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principles week 3 > biochemistry > Flashcards

biochemistry Flashcards

1
Q

What is a nucleoside?

A
  • a base

- a sugar

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2
Q

What is a nucleotide?

A
  • a nucleoside

- a phosphate group

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3
Q

What are the purines?

A
  • guanine

- adenine

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4
Q

What are the pyrimidines?

A
  • cytosine
  • thymine
  • uracil
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5
Q

Where are phosphodiester bonds formed?

A

Between a free 3’ OH group and a 5’ triphosphate group

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6
Q

Where a new nucleotides are added?

A

To the free 3’ end

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7
Q

What unwinds DNA?

A

Helicase

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8
Q

What removes wrong nucleotides during replication?

A

3’ to 5’ exonuclease

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9
Q

What type of RNA polymerase synthesises all mRNA?

A

Pol 2

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10
Q

What are the 5 stages of transcription?

A
  • RNA polymerase binding
  • DNA chain separation
  • transcription initiation
  • elongation
  • termination
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11
Q

What binds promotors?

A

RNA polymerases

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12
Q

Describe steroid receptors

A
  • family of transcription factors
  • dna binding and ligand binding domains highly conserved
  • bind at SREs, steroid response elements
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13
Q

Where would you find a poly A tail or 5’ cap?

A

At the end of mRNAs

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14
Q

What binds amino acids to their corresponding tRNA molecules?

A

amino-acyl tRNA synthetases

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15
Q

What are the three binding sites of ribosomes?

A
  • E (exit site)
  • P (peptidyl site)
  • A (acceptor site)
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16
Q

Name the types of gene mutation

A
  • point mutation
  • missense mutation
  • nonsense mutation
  • silent mutation
  • frameshift mutation
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17
Q

Name the types of chromosomal mutations

A
  • deletions
  • duplications
  • inversions
  • translocations
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18
Q

What is targeting (a finished protein)?

A

Moving protein to its final cellular destination

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19
Q

Free ribosomes in the cytosol make proteins for where?

A
  • cytosol
  • nucleus
  • mitochondria
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20
Q

Bound ribosomes in the endoplasmic reticulum make proteins for where?

A
  • plasma membrane
  • secretion
  • Golgi apparatus
  • er
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21
Q

Describe enzymes

A
  • efficient
  • potent
  • specific
  • does not affect equilibrium
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22
Q

Describe glycogen storage disease

A

Enzyme deficiency that results in failure of glycogen to enter transition ‘phosphorylated’ state

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23
Q

Describe co-factors

A
  • metal ions
  • inorganic
  • involved in redox reactions
  • stabilise transition states
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24
Q

Describe co-enzymes

A
  • organic molecules
  • associated with the enzyme only transiently
  • can change charge or structure during the course of the reaction but are regenerated
  • many are derived from vitamins
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25
Q

What are prosthetic groups?

A

Tightly bound coenzymes

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26
Q

What is an apoenzyme?

A

An enzyme without a cofactor

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27
Q

What is a haloenzyme?

A

An enzyme with a cofactor

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28
Q

Describe isozymes

A

Isoforms of enzymes, they catalyse the same reaction but have different properties, structure and sequence

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29
Q

Describe creatine kinase (CK)

A
  • a dimeric protein

- binds to the muscle sarcomere

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30
Q

The presence of creatine kinase can indicate what?

A
  • the appearance of the brain form in the blood suggests a stroke
  • the appearance of the heart type suggests a heart attack
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31
Q

What molecule carries out phosphorylation reactions?

A

Protein kinases

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32
Q

Describe zymogens

A

Inactive precursors of an enzyme, irreversibly transformed into active enzymes by cleavage of a covalent bond eg. digestive enzymes, blood clotting enzymes

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33
Q

What is Vmax?

A

The maximum velocity of a reaction, no active sites are left

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34
Q

What is Km?

A

The concentration in moles of S which gives 1/2 Vmax

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35
Q

What does the michaelis-menden equation describe?

A

Describes the rate of catalysis as a function of substrate concentration. Describes a hyperbola

36
Q

What are the units of Km?

A
  • molar
  • moles/l
  • moles/dm3
37
Q

What does low and high Km mean?

A

Low- efficient enzyme

High- rate is slower, less efficient enzyme

38
Q

What does the y-intercept indicate?

A

Vmax

39
Q

What does the x-intercept indicate?

A

Km

40
Q

Define electronegativity

A

The attractive force that an atomic nucleus exerts on electrons within a bond

41
Q

What is acylation?

A

The addition of an acyl group

42
Q

What is carboxylation?

A

addition of a carboxyl group

43
Q

What is condensation and hydrolysis?

A

Condensation- water is removed

Hydrolysis- water is added

44
Q

What is the most oxidised and most reduced forms of carbon?

A

Most reduced is CH2 (alkane group) and the most oxidised is CO2 (carbon dioxide)

45
Q

Name functions of biomolecules

A
  • information storage
  • structural
  • energy generation
  • energy currency/ storage
  • recognition / communication / specificity
46
Q

What are the three types of carbohydrates?

A
  • monosaccharides
  • polysaccharides
  • disaccharides
47
Q

What is the first law of thermodynamics?

A

Energy is neither created or destroyed

48
Q

What is the second law of thermodynamics?

A

When energy is converted from one form to another, some of that energy becomes unavailable to do work (not 100% efficient)

49
Q

What is the free energy equation (ΔG)?

A

ΔG= ΔH- TΔS

50
Q

What is an exergonic reaction?

A

A reaction in which the total free energy of the products is less than the total free energy of the reactants ΔG is negative. It can occur spontaneously

51
Q

What is an endergonic reaction?

A

A reaction in which the total free energy of the products is more than the total free energy of the reactants. ΔG is positive. Reactions don’t occur spontaneously, they need an input of energy to proceed

52
Q

Describe standard conditions

A
  • T= 298k
  • 1 atmosphere pressure
  • 1M (mol/l) concentration of reactants
  • pH= 7
53
Q

Define metabolism

A

All the reactions taking place in the body divided into anabolism and catabolism

54
Q

Define catabolism

A

Breaking down complex molecules into smaller molecules and releasing energy

55
Q

Define anabolism

A

Synthesising complex molecules out of smaller molecules through energy-consuming reactions

56
Q

Describe glycolysis (catabolic reaction)

A

Initial breakdown of glucose for the generation of ATP. Net gain of 2 ATP molecules per glucose molecule

57
Q

Describe gluconeogenesis (anabolic reaction)

A

Making new glucose from non-carbohydrate precursors eg. pyruvate. Costs energy

58
Q

Describe the shape of water

A

It is a bent molecule, it is polar and forms a dipole

59
Q

Describe amphipathic molecules

A

They have regions (domains) which are either hydrophilic or hydrophobic. They form micelles in water. Example, phospholipids on the cell membrane

60
Q

What do all amino acids contain?

A
  • an amine group (NH2)
  • a carboxyl group (COOH)
  • a hydrogen
  • a side chain

All bonded to an alpha carbon atom

61
Q

What are D and L forms of amino acids?

A

Non superimposable mirror images. Stereoisomers

62
Q

Describe non-polar amino acids

A
  • no charge difference between amino and carboxyl ends of the molecule
  • don’t dissolve in water
  • will interact with lipid or non-polar molecules
  • common in membrane spanning parts of proteins
63
Q

Describe polar, uncharged amino acids

A
  • no charge difference between amine and carboxyl groups
  • hydrogen bonding interaction with water
  • dissolves in water
  • variable solubility
  • amphiphilic nature
64
Q

Describe peptide bonds

A

Have a partial double bond character, planar, strong and rigid, important for folding of proteins

65
Q

What molecules are proton donors and proton acceptors?

A

Acids are proton donors

Bases are proton acceptors

66
Q

What does pH measure?

A

The amount of protons in a solution

67
Q

Describe the pH formula

A

pH= -log10 [h+]

68
Q

What are zwitterons?

A

Amino acids without charged side groups (in neutral solution) They have two pKa values

69
Q

What is the isoelectric point?

A

The pH at which a molecule has no net charge

70
Q

What is the primary structure of a protein?

A

The sequence of amino acid residues

71
Q

What is the secondary structure of a protein?

A

The localised conformation of the polypeptide backbone

72
Q

What is the tertiary structure of a protein?

A

The 3d structure of the entire polypeptide, including all side chains, consists of local regions with distinct secondary structures

73
Q

What is the quaternary structure of a protein?

A

The spatial arrangement of polypeptide chains in a protein with multiple subunits

74
Q

Describe alpha helices

A
  • rod like

- one polypeptide chain

75
Q

Describe beta sheets

A
  • hydrogen bonds between neighbouring peptides
  • two directions (parallel, antiparallel)
  • turns between strands
  • zig zag structure
76
Q

Describe the collagen triple helix

A
  • component of bone and connective tissue
  • very strong
  • water insoluble fibres
  • covalent inter and intra molecular bonds
77
Q

Describe fibrous proteins

A
  • contain polypeptide chains organised parallel along a single axis
  • long fibres or sheets
  • insoluble in water
  • eg. keratin in hair
78
Q

Describe globular proteins

A
  • folded into a spherical shape
  • soluble in water
  • eg. myoglobin, haemoglobin
79
Q

What forces stabilise tertiary structure?

A
  • covalent disulphide bonds
  • electro static interactions
  • hydrophobic interactions
  • hydrogen bonds
  • complex formation with metal ions
80
Q

Describe haemoglobin

A
  • four subunits
  • two alpha and 2 beta chains
  • each contains a haem group
  • allosteric (binding of one oxygen changes affinity for other subunits)
81
Q

Describe competitive inhibition

A
  • Orthosteric inhibition (at same site)

- inhibitor binds to the active (catalytic) site and blocks substrate access

82
Q

Describe non-competitive inhibition

A
  • allosteric inhibition

- Inhibition binds to a site other than the catalytic centre, inhibits enzyme by changing conformation

83
Q

Describe the effects of competitive inhibition on vmax and km

A

Enzymes reach the Km later, Vmax is not affected

84
Q

Describe the effects of non-competitive inhibition on vmax and km

A

Km doesn’t change but Vmax varies. A non-productive complex is formed

85
Q

Describe feedback inhibition

A

Inhibition of rate limiting enzymes by end product (allosteric control)

86
Q

What graph shape is created when the substrate concentration of allosteric enzymes is increased?

A

A sigmoidal curve

principles week 3 (2 decks)

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