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1. Principles > Biochemistry > Flashcards

Biochemistry Flashcards

1
Q

Name the bonds : strongest - weakest

A 
Covalent
Ionic
hydrogen
Hydrophobic interaction 
Van der Waals
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2
Q

Explain OILRIG?

A 
OIL = reducing agent (it loses its friend)
RIG = oxidising agent (it gains a friend)
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3
Q

Name the 4 major classes of biomolecules?

A

Peptides and proteins
Carbohydrates
Lipids
Nucleic Acids

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4
Q

Give an example of a peptide and protein?

A

amino acid

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5
Q

Give an example of a carbohydrate?

A

mono-
di-
poly-saccharide

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6
Q

Give an example of a lipid?

A

triglycerides
phospholipids
steroids

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7
Q

Give an example of a nucleic acid?

A

DNA

RNA

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8
Q

Descirbe the steps in the oxidation of carbon

A 
Alkane (fats) > 
Alcohol (in carbs) > 
aldehyde > 
carboxylic acid > 
Carbon dioxide (final product of catabolism)
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9
Q

What is an exergonic reaction?

A 
free energy change = negative
drives diseases (i.e. muscular distrophy)
spontaneous
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10
Q

What is an endergonic reaction?

A

free energy change = positive
needs energy input to proceed
not spontaneous

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11
Q

Name a type of mono, di and polysaccharide

A

Monosaccharides – glucose (can exist as multiple structures)
Disaccharides – Lactose
Polysaccharides – cellulose (poly glucose chain), glycogen (Alpha 1,4 occasionally branches into alpha 1,6)

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12
Q

What is the 1st law of thermodynamics?

A

energy is neither created nor destroyed

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13
Q

What is the 2nd law of thermodynamics?

A

energy is only converted from one form to another, some of that energy becomes unavailable to do work

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14
Q

What is the change in free energy (delta G) reaction?

A

DeltaG = (energy of products) – (energy of reactants)

kJ/mol

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15
Q

What does kinase do to proteins?

A

phosphorylates them

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16
Q

What does phosphatase do to proteins?

A

dephosphorylates them

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17
Q

What are amphipatic molecules?

A

both hydrophilic and hydrophobic - forms micelles in water

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18
Q

Explain the 4 structures of proteins?

A

Primary – sequence of amino acids
Secondary – formation of backbone (polypeptide)
Tertiary – 3d structure
Quaternary – Spatial arrangement of multiple subunits (disulphide bonds hold proteins together)
Collagen triple helix (abundant in connective tissue)

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19
Q

Describe the basic structure of every amino acid

A

Carbon bonded to:

  • an amino group (NH)
  • a carboxyl group (COOH)
  • a hydrogen (H)
  • a side chain (R)
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20
Q

Where do peptide chains run from and to?

A

N terminus to C terminus

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21
Q

What is a molecules iso electric point?

A

The pH at which they have no net charge

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22
Q

What is pH?

A

Measurement of the amount of protons in a solution

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23
Q

What occurs at the smooth ER?

A

synthesis of steroid hormones

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24
Q

What occurs at the rough ER?

A

synthesis of polypeptides

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25
Q

What is the mitochondria?

A

powerhouse of cell can multiply independently

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26
Q

What is the role of the Golgi apparatus?

A

receives materials from ER and distributes, can also modify proteins.

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27
Q

What occurs at the ribosomes?

A

where RNA is translated into protein

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28
Q

What is a prokaryote?

A

microscopic single cell organism that does not have a defined nucleus

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29
Q

What is a eukaryote?

A

just a normal cell with nucleus

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30
Q

What is a nucleoside?

A

base + sugar

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31
Q

What is a nucleotide?

A

nuceloside + phosphate

32
Q

What are purines?

A

Adenine and Guanine

33
Q

What are pyrimidines?

A

Uracil, Thymine and Cytosine

34
Q

Where do phosphodiester bonds form?

A

between 3’ OH group and 5’ triphosphate

35
Q

Describe the key points of DNA replication?

A

Always in a 5’-3’ direction
Catalysed by DNA polymerases
RNA primer is required for DNA replication
Leading strand – always has free 3’ end
Lagging strand is replicated in short fragments called Okazaki fragments
Helicase unwinds DNA

36
Q

What are the 3 main classes of RNA?

A

rRNA (ribosomal) - combines with proteins to form ribosomes where protein synthesis takes place
tRNA (transfer) -carries amino acids to be incorporated into protein. Anticodons consist of 3 nucleotides.
mRNA (messenger) – carries genetic information for protein synthesis

37
Q

What are the 3 types of eukaryotic cells?

A

Pol I, II, III

38
Q

What does Pol II synthesise?

A

all mRNA

39
Q

What is contained in collagen?

A

tropocollagen: made up of any amino acid, proline or hydroxyproline and Gylcerol
found in bones and influences the strength of the connective tissue

40
Q

What is the genome?

A

total DNA in each cell

41
Q

Describe transcription?

A

RNA polymerase binding
o Detects initiation sites on DNA (promoters)
o Requires transcription factors
DNA chain separation
o Unwinding of DNA
Transcription initiation
o Selection of first nucleotide of growing RNA
o Required additional general transcription factors
Elongation
o Addition of further nucleotides to RNA chain
o RNA synthesised in 5’ – 3’ direction
Termination
o Release of finished RNA

42
Q

What is TFIID?

A

general transcription factor required for all Pol II transcribed genes

43
Q

What are exons?

A

coding regions

44
Q

What are introns?

A

non coding regions - removed by splicing

45
Q

Describe translation?

A

Anticodons of tRNA form base pairs with codons of mRNA
Initiation
o GTP provides energy
o Ribosomal subunit binds to 5’ end of mRNA, moves along until start codon found
o Initiator tRNA pairs to start codon (AUG)
o Large subunit joins assembly and initiator tRNA is located in P site
Elongation
o Elongation factor brings aminoacyl-tRNA to A site
o Second elongation factor regenerates the first to pick up next aminoacyl-tRNA
Peptidyl transferase catalyses peptide bond formation between amino acids in P and A sites
Termination
o Occurs when A site of ribosome encounters a stop codon (UAA, UAG, UGA)
Finished proteins cleaves off tRNA

46
Q

What are the three tRNA binding sites?

A

Exit
Peptidyl
Aminoacyl

47
Q

What are post translational ribosomes?

A

Free ribosomes in cytosol proteins for - cytosol, nucleus, mitochondria

48
Q

What are co translational ribsomes?

A

Bound ribosomes on rough ER - plasma membrane, ER, Golgi, secretion

49
Q

Describe the terms degenerate and unambiguous in terms of the genetic code?

A

Degenerate – many amino acids have more than one codon

Unambiguous – each codon codes only for one amino acids

50
Q

What are enzymes without a cofactor called?

A

apoenzymes

51
Q

What are enzymes with a cofactor called?

A

holoenzymes

52
Q

Name some post translational modifications

A

glycosylation - addition and processing of carbohydrates in the ER and Golgi
proteolic cleavage in the ER, Golgi and secretory vesicles
folding and assembly of multisubunit proteins in the ER
formation of disulfide bonds in the ER

53
Q

What are prosthetic groups?

A

tightly bound enzymes

54
Q

What is a zymogen?

A

inactive precursors of an enzyme

55
Q

What is explained in the Michaelis Menten model?

A

the relationship between Vmax and Km

56
Q

What is Vmax?

A

Maximum velocity of a reaction

57
Q

What is Km?

A

concentration (in moles) of substrate which gives 50% Vmax

58
Q

On a Lineweaver-Burk plot, what is Vmax?

A

the intersection of the straight line with the Y axis

59
Q

On a Lineweaver-Burk plot, what is Km?

A

the line’s intersection with the X axis

60
Q

What is indicated by a low Km?

A

enzyme only needs a small amount of substate to work at 50% Vmax

61
Q

What occurs in reversible competitive enzyme activity?

A
  • Vmax does not change
  • Km varies
  • enzyme binds to the active site
62
Q

What occurs in reversible non competitive enzyme activity?

A
  • Vmax varies
  • Km no change
  • enzyme binds to an allosteric site
63
Q

Do catalysed or non catalysed enzymes have a lower activation energy?

A

catalysed

64
Q

What occurs in irreversible non competitive enzyme activity?

A

-innhibation cannot be reversed

65
Q

What relationship allosteric enzymes have?

A

sigmoidal curve relationship - not a hyperbole (michaelis menten)

66
Q

What is the function of the lipid - cholesterol?

A 
Present in cell membranes 
Component of myelin sheath 
Precursor molecule for 
	Steroid hormones 
	Vitamin D 
	Bile acids
67
Q

What is the function of the lipid - triglyceride?

A

Present in all cell membranes – lipid bilayer

Highly concentrated energy stores

68
Q

Describe anabolism?

A

requires energy – endergonic and reductive

69
Q

Describe catabolism?

A

breakdown of molecules to yield energy – exergonic and oxidative

70
Q

What is the initial pathway for the conversion of glucose to pyruvate?

A

Glycolysis - glucose is oxidised to CO2 and H2O

Per glucose there is a net gain of 2 ATP

71
Q

What is the final balance after each step of the glucose cycle?

A
  • Glycolysis – 2 ATP
  • TCA cycle (2 GTP) – 2 ATP
  • Glycolysis, PDH, TCA cycle (10 NADH + H+) – 25 ATP
  • TCA cycle (2 FADH2) – 3 ATP
  • 1 glucose molecule yields 30-32 ATP molecules
72
Q

What is oxidative phosphorylation?

A

Electrons from NADH and FADH2 used to reduce O2 to H2O
Their energy used to pump protons from mitochondrial matrix to intermembrane space
Protons flow back across membrane
Energy of proton flow used to phosphorylate ADP to ATP

73
Q

What are the aerobic and anaerobic fates of pyruvate?

A

Anaerobic – alcoholic fermentation, lactic acid formation in humans
Aerobic – further oxidised in the Citric Acid Cycle

74
Q

What are the fates of glucose?

A

Storage
Oxidation through: aerobic gylcolysis or pentose phosphate pathway
Fermentation through anaerobic glycolysis

75
Q

What is the role of GLUT1 receptor?

A

allows glucose to enter a cell

1. Principles (9 decks)

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