Biochemistry Flashcards
Is Carbon reduced or oxidised as
- Hydrogen is added
- Chlorine is added?
- Reduced
2. Oxidised
What is acylation?
Addition of COR
Rank the following in increasing States of carbon oxidation:
- Aldehyde
- Alkane
- Carbon dioxide
- Carboxylic acid
- Alcohol
Alkane < Alcohol < Aldehyde < Carboxylic acid < Carbon dioxide
What is the first law of thermodynamics?
Energy is neither created nor destroyed
What is the second law of thermodynamics?
When energy is converted from one form to another some is unavailable to do work
What is the definition of entropy?
Free energy tends towards an unstable state after multiple transformations
Equation for DeltaG
DeltaG = DeltaH - (T x DeltaS) or DeltaG = (energy of products) - (energy of reactants) Where: G - Free energy H - Enthalpy T - Temperature in K S - Entropy
Is DeltaG negative or positive in an
- Exergonic reaction
- Endergonic reaction
Exergonic - Negative (spontaneous reactions)
Endergonic - Positive
Why does coupling of reactions occur?
It allows reactions with a positive DeltaG to proceed as highly favourable reactions when coupled with a highly negative DeltaG reaction
Why is the breakdown of ATP highly favourable?
DeltaG = -30kJ/mol
What is catabolism?
Breakdown of molecules - releasing energy
What is anabolism?
Synthesis of complex molecules - using energy
What shape is the water molecule?
Bent dipole
What are micelles?
Arrangement of amphipathic molecules in water
Hydrophilic head out and hydrophobic tail in
What is the only amino acid without a D or L isomer?
Glycine
What enzyme catalyses peptide bond formation?
Peptidyl transferase
What direction do peptides run in?
From N-terminal residue to C-terminal residue
What is the Henderson-Hasselbalch equation?
pH = pKa + log([A-]/[HA])
ie
pH = pKa + log([base]/[acid])
What is the primary structure of a protein?
Amino acid sequence
What is the secondary structure of a protein?
Conformation of polypeptide backbone
What bond(s) are present in the secondary structure?
Hydrogen bonds
What are the types of secondary protein structure?
Alpha-helix - one right handed, rod-like chain
Beta-sheets - two directions (parallel and anti-parallel) and turns between strands (glycine and proline)
Collagen triple helix - three left handed chains - Tropocollagen
What effect does proline have on an alpha-helix?
Breaks it as it puts in a left handed 90 degree turn
What is the repeated sequence in all strands of collagen?
X-Y-Gly
Where:
X - any amino acid
Y - proline or hydroxyproline
What holds the chains together in collagen?
Inter-chain H bonds involving hydroxyproline and hydroxylysine
Also inter-chain covalent bonds
What is the tertiary structure of a protein?
Arrangement of the atoms in three-dimensional space
What are the two types of tertiary structure/protein?
Fibrous
Globular
What are some examples of fibrous proteins?
Keratin
Collagen
What are some examples of globular proteins?
Myoglobin
Haemolytic
What forces are present in the tertiary protein structure?
Disulphide bonds Electrostatic interactions Hydrophobic interactions Hydrogen bonds Metal ion complexes
What can cause protein desaturation?
Heat - increase in vibrations
pH extremes - interrupts electrostatic interactions
Detergents/Urea/Guanidine hydrochloride - disrupt hydrophobics
Thiol agents/Reducing agents - reduce and disrupt disulphide bonds
What is a haem group an example of?
A prosthetic group
What is the quaternary structure of a protein?
A protein with more than one subunit eg haemolytic
What is allosteric regulation in haemoglobin?
Binding of one oxygen molecule changes affinity for other subunits
What direction do nucleic acids run in?
5 prime to 3 prime
What is DNA replication catalysed by?
DNA polymerase
How is DNA replication described?
It is semi-conservative
What enzyme unwinds DNA?
Helicase
How is the lagging strand replicated?
As Okazaki fragments
What are the three classes of RNA?
Ribosomal
Transfer
Messenger
How many nucleotides comprises an anticodon?
Three
What are the steps of transcription?
RNA polymerase binding DNA chain separation Transcription initiation Elongation Termination
How does transcription terminate?
Stem-loop created
Stretch of uracils forms
Enzyme cleaves the finished RNA
How are the ends of mRNA processed?
Addition of a poly-A tail
Addition of five prime cap
Codons and anticodons consist of three nucleotides; the genetic code is based therefore on…
…triplets
How can the genetic code be described? (3 terms)
Degenerate (many AAs have more than one codon)
Unambiguous
Nearly universal
What are the start and stop codons?
Start - AUG (methionine)
Stop - UAA, UAG, UGA
What are the three tRNA binding sites on ribosomes called?
E - Exit (tRNA leaves)
P - Peptidyl (holds growing peptide)
A - Aminoacyl (Binds tRNA - site of bond formation)
What is the special initiator tRNA anticodon triplet?
UAC (matches start codon AUG)
What is the process of translation?
Initiator tRNA amino acid moves to P site
Next aminoacyl-tRNA binds to A site
Peptidyl transferase catalyses peptide bond formation between amino acids at P and A sites
Ribosome moved along mRNA by one triplet
Empty tRNA moves to E site
tRNA with growing peptide moves from A to P site
Repeat
What are the types of mutation?
Point Missense Nonsense Silent Frameshift
What happens to a finished protein?
Targeting
Modification
Degradation
What is an apoenzyme?
An enzyme without a cofactor
What is an enzyme with a cofactor called?
A holoenzyme
What are the models of enzyme function?
Lock-and-key
Induced fit
What are zymogens?
Inactive precursors of enzymes
What is the equation for glycolysis?
Glucose + 2ADP + 2Pi + 2NAD+ —> 2Pyruvate + 2ATP + 2H2O + 2NADH + 2H+
Describe glycolysis
First section - Three reactions - Phosphorylation of glucose - Uses two ATP per glucose - Forms fructose-1,6-bisphosphate (6 carbon sugar with 2 phosphates) Second section - One reaction - Splits fructose bisphosphate into two triose-phosphates Third section - Generates energy - Triose-phosphates converted to pyruvate - For each, 2ADP + 2Pi ---> 2ATP - Produces 4 ATP - Net gain of 2 ATP - Electrons transferred to NAD+
What are the regulators of glycolysis and how do they regulate it?
ATP - if in high amounts it is inhibited
Citric acid - an intermediate; large amounts inhibits cycle
Hydrogen ions - buildup leads to acidification and so inhibits cycle
AMP - high amount means cell is low in energy so promotes cycle
Fructose - promotes cycle
What are the important enzymes in the glycolysis?
Hexokinase - first reaction
Phosphofructokinase - third reaction
Pyruvate kinase - ninth (final) reaction
What is the name of the cycle through which Pyruvate is catabolised?
Citric acid/Krebs/Tricarboxylic acid cycle
Describe the TCA cycle
- Acetyl Co-A (C2) condensed with Oxaloacetate (C4) -> citric acid (C6)
- C6 -> C5 -> C4 releasing CO2
- Four oxidations (three make NADH, one makes FADH)
- One round generates (two CO2, three NADH, one FADH)
What is a transcription factor?
A protein other than RNA polymerase that is involved in transcription
How many ADP molecules are phosphorylated to ATP during glycolysis?
4
Net gain of 2
What molecules do ribosomes consist of?
RNA and proteins
What subunits are the nicotinic ACh receptors made of?
Alpha 3 and Beta 4
What protein is activated in Burkitts lymphoma?
c-myc
