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FOM1 > Biochemistry > Flashcards

Biochemistry Flashcards

1
Q

what are Monosaccharides?

A

carbohydrates with a single ring structure

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2
Q

what are disaccharides?

A

carbohydrates with a double ring structure

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3
Q

what are polysaccharides?

A
  • long chains of monosaccharides, storage carbohydrates
  • branching of glycogen enables fast metabolism of glucose
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4
Q

what is the 1st law of thermodynamics?

A

energy is neither created nor destroyed

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5
Q

what is the 2nd law of thermodynamics?

A

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

  • NO ENERGY TRANSFORMATION IS 100% EFFICIENT
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6
Q

In thermodynamic reactions, reactions involve change in……+ what does this mean?

A

enthalpy - heat content
entropy - disorder/randomness

  • means free energy will tend towards an unusable state after multiple reactions
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7
Q

how do you calculate change in free energy?

A

= (energy of products)-(energy of reactants)

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8
Q

what is free energy related?

A
  • free energy is related to the point of equilibrium
  • Delta G near 0 means reaction os readily reversible
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9
Q

what is a exergonic reaction?

A
  • total free energy of products is less than the total free energy of reactants
  • reaction can occur spontaneously
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10
Q

what is a endergonic reaction?

A
  • total free energy of products is more than total free energy of reactants
  • reaction requires input of energy
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11
Q

what does coupling of reactions involve?

A
  • many reactions within the body occur by coupling an unfavourable reaction (positive delta G) with a favourable reaction - e.g ATP + H20 = ADP + Pi + H+
  • therefore ATP is widely used as energy for many cellular processes
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12
Q

what is metabolism?

A

all reactions taking place in the body

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13
Q

what is catabolism?

A

breaking down complex (bigger) molecules into smaller ones and releasing energy

  • exergonic
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14
Q

what is anabolism?

A

synthesising complex molecules out of smaller ones in energy-consuming reactions

  • requires energy
  • endergonic
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15
Q

what is the definition of polar?

A

electrons shared unequally causing a difference in change from one side to the molecule to the other

  • enables water to act as a universal solvent
  • molecules form a dipole, tetrahedral shape
  • molecules are held together by hydrogen bonds
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16
Q

what is the hydrophobic effect?

A

the observed tendency of non polar substances to aggregate in aqueous solution and exclude water molecules - micelles, lipid bilayer

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17
Q

what are amphipathic molecules?

A

amphipathic molecules are molecules with a polar (hydrophilic) ‘head’ and a non polar (hydrophobic) ‘tail’

  • form micelles and the lipid bilayer of membranes
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18
Q

what are the 4 classifications of amino acids?

A
  • non polar (hydrophobic)
  • polar (hydrophobic)
  • Acidic
  • Basic
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19
Q

how are peptide bonds produced?

A

condensation reaction

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20
Q

what is the central dogma of molecular biology?

A

DNA - RNA - PROTEIN

  • DNA is transcribed into RNA, then RNA is translated into a protein
  • essentially, the DNA nucleotide seqence determines amino acid sequences of polypeptide chains
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21
Q

describe the structure of DNA and its constitutes?

A
  • anti parallel double helix
  • one strand 5’ to 3’ and other strand 3’ to 5’ (5’ end contains a phosphate group, 3’ end contains a deoxyribose sugar)
  • supported by sugar phosphate backbone (of alternating deoxyribose and phosphate groups)
  • Base pairs A-T, C-G held together by hydrogen bonds
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22
Q

explain DNA replication

A
  1. DNA primer required
  2. Helix unwound by helicase
  3. Replication fork with leading and lagging strand
  4. leading strand synthesised in 5’-3’ direction, catalysed by DNA polymerase
  5. lagging strand synthesises in OKAZAKI FRAGMENTS, which are then joined by DNA ligase
  • in eukaryotes, replication starts at simultaneously at several points in the genome
  • speeds up replication
  • bidirectional
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23
Q

what are Okazaki fragments?

A

short sequences of DNA nucleotides that are synthesised discontinuously and later linked by DNA ligase

24
Q

explain the types of tRNA

A

rRNA: combines with proteins to from ribosomes

tRNA: carries amino acid to be incorporated into protein

mRNA: carries genetic information for protein synthesis

25
Q

what is RNA polymerase?

A

multi-subunit complexes which make RNA

  • eukaryotes have 3 types: Pol l, Pol ll, Pol lll
  • Pol 11 synthesises all mRNA
26
Q

explain the steps of transcription

A
  1. TATA box at (-25) - TATA box binding protein introduces a kink in the DNA to determine the start and direction of transcription and provides landing platforms for further transcription factors and RNA pol
  2. TFIID - first general transcription factor to bind to the promotor, bings to TATA box through TBP (general transcription factor required for all POL II transcribed genes)
  3. RNA poly II bings to specific promotor (0)
  4. Transcription belongs at nucleotide +1
  5. DNA chain separation - unwinding of DNA, catalysed by helicase
  6. INITIATION - selection of first nucleotide of growing RNA (requires additional general transcription factors)
  7. ELONGATION - addition of further nucleotides to RNA chain in the 5’ -> 3’ direction
  8. TERMINATION - release of finished mRNA
27
Q

how is premature mRNA converted to mature mRNA?

A

-splicing
- splice out introns
- add poly-adenosine tail
- add 5’ cap

28
Q

explain the steps of translation

A
  1. INITIATION - formation of initiation complex, energy provided by GTP
  2. ELONGATION - anticodons of tRNA form base pairs with codons on mRNA, aminoacyl-tRNA synthetases catalyse the covalent attachment of amino acids to their corresponding tRNA molecules
  3. Peptide bond formation and translocation - peptidyl transferase catalyses peptide bond formation between amino acids in P and A sites, EF-2 moves ribosome along mRNA
  4. TERMINATION - A site encounters a stop codon, termination protein binds to the codon and the ribosome dissociates, leads to a change in peptidyl transferase activity which results in the release of the protein from the last tRNA to which it was attached
29
Q

what are the post-translational modifications?

A
  • glycosylation
  • Disulphide bonds (ER)
  • Folding/assembly of multi-subunit proteins (ER)
  • Specific proteolytic cleavage (ER, Golgi, secretory vesicles)
30
Q

describe the action of ribosomes

A

bind to 3 tRNA binding sites:
- P (peptidyl site)
- A (acceptor site)
- E (exit site)

  • free ribosomes in cytosol produced proteins in the cytosol, nucleus and mitochondria
    — post-translational - produces in cytosol then translocated (after translation)
  • Bound ribosomes on rough ER produce proteins for plasma membrane, ER, Golgi , secretion
31
Q

what are point mutations?

A

change in single name of DNA

32
Q

what are missense mutations?

A

results in a change of amino acid sequence

33
Q

what is a nonsense mutation?

A

creates new termination codon

34
Q

what is a silent mutation?

A

no change of amino acid sequence

35
Q

what is a frame shift mutation?

A

addition or deletion of 1 or 2 based which changes the reading frame of translation

36
Q

what are the features of genetic code?

A
  • degenerate
  • unambiguous
  • near universal
37
Q

what are the roles of enzymes (biological catalysts) in chemical reactions?

A
  • enzymes (biological catalysts) catalyse the many chemical reactions which together make p the process of metabolism
  • an enzyme speeds up the rate at which a reaction reaches equilibrium, without being used up itself
  • enzymes DO NOT affect the equilibrium position of a reaction
38
Q

What are enzymes?

A
  • biological catalysts
  • mostly proteins (exception -> : some types of RNA - ribozymes
  • work at body temperature
  • SPECIFIC - each enzyme has a limited range of substrates
  • POTENT - can enzyme molecule can convert many substrate molecules into product per second
39
Q

describe the term free energy change

A

the amount of energy released in the conversion of reactants to products under standard conditions

40
Q

describe the term of transition state

A

the transition state is the reaction intermediate species which has the greatest free energy

41
Q

describe the term activation energy + what enzymes do to the activation energy

A

the minimal amount of energy required to the reactants for a chemical reaction to occur

  • enzymes reduce the activation energy by providing alternative reaction pathways
42
Q

Describe the importance of co-factors and co-enzymes. (+ examples of them)

A

catalyse activity of many enzymes depends on presence of small molecules, called COFACTORS OR COENZYMES

2 types:
- metal ions (inorganic, COFACTORS) (ex zinc, iron, copper)

  • organic molecules (organic origin, COENZYMES) (ex derived from vitamins)

(BOTH INVOLVED IN REDOX REACTIONS)

43
Q

Describe the function of cofactors.

A

Metal cofactors form a metal co-ordination centre in the enzyme

  • enzyme referred to as ‘metalloprotein’
44
Q

what is an enzyme with a cofactor called?

A

holoenzyme

45
Q

what is an enzyme without a cofactor called?

A

Apoenzyme

46
Q

Describe the function of coenzymes

A

coenzymes mostly associate with the enzyme only transiently (for a short time)

  • coenzymes change charge or structure during the reaction, but are regenerated
47
Q

what are tightly bound coenzymes called?

A

prosthetic group
- e.g haem in haemoglobin

48
Q

Explain the concept of the substrate binding to the active site of the enzyme

A

substrate binds to the active site of the enzyme
- active site contains amino acids for catalytic activity

fits like a lock and key:
- active site of unbound enzyme is complementary to the shape of the substrate

49
Q

what is the induced fit model?

A
  • binding of a substrate induces a conformational change in the enzyme
  • results in a complementary fit
50
Q

How are enzymes effected by temperature and pH?

A
  • each enzyme will have an optimum temperature and pH
  • Increasing/decreasing the temperature and pH away from the optimum will alter the active site of the enzyme
  • denaturing the enzyme
51
Q

examples of active sites

A

3 pancreatic serine proteases (contain reactive serine reside)
- catalyse hydrolysis of peptide at specific sites

CHYMOTRYPSIN
- hydrophobic pocket binds aromatic amino acids

TRYPSIN
- negatively charged Asp interacts with positively charged Lys or Asp

ELASTASE
- active site partially blocked, only amino acids with small or no side chains can bind

51
Q

what are Isozymes?

A

Isozymes are isoforms of enzymes

They catalyse the same reaction but have different properties and structure

52
Q

what can isozymes be?

A
  • synthesised during different stages of foetal and embryonic development
  • present in different tissues
  • present in different cellular locations
52
Q

what are clinical uses of Isozymes?

A
  • relative amounts of isoenzymes in tissue & blood are useful for diagnostic purposes
52
Q

what is an example of tissue specific isozyme (isoforms of enzymes)?

A

Lactate Dehydrogenase

2 subunits:
- H (Heart) > promotes aerobic metabolism
- M (Muscle) > promotes anaerobic metabolism

FOM1 (14 decks)

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