Biochemistry Flashcards
Describe protons, electrons and neutrons in terms of :
- charge
- mass
Protons - charge = +1
- mass = +1
Electrons - charge -1
- mass = 0
Neutrons - charge = 0
- mass = +1Explain covalent bonding
sharing of electron pairs
Explain ionic bonding
attraction of opposite charges
Explain hydrophobic interactions
interaction of non polar substances in the presence of polar substances
Define electronegativity
the attractive force that an atomic nucleus experts on electrons within a bond
Define REDOX
- OILRIG
- Oxidation - is loss of electrons
- Reduction - is gain of electrons
Final product of catabolism?
Carbon dioxide
Example of a monosaccharide
Glucose
Example of a disaccharide
- sucrose
- lactose
Example of a polysaccharide
glycogen
Define thermodynamics
biophysical discipline which deals with the question if a process if energetically favourable
1st law of thermodynamics is….
energy is neither created nor destroyed
2nd law of thermodynamics is…
when energy is converted from one form to another, some of that energy becomes unavailable to do work
Define entropy
free energy will tend towards an unusable state after multiple transformations
ΔS
What is enthalpy
- heat constant
- ΔH
Equation for free energy
ΔG = ΔH – TΔS
T - is the temp in K
or
ΔG= (energy of the products)- (energy of the reactants)
ΔG= -ve
what does this imply?
- exergonic reaction
- energy of the products is less than that of the reactants
- can occur spontaneously
ΔG= +ve
what does this imply?
- endergonic reaction
- energy of products is more than that of reactants
- cannot occur spontaneously, requires the input of energy
What is the relationship between ΔG and equilibrium?
ΔG values near zero are characteristic of readily reversible reaction
ADP is more stable than ATP: True/False
True
The negative charges close together in ATP put a strain on the molecule, making it less stable than ADP
Anhydride bonds are low energy:
True/False
False
Anhydride bonds are high energy
Define metabolism
- all the reactions taking place in the body, divided into catabolism and anabolism
Define Catabolism
breaking down complex molecules into smaller ones, releasing energy
Define Anabolism
Synthesising complex molecules out of smaller ones in energy consuming reactions
There are always energy consuming steps in catabolic pathways.
True/ False
True
although catabolism releases energy, there are always energy consuming steps involved
Give an example of a catabolic pathway
Glycolysis
- initial breakdown of glucose
Give an example of an anabolic pathway
Gluconeogenesis
- making glucose from pyruvate
Reactions with large negative ΔG values are useful control points
True/False
True
What does hydrophilic mean?
- water loving
What does hydrophobic mean?
- water hating
What are hydrogen bonds?
- covalent bonds
- hydrogen bonded to a more electronegative atom
- hydrogen gets a partially positive charge
Do hydrogen bonds tend to be _____
a) bent
b) linear
- linear
What are amphipathic molecules?
- have regions which are either hydrophobic or hydrophilic
What do amphipathic molecules form when in a polar substance?
- micelles
hydrophilic heads in contact with water, hydrophobic tail towards the centre
What are the chemical groups that make up an amino acid?
- amino group (NH2)
- carboxyl (COOH)
- hydrogen (H)
- side chain (R)
What is the alpha carbon?
- the carbon bonded to the amino group, carboxyl, hydrogen and side chain
What does D & L mean in terms of amino acids?
- Sterochemistry
- D & L are stereoisomers
( cannot be superimposed on each other)
What makes amino acids acidic?
- additional COOH group
What is a useful property of acidic buffers?
- can be used as buffers
What is a useful property of basic buffers?
- used as buffers
How can you identify a basic buffer?
- long hydrocarbon chain
What are the 4 elements that make up a peptide bond?
- carbon
- oxygen
- nitrogen
- hydrogen
What does it mean “peptides have direction”
- depending on the end terminal will say if it is N or C terminal
- N terminal - amino group
- C terminal - Carboxyl group
In which direction is a peptide chain?
- N –> C
Peptide bonds are _____ in shape
a) planar
b ) 3 dimensional
- a
- peptide bonds are planar
Peptide bonds are ____
a) strong
b) weak
- a
strong and rigid
Acids are proton ____
donators
Bases are proton ____
acceptors
What is the strength of an acid based on?
- how readily it donates a proton to a base
What is the equation for the acid dissociation?
Ka = [H+][A-]
—————
[HA]
pH is equal to—-
pH = -log10 [H+]
What is a buffer?
- a solution to control the pH of a reaction
Name of an amino acid that exists without charged groups?
- zwitterions
- no net charge
- contains 2 tritatable groups
name given to the pH where a molecule has no net charge?
- isoelectric pH
What is the primary structure of a protein?
- sequence of amino acids
what is the secondary structure of a protein?
- localised confirmation of the polypeptide backbone
what is the tertiary structure of a protein?
- 3d shape
What is the quaternary structure of a protein?
- the spatial arrangement of polypeptide chains with multiple subunits
where can a polypeptide rotate?
- between:
- a carbon and amino group
- a carbon and carboxyl group
3 types of secondary structures?
- a helix
- b sheet
- triple helix
Explain a helix?
- secondary structure
- 1 rod like chain
- right handed
explain beta sheets?
- secondary structure
- may be parallel or antiparallel
- may contain turns
explain triple helix?
- secondary structure
- 3 left handed rods
example of a triple helix protein?
- collagen
2 types of tertiary structures?
- fibrous (paralel along single axis)
- globular (folded spherical)
tertiary protein interactions?
- covalent disulphide bonds
- hydrogen bonds
- hydrophobic interactions
- salt bridges
“polar groups are more likely to be in the inside of a polypetide”
true or false?
- false
- more likely to be on outside for interactions with water
explain myoglobin
- globular protein
- haem group
- stores oxygen in muscle
explain haemoglobin
- globular protein
- 4 subunits
- 2 alpha + 2 beta chains
- transports oxygen in blood
what is the name of the molecule which helps protein folding?
- chaperones
What is a nucleoside?
- base + sugar
What is a nucleotide?
- nucleoside + phosphate group(s)
What end are nucleotides added to?
- 3’ end
DNA is a continuous process
true or false?
- false
- discontinous
What are okazaki fragments
- formed from the laggin strand
what in built mechanism does DNA have to pick up errors?
- exonuclease activity
- 3’ –> 5’ direction
- removes incorrect nucleotides
3 types of RNA?
- tRNA
- mRNA
- rRNA
What is tRNA
- carries amino acids to be incorportated in a protein
What is mRNA
- carries genetic information for protein synthesis
What is rRNA
- combines with a protein to form a ribosome
What is a TBP?
- TATA Box Binding Protein
- recognises TATA boc
- part of TFIID
Name a transcription factor?
TFIID
What are introns
- non coding regions
- must be spliced
In relation to amino acids what does degenerate mean?
- many amino acids have more than one codon
In relation to amino acids what does unambiguous mean?
- each codon only codes for 1 amino acid
What protein binds amino acids to corrosponding tRNA/
- aminoacyl-tRNA sythatase
What are the names of the 3 binding sites in a ribosome?
- A (amioacyl)
- P (peptidyl)
- E (Exit)
An example of a start codon
AUG
Nonsense mutation?
- creates a premature stop codon
Missense mutation?
amino acid sequence changed
Free ribosomes make proteins for where?
- nucleus
- cytosol
- mitochondria
Bound ribosomes make proteins for where?
- plamsa membrane
- golgi apparatus
- ER
What are enzymes?
- catalyse chemical reactions
- speeds up a reaction without altering the equilibrium
- provide an alternative pathway
What is a cofactor and name an example?
- required for the action of an enzyme
- inorganic –> metals
- zinc, iron, copper
What is a coenzymes and name an example
- required for the action of an enzyme
- organic —> vitamins
- NAD+
What is an isozyme?
- isoform of an enzyme, catalyse the same reaction but have different properties/structure
What is a zymogen?
- inactive precursors of an enzyme
- needs to be cleaved to become active
Describe what enzyme behavior would look like on a Michaelis Menten model?
- hyperbolic in shape
- Vmax and Km values
- Sustrate on x axis
- rate on Y axis
What is Vmax?
- infinite substrate will approach a maximal rate
What is Km?
- the concentration of substrate required to produce a half maximal effect
How can Km be calculated?
Km= k-1+k2/k1
Why is a lineweaver plot better than michaelis menten model for determining Km and Vmax?
- kinetics is never linear, will never reach exact Vmax on michaelis menten
Where is 1/Vmax seen on lineweaver plot?
- Y axis
Where is -1/Km seen on lineweaver plot?
- X axis
What effect does a competitive inhibitor have on a lineweaver plot?
- Vmax remains the same
- Km is increased
What effect does a non-competivite inhibitor have on a lineweaver plot?
- Vmax is reduced
- Km remains the same
Explain feedback inhibition
- the end product of a reaction may inhibit one of the beginning rate limiting enzymes
- prevents a build up of intermediates that may be harmful
- allosteric control
What is different about allosteric enzymes in terms of the Michaelis Menten model?
- do not follow a hyperbolic graph
- instead they are sigmoidal
- show co-operativity
What can be used to control allosteric enzymes?
- activators
- inhibitors
Define metabolism
- all chemical reactions that maintain the living state of cells and organisms
Define anabolism?
- assimilation of molecules from building blocks of life
- requires energy
Define catabolism?
- breakdown of molecules to obtain building blocks
- energy yielding
Name a monosccharide
- glucose
Name a disaccharide
- lactose
Name a polysaccharide
- glycogen
How does glucose get transported from cells?
- GLUT receptors
- conformational changes allowing binding at one side and then release at the other
Define glycolysis
- the initial pathway which is involved in the conversion of glucose to 2 pyruvate
Explain the intermediates of glycolysis?
- glucose
- fructose-1,6-bisphosphate
- 2 triose phosphate
- 2 pyruvate
What are the names of the 3 enzymes that control glycolysis?
- hexokinase (controls subsrate entry)
- phosphofructokinase (rate flow control)
- pyruvate kinase (end product formation)
What is the name given to the ATP/AMP ratio?
- energy charge
In the environment of not enough oxygen what occurs?
- mitochondrial metabolism inhibited
- NADH ferments pyruvate –> lactic acid
- NADH regenerated
How is NAD+ regenerated?
- oxidative metabolism of pyruvate
Where does the TCA occur?
- mitochondria
How does pyruvate enter the mitochondrial matrix?
- H+ gradient
- pyruvate transporters
what catalyses pyruvate to acetyl CoA?
- Pyruvate dehydrogenase complex
What can the reaction from pyruvate to acetyl CoA be called?
- oxidative decarboxylation
Where are enzymes for the TCA located?
- mitochondrial matrix
- except succinate dehydrogenase (inner mitochondrial membrane)
Electrons from NADH and FADH2 are used to reduce ___ to ____
- electrons are used to reduce O2 to H20
The energy of NADH and FADH2 is used to ____
- pump protons from mitochondrial matrix
What are the names of the 2 transporters of NADH and FADH2?
- Glycerol-3-phosphate
- malate-aspartate
How is phosphoryl tranfer potential measured?
- measured by the free energy change for hydrolysis of ATP
How is electron transfer potential measure?
- measured by the redox potential of a compound
NADH enter what complex?
- complex I
FADH2 enter what complex?
- complex II
Final electron acceptor in the electron transport chain?
- O2
1 Glucose molecule can make how many ATP molecules?
- 30-32 ATP molecules
