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Foundation of Medicine > Biochemistry > Flashcards

Biochemistry Flashcards

1
Q

What is the basic structure of atoms

A

Nucleus with protons (+) and neutrons (No charge) Both mass=1
Electrons in outer ring (-) mass is negligible

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2
Q

What is the basic periodic table structure

A

Groups= Vertical (Shared chemical properties, increasing electron orbitals)
Periods= Horizontal rows (same number of electron shells, increasing from 1-7)

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3
Q

What is ionisation energy

A

Energy required for 1 mole of electrons to be discharged
Increases along periods
Decreases down groups

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4
Q

What is electron affinity

A

Energy released when electron is attached to neutral atom forming -‘ve ion
Increases along periods
Decreases down groups

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5
Q

What are the main types of bonds

A

Covalent (shared pair of electrons)
Ionic (opposite charges attract)
Hydrogen (H-O, H-F, H-N)
Van der Waals (non polar Pd-Pd & LDF’s)
Hydrophobic (Non polar & polar substance)

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6
Q

What shape do carbon molecules make

A

Tetrahedral as 4 bonds can be made- valency

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7
Q

What is electronegativity

A

Measures how strongly atoms attract bonding electrons
High number- more likely to attract electrons

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8
Q

What are common reactions of O2

A

Phosphorylation/dephosphorylation
Acylation
Carboxylation
Esterification

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9
Q

What is condensation reaction

A

2 small molecules join to make 1 large molecule and eliminate H2O

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10
Q

What is hydrolysis reaction

A

H2O is added to a large molecule to break it into 2 constituents

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11
Q

What are redox reactions

A

Transfer of electrons

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12
Q

What is oxidation and reduction

A

Oxidation is LOSS
Reduction is GAIN

as 1 is oxidised the other is reduced

Oxidising agent is reduced
Reducing agent is oxidised

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13
Q

What functional groups are common in biological molecules

A

Methyl groups
Amino groups
Carboxyl groups
Ester links
Carbonyl groups
Phosphates

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14
Q

What are some functions of biomolecules

A

Information storage (DNA)
Structure (Teeth, bone, cartilage)
Energy generation (Glycolysis, citric acid cycle electron transport chain)
Energy storage (ATP)
Specificity (Receptors, enzymes, hormones)

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15
Q

Major classes of biomolecules

A

Peptides (amino acids)
Proteins (amino acids)
Lipids (steroids, phospholipid)
Nucleic acids (DNA, RNA)
Carbohydrates (mon- ,di-, polysaccharides)

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16
Q

What is the 1st law of thermodynamics

A

Energy is neither created nor destroyed (in conversion of 1 energy form to another)

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17
Q

What is the 2nd law of thermodynamics

A

When energy is converted from one form to another, some energy become unavailable to do work

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18
Q

What is entropy (ΔS)

A

the randomness and disorder of a reaction

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19
Q

What is enthalpy (H)

A

Measurement of energy (heat content) in a given reaction
Change is also calculated (ΔH)

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20
Q

What is free energy change (ΔG)

A

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

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21
Q

How is free energy change calculated

A

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

ΔG= ΔH- TΔS

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22
Q

What is an exergonic reaction

A

Total free energy of product is LESS than that of reactant
(NEGATIVE ΔG so occurs spontaneously)

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23
Q

What is an endergonic reaction

A

Total free energy of the reaction product is GREATER than that of reactant
(POSITIVE ΔG so cannot occur spontaneously)

Input of energy needed to proceed

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24
Q

How is ΔG determined for a given reaction A + B→ C + D

A

ΔG = ΔGo’ + RTln([C][D]/[A][B])

R is universal gas constant (8.3JK-1mol-1)
T = absolute temperature (Kelvin)

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25
Q

Free energy change is always under standard conditions, What are these in the body?

A

T = 298 K
1 atmosphere pressure
1 M (1 mol/l) concentration of reactants (except for H+)
pH = 7

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26
Q

How is ΔG related to equilibrium

A

The further towards completion the point of equilibrium is, the more free energy is released

ΔG values near zero are characteristic of readily reversible reactions

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27
Q

What cellular processes are unfavourable for spontaneous reactions

A

having to proceed in +’ve ΔG direction
transport against gradient
synthesis of large molecules

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28
Q

What is ATP structure

A
  • Less stable than ADP due to electrostatic repulsion of close negative charges on phosphates

Phosphate groups linked by anhydride bonds(high energy)
Which attach to a sugar and a base

29
Q

What is metabolism

A

All reactions taking place in the body divided into 2 subsections

30
Q

What are the 2 subsections of metabolism

A

Catabolism- Break down complex molecule into smaller ones releasing energy

Anabolism- Synthesise complex molecules from smaller ones requiring energy

31
Q

What can be used as a control point in metabolic pathways

A

Reactions with large negative ΔG values

32
Q

What are characteristics of water

A

Polar- electrons shared unequally
Forms a dipole
Ionic + polar substances dissolve in it i.e hydrophilic
Has hydrogen bonding between molecules

33
Q

What happens when non-polar substances go into water

A

Solid types do not dissolve and liquids form 2 layer system as non-polar molecules are hydrophobic

34
Q

What are amphipathic molecules

A

A molecule that is both hydrophilic and hydrophobic

-Polar head and non-polar tail
-Form micelles in water

35
Q

how does amphipathic molecule- Sodium palmitate work

A

Is a fatty acid that’s the sodium salt of palmitic acid- soap

-Forms micelles with tails gathering at centre and heads protecting around

36
Q

What groups do all amino acids contain

A

-Amino -NH2
-Carboxyl -COOH
-Hydrogen -H
-Side R group
ALL ATTACHED TO CENTRAL C

37
Q

What are stereoisomers

A

Non-superimposable mirror images

All D- and L- forms of amino acids are stereoisomers

38
Q

What are the types of amino acids

A

Basic (positively charged)
Acidic (negatively charged)
Polar (Hydrogen bonding)
Hydrophobic (Hydrocarbons)

39
Q

What are basic amino acid examples

A

Lysine
Arginine
Histidine

40
Q

What are acidic amino acid examples

A

Aspartic acid
Glutamic acid

41
Q

What are polar amino acid examples

A

Glycine
Serine
Asparagine
Glutamine
Cysteine
Tyrosine
Threonine

42
Q

What are hydrophobic amino acid examples

A

Leucine
Proline
Alanine
Valine
Methionine
Tryptophan
Phenylalanine
Isoleucine

43
Q

How do peptide bonds form

A

Two amino acids join by attraction of negatively charged COO- group and positively charged NH3+ group
Eliminates H2O

44
Q

What is the direction of a peptide

A

Runs from N-Terminal residue at 1 end to C-terminal residue at the other

45
Q

What are the characteristics of peptide bonds

A

partial double bond character
Planar structure
strong and rigid- important in folding proteins

46
Q

What are acids and bases in terms of protons

A

Acid molecules can donate a proton
Bases accept protons

47
Q

What does the strength of an acid depend upon and how is it calculated

A

How readily it can donate a proton (hydrogen ion) and is measure by acid dissociation constant Ka

pKa= -log10[Ka]

48
Q

What is pH and how is it calculated

A

The measurement of amount of proteins in a solution

pH= -log10[H+]

49
Q

What is a buffer

A

Solution used to control the pH of a reaction mixture

50
Q

What are zwitterions

A

amino acids without charged side groups in a neutral solution -NO NET CHARGE
-Gives buffering properties to proteins influencing function

51
Q

What are the different protein structures

A

Primary
Secondary
Tertiary
Quaternary

52
Q

What is a primary protein

A

The sequence of amino acids in polypeptide

53
Q

What is secondary structure

A

Localised conformation of the polypeptide backbone

54
Q

What are the types of secondary proteins

A

Alpha helix
Beta pleated sheet & strands
Triple helix

Some proteins have more than 1 of these elements

55
Q

What is alpha helix

A

Rod like, with 1 polypeptide chain, spirals

56
Q

What is a beta pleated sheet/strand

A

Backbone almost completely extended, can involve more than 1 chain
Can run antiparallel or parallel with turns between strands
-Also can be a repeated zig zag structure

57
Q

What is a collagen triple helix structure

A

Triple helix- Three left-handed helical chains twisted around each other form a right-handed superhelix

Influences strength of connective tissue, weakened collagen= bleeding gums

58
Q

What is a tertiary protein

A

the three-dimensional structure of an entire polypeptide, including all its side chains

Has fibrous and globular proteins

59
Q

What are fibrous proteins

A

Have polypeptide chains organised approximately parallel along a single axis

  • consist of long fibers or large sheets
  • tend to be mechanically strong
  • are insoluble in water and dilute salt solutions
  • play important structural roles in nature
60
Q

What are examples of fibrous proteins

A

Keratin of hair
Wool
Collagen of connective tissue of animals

61
Q

What are globular proteins

A

Proteins which are folded to a more or less spherical shape

  • they tend to be soluble in water and salt solutions
  • most of their polar side chains are on the outside and interact with the aqueous environment by hydrogen bonding and ion-dipole interactions
  • most of their nonpolar side chains are buried inside
  • nearly all have substantial sections of alpha-helix and beta-sheet
62
Q

What are examples of globular proteins

A

Myoglobin
Haemoglobin

63
Q

What forces stabilise tertiary structures

A

Covalent disulphide bonds
Hydrophobic interactions
Hydrogen bonds
Electrostatic interactions-salt bridge

64
Q

What do amino acid substitutions do to protein structure- sickle cell anemia example

A

Significant functional changes

Single nucleotide change makes altered protein (Glutamic acid swapped for valine)
Valine= Hydrophobic
Glutamic acid= Acidic

so low O2: haemoglobin polymerises blocking capillary blood flow

65
Q

What causes denaturation of proteins

A

Heat
Extreme pH change
Detergents, urea
Reducing agents

66
Q

What is quaternary protein structure

A

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

67
Q

what is a quaternary protein example

A

Haemoglobin

-Has 4 subunits
Each ahs a haem group binding to 1 O2 molecule

Binding of 1 molecule changes the affinity at other subunits - allosteric regulation

68
Q

What does haemoglobin do

A

Transports oxygen in the blood

Foundation of Medicine (23 decks)

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