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Nutrition > Biochemistry > Flashcards

Biochemistry Flashcards

1
Q

What is mRNA? tRNA? rRNA?

A

Carries genetic information from DNA - read in codons

tRNA - molecules that take amino acids and anticodons to the ribosomes, this anticodon complements to the codon.

rRNA - form ribosomes.

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2
Q

Crick’s Adapter Hypothesis

A

Adapter is tRNA, two sides. One side is for amino acid specific. A separate part recognises the nucleotide sequence.

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3
Q

Degenerate

A

More than one codon codes for an amino acid

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4
Q

1 start codon

3 stop codon

A

AUG - methionine (START)

UAA, UAG, UGA (STOP)

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5
Q

Translation

3 RNA

A

Process by which mRNA forms a polypeptide chain in the correct order

  • mRNA
  • tRNA
  • rRNA
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6
Q

Open reading frames

A

No termination codon for 50 codons

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7
Q

Mutations- deletions or insertions, point mutations

A

Deletions or insertions - dangerous, change reading frame

Point mutations - not dangerous, single base substitution

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8
Q

Aminoacyl tRNA synthesases

A

Recognise a amino acid, and help bind the anticodon to the codon.

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9
Q

What is tRNAfmet

A

Recognises the AUG codon (bacteria)

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10
Q

Shine - Dalgarno sequence

A

sequence that guides mRNA to the correct position to start initiation

Only in prokaryotes

8 base pairs upstream of AUG

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11
Q

P site

A site

E site

A

A-site : where initial binding of AUG and MRNA occurs

P-site : mRNA binds to AUG

E-site : exit path for tRNA molecule

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12
Q

Translocation

A

Ribosome moves single codon downstream

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13
Q

Post-translational modification

A
  1. Removal of signal sequence
  2. Folding
  3. Modification of amino acids
  4. Addition of groups
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14
Q

Recombinant DNA

A

Artificial recombinant molecule created from 2 or more sources

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15
Q

Reporter proteins

A

Organism that expresses a gene, it can be identified due to the fluorescence.
GFP -

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16
Q

GFP

A

barrel structure, B sheet, a helix

Shows green light, when exposed blue light

Hydrogen bonding

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17
Q

Viruses

A

Replicate in host cells,

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18
Q

cDNA

A

Made from mRNA template, plasmid put into host cell, amplified.

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19
Q

Vectors

A

Are DNA molecules used as a vehicle to transfer foreign genetic material

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20
Q

cloning vectors - ORI

Selectable markers

A

Plasmid is replicated into the cell

Selectable markers - allows u to tell if the plasmid is present in the host cell (reporter gene gfp)

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21
Q

Cloning vectors - multiple cloning site

A

Is used to insert gene of ur interest (has cut sites)

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22
Q

Procedure for cloning

A
  1. Find vector
  2. Cut DNA (restriction endonuclease)
  3. Joining DNA (ligase)
  4. Amplify PCR
  5. Identify host cells with recombinant DNA
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23
Q

What is PCR?

A

PCR is the process of amplifying DNA of interest multiple times .

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24
Q

What is required for PCR?

A 
Taq polymerase 
Primers 
Nucleotides
DNA template
Buffer at ph = 7
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25
Q

What is taq polymerase?

A

Can survive 95C and is used to separate the DNA double strands and catalyse more DNA at 72C

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26
Q

How is PCR used in medicine?

A

It identifies infectious diseases and diagnoses genetic disorders and cancers

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27
Q

What are the biological role of proteins?

A 
Catalytic roles - speed up chemical reactions
Structural support - strength
Ligand binding roles - 
Storage facility - ferritin for iron
Transport role - Hb movement 
Defensive functions - act as antibodies
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28
Q

The central dogma

A

DNA —————–> mRNA —————-> protein

Transcription. Translation

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29
Q

Configuration? Chirality? Enantiomers?

A

Spatial arrangement of groups around a carbon atom

x/y/z/a all 4 groups differ therefore they are chiral or asymmetric.

Enantiomers - 2 diff arrangement of groups around the C atom, mirror images, cannot be superimposed

Glycine is the only molecule that is not chiral, due to H atoms.

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30
Q

What does this mean; “biological systems are stereo-specific”

A

They can tell the difference between left and right hands. So shape (topology) is also important

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31
Q

If pH

A

PRONATED FORM

COOH
NH3+

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32
Q

If ph > pKa

A

DEPRONATED FORM

COO-
NH2

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33
Q

Zwitterion

A

At ph =7; acts as a base and acid (amphiprotic)

COO- and NH3+

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34
Q

Titrations show the pI, what is the pI?

A

Is the pH at which the molecule has a zero net charge,

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35
Q

Difference between pKa and pH?

A

pKa values are fixed, a constant that cannot change

Ph can be changed by adding an acid or base

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36
Q

Describe polar molecules

A

Hydrophilic molecules
Interact with water in an energetically favourable way
Reduce delta G and increase entropy

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37
Q

Describe non polar molecules

A

Hydrophobic
Interact with water in an energetically unfavourable way
Increase G and decrease S
Burry themselves in the core of enzymes

38
Q

Give examples for non polar, aromatic, polar uncharged, basic and acidic.

A

non polar, glycine gly
aromatic, phenylalanine Phe
polar uncharged, Serine Ser
basic Lysine Lys
acidic. Aspartate. Asp

39
Q

Importance of histidine (BASIC)

A

Only standard amino acid with pKa of 7; therefore it can act as an acid or base

40
Q

Carboxylic acid pKa

Amino acid pKa

A

A- COOH pKa - 2. Side chain pKa - 4

A- NH2 pKa - 9. Side chain pKa- 11

41
Q

Describe protein turnover

A

Protein synthesis and protein degradation

42
Q

How to calculate MW of proteins?

A

MW of proteins = no of residues x 110

110 (weighted average mass for smaller amino acids)

43
Q

Where is rotation allowed on proteins?

A

Only on single COVALENT bonds

44
Q

What are NATIVE proteins?

A

Native proteins are thermodynamically stable; low free energy (G)

45
Q

Primary structure

A

The linear sequence of amino acids with covalent bonds (includes peptide and disulphide bonds)

46
Q

Secondary structure general

A

Include short chain interactions in the LOCALISED region of primary structure.

47
Q

Rotation

A

No rotation is possible in double bonds or bonds with partial double bond character, so peptide is rigid.

Ca - C = N - Ca

No rotation in C-N bond, but allowed in Ca - C (psi) and N - C (phi)
Both psi and phi are +180

48
Q

What reduce the range of conformations (spatial arrangement for groups around a carbon atom) for protein chains?

A

Rigid - no rotation in double bonds

planar arrangement - co planar (arranged in 2D plane)

Steric hindrance

49
Q

Secondary structure a-helix

A

🔴 simplest form of secondary structure
🔴 has a tight, compact structure with R groups pointing outwards
🔴 has rotations in all bonds expect the peptide bond (C=N)
🔴 held together by internal H - bonds formed every 4 residues

Stabilising - polar amino acids interact in favourable way

Destabilising - glycine - small molecule and forms different coils to a helices

Proline - ‘imino’ N atom has no H atom, so can’t form H -bonds

50
Q

Secondary structure - B conformation

A

Is the formation of strands and pleates in an antiparallel or parallel arrangement.

  • B strands: the polypeptide forms zig zag shape (not inherently stable)
  • B pleates: multiple B strands arranged side by side forming pleats (inherently stable)
  • B turns: turns and coils allows protein to reverse direction

Held together by H-bonds

Proline and glycine - allow for tight turns and kinked peptide formation

51
Q

Tertiary structure

A

Multiple secondary structures coming together to form a 3D structure
A helices, b sheets, turns, pleates.
Defines globular and fibrous proteins.
Stabilised by hydrophobic interactions (internal- less interaction with water)

52
Q

Quaternary structure

A 
Is the overall arrangement of multiple separate protein chains coming together to form a complex subunit structure. 
Monomer - 1 subunit - ribonuclease 
Dimer - ADH
Trimer - collagen 
Tetramer - haemoglobin

Held together by hydrophobic interactions

53
Q

⬆️ products ⬇️ reactants = G positive, goes backwards, energetically unfavourable Keq 1

A

Delta G = 0, when Keq = 1

54
Q

When equilbrium is established equation

A

delta G = -R . T . Log e (Keq)

55
Q

Transition state

A

Is the intermediate between ️products and substrate
S*
A high energy molecule, but unstable

56
Q

Activation energy

A

An energy barrier that must be overcome in order for a reaction to occur

57
Q

Denature or enhance!

A

ph extremes can denature or enhance rxn rate
Temperature (heat) to denature molecule or increase rxn rate
Chemical solvents to denature molecules or enhance reactions

58
Q

What are catalysts

A

Speed up chemical rxns by lowering the activation energy, are not consumed in the process and can be reused again. Do not effect delta G or Keq

59
Q

What is binding energy

A

Is the sum of free energy released from weak interactions

60
Q

Lock and key model

Induced fit model

A

Lock and key - substrate binds to the enzyme with a perfect fit at the active site

Induced fit - substrate induces a fit at the active site, involves formation of transition state

61
Q

Define Km

A

Is the maximal rate of rxn (the speed of the rxn)

62
Q

Define Vmax

A

Is the substrate concentration when V0 = 1/2vmax, describes the affinity of the enzyme to bind to its substrate.

63
Q

PH graphs

A

Are symmetrically shaped
Bell shaped curve
High or low ph can denature enzymes but breaking weak interactions and hence losing its biological function

64
Q

Temperature graphs

A

At low temps; enzyme activity is low

At extreme temperatures; weak interactions distabilise, thermal desaturation, loss of structure, function and enzyme activity

65
Q

The wobble case

A

The third base is different in codon

66
Q

Chemical denaturents

A

Acetate (organic solvents), detergents and urea denature proteins by interacting with internal hydrophobic interactions. This disrupts hydrophobic interactions that stabilise the protein and hence loss of function.

67
Q

Define specificity

A

enzyme can tell the difference between its normal substrate and another molecule

68
Q

What is an enzyme inhibitor?

A

Interfere with the catalytic action of an enzyme and finished the reaction rate

69
Q

Competitive inhibition

A

Competes with the substrate and binds at the active site, this reduces reaction rate as products aren’t formed
Vmax is unaffected
km increases

70
Q

Uncompetitive

A

Inhibitor does not compete with the substrate and binds at a place other than the active site, which changes the shape of the active site and this dimishes the activity of the enzyme.

Vmax and km reduced

71
Q

Define protein purification

A

Isolation of a single protein via the physical separation and complete removal of other proteins,

72
Q

What properties need to be exploited to seperate proteins

A

Size
Charge (pI)
Binding affinity

73
Q

Tech 1 - COLUMN CHROMATOGRAPHY (exploit all 3 properties - charge, binding affinity and size)

2 phases and separation

A

Stationary phase - solid porous material

Mobile phase which contains buffer solution is what passes through the stationary phase (eluate)

Proteins travel through the coloumn at different rates, how seperation occurs

Large proteins come out quick, small proteins come out slow

74
Q

Tech 2 - ion exchange chromatography

A

Exploits differences in magnitude of the net charge of proteins at a ph.

Anion (-) moves towards the anode (+)

Cation (+) moves towards the cathode (-)

75
Q

Tech 3 - affinity chromatography

A

Seperation depends on binding affinity of protein to a ligand.

Colomn has ligand, and protein that binds to that ligand will stay in the coloumn, proteins that don’t bind will pass through (eluted). E.g antibody antigen seperation

76
Q

How Do we know when proteins are PURE .

A

Use seperation techniques with high power

Visualise protein with stains

Ur protein is pure if only one species is appearing

77
Q

SDS page

A

Separates based on size and shape

  • makes all proteins carry -Ve charge and linearise them
  • then seperates them (-Ve charges move to anode)
  • one protein shown means it’s pure
78
Q

Define homogeneity

A

Is 100% protein purification

79
Q

isoelectric focusing

2D Page

A

IEF — Seperation of proteins based on isoelectric points.

2D page — seperation by IEP first then SDS page

80
Q

Specific activity

A

Measure of the purity of enzyme preperation

Units of enzyme activity /mg of protein

81
Q

Turnover number of enzymes

A

Number of substrate molecules that are turned into products by an enzyme per second “kcat”

82
Q

Laws of thermodynamics

A

1st - energy is neither created nor destroyed

2nd - all natural process increase the entropy of the universe

83
Q

Why is second law broken?

A

Living organisms are open systems, they require food/energy to maintain order and structure.

84
Q

ATP act as an energy source for

A

Chemical work - production of macromolecules

Physical work - muscle contraction

Transport - moving solutes against concentration gradients

85
Q

Define free energy

A

The amount of energy available to perform work

Delta G - change in free energy

86
Q

Define entropy

Explain information as energy and NEGATIVE entropy

A

Delta S - degree of disorder and randomness

Randomised letters have no meaning, but are rich in entropy

Negative entropy - eg. information

87
Q

Equation for delta G

A

Delta G = delta H - T . Delta S

88
Q

What is standard free energy change?

A 
Free energy change under standard conditions 
1M 
Ph= o
1atm 
101.3 kpa
89
Q

What is delta G prime?

A

Standard free energy at a ph other then 0. Most reactions occur at ph=7

90
Q

Coupling

A

Drive unfavourable reactions by coupling reactions with a common intermediate

Nutrition (2 decks)

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