Biochemistry Flashcards
First law of thermodynamics?
Energy is neither created or destroyed
Second law of thermodynamics?
When energy is converted from one form to another, some of it becomes unavailable for work
2 formulas for ΔG?
ΔH – TΔS or (energy of the products) – (energy of the reactants)
2 things ΔG represents?
Energy available to do work and how close a reaction is to equilibrium
What ΔG value would a reaction close to equilibrium have?
ΔG = 0
Highly +ve or -ve ΔG values are readily reversible reactions? True or False?
False
4 key points of an exergonic reaction + an example?
- free energy of products is less than reactants
- ΔG is negative
- reaction can occur spontaneously
- reactions like these are used for control points
- ATP hydrolysis is a negative ΔG reaction
3 key points of an endergonic reaction?
- free energy of the products is more than reactants
- ΔG is positive
- reaction needs input of energy
What is coupling of reaction?
Reactions with +ve ΔG are coupled with a -ve ΔG reaction to make them occur more spontaneously
Do cells store a lot of ATP?
No
Is ATP or ADP more unstable and why?
ATP due to repulsion of 3 phosphates
Name of bonds that join phosphate groups?
Anhydride bonds
Is water polar or non-polar + shape?
Polar + bent
What types of substances can water dissolve and how?
Ionic and polar via dipole-dipole interactions
Polarity of hydrophic, hydrophillic and amphipathic molecules?
Non-polar, polar and both
Example of amphipathic molecules?
Phospholipids in the cell membrane and micelles
How many amino acids are there + how many bases in amino acid?
20 + 3
What is the alpha carbon?
The carbon that has 4 different groups bound to it
What is the shape of an amino acid?
Tetrahedral
D and L amino acids are + what does that mean?
Sterioisomers + they are non-superimposable versions of eachother
Name the components of an amino acid?
Alpha carbon, NH2 (amino) group, COOH (carboxyl) group, H and an R side chain
Direction of an amino acid + charges of each side?
N-terminal (+ve) to C-terminal (-ve)
Key feature of peptide bonds + what they join?
They are planar + amino acids
How do amino acid chains rotate?
Around the alpha carbons
Describe how amino acids form resonance structures?
The 2 free electrons of the N of a peptide bond are given to the nearby oxygen to form a C=N
4 key features of zwitterions?
- 2 titratable end groups
- act as buffers for acids and bases
- 2 pKa values
- no net charge
Acids …. protons to form …. and bases accept ….. to form …..?
Give, conjugate bases, electrons and conjugate acids
What does Ka + pKa mean?
How readily an acid loses protons + value at which pH does not change upon addition of OH
What is pH a measure of + change in x pH = ?
Protons in a solution + 10 to the power of x
As an acid strengthens its Ka value ….. and pKa value …..?
Increases and decreases
Primary protein structure?
Sequence of amino acids
Bonding that holds secondary structure?
Hydrogen bonding
3 types of secondary structures?
Alpha helix, beta sheets 1 & 2 and triple helix
What are alpha helices + what molecule breaks them?
Single stands where a C-O binds an N-H 4 residues away + proline residues
2 types of beta sheets?
1 = parallel and anti-parallel 2 = zigzag pleated sheets
What are triple helices + where are they found?
3 chains of collagen made from proline residues + connective tissue
What is tertiary structure + additional feature?
Final 3D shape of the polypeptide + prosthetic group
Describe fibrous vs globular proteins + examples?
Fibrous are insoluble sheets (kertain) and globular are soluble spheres (haemoglobin)
What is quaternary structure?
Binding of subunits together
Amino acid substitution in sickle cell anaemia?
Valine (hydrophobic) for glutamic acid
Examples of disease that arise from incorrect protein folding?
Parkinson’s and Alzheimer’s
Examples of prion diseases?
Mad cow and Creutzfeldt-Jacob
3 differences between DNA and RNA?
DNA (deoxyribose sugar, ACTG and double stranded) vs RNA (ribose sugar, AUCG and single stranded)
How to differentiate between ribose and deoxyribose?
Ribose has an OH on carbon 2 and deoxyribose has an H
Building blocks of bases?
dATP/TTP/CTP/GTP (DNA) vs ATP/UTP/GTP/CTP (RNA)
A nucleoside + nucleotide is made of a?
Base and sugar + nucleoside and phosphate
A nucleic acid is?
RNA and DNA
5 step summary of DNA replication?
- Helicase unwinds
- RNA primer joins 3’ end
- Nucleotides added
- DNA polymerase fills gaps on leading strand
- DNA ligase bonds Okazaki fragments on lagging strand
2 steps in how nucleotides added in DNA replication?
- Triphosphate breaks leaving base + monophosphate
- 5’ phosphate forms phosphodiesterase bond with 3’ OH of DNA chain
What is essential for DNA replication?
A 3’ end
Bonding between A and T + C and G?
A=T and C≡G
Enzyme that adds TTAGGG repeat?
Telomerase
Extra function of DNA polymerase?
Exonuclease activity removes incorrect nucleotides
General structure of RNA?
Stem-loop with intramolecular pairing
Most unstable RNA?
mRNA
Structure of tRNA?
Anticodon (3 bases) determines which amino acid binds to attachment site on opposite side of molecule
What is RNA made by?
RNA polymerase (Pol)
How many Pols in prokaryotes vs eukaryotes?
1 vs 3
What Pol is needed to synthesise mRNA?
Pol II
Transcription + splicing summary?
- TATA BBP (part of TFIID) binds TATA box and kinks DNA to provide landing platform
- Pol II binds TATA promoter region and unwinds DNA within itself
- Nucleotides added to form mRNA complimentary to DNA template
- Introns are removed leaving exons
- Addition of 5’ cap and 3’ poly A tail
What are the 2 essential components needed for translation?
Initiation factors and GTP hydrolysis
Three binding sites of a ribosome?
APE
Start and tRNA initiator codon?
AUG and UAC
7 step translation summary?
- IF binds ribosome and GTP hydrolysis occurs
- A binds mRNA 5’ end of mRNA and finds start codon
- Initiator tRNA binds start codon which moves to P
- EF-1 alpha brings next tRNA into A
- GTP is hydrolysed and EF-1 alpha dissociates
- EF-2 moves mRNA along one triplet
- Continues until stop codon is reached
Role of EF-1 and 2 in transcription + which molecule regenerates EF-1?
1 = bring tRNA in to A site 2 = move mRNA along ribosome + EF-alpha beta
Role of GTP hydrolysis in translation?
Allows EF-1 alpha to be released from tRNA
Enzyme that bonds tRNA and amino acid?
Aminoacyl-tRNA synthetase
Energy released from GTP, ATP and UTP is different? True or False?
False - energy is the same
Enzyme that forms peptide bonds?
Peptidyl transferase
Where does post-translational modification take place?
In the ER and golgi apparatus
What is glycosylation and when does it take place?
Adding carbohydrates to proteins during post-translational modification
Disease of incorrect lysosome protein sorting?
Mucolipidosis
Disease of alpha-1 antitrypsin (A1AT) incorrect folding?
Emphysema
How are enzymes activated?
Phosphorylation via kinases
What is a zymogen?
Inactive enzyme precursor that is activated via cleaved covalent bond
How do enzymes lower activation energy?
Bind to intermediate complex and stabilise it
Examples of cofactors vs coenzymes?
Iron/zinc vs NAD/FAD/vitamins
Enzyme - cofactor?
Apoenzyme
Enzyme + cofactor?
Holoenzyme
Name of an enzyme in a cofactor metal coordination complex?
Metalloprotein
Coenzymes can tightly bind to form?
Prosthetic groups
What is an isoenzyme + example?
Different structure but same reaction
Lactate dehydrogenase is H in the heart (promotes aerobic) and M in the muscle
What is Vmax and Km + name of graph used to determine their values + what the graph compares?
- Vmax = max velocity of a rection
- Km = 0.5 Vmax
- Line-weaver burk graph plots substrate concentration vs rate of reaction
How are Vmax and Km determined on a graph?
Vmax = Y axis intersection Km = X axis intersection
Change in Vmax and Km with competitive inhibition + give an example?
Vmax = no change and Km = increased + methanol poisoning
Change in Vmax and Km with non-competitive inhibition?
Vmax = decreased and Km = no change
2 key points about allosteric enzymes + an example?
- Do not follow Michaelis-Menten kinetics
- Produce sigmoidal curve
- Haemoglobin
2 ways glucose enters the cell?
Na/glucose symport or GLUT transporters
Control points of glycolysis?
Hexokinase, PFK and pyruvate kinase
Hexokinase catalyses?
Glucose to glucose-6-phosphate
PFK catalyses?
Fructose-6-phosphate to frucotse-1,6-biphosphate
What activates and inhibits PFK?
AMP + fructose-2,6,-biphsophate and ATP + citrate + H
Where is ATP used in glycolysis?
Hexokinase + PFK reactions
2 triose phosphates to 2 pyruvates produces?
4 ATP + 2 NADH + 2 H
Products of anaerobic glycolysis?
2 ATP + 2 NADH + NAD
Function of NADH in anaerobic glycolysis?
Converts pyruvate to lactic acid
All enzymes for CAC in matrix except what + function?
Succinate dehydrogenase + makes FADH2
How does pyruvate enter the martix?
H/pyruvate symport
Enzyme that converts pyruvate to acetyl co-A?
Pyruvate dehydrogenase complex
Irreversible step of the CAC?
Pyruvate 3C to acetyl co-A 2C
Summary of the CAC complexes?
Pyruvate (3C) -> acetyl co-A (2C) -> citrate (6C) -> oxaloaceteate (4C)
Products of the CAC?
3 CO2, 1 FADH, 3 NADH, 2 H, 1 GTP (which forms 1 ATP)
Yield per glucose molecule from glycolysis + CAC?
4 ATP, 10 NADH, 10 H, 2 FADH2, 6 CO2,
How many electrons do NADH or FADH2 carry?
2
Purpose/journey of electrons from NADH/FADH2 carriers?
Transferred along the ETC to reduce O2 to H2O which provides energy for H to cross the inner membrane
How does NADH cross the mitochondrial membrane?
Glycerol and malate shuttles
Eo’ = ?
The redox potential - how readily X loses electrons
NADH electrons enter at?
Complex I
FADH2 electrons enter at?
Complex II
Complex IV is a?
Cytochrome
What is a cytochrome?
A protein with a haem group (cofactor) that takes up/releases electrons
Which complexes are H pumps in the ETC?
I, III and IV
2 step ETC summary?
- Complex I, II and IV couple H transfer across inner membrane with electron transfer along membrane
- H moves back in through ATP synthase
1 glucose molecule produces .. ATP ?
30-32
Explain uncoupling of the ETC?
H is redirected back through uncoupling protein/thermogenin instead of ATP synthase to produce heat instead of energy
Where is uncoupling seen?
In newborn adipose tissue
How does cyanide inhibit the ETC?
Stops electron transfer to O2
Electrons are moves from …. to ….. energy but ….. redox potential?
Higher to lower and higher
Coenzyme Q is …. and shuttles between which complexes?
Ubiquinone and I, II and III
Which complex is part of the CAC?
II
Why do allosteric enzymes produce a sigmoidal curve?
They have more than one active site
Term for 3 bases on DNA, mRNA and tRNA?
Triplet, codon and anticodon
Protons are pumped …. the inner mitochondrial membrane/ETC and electrons are pumped …. the inner mitochondrial membrane/ETC?
Across and along
Hydrophillic signal molecules like ….. and ….. do/do not cross the cell membrane easily?
Peptide hormones and Ach + do not
Hydrophobic signal molecules like …… and …… do/do not cross the cell membrane easily?
Glucocorticoids and thyroid hormones + do
Molecule used in muscles for short-term energy production?
Creatine phosphate
What is Von Gierke’s disease + how it it treated?
Failure to break down glycogen into glucose + slow release glucose foods and small portions
Does GLUT 1 in the brain have a high or low Km?
Low
Diagnostic test for prostate cancer + disadvantage?
Prostate specific antigen (PSA) + some men with benign prostatic hyperplasia also have raised PSA
Gland that controls calcium levels?
Parathyroid
Hypercalcaemia does what to kindeys?
Increases urine and Na loss
Give an example of a monsaccharide, disaccharide and polysaccaharide?
Glucose, lactose and glycogen
4 amino acid groups + examples?
Non-polar hydrophobic, polar uncharged, acidic (COOH) and basic (NH)
