Biochemistry Flashcards
What are examples of lipids?
Triglycerides, phospholipids, steroids
What is an example of a monosaccharide?
Glucose
Which carbons react with each other in monosaccharides and what do they form?
Carbon 1 and carbon 5 to form a cyclic compound
What type of reaction is combining carbons of the same monosaccharide to form a cyclic compound?
Intermolecular reaction to change the structure of a molecule
What type of bonds can disaccharides be held together with?
Alpha or beta linkages
What is the importance of different types of bonds in disaccharides?
Important in our ability to break bonds apart during metabolism
In disaccharides, which carbons are the alpha or beta linkages between?
1 and 4
What two things do reactions involve a change in?
Entropy and enthalpy
What is the equation for a free energy change in a reaction?
delta G= delta H - T(deltaS)
What are exergonic reactions?
Total free energy of products is less than reactants- delta G is negative and these can occur spontaneously
What are endergonic reactions?
Total free energy of products is more than reactants- delta G is positive and these need energy to occur
What are delta G values of near 0 characteristic of?
Readily reversible reactions
What are examples of unfavourable cellular processes (+ delta G)?
Transport against a gradient or synthesis of large molecules
What are unfavourable cellular processes driven by?
Coupling
What reaction is very favourable and is often coupled?
Formation of ADP + Pi
What causes ATP to be less stable than ADP?
negative charges are very close together
How is the strain on ATP reduced partially?
Removal of a phosphate group
What are anhydride bonds?
High energy bonds
What are reactions with large negative delta G values used for in metabolic reactions?
Control points
What is metabolism?
All reactions taking place in the body
What is catabolism?
Breaking down smaller molecules into complex ones to release energy (favourable)
What is anabolism?
Synthesising complex molecules out of small ones in energy consuming unfavourable reactions
What is an example of a catabolic reaction?
Glycolysis (breakdown of glucose to generate ATP)
What is the net gain of glycolysis?
2 ATP
What is an example of anabolism?
Gluconeogenesis- making new glucose from non-carbohydrate precursors
What is the polarity of water?
Polar
What is the shape of water?
Bent
Water is hydrophilic. What dissolves in it?
Ionic and polar substances
What substances are insoluble in water?
Non-polar substances
How strong are hydrogen bonds compared to covalent ones?
Weaker individually but may be stronger collectively
What are amphipathic molecules?
Both hydrophobic and hydrophilic
What do amphipathic molecules form in water?
Micelles
What does the chiral carbon of an amino acid bind to?
An amino group, carboxyl group, hydrogen and side chain
What are the D and L forms of amino acids?
Stereoisomers
What bonds form between amino acids?
Peptide
What describes an acid?
Donates protons
What describes a base?
Accepts protons
What is the strength of an acid based on?
How readily it dissociates
What is the equation for the dissociation constant of an acid?
Ka= [H+] [A-] / [HA]
What is pH a measure of?
Concentration of protons in a solution
What does the Henderson-Hasselbach equation do?
Connects the Ka of a weak acid with the pH of the solution containing it
What is the Henderson-Hasselbalch equation?
pH= pKa + log ([A-] / [HA])
What is the isoelectric point?
pH at which a molecule has no net charge
How many pKa values do amino acids have?
2
What is primary protein structure?
The amino acid sequence
What is secondary protein structure?
Localised conformation of polypeptide backbone
What is the 3D structure of a polypeptide, including side chains?
Tertiary structure
What is the arrangement of polypeptide chains in a protein with multiple subunits?
Quaternary structure
What type of bonds are involved in secondary structure?
Hydrogen bonds
Secondary structure is localised. What does this mean?
Similar features are kept together
What are types of secondary structure?
Alpha helices, beta sheets, triple helices
What forms hydrogen bonds in secondary structure?
CO group of one amino acid and the NH group of another- 4 amino acids away
What residues break alpha helices?
Proline
How many polypeptide chains are involved in alpha helices?
1
How many polypeptide chains are involved in beta sheets?
Can be more than 1
What two types of bets-sheets are there?
Parallel or anti-parallel
Can different elements of secondary structure occur between the same protein?
Yes
What forms a triple helix?
Collagen
Where is collagen found in the body?
Bone and connective tissue
What is a repeating sequence of an amino acid?
Triple helix
What type of inter-chain bonds are present in triple helices?
Hydrogen
Apart from hydrogen, what other type of bonds are present in triple helices?
Covalent bonds
What are globular proteins?
Proteins folded into a spherical shape
What is an example of a globular protein?
Haemoglobin
What is the solubility of globular proteins like?
Soluble in water and salt solutions
What are fibrous proteins?
Contain polypeptide chains organised approximately parallel along a single axis
What are examples of fibrous proteins?
Keratin, collagen
What is the solubility of fibrous proteins?
Not soluble in water and salt
What are stronger, fibrous or globular proteins?
Fibrous
What are some different bonds involved in tertiary structure?
Hydrogen bonds, hydrophobic interactions, salt bridges, disulfide bridges
What are disulphide bridges?
Covalent bonds between cysteine amino acids
What are proteins which aid the folding process known as?
Chaperones
What conditions can cause denaturation of proteins?
pH, heat, detergents, urea, thiol or reducing agents
What are prosthetic groups?
A type of tertiary structure- proteins which contain another non-protein structure
What is an example of a prosthetic group?
Haem
What is quaternary structure involved in?
Proteins involving more than one polypeptide chain
What happens when one subunit of a protein binds to oxygen and what is this process known as?
Increases the other subunits affinity for oxygen- allosteric regulation
What is the genome?
The total DNA in each cell
What are the sugars in RNA and DNA?
Ribose and deoxyribose
What is a nucleoside?
Base and sugar
What is a nucleotide?
Nucleoside and phosphate group
What bonds are involved in nucleotides?
Phosphodiesterase
What are phosphodiesterase bonds formed between in nucleotide binding?
Free 3’ OH group and 5’ triphosphate
How many high energy bonds does the phosphodiesterase bonding of nucleotides take up?
2
Where are new nucleotides added?
To the free 3’ end only
How many nucleotide strands does DNA contain?
2
What is on the outside of the DNA strand?
Sugar phosphate backbones
What is on the inside of the DNA strand?
Bases
How are base pairs bonded?
Hydrogen bonds
What are the differences in bonds between AT and CG pairs?
AT- double bond
CG- triple bond
What must happen to DNA before cell division?
Replication
DNA replication is semi-conservative and catalysed by what?
RNA polymerase
What is needed to start DNA replication?
RNA primer
Where can DNA be added?
Only to existing nucleotides
Where does DNA replication start?
Simultaneously at multiple points in the genome
How is the lagging strand replicated?
In small short segments known as Okazaki fragments
What does helicase do?
Unwinds the DNA helix and stops it rewinding
What does 3’-5’ exonuclease do?
Removes incorrect nucleotides to improve error rate
What is rRNA?
Combines with proteins to form ribosomes where protein synthesis takes place
What is tRNA?
Carries amino acids to be incorporated into the protein
What is mRNA?
Carries genetic information for protein synthesis
Where does the specific amino acid attach to tRNA?
3’ end
What happens at the RNA polymerase binding stage of transcription?
Detection of initiation sites on DNA, requires transcription factors
What is the 2nd stage of transcription?
DNA chain separation
What is the 3rd stage of transcription?
Transcription initiation
What are the 4th and 5th stages of transcription?
Elongation and termination
Where does transcription start?
Nucleotide +1
What is a TATA box?
A nucleotide sequence which specifies to other molecules where transcription begins
Where is the TATA box found?
About 25 nucleotides infront of the transcriptional start
What does the TATA box binding protein do?
Recognises TATA and introduces a kink into DNA which determines the transcriptional start and direction
What direction is the RNA chain synthesised in?
5’-3’
What is new RNA identical and complementary to?
Identical to coding strand
Complementary to template strand
What does regulation of transcription require?
DNA binding proteins
What are the functional domains of DNA binding proteins?
DNA binding domain and transcription activation domain
What are non-coding sequences that eukaryotic genes have?
Introns
Introns have to be removed before translation- how?
Splicing
Why does one end of mRNA receive a GTP cap?
To prevent degradation
Why does one end of mRNA receive a polyA tail?
To make it ready to be recognised for translation
What do anticodons of tRNA molecules form base pairs with?
Codons on mRNA
What does degenerate genetic code mean?
Amino acids have more than 1 codon
What does unambiguous genetic code mean?
Each codon codes for only 1 amino acid or a stop
How many different frames can an RNA molecule be translated in?
3
What do aminoacyl-tRNA synthetases do?
Bind amino acids to their tRNA molecule
How many rRNA molecules and protein compounds do ribosomes contain?
4
How many tRNA binding sites do ribosomes have?
3
What happens to GTP in the initiation phase of translation?
Hydrolysed
Where do ribosomal subunits bind in initiation of translation?
5’ end of mRNA
What is the start codon?
AUG
At the end of initiation, where is the initiator tRNA located?
P site
In elongation of translation, where does elongation factor bring the next tRNA to?
A site
What do peptidyl transferases do?
Catalyse peptide bond formation between amino acids
During translocation, where does tRNA with the growing peptide move?
P site
When does termination of translation take place?
When the A site of the ribosome encounters a stop codon
What is a point mutation?
Change in a single base of DNA
What is a missense mutation?
Change of amino acid sequence
What is a nonsense mutation?
Creates a new termination codon and leads to premature stop
What is a silent mutation?
No change in amino acid sequence
What is a frameshift mutation?
Addition/deletion of 1 or 2 bases
What kind of mutations affect a larger portion of the genome?
Chromosomal
What are different types of chromosomal mutation?
Deletion, duplication, translocation, inversion
What is targeting after translation?
Moving a protein to its final location
What is modification after translation?
Addition of further functional chemical groups to a protein
What is degradation after translation?
Removal of unwanted/damaged proteins
What do free ribosomes in the cytoplasm make proteins for?
Cytoplasm, nucleus, mitochondria
What do bound ribosomes in the RER make proteins for?
Plasma membrane, ER, golgi
What do enzymes do?
Speed up the rate at which a reaction reaches equilibrium
What do enzymes not do?
Affect the equilibrium position of a reaction
What is the transition state?
Reaction intermediate species which has the greatest free energy
Where do enzymes specifically bind and stabilise?
Transition state
What do enzymes provide alternative reaction pathways to do?
Reduce the activation energy
What is glycogen storage disease?
An enzyme deficiency which results in the failure of glycogen to enter a phosphorylated state
What are some symptoms of glycogen storage disease?
Hypoglycaemia, hepatomegaly, skin and mouth ulcers, bacterial and fungal infections, bowel inflammation and irritability
What does the catalytic activity of many enzymes depend on?
Small molecules- cofactors and coenzymes
What are co-factors?
Inorganic metalions
What are coenzymes?
Organic molecules
Which out of coenzymes and cofactors are permanently associated with the enzyme?
Cofactors
What happens to coenzymes during a reaction?
They change charge and structure but are regenerated in the end
What are tightly bound co-enzymes known as?
Prosthetic groups
What does: the active site of unbound enzymes is complementary to the shape of the substrate describe?
Lock and key model of substrate binding
What does: the binding of the substrate induces a conformational change in the enzyme which results in a complementary fit describe?
Induced fit model of substrate binding
What are isoforms of enzymes known as?
Izozymes
What do isozymes do?
Catalyse the same reaction but have different properties and substrates
What is creatinine kinase?
A protein which binds to muscle sarcomere
Where is the M form of creatinine kinase produced?
Skeletal muscle
Where is the B form of creatinine kinase produced?
Brain
What type of creatinine kinase does the heart produce?
Both B and M type heterodimer
What does B type creatinine kinase in the blood suggest?
Stroke/tumour
What does the heart heterodimer of creatinine kinase in the blood suggest?
Heart attack
What does kinase do?
Phosphorylates other proteins
What does phosphatase do?
Dephosphorylates other proteins
What are zymogens?
Inactive precursors of enzymes
How are zymogens transferred into active enzymes?
Cleavage of a covalent bond
Where do zymogen reactions commonly occur?
Small intestine with digestive enzymes
In enzyme kinetics, what is Vmax?
Maximum speed of catalysis
In enzyme kinetics, what is Km?
The concentration of substrate which gives half Vmax
In enzyme kinetics, what does k1 describe?
Forward rate constant for enzyme association with the substrate
In enzyme kinetics, what does k2 describe?
Forward rate constant of enzyme conversion of substrate to product
In enzyme kinetics, what does k-1 describe?
Backwards rate constant for enzyme dissociation with the substrate
If given the graph of V and S moles in log form, which way is increasing substrate concentration?
Right to left
If given the graph of V and S moles in log form, which way is velocity increasing?
Towards the x-axis
If given the graph of V and S moles in log form, where is Vmax?
Y- intercept
If given the graph of V and S moles in log form, where is Km?
Where the slope intersects with the x-axis
Does Vmax change in competitive inhibition?
No
Does Vmax change in non-competitive inhibition?
Yes, the competitors will have different Vmax values
What type of curve to allosteric enzymes result in?
Sigmoidal
What do allosteric enzymes show?
Co-operative behaviour
What do allosteric factors modulate?
Enzyme kinetics behaviour
What physiological term is associated with moving the oxygen haemoglobin curve left?
Haldane effect- increased saturation of haemoglobin with oxygen but less oxygen delivery to tissues
What physiological term is associated with moving the oxygen haemoglobin curve right?
Bohr effect- decreased saturation of haemoglobin with oxygen but more oxygen delivery to the tissues
What way will foetal haemoglobin, methaemoglobin and carboxyhaemoglobin move the oxygen haemoglobin curve?
Left
What else moves the oxygen haemoglobin curve left?
Low [H+] (alkali), low pCO2, low 2,3-DPG, low temp
What moves the oxygen haemoglobin curve right?
High [H+] (acid), high pCO2, high 2,3-DPG, high temp
What type of reaction is the anabolism of glucose?
Endergonic and reductive (requires energy)
What type of reaction is the catabolism of glucose?
Exergonic and oxidative (yields energy)
What does ATP do during redox reactions?
Energy carrier
What does NADPH + H+ and NADP + H+ do during redox reactions?
Electron carrier
What does oxygen do in redox reactions?
Combines with leftover hydrogen to form water
How can glucose be stored?
Glycogen, starch, sucrose, converted to lipids
What is glucose oxidised to form?
CO2 and O2
What does oxidisation of glucose through the pentose phosphate pathway form?
Ribose-5-phosphate
What does ribose-5-phosphate do?
Precursor for nucleotide synthesis and DNA repair- essential for growth
What is produced when glucose is fermented by anaerobic glycolysis?
Lactate
What does lactate cause?
Rapid, inefficient ATP production
What is formed when glucose is oxidised through aerobic glycolysis?
Pyruvate
What does pyruvate produce?
ATP efficiently
How can glucose be transported?
Via Na+/glucose symporters or passive facilitated diffusion glucose transporters
Which glucose transporters are found in the brain and have low Km?
GLUT 1 and 3
What glucose transporter is found in liver/beta cells, has a high Km and is insulin dependent?
GLUT2
Where is GLUT4 found?
In muscle and adipose tissue- insulin dependent
What does GLUT5 do?
Transports fructose in the gut
What is glycolysis?
Conversion of glucose to pyruvate
What is formed in glycolysis?
2 pyruvate, 4ATP, 2H2O, 2NADH, 2H+
What is the end point of pyruvate?
3 carbon chain with no phosphate
How often does the 2nd part of glycolysis occur?
Twice for every mole of glucose
What is the net gain of glycolysis?
2ATP
What does hexokinase control?
Rate of substrate entry
What does phosphofructokinase control?
Rate of flow
What does pyruvate kinase control?
Product exit
What is the ATP/AMP ratio known as?
Energy charge
If adenyl nucleotides are in the shape of ATP what is the ATP/AMP ratio?
Charged
What makes the ATP/AMP ratio discharged?
Cell only contains AMP and Pi
What happens if the mitochondrial metabolism is inhibited by lack of oxygen?
NADH is used to ferment pyruvate to lactic acid
When is NADH regenerated after anaerobic respiration?
Stage 3
What is the Warburg effect?
Cancer cells produce energy by a high rate of glucose metabolism to lactate. They have a low Km.
What are advantages of the Warburg effect?
Rapid energy production and rapid cell growth
What are disadvantages of the Warburg effect?
Uses lots of glucose and causes weight loss
What happens to NAD+ after glycolysis?
It turns to NADH + H+
What must happen to NADH + H+ for glycolysis to continue?
Must be re-oxidised
How is NAD+ regenerated?
Oxidative metabolism of pyruvate
Before being re-oxidised, what does NADH do?
Delivers electrons to the respiratory chain (cytochrome system)
Where does the TCA cycle occur?
Mitochondrial matrix
How does pyruvate enter the mitochondrial matrix?
H+ gradient from the cytosol allows transport which occurs through facilitated diffusion
What does pyruvate dehydrogenase complex do?
Catalyses the pyruvate to acetyl CoA reaction
What does pyruvate dehydrogenase complex consist of and how is it regulated?
Consists of 3 enzymes which are allosterically regulated by phosphorylation
Is the reaction of pyruvate to acetyl CoA reversible?
No
Apart from pyruvate, what else can acetyl CoA be generated from?
Lipids or amino acids
How many reactions are there in the TCA cycle?
8
What does the 2C unit (acetyl CoA) combine with in the TCA cycle?
4C unit
In the TCA cycle, the 6C unit is decarboxylated twice- what does this yield?
CO2
What else do oxidation reactions in the TCA cycle form?
NADH + H+ and FADH2
What energy is formed in the TCA cycle?
1 GTP
What happens to the 4C unit at the end of the TCA cycle?
It is regenerated
Where are all TCA enzymes found apart from one?
Mitochondrial matrix
Where is the succinate dehydrogenase enzyme found?
Inner mitochondrial membrane
What is high ATP, NADH and acetyl CoA suggestive of?
Plenty of energy
What is high ADP and NAD+ suggestive of?
Lack of energy
In the TCA cycle, what is generated per molecule of glucose?
4ATP, 10 NADH, 10 H+, 2 FADH2 and 6CO2
What is pyruvate dehydrogenase complex deficiency?
X linked disease
What will XX and XY forms of pyruvate dehydrogenase complex deficiency show?
XX- symptoms will show in adolescence
XY- stillborn
What are some symptoms of pyruvate dehydrogenase complex deficiency?
Poor muscle tone, lack of coordination, retardation and seizures, persistent lactic acidosis and respiratory problems
What does fumarate hydratase deficiency show?
Multiple systemic benign and malignant tumours- particularly tumours
From both previous cycles, what does NADH + H+ and FADH2 carry at the start of oxidative phosphorylation?
Each molecule carries 2 high energy electrons
What are the high energy electrons carried by NADH + H+ and FADH2 used for in oxidative phosphorylation?
To reduce O2 to H2O
In oxidative phosphorylation, protons flow from the matrix to the inner membrane and back again following their concentration gradient. What does this do?
Provides energy to allow ADP to be phosphorylated to ATP
What is used to overcome the fact that NADH cannot cross the inner mitochondrial membrane?
Glycerol 3 phosphate and aspartate shuttles
What is the standard electron transfer of a reduced substance a measure of?
How readily substance X will donate an electron (compared to H2)
What does a negative electron transfer value mean?
Reduced forms of substance X have a lower affinity for electrons than H2
What does a positive electron transfer value mean?
Reduced forms of substance X will have a higher affinity for electrons than H2
What is the standard free energy change proportional to?
Change in standard redox potential and the number of electrons transferred
What is the driving force of oxidative phosphorylation?
Redox of O2 by NADH
How many multisubunit respiratory complexes are involved in the electron transfer stage of oxidative phosphorylation?
4
What do the multisubunit respiratory complexes are involved in the electron transfer stage of oxidative phosphorylation do?
Take energy from NADH and transfer it to oxygen to form water
What are cytochromes?
Proteins which contain a haem group as a co-factor
What does the Fe (II) in haem do?
Take up and release electrons
What is transport of electrons through the respiratory chain coupled to?
Transport of H+ from the matrix to membrane
How do protons travel back to the mitochondrial matrix from the inner membrane?
Through ATP synthase in 2 proton pumps
What does the F1 subunit of ATP synthase do?
Protrudes into the mitochondrial matrix
What does the F0 subunit of ATP synthase do?
Hydrophobic complex in the inner membrane
What does the flow of proteins through ATP synthase do?
Causes ATP synthesis
What are examples of competitive inhibitors of the electron transport chain?
Cyanide, azide and CO
What provides a route for protons to be returned to the matrix?
Uncoupling proteins
How many ATP molecules does 1 glucose make?
30-32
What is lipolysis?
The breakdown of lipids
What does lipase do?
Releases free fatty acids and glycerol when energy is needed
Where are ketone bodies found?
They are formed in liver mitochondria and diffuse into the bloodstream
What are important molecules of energy metabolism which are strongly acidic?
Ketone bodies
What does cholesterol do?
Maintains structure and fluidity of cell membranes, involved in cell signalling and act as precursors for bile/bile acids
What do triglycerides require for transport?
Lipoproteins
