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Biology - Year 1 > Biochemistry - A Conceptual Overview > Flashcards

Biochemistry - A Conceptual Overview Flashcards

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0
Q

What is the only imino acid?

A

Proline

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1
Q

What is the general structure of an amino acid?

A 
An alpha carbon surrounded by
A carboxyl group (COO-)
An amino group (NH3+)
A side chain (R group)
A hydrogen atom
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2
Q

What is the difference between a carboxylic acid and carboxylate?

A

Carboxylic acids COOH can donate a proton.

A carboxylate is its conjugate base and has lost its proton.

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3
Q

In humans what sterioisomer are amino acids?

What is the only amino acid not to have a stereoisomers?

A

L-isomers

Glycine

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4
Q

What is the isoeletric point of an amino acid?

A

When the AA is neutral charge

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5
Q

Classify nonpolar, aliphatic R groups.

Classify polar uncharged R groups.

A

Include the amino acids glycine, alanine, proline, valine, leucine, isolecuine and methionine.
Can’t form H bonds. Are hydrophobic.

Include the amino acids serine, threonine, cysteine, asparagine and glutamine.
Component in their side chain can form H bonds (e.g. O, N or S).
Don’t have a distinctive charge.
Interact with water due to H bonds.
Serine and threonine have hydroxyl (alcohol group) which is a target for phosphorylation in cell signalling.
Cysteine has reduced sulfur atom. Disulfides important for cross links in 3D proteins.

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6
Q

Classify aromatic R groups.

A

Includes the amino acids phenylalanine, tyrosine and tryptophan.
All have benzene ring.
Often called bulky AA.
The only 3 AA to absorb light in the UV range.

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7
Q

Classify positively charged R groups.

A

Include amino acids lysine, arginine and histidine.
Basic AA, positively charged at physiological pH (7.4).
Histidine is hard to classify, neutral or positive at physiological pH but has ring. Enzymes use it in catalytic mechanisms.

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8
Q

Classify negatively charged R groups.

A

Include the amino acids aspartate and glutamate.
Have carboxylate COO-.
Can form salt bridges and interact with metals.

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9
Q

Describe these post transational modded amino acids:

  • Hydroxy proline and lysine
  • 6-N-Methyllysine
  • Gamma-carboxyglutamate
  • Desmosine
  • Selenocysteine

What is the name of the other two types?

A

Have OH group added to parent AA. Important for collgen formation. Enzyme that adds OH group needs vitamin C.

Adds CH3 to lysine. Found in myosin for muscle contraction. Parent has positive charge addition of CH3 makes it neutral.

Found in prothrombin - blood colagulation. Carboxyl group added to gamma carbon. Allows binding to calcium.

Four lysine residues bind to ring structure. Found in elastin.

Exception to rule - incorporated during translation. Parent AA cerine. Found in GSH peroxidase protein. Involved in detoxification of peroxides.

Ornithine and citrulline

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10
Q

What is a cofactor?

A

A non amino acid component of proteins. Usually derived from micronutrients.

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11
Q

What are the types of mutation?

A

Silent

Conservative

Non-conservative

Stop mutations

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12
Q

What direction are peptides chains written?

A

N terminus to C terminus

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13
Q

What are the destabilising factors of alpha helices?

A

High concentration of high charged AA

Bulky side chains

High glycine concentration

Proline added in the middle of a chain

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14
Q

How many amino acids do beta turns contain?

A

4

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15
Q

What are the two types of tertiary protein structure? Give an example.

A

Globular e.g. myoglobin and structural e.g. alpha keratin

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16
Q

Why is the haem group of myoglobin in a cleft?

Why do you need a relative large protein for myoglobin?

A

To protect the iron from being oxidised and converted to the Fe3+.

Need to form a structure that forms a hydrophobic cavity that will protect the heam.
Most of the AA are there to form the 3D structure that will bind to oxygen.

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17
Q

Why do viruses need a protein capsid?

A

RNA is very unstable, the protein capsid protects RNA and DNA.
Viruses use cell receptors to enter a cell, cell receptors recognise proteins in the capsid.

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18
Q

In a rate equation what is k?

A

Rate constant, but is only truly constant if all that is changing is the concentration of the reactants

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19
Q

What is a zero order reaction, what is its rate?

What is a first order reaction, what is its rate?

What is a second order reaction?

A

Where the rate does not depend on the concentration of the reactants. Rate = -k

Where the rate of reaction depends on the concentration of just one reaction. Rate = -k1[A] or rate = k1[C]

Where the rate of reaction depends on the concentration of one reactant squared or the concentration of two reactants

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20
Q

What is the order of a reaction?

A

The number of components involved in the rate-determining step. E.g. A first order reaction depends on only one component in the reaction mixture.

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21
Q

What is the rate limiting step?

A

The slowest step in a reaction

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22
Q

How does delta G relate to the equilibrium constant (i.e. what is the equation linking deltaG and Keq)?

A

Delta G = -RTlnKeq

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23
Q

Describe an amino terminal modification?

A

AA are usually capped so amino terminus can’t undertake further reactions
In eukaryotes methionine is modified by acetic acid
Capping is sometimes removed in further processing of proteins

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24
Q

Describe a protein signal sequence?

A

A intracellular “post code” directs a protein to its appropriate location within the cell
Often removed when a protein reaches its target, removal of SS often activates a protein

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25
Q

Describe phosphorylation, why is it important? How is it triggered?

What are the three amino acids that are phosphorylation, what do they have in common?

What are enzymes that phosphorylated called?

What are enzymes that dephosphorylate called?

A

Important for signal transduction mechanism by which many hormones activate or deactivate metabolic pathways.
Hormones bind to receptors and can trigger phosphorylation.

Serine, threonine and tyrosine are the three AA that are phosphorylated they all have an OH group which is changed to a phosphate causing the side chain to become negative impacting the protein.

Kinases

Phosphatases

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26
Q

Describe acetylation, what is it for?

A

Lysine residues in histones are acetylated.
Lysine has positive side chain which interacts with negative phosphates on DNA.
Lysine residues are acetylated to turn side chain neutral so DNA can be unwound and a gene transcribed

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27
Q

What is glycosylation? What are the two types?

What amino acid is involved in O-linked glycosylation?

What amino acid is involved in N-linked glycosylation?

What do glycosylated proteins do?

A

Addition of sugar groups to a protein. N-linked and O-linked.

Serine

Asparagine

Often point out of the cell and are used for recognition.

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28
Q

What is acylation?

What is it important for?

A

Addition of a acyl group. Most acylation takes place by addition of a fatty acid.

Important for peripheral membrane proteins these always sit on the outside of membranes. Two components needed for binding of PMP: fatty acid which acts as anchor into membrane, and an interaction between protein an phospholipids e.g. electrostatic.

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29
Q

What are prosthetic groups?

What are the types?

A

Non-protein co-factor that are: required for the function of a protein, irreversibly bound and stay with the protein for its lifetime.

Metal type or organic

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30
Q

Why are disulfide bonds important?

A

For the protein to form it’s 3D shape.

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31
Q

What are the two ketogenic amino acids?

A

Leucine and lysine

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32
Q

What is a cofactor in respect to enzymes?

A

A small molecule (vitamins or minerals) often associated with active site of enzyme, often increase protein reactivity to substrate.

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33
Q

What type of binding pocket does chymotrypsin have? What amino acids does it bind?

What type of binding pocket does trypsin have? What amino acids does it bind?

What type of binding pocket does elastase have? What amino acids does it bind?

A

CT has a large and hydrophobic binding pocket. It’s is specific for amino acids that are large and hydrophobic such as the aromatic amino acids.

Trypsin’s substrate binding point has a negatively charged asparagine. It is specific for two positively charged amino acids: arginine and lysine, which form electrostatic interactions with asparagine.

Elastase has a few valine amino acids that restrict the size of the substrate binding pocket so elastase is specific for an amino acid with small side chains e.g. Glycine, alanine etc…

34
Q

What are the mechanisms of rate enhancement used by chymotrypsin?

A

Acid base catalysis

Covalent bond

Orientation and proximity

Environmental effects (oxyanions)

35
Q

What are the mechanisms of rate enhancement?

A

Acid base catalysis

Covalent catalysis - covalent bond formed and broken rapidly

Metal ion catalysis - binds and orientates substrate

Environmental effects

Proximity and orientation

Strain distortion

36
Q

What is the i+4 rule?

A

In alpha helices, where the carbonyl group attached to amino acid i forms a hydrogen bond with the NH attached to the i4 alpha carbon

37
Q

What is the half life of a reaction?

For a first order reaction how do you calculate half life?

A

It’s a measure of rate of reaction, the time taken for half the original amount of substrate to react

T1/2 = ln2/k

38
Q

What it the equilibrium constant represented by?

What actually is the equilibrium constant?

How do you calculate Keq?

What does a small and large Keq tell you about substrate and product concentration?

A

Keq

A ratio of the concentration of the products to the concentration of the reactants.

Keq = [B]/[A]

Small Keq = higher [A]
Large Keq = higher [B]

39
Q

What effect do catalysts have on the transition state?

A

Decrease the energy required to reach the transition state and so increase reaction rate

40
Q

What is Vmax?

A

The max rate when the enzyme is saturated with substrate. Vmax = K2[E]T

41
Q

What is the Michaelis-Menten equation?

A

V = Vmax ([S]/[S] + Km)

42
Q

What effect does a competitive inhibitor have on Km?

A

Competitive inhibitors reduce enzyme substrate affinity so Km increases

43
Q

What is a classical non-competitive inhibitor? What is its effect on Km?

What is a mixed inhibitor? What is its effect on Km?

A

Has no effect on substrate binding, no effect on Km

Change in active site modifies binding ability of S, affinity is reduced, Km increases

44
Q

What is an uncompetitive inhibitor?

What effect does it have on Km and Vmax?

A

It cannot bind with a free enzyme and needs the presence of a substrate to bind. The substrate promotes a conformation change so the inhibitor can bind

Km decreases and Vmax decreases

45
Q

Describe amino acid catabolism.

A

Starts with the removal of an amino group (transamination).
Every amino acid has an enzyme to catalyse the transamination process.
The enzyme has two substrates it’s amino acid and alphaketoglutarate.
The amino group is transferred to alphaketoglutarate to make glutamate.

46
Q

Describe the oxidative deamination of glutamate.

A

Ammonium NH4+ is produced.
Catalysed by glutamate dehydrogenase.
Glutamate is deaminated to alphaketoglutarate and ammonia.
The ammonia is used by the liver (urea cycle)
In the liver ammonia is combined with glutamate to form glutamine.

47
Q

How are amino acids catabolised in muscles?

A

Muscle proteins are transaminated to form glutamate.
Glutamate and pyruvate combine to form alanine (catalysed by alanine amino transferase).
Alanine is transported to the liver (where it is converted back to pyruvate).
Pyruvate is used for gluconeogenesis to make glucose to use in glycolysis for energy

48
Q

What are some of the main liver function tests?

A

AST (serum aspartate aminotransferase) and ALT (serum alanine aminotransferase) are important in amino acid metabolism and are expressed in large concentrations in the liver and can be used to find the location of liver damage

Lactate dehydrogenase (LDH) test

Alkaline phosphatase indicates damage to/ blocked bike duct

Gamma-Glutmyltranaferase - indicates cirrhosis and metastatic invasion

49
Q

What are some other markers of liver function?

A

Prothrombin time - required for blood coagulation, time for patients blood sample to coagulate is measured liver damage = longer time

Albumin - most common protein in blood, produced in the liver, liver damage = decreased albumin

Bilirubin - builds up when liver is damage causes jaundice

50
Q

What are the criteria for a heart attack diagnosis?

How many of these criteria are needed for a heart attack to be diagnosed?

A
  • History of ischemic chest pain longer than 20 minuets.
  • Changing in ECG tracing
  • Rise and fall of serum cardiac biomarkers

2/3

51
Q

What are two tests used to diagnose a heart attack?

A

Creatin kinase - specific for muscle and brain tissue so most sensitive test

AST and LDH - however are unspecific to heart tissue

52
Q

What are the two approaches to drug design?

A

Targeted - designing an inhibitor for a target
Molecular target&raquo_space; compound&raquo_space; physiological effect

Untargeted - molecular target is unknown
Compound&raquo_space; physiological effect&raquo_space; molecular target

53
Q

What type of antibiotic is penicillin?

In drug design what is:

  • IC50
  • LogP
  • Cmax
A

A beta-lactam antibiotic

Concentration of drug that inhibits an enzyme by 50%
Measure of hydrophobicity
Max concentration of a particular compound in blood a low number indicates drug is not getting into the blood

54
Q

Metal ion catalysis is a type of rate enhancement, give example of two types of enzyme that involve metal ions?

A

Cytochrome p-450: the main enzyme in drug metabolism

Restriction enzymes: produced by bacteria to cut DNA at specific sites, Mg2+ used as a cofactor to reduce electrostatic repulsion

55
Q

What is a protease?

Give examples of three digestive proteases found in the small intestine.

Where are these digestive enzymes originally produced? In what form, what is this form called?

A

They break peptide bonds into peptides which are further broken into amino acids.

Chymotrypsin, trypsin and elastase

In the pancreas in an inactive form called a zymogen

56
Q

What amino acids form the catalytic triad?

A

Asp102, Histadine57 and serine195.

57
Q

What is an iso enzyme?

A

Enzymes that all catalyse the same type of reaction e.g. there are 5 LDH isoenzymes that all do the same thing

58
Q

In a Trp operon either a 2-3 stem loop or 3-4 stem loop is formed depending on weather Tryptophan is present?
Which stem loop terminates transcription?

A

3-4 stem loop terminates transcription

2-3 stem loop doesn’t terminate transcription

59
Q

What is a defining feature of temperate bacteriophages?

A

They can be in either a lytic cycle or in a lysogenic state

60
Q

What are some of the ways of introducing DNA into cells?

A

Protoplast transformation - remove cell wall by enzymatic treatment prior to mixing with DNA.
Precipitation - of DNA onto a cell mono layer culture
Electroporation - electrocuting cells in the presence of DNA
Biolistics - bombardment of tissues with gold or tungsten microprojectiles coated in DNA
Direct micro injection of DNA into host cells nucleus (only large eukaryotic cells).

61
Q

Outline the general stages of genetic engineering.

A
  • DNA is digested with a restriction enzyme the cloning vector is also digested with the same restriction enzyme
  • DNA fragments are mixed together and ligated to produced recombinant DNA
  • Ligation mixture is introduced to the cloning host
  • Transformants are screened for desired recombinant molecule
62
Q

The enzyme lactate dehydrogenase catalyses the conversion of…

Why can lactate dehydrogenase be used as a marker of injury and disease?

A

Pyruvate to lactate and vice versa (its a reversible reaction).

It is released during tissue damage

63
Q

Penicillin antibiotic resistance can be countered by using…

A

Amoxicillin (a penicillin analogue) and Clavalanic acid (a lactamase inhibitor)

64
Q

What are some of the potential targets in a cell that could be targeted to reduce HIV infection?

A

Entry inhibitors
Reverse transcriptase inhibitors
Intergrase inhibitors
Protease inhibitors

65
Q

Base catalysis is defined as…

A

Temporary proton abstraction

66
Q

What type of covalent bond is formed in covalent catalysis?

A

Transient (bond formed and broken rapidly)

67
Q

In the chymotrypsin catalytic triad what does

  • serine 195 do
  • histidine 57 do
  • aspartate 102 do
A

Provides nucleophile

Acts as base catalyst to activate Ser

Stabilises protonated His

68
Q

What is an inborn error (of amino acid catabolism)?

Give 3 examples of diseases caused by inborn errors, what causes them?

A

Genetic errors (mutations) that can affect the structure of a protein

Phenylketonuria (PKU) - caused by deficiency in phenylalanine hydroxylase which converts phenylalanine to tyrosine

Biopterin deficiency - caused by a defect in the enzyme needed to form biopterin, biopterin is a cofactor required by phenylalanine hydroxylase

Alkaptonuria - deficiency of homogentisic acid oxidase, build up of homgentisitc acid

69
Q

In photosynthesis what is P700?

What is P680?

A

Photosystem 1

Photosystem 2

70
Q

In photosynthesis what is the name of the electron acceptor that accepts electrons from photo system two?

What is the name of the electron acceptor that accepts electrons from photosystem one?

A

B-6f complex

NADP reductase

71
Q

What is the point of the Calvin cycle?

A

A series of reactions are carried out to reduce carbon dioxide to produce glyceraldehyde 3-phospahte

72
Q

When considering free energy what does:

  • deltaG less than 0
  • deltaG equal to 0
  • deltaG greater than 0

Signify?

A

The reaction is spontaneous, it’s and exergonic reaction and energy is released

The reaction is in equilibrium, there is no net exchange of energy

The reaction cannot occur spontaneously, the reaction is endergonic and energy is required for to to proceed

73
Q

What is the name of the enzyme that catalyses the oxidative deamination of glutamate?

A

Glutamate dehydrogenase

74
Q

What do beta-lactamase antibiotics do?

A

Inhibit peptidases (which form cross links between peptidoglycan in bacterial cell wall) so prevent the proper formation of the outer cell wall

75
Q

What amino acid is usually found at acid base catalysis sites? Why?

A

Histidine because it’s pKa value is close to physiological pH

76
Q

In protein turnover what processes affect the input into the amino acid pool?

What processes affect the output of the amino acid pool?

A

Degradation of proteins, dietary proteins, synthesis of non-essential amino acids

Protein synthesis, AA degradation, production of nitrogen containing compounds

77
Q

In the urea cycle the two nitrogens are provided by what substrates?

A

Carbamoyl phosphate and aspartate

78
Q

Roughly outline the steps of the urea cycle.

A
  1. Carbamoyl phosphate synthesised
  2. Citrulline formed from carbamoyl phosphate and ornithine
  3. Arginosuccinate formed - an amino group is incorporated in this step
  4. Arginosuccinate cleaved to form arginine and fumarate, arginine is the immediate precursor for urea
  5. Urea formed
79
Q

Briefly outline the citric acid cycle.

A
  1. Oxaloacetate combines with acetly CoA to form citric acid.
  2. Citric acid is converted to isocitrate (catalysed by aconitase)
  3. Isocitrate is converted to alpha-ketoglutarate (NADH and CO2 are produced at this stage)
  4. Alpha-ketoglutarate is converted to succinyl-CoA (CO2 lost and NADH produced)
  5. Succinyl-CoA is converted to succinate (by succinyl-CoA synthetase, GTP also produced)
  6. Succinate is converted to fumarate (FADH2 is produced)
  7. Fumarate is converted to L-malate
  8. L-malate is converted to oxaloacetate (NADH is produced)
80
Q

In the Krebs cycle how much NADH is produced per pyruvate molecule? How much ATP

How many NADH are produced per glucose molecule? How much ATP

A

3 NADH 1 FADH2 and 1ATP

6 NADH and 2 FADH2 and 2 ATP

81
Q

What is the purpose of the urea cycle?

Where in the cell does the urea cycle take place?

A

To detoxify ammonia and form urea. Urea contains two N’s that can be released via the kidney into the urine

Mitochondria and cytosol

82
Q

What is the amino acid involved in the formation of disulfide bonds?

A

Cysteine

Biology - Year 1 (6 decks)

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