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biochemistry and molecular biology > module 1 > Flashcards

module 1 Flashcards

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AP® Biology flashcards Biology 101 flashcards
1
Q

what is gibbs free energy

A

is the energy of the reaction to do work “available energy”

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2
Q

that is the formula for gibbs free energy

A

Delta H-(tempreature x delta entropy)

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3
Q

a negative delta G is given by

A

§ Negative enthalpy (exothermic)
§ Positive entropy (increase in entropy)
Or any combination that leaves negative DeltaG

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4
Q

what are stardard conditions in biochemistry

A

25 degrees
gas pressures at 101.3kpa
reactants and products of 1 M

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5
Q

what happens when delta G is zero

A

it means the reaction can do no work

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6
Q

how do you keep the concentration of products much lower then the reactants

A

Remove one or more of the products at a rate which is faster then it is produced then the reaction is now kinetically driven

Replenish one or more of the reactants at a rate which is faster then it is removed

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7
Q

why is ATP energy rich

A

Energy is required to break any bond

Energy is released when any bond forms therefore when ATP+Pi are formed they released energy!!!!!

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8
Q

what are the biological functions of proteins

A
  • Catalysis
    • Transport
    • Structure
    • Motion
      Signalling
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9
Q

what is the structure of an amino acid (components)

A

An acidic carboxyl group
A basic amino group
R group which different between the amino acids

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10
Q

is the alpha carbon chiral or not

A

yes it is chairal

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11
Q

how are D amino acids made

A

Made by starting synthesis of D-glyceraldehyde

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12
Q

how are L amino acids made

A

Made by starting synthesis from L-glyceraldehyde

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13
Q

what are the acidic amino acids

A
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14
Q

what are the polar uncharged amino acids

A
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15
Q

what are the non polar hydrophobic amino acids

A
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16
Q

what are the aromatic amino acids

A
17
Q

what are aromatic sides responsible for

A
  • Aromatic side chains are responsible for most ultralight absorbance and fluorescence properties of proteins
    • This is useful in protein detection
      These properties are however sen
18
Q

what formula is used for adsorption of aromtoc amino acids

A

beer-lambert laws

19
Q

what is beer-lambert law

A

Absorption= molecular coefficient x concentration x path length

20
Q

what are disulfide bonds

A

bonds between two cysteine amino acids

21
Q

what are the two types of disulfide bonds

A

1) Interchain disulfide bonds
2) intrachain disulfide bonds

22
Q

how is a disulfide bond made

A

formed by the oxidation of Cysetine where covalent bonds are formed between two Cys amino acids

23
Q

what are the four ways to represent proteins

A

Worm/tube backbone
Ribbon backbone
Space filling heavy atoms
Line (all atoms)

24
Q

proteins are most stable when

A

Folded shape of a protein (conformation) is specified by its amino acid sequence

25
Q

what does the amino acid sequence determine

A

The amino acid sequence of a protein encodes the folded structure it will adopt

26
Q

what is the rotation like on the aminde bondand why faggot!!!!

A
  • Peptide bonds have limited rotation
    § The peptide bonds has a partial double bond character due to resonance
    § As a result the CO-NH bond is not free and the groups are co planar
    § As a result there is 40% resonance structure double bond character
27
Q

a peptide bond has 2 isomerism. what are they

A

cis and trans

28
Q

what is the most stable isomerism for the amide bond and why

A
  • The trans form is favoured energetically due to less steric hinderance
    -Due to severe less steric hinderance (van de waals repulsion) of the side chains in cis
29
Q

what is the ratio for trans amino acids

A

1000:1

30
Q

what is the ratio for protein for trans to cis for proline

A

4:1 due to steric hinderance in both the cis and trans

31
Q

what are the 3 dihedral angles

A

omega
psi
phi

32
Q

the omega angle is looking along the

A

C-N bond (omega) desribes the dihedral angle or “torsion angle” between the C alpha and C bond and the N-C alpha bond)

33
Q

the phi angle is looking at the

A

The bond between the N-C alpha and C-C alpha is a pure single-single double bond

34
Q

what is the psi angle looking along

A

Rotation about the Ca-C bond is described by the Psi angle

35
Q

why are phi and psi important

A

phi and psi are important because: assuming all peptide bonds are trans all conformational freedom in the backbone of a polypeptide is due to these rotations. Eveything else in this diagram is fixed

36
Q
A

biochemistry and molecular biology (4 decks)

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