymes?
Increase the speed a reaction reaches equilibrium by reducing the energy needed for substrates to reach transition state
What is a co-factor?
metal ion that forms metalloprotein complex, involved in redox reactions to stabilise transition state
What is a co-enzyme?
Organic molecule that transiently alters charge and structure of enzyme, which is regenerated after
What is the difference between apoenzymes and holoenzymes?
Apoenzyme - enzyme that is inactive without co-factor
Holoenzyme - enzyme with a co-fector, therefore complete and catalytically active
What is a zymogen?
Inactive precursor
What is V max?
The maximum possible rate of reaciton
What is Km?
The concentration of substrate at which the reaction occurs at 50% of its maximum possible rate
In a Lineweaver Burke plot, what is represented by the x and y axis?
1/[V] is y
1/[S] is x
In a Lineweaver Burke plot, what is represented by the intersections of the x and y axis?
Vmax - intersection with y-axis
Km - intersection with x-axis
How does competitive inhibition affect a Lineweaver burke plot?
Vmax doesn’t change but Km is reduced
How does non-competitive inhibition affect a Lineweaver burke plot?
Vmax is reduced but Km doesn’t change
What are the possible functions of glucose?
Stored as glycogen, starch, sucrose of converted into lipids
Oxidosed to precursor for nucleotide synthesis (ribose-5-phosphate)
Fermented by anaerobic glycolysis to lactic acid
Oxidised by aerobic glycolysis to pyruvate
How does glucose enter cells?
Na+/glucose symporters
What is the equation for glycolysis?
Glucose + 2ADP + 2Pi + 2NAD+ –> 2 pyruvate + 4ATP + 2H2O + 2NADH + 2H+
What is the rate limiting enzyme for glycolysis?
Phosphofructokinase
What is the enzyme that limits substrates in glycolysis, and which reaction does it catalyse?
Hexokinase
Glucose to G-6-P
What are the activators and inhibitors for glycolysis?
Activators: AMP and fructose-2,6-biphosphate
Inhibitors: ATP/citrate and H+
What happens instead go glycolysis in anaerobic conditions?
NADH ferments 2 pyruvate to lactic acid and 2ATP
Where does the TCA cycle occur?
Mitochondrial matrix
What are the products of the TCA cycle?
2CO2
3NADH + 3H+
FADH2
GDP + Pi (converted to GTP, converted to ATP)
How many ATP does 1 glucose molecule produce?
2
How does NADH enter?
Malate-aspartate shuttle
What is the TCA cycle activated and inhibited by?
Activated by: ADP, NAD+ (lack of energy)
Inhibited by: ATP, NADH, acetyl-CoA (excess energy)
What happens to the products of the TCA cycle NADH and FADH2?
Electron transport chain
What is the electron transport chain?
NADH and FADH2 donate electrons which are passed along the chain which produces energy
The energy is used to pump H+ across the inner mitochrondrial matrix.
The flow of H+ back into the mitochrondria through ATP synthase produces ATP
Which stage of glycolysis produces the most ATP, and how much does it produce per glucose molecule?
Electron transport chain - 30-32 ATP
What is the electron transport chain inhibited by?
Cyanide, azide and CO
What is the function of UCP?
Uncoupling Protin
Short-circuit mitochondrial battery that pumps out H+ without the electron transport chin
Where is UCP found int he body?
Brown fat in newborns
