Biochemistry Flashcards
What has more carbon oxidation: alkane (in fats) or carbon dioxide?
Carbon dioxide
What is phosphorylation and de-phosphorylation?
The addition or removal of PO4
What is the final product of catabolism?
Carbon dioxide
What is more reduced: alcohol or aldehyde?
Alcohol
What are three biomolecules used for information storage?
DNA
RNA
NADH/NAD
What is the energy currency?
ATP
What do peptides and proteins consist of?
Amino acids
Give three types of lipids
Triglycerides
Phospholipids
Steroids
What are the two nucleic acids?
DNA
RNA
Name 4 disaccharides
Lactose
Maltose
Sucrose
Cellobiose
Name two polysaccharides
Cellulose
Glycogen
What is the first law of thermodynamics?
Energy is neither created or destroyed
What is the second law of thermodynamics?
When energy is converted from one form to another, some of that energy becomes unavailable to do work
What are reactions in which the total free energy of the product is less that the total free energy of the reactant?
Exergonic reactions
In an exergonic reaction, what is deltaG? and are the reactions spontaneous or not?
Negative and spontaneous
What are reactions in which the total free energy of the products is more than the total free energy of the reactants?
Endergonic
What is deltaG in endergonic reactions?
positive
deltaG values of near zero are characteristic of what?
Readily reversible reactions
What enzyme catalyses the reaction of glucose-6-phosphate to glucose-1-phosphate?
Phosphoglucomutase
What are anhydride bonds?
High energy bonds
What is catabolism?
breaking down complex molecules into smaller ones and releasing energy
What is anabolism?
Synthesising complex molecules out of smaller ones in energy-consuming reactions
Give an example for a catabolic pathway?
Glycolysis
What pathway is the initial breakdown of glucose for the generation of ATP?
Glycolysis
What is the net gain of ATP molecules per glucose molecule in glycolysis?
Net gain of 2 ATP
Give an example of an anabolic pathway?
Gluconeogenesis
What pathway involves making new glucose from non-carbohydrate precursors such as pyruvate?
Gluconeogenesis
What are useful control points in metabolic pathways?
Reactions with large negative deltaG values are useful control points
Is water polar or non-polar?
Polar
What shape are water molecules?
Tetrahedral shape and forms a dipole
What are amphipathic molecules?
Both hydrophilic and hydrophobic
What type of molecule is sodium palmitate?
Amphipathic
What do peptides have at each end of their molecules?
N-terminal residue and C-terminal residue
What direction is the peptide chain in?
From N-terminal to C-terminal
State three things about peptide bonds?
Peptide bonds have a partial double bond character
Peptide bonds are planar
Peptide bonds are strong and rigid
What is pH?
The measurement of the amount of protons in a solutions
What important equation lets us calculate the properties of buffer solutions?
Henderson-Hasselbalch equation
State the Henderson-Hasselbalch equation
pH = pKa + log [A-]/[HA]
What substances tend to resist a change of pH on addition of moderate amounts of acid or base?
A buffer solution
What are zwitterions?
Amino acids without charged side groups exist as these in neutral solution
What is the pH at which a molecule has no net charge called?
The isoelectric pH
What can act as buffers?
Proteins e.g. haemoglobin in the blood
What is the primary structure of a protein?
The sequence of amino acid residues
What is the secondary structure of a protein?
The localised conformation of the polypeptide backbone
What is the tertiary structure of a protein?
The three-dimensional structure of an entire polypeptide chain, including its side chains
What is the quaternanry structure of a protein?
The spatial arrangement of polypeptide chains in a protein with multiple subunits
What two angles can polypeptides rotate around?
angle between:
The alpha-carbon and the amino group
The alpha-carbon and the carboxyl group
What are the three types of secondary protein structures?
- Alpha helix
- Beta strands and sheets
- Triple helix
How many polypeptide chains does an alpha helix have?
One
What residues break alpha helixes?
Proline residues
What two directions could betasheets be in?
Parallel or antiparallel
What are the turns between strands on beta sheets?
Glycine and proline
Give an example of a triple helix?
Collagen triple helix
What type of protein structure is the component of bone and conective tissues?
Collagen triple helix (secondary)
In what protein structure does this occur: three left handed helical chains twisted around each other form a right-handed superhelix?
Collagen triple helix
What 2 types of bonds do collagen triple helixes have?
Inter-chain H-bonds - involving hydroxylysine and hydroxyproline
Covalent inter- and intra-molecular bonds
What type of protein structure are fibrous proteins and globular proteins?
Tertiary structures
What type of proteins contain polypeptide chains organised approximately parallel along a single axis?
Fibrous proteins
Give two examples of fibrous protein?
- Keratin of hair and wool
2. Collagen of connective tissue of animals including cartilage, bones, teeth, skin and blood vessels
What proteins are folded into more or less spherical shapes?
Globular proteins
Which are soluble in water: Globular proteins or Fibrous protiens?
Globular protiens
Give two examples of globular proteins?
Myoglobin
Haemoglobin
What 5 forces stabilise tertiary protein structures?
- Covalent disulphide bonds
- Electrostatic interactions = salt bridges
- Hydrophobic interactions
- Hydrogen bonds: back bone, side chain
- Complex formation with metal ions
Where are charged (polar) side groups normally located?
On the outside of proteins
Where do amino acids with hydrophobic side-chains tend to cluster?
In the centre of globular proteins
In sickle cell anaemia - what is the single nucleotide sequence change?
In coding region of the beta-chain of haemoglobin A
What does the single nucleotide sequence change in sickle cell anaemia result in?
Valine instead of glutamic acid
What happens to haemoglobin under low oxygen conditions?
Haemoglobin polymerises which results in rigid, sickle shape cells
Give 2 examples of disease caused by malfunctions with folding polypeptide chains
Alzheimers
Parkinsons
What are prion proteins?
Normal components of teh brain
Where are disease-causing forms of prion proteins?
Enriched in beta-sheets (aggregates into multimeric complexes, resistant to degradation)
What do Thiol agents and reducing agents do to disulphide bonds?
Reduce and therby disrupt disulphide bonds
In myoglobin - what does the haem group contain?
An iron ion (Fe II) and a prosthetic group
How many subunits does haemoglobin have?
4 - two alpha and two beta chains
How many oxygen molecules can each sub unit of haemoglobin bind?
ONE
What is nucleotide to nucleotide?
Transcription
What is nucleotide to amino acid?
Translation
What is a nucleoside?
A base and sugar
What is a nucleotide?
A nucleoside and a phosphate group
What does ribose have attached to carbon 2?
OH
What does 2-deoxyribose have attached to its carbon 2?
H
What are the purines?
Adenine and Guanine
What are the pyrimidines?
Uracil, Thymine and Cytosine
What is a phosphodiester bond formed between?
A free 3’ OH group and a 5’ triphosphate group
What end of the DNA strand are new nucleotides added to?
3’
What drug is used to suppress HIV?
Retrovir
How many hydrogen bonds are between A and T?
2
How many hydrogen bonds are between C and G?
3
What type of replication is semi-conservative?
DNA replication
What is DNA replication catalysed by?
DNA polymerase
What is required to start DNA replication?
An RNA primer
What are the fragments called on a lagging strand?
Okazaki fragments
What unwinds the double helix?
DNA helicase
What are the 4 building blocks of DNA replication?
dATP
dTTP
dCTP
dGTP
During DNA replication one phosphate group froms phosphodiester bond, what do the other two leave as?
Pyrophosphate - energy supply
What strand is the leading strand?
(3’ - 5’)
What strand is the lagging strand?
(5’ - 3”)
What is the RNA primer synthesised by?
Primase
What are the 3 main classes of RNA?
- Ribosomal RNA (rRNA) - combines with proteins to form ribosomes where protein synthesis takes place
- transfer RNA (tRNA) - carries the amino acids to be incorporated into the protein
- messenger RNA (mRNA) - carries the genetic information for protein synthesis
What are the two stable types of RNA?
Ribosomal RNA and Tranfer RNA
How many types of RNA polymerases do prokaryotic cells have?
One
How many types of RNA polymerase fo eukaryotic cells have?
Pol I, Pol II and Pol III (3 types)
How can Pol I, Pol II and Pol II be distinguished?
By their sensitivity to toxins like alpha-amanitin
What does Pol II synthesise?
All mRNA
What are the five steps of transcription?
RNA polymerase binding DNA chain seperation Transcription initiation Elongation Termination
What does RNA polymerase binding require?
Transcription factors
What are initiation sites on DNA called?
Promoters
Where is the TATA box found?
In a promoter
What does a TATA box binding protein do first?
Recognises TATA box
What is TFIID?
a general transcription factor
What is TFIID required for?
All Pol II transcribed genes
What two steps occur after TATA box binding protein has recognised a TATA box?
- Introduces a kink into DNA - determines transcriptional start and direction
- Provides a landing platform for further transcription factors and for RNA polymerase
What do Pol II and TFIID do on their own?
Extend transcript
What kind of structure does newly synthesised RNA make?
A stem loop structure
Specific regulation of transcription requires ‘specific’ transcription factors - what are they?
DNA-binding proteins
What do DNA-binding proteins do?
Bind to specific DNA sequences in the vicinity of a promotor
Regulate transcription postively or negatively
Name a family of transcription factors
Steroid receptors
What 3 domains do steroid receptors have?
Transactivation domain
DNA-binding domain
Ligand-binding domain
What can be said about the DNA-binding and ligand-binding domains on a steroid receptor?
They are highly conservative
Where are steroid receptors located?
In the cell cytoplasm (inactive)
What do steroid receptors do once they have binded to a ligand?
Move to nucleus and bind to DNA at steroid-response elements
In eukaryotic genes what are the coding regions (exons) interrupted by?
Non-coding regions (introns)
What has to be removed before translation into a protein?
Introns (splicing)
When processing the ends of mRNAs, what two things are added?
- Addition of poly(A) TAIL
2. Addition of 5’ cap
During translation, anticodons of tRNA molecules form base pairs with what?
Codons on mRNA
What are the 7 components of translation?
- Amino acids
- tRNAs
- Aminoacyl-tRNA synthetases
- Set of protein factor for initiation of protein synthesis, elongation of polypeptide chain and translocation and termination
- ATP and GTP as sources of energy
- Ribosomes
- mRNA
What binds amino acids to their corresponding tRNA molecules?
Aminoacyl-tRNA synthetase
How many rRNA molecules do ribosomes contain?
4
What are the 3 tRNA binding sites on ribosomes?
E = exit P = Peptidyl A = aminoacyl
What does inititation require?
Initiation factors
What gives the energy required for initiation?
GTP is hydrolysed to provide energy for inititation
What is AUG?
Start codon
What base pairs with the start codon?
Special ‘initiator’ tRNA with UAC anticodon base pairs
During elongation: what brings the next aminoacyl-tRNA to the A site?
An elongation factor (EF-1alpha)
What regenerates EF1alpha to pick up the next aminoacyl-tRNA?
A second elongation factor (EFbetagamma)
What does peptidyl transferase catalyse?
Peptide bond formation between amino acids in the P and A sites
What moves the ribosome along the mRNA?
Elongation factor EF-2
When does termination of protein synthesis occur?
When the A site of the ribosome encounters a stop codon
What does release factor RF do in termination of protein synthesis?
Binds to stop codon - GTP hydrolysis
What is a point mutation?
A change in a single base in DNA
What is a missense mutation?
Results in a change of amino acid sequence
Can change protein function e.g. altered haemoglobin in sickle cell anaemia
What mutation creates a new termination codon and changes the length of protein due to premature stop of translation?
Nonsense mutation
What mutation is due to degeneracy of the genetic code, has no effect on protein function and has no change of amino acid sequence?
Silent mutation
What is a frameshift mutation?
Addition or deletion of a single base
What are the 4 chromosomal mutations?
- Deletions
- Duplications
- Inversions
- Translocations
What do free ribosomes in the cytosol make proteins destined for?
Cytosol
Nucleus
Mitochondria
Translocated post-trranslationally
Where do bound ribosomes on the rough endoplasmic reticulum make proteins destined for?
Plasma membrane ER Golgi apparatus Secretion Translocated co-translationally
What is glycosylation?
The addition and processing of carbohydrates in the ER and the Golgi
Give three examples of post-translational modifications?
- Proteolysis
- Glycosylation
- Phosphorlyation
What is I-cell disease?
Inherited recessive disorder of protein targeting
Proteins normally destined for lysosomes are not properly sorted in the Golgi
End up secreted from cell
Lysosomes cannot properly digest material and become clogged
What do enzymes do to the activation energy?
Reduce it by providing alternative reaction pathways
What does catalytic activity of many enzymes depend on the presence of?
Cofactors
What are the two types of cofactors?
- Metal ions
2. Organic molecules - also called coenzymes
What are tightly bound coenzymes called?
Prosthetic goup
What is an enzyme without a cofactor called?
Apoenzyme
What is an enzyme with cofactor called?
Holoenzyme
What are NAD+ and FAD?
Coenzymes
What does CoA (coenzyme A) do?
Transfers acetyl groups
Three pancreatic serine proteases contain reactive serine residue and they catalyse hydrolysis of peptides at specific sites. What are the three proteases and how do they work?
- Chymotrypsin: hydrophobic pocket binds aromatic amino acids
- Trypsin: negatively charged Asp interacts with positively charged Lys or Arg
- Elastase: active site partially blocked, only amino acids with small or no side chains can bind
Would trypsin active site be affected by a small change in pH?
Yes
What are isozymes?
They are isoforms of enzymes that catalyse the same reaction but have different properties and structure
What isozyme is involved in developmental variation?
Haaemoglobin
Give an example of a tissue specific isoform?
Lactate Dehydrogenase (LDH)
Where are the two types of subunit in LDH present?
One predominantly in the heart
One predominantly in skeletal muscle
What does an increase in LDH in blood suggest?
Tissue damage
What is Creatine Kinase (CK)?
A dimeric protein which binds to the muscle sacromere
Where is the M form of CK produced?
In the muscle
Where is the B form of CK produced?
In the brain
What are phosphorylation reactions carried out by?
Protein kinases
What are zymogens?
Inactive precursors of an enzyme - are irreversibly transformed into active enzymes by cleavage of a covalent bond
In the pancreas: what two zymogens are formed?
- Trypsinogen
2. Chymotrypsinogen
What is the formation of the enzyme-substrate complex (ES) described by?
KM - The Michaelis constant - a combination of all rate constants in the reaction
What is Vmax?
The maximal rate of reaction at unlimited substrate concentration
How is the initial rate of an enzyme reaction is measured?
The tangent at the curve at time 0
What is the Michaelis constant KM equivalent to?
The substrate concentration where the intitial reaction rate is half-maximal
KM = [S] at?
at 0.5 Vmax
What does a low KM mean?
That an enzyme only needs a little substrate to work at half-maximal velocity
What does a high KM mean?
That an enzyme needs a lot of substrate to work at half-maximal velocity
What describes the rate of catalysis as a function of substrate concentration?
The Michaelis-Menton equation
On a Lineweaver-Burk plot how can Vmax be determined?
From the intersection of the straight line with the Y axis
On a Lineweaver-Burk plot, how can KM be determined?
From the intersection with the X axis
What is glucokinase?
An isozyme in liver and pancreas
Where is hexokinase I found?
In red blood cells
What is caused by mutations in pancreatic glucokinase which affect KM or Vmax?
MODY - Maturity-Onset Diabetes of the Young
What is a reversible inhibitor?
A substance that binds to an enzyme to inhibit it, but which can be reversed
What is an irreversible inhibitor?
A substance that causes inhibition that cannot be reversed
How can the competetive inhibitor of an enzyme be ‘out-competed’?
By the addition of lots of substrate
How can a non-competitive inhibitor be ‘out-competed’?
It cannot
What are the 5 methods of enzyme control?
- Allosteric control
- Regulation of traanscription - varies rate of protein synthesis
- Reversible covalent modification - we have seen phosphorylation as one mechanism
- Irreversible covalent modification - we have seen proteolytic cleavage
- Degradation
Inhibition of rate limiting enzymes by end products is a common mechanism of what?
Allosteric control
What type of enzymes do not follow Michaelis-Menten kinetics?
Allosteric enzymes
Give an important example for allosteric regulation
Binding of oxygen to haemoglobin
What is the binding of oxygen to haemoglobin controlled by?
H+
CO2
2,3 bisphosphoglycerate (side product of glycolysis)
In the absence of substrate - what are most enzyme subunits in?
The inactive from (tight form)
The binding of a substrate induces a conformational change from which forms?
T form to R form
What do allosteric activators or inhibitors do to the binding of a substrate?
Lock subunits in the T or R form
Where is fat stored?
In adipose tissue
Where are ketone bodies formed?
In liver mitochondria
What type of process is catabolism?
Oxidative, endergonic
What type of process is anabolism?
Reductive, endergonic
What are proteins broken down into?
Amino acids
What are polysaccharides broken down into?
Simple sugars
What are lipids broken down into?
Fatty acids and glycerol
During catabolism: small molecules from the degradation of macromolecules enter cells and are converted into a small number of very simple molecules, what are they?
2- carbon acetyl-CoA
some ATP is produced
What group of acetly-CoA enters the Krebs cycle?
Acetyl group
What happens to the acetyl group one it has entered the Krebs cycle?
It is completely degraded to CO2 and water
What allows glucose to transport into cells?
Na+/glucose symporters, via passive facilitated diffusion glucose transporters
Where is GLUT 1 transporter present?
In teh brain
Where is GLUT 2 transporter present?
In the liver
Beta-cells
Where is GLUT 3 transporter present?
In the brain
Where are GLUT 4 transporters present?
In muscle and adipose tissue
Where are GLUT 5 transporters present?
In teh gut
What is the initial pathway for the conversion of glucose to pyruvate?
Glycolysis
What is hexokinase involved in?
The conversion of glucose to glucose-6-phosphate
What is phosphofructokinase involved in?
The conversion of fructose 6-phosphate to fructose 1,6-biphosphate
What controls the conversion of phosphoenolpyruvate to pyruvate?
Pyruvate kinase
What is the key enzyme in the control of glycolysis?
Phosphofructokinase
What are the 3 negative modulators of phosphofructokinase?
- ATP
- Citrate
- H+ - prevents the excessive formation of lactic acid
What are the 2 positive modulators of phosphofructokinase?
AMP
fructose 2,6-bisphosphate
The ATP/AMP ratio is called the energy charge: if all adenylate nucleotides are in the shape of ATP what is the cell said to be in?
A fully charged state
What does glycolysis reduce NAD+ to?
NADH + H+
What must happen to NADH for glycolysis to continue?
It must be re-oxidised
What are the 2 fates of pyruvate anaerobically?
- Alcohol fermentation - yeast can form ethanol from pyruvate
- Lactic acid fermentation - some microorganisms can convert pyruvate to lactate
What is the fate of pyruvate in aerobic conditions?
Further oxidation and more energy released
What enzyme is involved in the conversion of pyruvate to lactate?
Lactate dehydrogenase
In what cycle does further oxidation of pyruvate occur?
The citric acid cycle or Krebs cycle or TCA cycle
What does the matrix of the mitochondria contain?
Enzymes for the TCA cycle
What do the inner membranes of mitochondria contain?
Proteins for electron transport chain, ATP synthase and transport proteins
Once in the mitochondria what does the pyruvate dehydrogenase complex (PDC) do to pyruvate?
Catalyses the oxidative decarboxylation of pyruvate to acetyl-CoA
Is the reaction of pyruvate to acetyl-CoA reversible?
NO ACETYL-COA CANNOT BE CONVERTED TO PYRUVATE
The pyruvate dehydrogenase complex consists of 3 enzymes involved in the actual reaction - what are they?
E1, E2 and E3
Pyruvate dehydrogenase complex also contains 2 enzymes involved in the control of PDC - what are they?
A kinase and a phosphatase in a single polypeptide
Pyruvate dehydrogenase complex also contains 5 coenzymes - what are they?
Thiamine, lipoic acid, coenzyme A, FAD and NAD+
How many GTP is formed during the TCA cycle?
one GTP
What enzyme of the TCA cycle is not located in the mitochondrial matrix?
Succinate dehydrogenase - integrated in the inner mitochondrial membrane
What enzyme is involved in this reaction:
Succinate + FAD = fumerate + FADH2
Succinate dehydrogenase
What is acetyl-CoA oxidised completely to in teh TCA cycle?
Carbon dioxide
What does each turn of the TCA cycle involve?
The uptake of 2 carbon atoms in the form of acetyl-CoA and the release of 2 carbon atoms as carbon dioxide
Each turn of the TCA cycle involves the transfer of 3 pairs of electrons to NAD+ to form?
NADH + H+
Each turn of the TCA cycle also results in the transfer of 1 pair of electrons to reduce FAD to what?
FADH2
From each acetyl-CoA the TCA cycle generates what?
3 x NADH + H+
1 x FADH2
1 x GTP
2 x CO2
All together, the reactions of glycolysis, pyruvate dehydrogenase complex and the TCA cycle produce?
10 NADH + 10 H+
2 FADH2
In oxidative phosophorylation, the electron transfer potential of NADH+ and FADH2 is converted into what?
The phosphoryl transfer potential of ATP
What can phosphoryl transfer potential be measured by?
Free energy change for the hydrolysis of ATP
What can the electron transfer potential be measured by?
The redox potential of a compound
What is a measure of how readily a reduced substance donates an electron?
The standard redox potential
What is the driving force of oxidative phosphorylation?
The reduction of oxygen by NADH
What are the two stages of oxidative phosphorylation?
- Electron transport (electrons flow from NADH tand FADH2 to oxygen, respiratory chain, energy is used to pump H+ out of the mitochondrial matrix)
- ATP synthesis
During electron transport - where do electrons from NADH enter?
At complex I
During electron transport where do the electrons from FADH2 enter?
At complex II
What are proteins which contain a haem group as a functional co-factor?
Cytochromes
Where is the F1 subunit of ATP synthase located?
Protrudes into the mitochondrial matrix
Where is the F0 subunit of ATP synthase located?
As a hydrophobic complex in the inner memrbane - contains the proton channel
What forms stator (ATP synthase)?
a, b, alpha, beta and delta subunits form stator
What forms rotor (ATP synthase)?
c, gamma and (greek E) subunits form rotor
What turns the rotor in ATP synthase?
Flow of protons
What three things inhibit transfer of electrons to oxygen during oxidative phosphorylation?
Cyanide
Azide
CO
What does brown adipose tissue contain?
Uncoupling protein (UCP) = thermogenin
Where does glycolysis take place?
in the cytoplasm
How does NADH from the cytoplasm get into the oxidative phosphorylation pathway?
The glycerol-3-phosphate and malate shuttles overcome this
How much ATP does one glucose molecule yield?
30-32 ATP molecules
