Biochemistry Flashcards
What are exergonic reactions
Reactions in which total free energy of the product is less than total free energy of reactant, Delta G is -ve
What are endergonic reactions
Reactions in which total free energy of products is more than the reactants, Delta G is + ve
What do Delta G values towards zero signify?
These are characteristic of readily reversible reactions
How do we determine Delta G for a reaction?
Delta G = - R T ln K (eq) kJ/mol
R = Universal gas constant
T = Absolute temperature (Kelvin)
K (eq) = Product/Substrate concentration
How does the body compensate for the many unfavourable reactions necessary for life
By coupling an exergonic reaction (favourable) with an endergonic reaction (unfavourable)
What are amphipathic molecules?
Molecules that are hydrophobic and hydrophilic
Differentiate acids and bases based on proton donation
Acids donate protons, bases accept protons
Most abundant protein in vertebrates
Collagen
Deficiency of what vitamin can cause weak collagen
Ascorbic Acid - Vitamin C
Types of tertiary structure
Fibrous protein - Collagen, Kerain
Globular protein - Myoglobin, Haemoglobin
What are salt bridges in proteins
Electrostatic interaction between unlike charges
What catalyzes DNA replication
DNA dependant - DNA polymerase, requires RNA primers
Limitation of DNA polymerase
Can only add to 3’ end, called leading strand. Other strand is replicated in short fragments called Okazaki fragments.
Central dogma?
DNA - Transcription - mRNA - Translation - Protein
Nucleoside vs nucleotide
Nucleoside = Base + Sugar Nucleotide = Nucleoside + Phosphate group
What is DNA polymerisation
Formation of a phosphodiester bond between the 3’ OH group and 5’ Triphosphate group
Name a HIV drug that is a nucleotide analogues
Zidovudine or Azidothymidine. Lack a 3’ OH group and hence terminate chain elongation
What direction is DNA polymerase exonuclease activity?
3’ to 5’
What are the stable RNAs
tRNA, mRNA and rRNA
Types of RNA Polymerase
Pol I, Pol II and Pol III. Pol II synthesizes all mRNA
Transcription steps
RNA polymerase detects initiation sites and binds to to these. Requires transcription factors
DNA chain separation
Initiation - Selection of first nucleotide
Elongation - Addition of further nucleotide
Termination - Release of finished RNA
What is the TATA box
Sequence of TATAT around 25 nucleotides before transcriptional start. RNA Pol II specific promoter. This is recognised by TATA box Binding Protein (TBP), part of TFIID - General transcription factor
What is the direction of newly synthesized RNA strand
5’ to 3’
What are transcription factors
DNA binding proteins that regulate transcription positively or negatively
What happens when a ligand (steroid) binds to steroid receptors
Steroid receptors consists of three domains: transactivation domain, DNA-binding domain, ligand-binding domain. Steroid binds to the ligand-binding domain. This causes it to move into the nucleus and bind to DNA at steroid-response element (SRE)
What is splicing
Removal of non-coding regions (introns) from coding regions (exons)
How is mRNA processed
GTP cap is added to 5’ end
Poly A-tail is added to 3’ end
Properties of genetic code
64 possible combinations 20 amino acids AUG - Start UAA, UAG, UGA - Stop Unambiguous, degenerate, universal
Function of Aminoacyl-tRNA Synthetases
Aminoacyl-tRNA Synthetase bind amino acids to their corresponding tRNA molecule. ATP for energy
Ribosomal subunits in eukaryotes
60s - Large
40s - Small
Initiation of translation
GTP hydrolysed to provide energy
40s subunit moves from 5’ end of mRNA to find AUG. UAC tRNA brings Methionine. 60s subunit joins assembly and initiator tRNA is located at P site
Elongation of translation
Elongation factor - 1 alpha (EF-1alpha) brings the next aminoacyl-tRNA to Aminoacyl site
Anticodon base pairs with codon
GTP hydrolysed, elongation factor released
Elongation factor - Beta Gamma regenerates EF-1 Alpha to pick up next tRNA
What catalyzes peptide bond formation in translation
Peptidyl transferase catalyses peptide bond formation between Peptidyl and Aminoacyl site
Termination of translation
Release factor (RF) binds stop codon
GTP hydrolysed
rRNA, mRNA and tRNA dissociate
What is a polysome
A cluster of ribosomes held together by a strand of mRNA which each is translating
Common post translation modifications
Proteolysis - Cleaving polypeptide allows fragments to fold into different shapes
Glycosylation - Adding sugars
Phosphorylation - Added phosphate group alter shape of protein
Cofactors vs Coenzymes
Cofactors - Metal ions
Coenzymes - Organic molecules
What are metalloproteins
Metal cofactors form a metal coordinating centre in the enzyme. This is called metalloprotein
What are prosthetic groups
Tightly bound coenzymes such as Haem group
Apoenzyme vs Holoenzyme
Apoenzyme is an inactive enzyme
Holoenzyme = Apoenzyme + Cofactor, catalytically active
Common coenzyme for redox reactions
Nicotinamide adenine dinucleotide, NAD+
What are Isozymes
Isozymes are isoforms of enzymes, they catalyse the same reaction but have different properties and structure
Example of Isozyme
Lactate dehydrogenase, 2 subtypes -
Heart - Promotes aerobic metabolism
Muscle - Promotes anaerobic metabolism
What is a kinase enzyme
Kinase is an enzyme that adds a Phosphate group - Phosphorylation
What is a Phosphatase
Phosphatase is an enzyme that uses water to cleave a phosphoric acid monoester
What are Zymogens
Inactive precursors of enzymes. Transformed into active enzymes by cleavage of covalent bond. Ex: Trypsinogen and Chymotrypsinogen
What is Vmax and Km in enzymatic behaviour
Vmax is the maximum rate an enzyme can operate at
Km is the concentration of solutes at which half Vmax is obtained
What does a low Km signify?
An enzyme with a low Km requires little substrate to work at half maximum velocity
Glucokinase vs Hexokinase
Glucokinase Km = 5 mM Glucose. Hence it’s involved in homeostasis as it can sense high concentrations of glucose. Maturity Onset Diabetes is caused by the lack of Glucokinase activity. Hexokinase in RBC has a Km = 0.05mM Glucose. Useful in energy production during low Glucose levels.
What is Prolyl Hydroxylase
Uses Oxygen as a substrate to regulate Hypoxia Inducible Factor. Has a high Km for Oxygen; this keep is sensitive to fluctuations. Absence leads to expression of genes for surviving Hypoxia - RBC synthesis, angiogenesis and anaerobic survival pathways
Orthosteric vs Allosteric inhibition
Orthosteric - Inhibitor binds to active site
Allosteric - Inhibitor binds to site other than catalytic centre
Competitive vs noncompetitive inhibitor graphs
Km changes in competitive inhibition; using Ethanol to treat Methanol poisoning
No change in Km in non-competitive inhibition
What are allosteric enzymes
Allosteric enzymes don’t follow Michaelis-Menten kinetics. Increasing substrate concentration results in sigmoidal curve. Ex: Haemoglobin
What involves exercise, Anabolism or Catabolism
Anabolism
Process from oxidised precursor to reduced biosynthetic products
Anabolism
Process from reduced fuel to oxidised product
Catabolism
Fate of glucose in the body
Can be stored as glycogen, starch and sucrose
Aerobic glycolysis to Pyruvate
Anaerobic glycolysis to Lactate
Oxidation through the pentose phosphate pathway - Ribose-5-phosphate (precursor for nucleotide synthesis and DNA repair)
How is glucose transported into cells
Via Na+/Glucose symporters
Passive facilitated diffusion glucose transporters
How many ATP generated at the end of Glycolysis
2 net ATP, 2 used in the process, 4 produced
Control points in Glycolysis
Hexokinase, Phosphofructokinse and Pyruvate kinase
Key enzyme controlling rate of substrate movement along glycolytic pathway
Phosphofructokinase
What inhibits phosphofructokinase
ATP - Energy abundance slows glycolysis
Citrate - TCA intermediate, slows downstream pyruvate entry to TCA cycle
H+ - Slows glycolysis if too much lactic acid produced
What activates phosphofructokinase
AMP - Energy is needed
What is energy charge
Ratio of ATP/AMP is energy charge. This controls phosphofructokinase
What happens to the products of glycolysis
4ATP - Energy, 2 pyruvate as substrate for TCA cycle, 2 NADH+ for the electron transport chain and ATP synthesis
What happens if mitochondrial metabolism is inhibited by lack of oxygen
NADH is used to ferment pyruvate to lactic acid
Why do cancer patients lose weight
Due to the Warburg effect, upregulation of anaerobic glycolysis in cancer cells. High glucose demand
Anaerobic respiration
Pruvate to Lactate
Where does the TCA cycle occur in the Mitochondria
Inner membrane and matrix
How does Pyruvate, ADP and P get into the matrix
pH gradient drive Pyruvate and phosphate (P) import
Voltage gradient drives ADP-ATP exchange
What catalyzes pyruvate to acetyl-CoA
Pyruvate dehydrogenase complex (PDC)
Yields in oxidative decarboxylation of pyruvate
CO2, NADH + H+ and Acetyl-CoA
Only enzyme of TCA cycle not in mitochondrial matrix
Succinate dehydrogenase, located in inner mitochondrial membrane which oversees Succinate + FAD = Fumarate + FADH2
Each turn of TCA cycle involves
3 NADH, 3 H+, GTP, FADH2, CO2
What can inhibit TCA cycle
High levels of ATP, NADH, acetyl-CoA
What can stimulate TCA cycle
High levels of ADP, NAD+
New yield of glucose to acetyl-CoA to TCA cycle
6-2 = 4 ATP, 10 NADH, 10 H+, 2 FADH2, 6 CO2
Can males have Pyruvate dehydrogenase complex deficiency
No as it’s present on the X chromosome. XY leads to still born whereas XX is survivable. Females be mosaic
Why does pyruvate dehydrogenase complex deficiency lead to persistent lactic acidosis
As Pyruate can’t be oxidatively decarboxylated to Acetyl-CoA to enter the TCA cycle. Pyruvate is instead fermented to lactate
What is hereditary leiomyomatosis and renal cell cancer
Defect in fumarate hydratase. Fumarate can’t be converted to Malate, causing a buildup of Fumarate in the mitochondria. Leads to tumours which can metastasize to kidney
Essence of oxidative phosphorylation
Electrons from NADH and FADH2 are used to reduce O2 to H2O. This energy is used to pump H+ from membrane to the intermembrane space. Protons flow back across the membrane, following their concentration gradient. Energy of proton flow is used to phosphorylate ADP to ATP
How does NADH form cytoplasm get in
Via Glycerol-3-Phosphate and Malate-Aspartate shuttle
Oxaloacetate is converted to Malate using NADH + H+. This is transferred to the mitochondrial matrix via Malate transporters. Malate enters TCA cycle to be converted to Oxaloacetate and release of NADH + H+
Transfer potentials in oxidative phosphorylation
Electron transfer potential of NADH+ and FADH2 is converted to phosphoryl transfer potential of ATP
What does a negative redox potential mean
Tend to donate electrons, strong reducers; NAD+
What does a positive redox potential mean
Tend to gain electrons, strong oxidisers; O2
What is the chemiosmotic hypothesis
Action of ATP synthase is coupled with that of a proton gradient. It is the action of proton gradient that causes a proton motive force that allows ADP + Pi = ATP
Where do electrons from NADh and FADH2 enter the electron transport chain
Complex 1 and 2 (2 is succinate dehydrogenase part of TCA cycle), all located on inner mitochondrial membrane
What are cytochromes
Proteins that contain a haem group as a functional co-factor. The Fe(II) can take up and release electrons
What pump is used to synthesize ATP
ATP synthase, Mitochondrial ATPase, F1F0ATPase
What can inhibit oxidative phosphorylation
Cyanide (CN-), Azide (N3-) and Carbon Monoxide can inhibit transfer of electron from complex IV to O2
What does brown adipose tissue contain
Uncoupling protein (UCP) = Thermogenin, generates heat by short-circuiting mitochondrial battery
How does non-shivering thermogenesis work
Protons that are pumped out into the intermembrane space flow back across the concentration gradient via Uncoupling Protein (UCP) instead of ATP synthase. This leads to generation of heat. Free fatty acids required
What can proton leak (non-shivering thermogenesis) be used for
Anti-obesity therapy, 2,4 - Dinitrophenol (DNP) can be used to create artifical proton leak, metabolic rate up
How does ecstasy (MDMA)cause death
Ecstasy targets UCP-3, involved in skeletal muscle thermogenesis. MDMA causes death by hyperthermia and rhabdomyolysis
1 glucose molecule yields how many ATP
30 - 32 ATP molecules
Normal presentation of diabeties
Breath smells funny, deep breathing and urine positive for glucose/ketones
Osmotic symptoms
Increased glucose in blood (hyperglycaemia), stimulates the thirst centre in the brain. This causes polyuria and nocturia.
Typical signs of undiagnosed diabetes in young
Dehydrated, polyuria, nocturia, vomiting, muscle waste
What can cause insulin resistance
Obesity as person have excessive fat stores, it wouldn’t make sense for body to response to Insulin, whose function is to make more energy stores.
What makes diabetic person nausea
Body used triglycerides as a source of fuel as glucose can’t be absorbed into cells. This is broken down into glycerol, fatty acids and ketones. Ketones are strongly acidic, dissociate and release protons
What causes Kussmauls breathing
Increase H+ ions, due to ketoacidosis drives reaction of
H + HCO3 - H2CO3 - CO2 + H2O to the right
However, CO2 is constantly blown off as a deep sighted respiration (Kussmauls breathing)
Can raised creatine kinase be physiological
Never, signifies damage to muscle tissue
Function of cholesterol in plasma membrane
Provide structure and fluidity
How are lipids transported
Via lipoproteins
Which is the densest lipoprotein
High density lipoprotein - Least triglyceride content
Earliest visible lesions in atherosclerosis
Fatty streaks, consists of foam cells
Ideal total cholesterol levels
< 5 mmol/L
Normal total HDL cholesterol levels
0.9 - 1.6 mmol/L
What leads to lipoproteins eventually attracting macrophages
Cholesterol from liver is transported on VLDL. Triglycerides are slowly stripped away leading to formation of IDL and LDL. If not enough LDL is cleared, this accumulates and gets oxidised. This triggers macrophages to mediate inflammation and swallow LDL becoming foam cells. This inflammation inhibits reverse cholesterol transport, starting a vicious feedforward
Mode of action of statins
Express more LDL receptors to increase reverse cholesterol transport and decrease cholesterol synthesis from acetate. Also less inflammation
