Biochemistry Flashcards
What are examples of macromolecules?
carbohydrates, proteins, nucleic acids, lipids
what are heteropolysaccharides?
composted of two or more different polysaccharides
What is an example of a heteropolysaccharide?
hyaluronic acid
Name a few functions of carbohydrates
selectins
molecular tags (PAMPs)
blood group antigens
cell adhesion molecules
Where can you find hyaluronic acid in the body?
surrounding an oocyte (part of the ZP)
major component of extracellular matrix and synovial fluid
What are carbohydrates?
organic molecules composed of carbon hydrogen and oxygen
what are lipids?
molecules that have key biological functions
What are saturated fatty acids
fatty acids without a double bond that compact tightly because there is a bend in the molecule
what are unsaturated fatty acids
does not pack because of the presence of a double bond and so created more fluid substances
What are essential nutrients
molecules (vitamins and fatty acids etc) that the body cannot obtain itself so requires this from the diet
What is a phospholipid
resembles a triglyceride but one fatty acid is replaced by a phosphate
are phospholipids hydrophilic?
They are ambivalent, hydrophobic tail and hydrophilic head
what does the hydrophobic tail consist of in a phospholipid
saturated fatty acid and unsaturated fatty acid on one of the tails
what does the hydrophilic head consist of?
a phosphate and glycerol
What are sphingolipids?
a class of lipids that play an important role in cellular structure and function, abundant in the myelin sheath
What is the role of sphingolipids?
essential for nerve function and signalling
what are steroids
molecules that have a carbon consisting of four fused rings
What are examples of steroids
sex hormones (testosterone, progesterone etc) cortisol, vitamin D , cholesterol
What is a polar bond
the covalent bond between hydrogen and a more electronegative atom
what is a hydrogen bond
the bond between hydrogen and an electronegative atom that is already in a covalent bond with an electronegative atom
Non-polar substances are soluble in water, true or false?
false, they are hydrophobic so insoluble
examples of amphipathic molecules
sodium palmitate
micelle formation
what are proteins
a chain made out of a chain of amino acids
What chemical groups makes up an amino acid
amino group NH2
carboxyl group COOH
hydrogen H
side chain -R (determines/varies in each the amino acid)
what are stereoisomers
omers non-superimposable mirror images
Acids are molecules which can accept a proton, true or false?
false, acids donate protons
Bases are proton acceptors, true or false?
true
what is pH
measurement of the amount of protons in a solution
a change of one pH changes the proton concentration how?
tenfold
what molecules can span both polar and non-polar environments?
amphipathic molecules
what is a zwitterionic amino acid
one which is overall neutral but contains a positively charged amine group and a negatively charged carboxyl
what are the benefits of a zwitterionic amino acid
increased solubility
can act as a buffer so maintains pH
influences the structure and folding abilities
What is the secondary stucture of the protein
the polypeptide chain conformation
what is the quaternary structure of the protein
in the spatial arrangement of polypeptide chain with its subunits
The tertiary structure of a protein is the sequence of amino acids
false, that’s the primary structure the tertiary structure is the three-dimensional structure of the entire polypeptide
where are the two rotational angles on a polypeptide chain
the alpha carbon of the amino group and the carboxyl group
Name three types of secondary structure of a protein
alpha helix, beta sheet or triple helix
what is the alpha heix
the carboxyl group of one amino acid shares a hydrogen bond with the amino group on another amino acid and forms a rod-like shape
beta sheets can only run in a parallel direction, true or false
false they can run both parallel and antiparallel
what is a collagen triple helix
where three left handed helical chains twist round each other to form a right handed supehelix
where can you find the triple helix
in bone and connective tissue
what are fibrous proteins
polypeptide chains that are organised parallel along a single axis
properties
long fibres or large sheets
mechanically strong
insoluble in water
structural importance
what are examples of fibrous proteins
keratin
collagen of connective tissues (cartilage bone skin blood vessels etc etc)
What are globular proteins?
proteins folded into a spherical shape somewhat
properties
soluble in water and salt solution
polar side chains interact with aqueous environment by hydrogen bonding
non-polar chains are internal
sections of both alpha helix AND beta sheets
What are examples of globular proteins
myoglobin and haemoglobin
What bonds are involved in tertiary structures
covalent disulphide
hydrophobic
hydrogen bonds (backbone and side chain)
electrostatic interactions
What is the mutation in sickle cell anaemia
single nucleotide sequence change that results in the alteration of valine instead of glutamic acid, glutamic acid is responsible for the folding of the haemoglobin so because of the lack the RBCs become sickle-shaped and can block blood flow through capillaries
In what diseases does the protein fold incorrectly
alzhiemers, parkisons, CJD
What are prions?
misfolded proteins that encourage other proteins to do the same tend to be preen tin the brain and affect this area
What is a nucleoside
nitrogenous base and pentose sugar
a nucleotide is a nucleoside and phosphate group, true or false?
True
What is the difference between purines and pyrimidines
purines are six-membered ringed molecules fused with a five-membered ring and pyrimidines are a singular six-membered ring
What are examples of pyrimidines
uracil thymine and cytosine
examples of purines are adenine uracil and guanine, true or false?
false, uracil is a pyrimidine
what bond holds the bases together
van der waals
why is it important to have weak bonds between the bases
to allow for bond breakage during DNA replication
where is the phosphodiester bond used
between nucleotides
give an example of a drug that is an analogue of thymidine
retrovir (anti-retroviral for HIV)
what enzyme catalyses DNA replication
DNA polymerase
what are the small individual strands created during replication called
Okazaki fragments
okazaki fragments are present on which strand
lagging strand
which enzyme stitches up the lagging strand after replication
DNA ligase
How are nucleotides added to the leading strand
5’ to 3’ direction continuously
what does the promoter consist of
TATA box, initiation site
Enzymes alter the equilibrium of a reaction, true or false
False, they do not alter the position of the equilibirum
Enzymes reduce the time for a chemical reaction to reach equilibrium, true or false?
True
Enzymes stabilise the intermediates that are formed as substrates are converted into products
True
Enzymes catalyse reactions to avoid the loss of free energy when substrates are converted to products
True (enzymes lower the activation energy)
Give three examples of a cofactor
zinc iron and copper
give three examples of a coenzyme
CoA NAD+ ATP
What is an apoenzyme
enzyme without a cofactor
A prosthetic group determines the chain of amino acids in the protein
false, it is part of an enzyme that determines its function
What is a zymogen?
precursor of an enzyme, irreversibly changed when it becomes an enzyme
What two form a holoenzyme?
zymogen and cofactor
What are the five characteristics of all enzymes?
specific, potent, mostly proteins, biological catalysts and increase rate of reaction
Enzymes reduce the activation energy of a reaction
true
What is an example of glycogen storage disease?
von-dierkes disease
what is von dierkes disease/glycogen storage disease?
mutation in glucose-6-phosphate, in these patients they cannot break glycogen down therefore resulting in a high level of glucose-6-phosphate
coenzymes are permanently bound to the enzymes, true or false
false, they are transiently bound they only associate for a short period of time
what is an example of a prosthetic group
haem in haemaglobin
what is meant by induced fit
where the binding of the substrate induces a confirmational change in the enzyme
What are isozymes
form of enzyme that catalyses the same reaction but may differ in structure and mechanisms
Give an example of isozymes used in hypoxia
lactate dehydrogenase has five isozymes and depending on the quaternary structure they will engage in lactate to pyruvate reaction or pyruvate to lactate (the latter in the presence of low oxygen)
How can isozymes be used in a clinical setting
examine the blood for specific forms - creatine kinase is a dimeric protein which can be found in muscle, brain and heart which has both types as a heterodimer (MB) but if say the brain form is found in circulation could suggest a stroke or tumour
- therefore useful for diagnostics
What are examples of zymogens
in the pancreas - trypsinogen and chymotrypsinogen
small intestine - enteropeptidase cleaves trypsinogen to active trypsin which cleaves chymotrypsinogen to chymotrypsin
What carbon of the nucleoside does the free hydroxyl sit on
3’
which carbon of the nucleoside does the phosphate group sit on
5’
nucleotides are always added to the 5’ end of the DNA chain, true or false
false, they are added to the 3’ end where the hydroxyl group sits
Which direction does the DNA strand get synthesised?
5’ to 3’
Name the steps of translation
initiation, elongation, translocation and termination
What is a polysome
multiple ribosomes engaging in translation at the same time
What is glycolysis?
the process by which one molecule of glucose produces two molecules of pyruvate
what are post translational modifications?
the addition of functional/chemical groups
What four fates can glucose have in the body?
stored as glycogen
lactic acid fermentation
pentose phosphate pathway
glycolysis
What is the role of hexokinase in glycolysis?
controls substrate entry of glucose
what is the function of the pentose phosphate pathway?
uses glucose to form nucelotides
what happens in the absence of oxygen during glycolysis?
pyruvate accepts electrons from NADH to produce lactic acid (lactate) from glucose
What two glucose transporters have a low Km and are present in the brain?
GLUT 1 and 3
Where can you find glucose transporters with a high Km?
in the liver and beta cells (GLUT2)
What glucose transporters are found in the adipose tissue and muscle?
GLUT 4
where are GLUT 5 transporters found?
the gut
What regulates PFK-1 and why?
AMP because it is more sensitive to fluctuating ATP
What is the function of phosphofructokinase?
rate of substrate (glucose) flow through glycolysis
what are the different allosteric effectors for PFK-1
ATP
citrate
H+
how does citrate modify PFK-1
slows downstream pyruvate entry
How does H+ modify PFK-1
slows down glycolysis if lactic acid is increased
What enzyme controls the production of pyruvate at the end of glycolysis?
pyruvate kinase
What are the products of glycolysis?
4ATP and 2NADH and H+
What is the mechanisms of action dichloroacetate?
promotes the conversion of lactic acid to pyruvate
What drug blocks further metabolism of glucose 6-phosphate
2 deoxy-glucose
how do cancer cells exploit lactate?
excess production to damage NK and T cells and activate suppressor cells
Why would the body produce lactate in the absence of oxygen?
during muscle exercise, hypoxemia and septic shock
Is the conversion of pyruvate to acetyl-CoA reversible?
No
What happens to the TCA if pyruvate supply is limited
acetyl-CoA diverts to ketones
Where does glycolysis take place?
cytosol
where does the TCA cycle take place?
in the mitochondrial matrix (predominantly)
What type of inheritance is PDC deficiency?
X-linked
How many ATP, NADH H+, FADH2 and CO2 are produced after the TCA cycle (including all previous steps - net accumulation)?
ATP - 4
NADH H+ - 10
FADH2 - 2
CO2 - 6
What molecule combines with acetyl CoA to form citrate?
oxaloacetate
What are the symptoms of PDC deficiency?
poor muscle tone and lack of coordination
retardation and seizures
persistent lactic acidosis
respiratory problems
What is the Warburg effect?
Cancer cells produce energy by high rate of glucose metabolism to lactate
Why is NADH needed for oxidative phosphorylation?
it provides the electrons to facilitate the production of ATP
What provides energy to pump protons across the membrane in oxidative phosphorylation?
electrons
What is E0
how likely a substance is going to gain or lose electrons
positive - it’ll gain electrons and be reduced
negative - it’ll lose electrons and be oxidised
Can NADH cross the membrane as itself?
No
donates its electrons to oxaloacetate forming malate which can cross the membrane into the matrix
