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Year 2 - University > Biochemistry > Flashcards

Biochemistry Flashcards

1
Q

Define drug

A

A chemical which changes biochemistry

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2
Q

Why do most drugs not make covalent bonds with their biomolecular targets?

A

This would require high reactivity which makes it hard to be selective. If covalent chemistry is used in the body it would need to be heated to 80-90 degrees under reflux which is not possible

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3
Q

How do electrostatic interactions come about?

A

The attraction between molecules bearing opposite electronic charges

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4
Q

How do ion-ion interactions happen?

A

The closer they get the more attraction they feel until a certain point when you get repulsion

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5
Q

Why are ion-ion interactions stronger in a hydrophobic environment than a polar environment?

A

Due to competition by water. Usually, binding site is more hydrophobic than the surface, so this increases the effect of an ionic interaction

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6
Q

What are hydrogen bonds?

A

Electrostatic interactions between a polarised proton with a nearby atom bearing a lone pair

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7
Q

Define amino acid

A

Bifunctional organic compounds that possess both a carbonyl and amino group

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8
Q

What is an alpha amino acid?

A

Where the carbonyl and amino group are attached to the same central carbon atom (alpha-carbon atom)

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9
Q

Why can amino acids act as nucleophiles?

A

Due to their lone pairs

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10
Q

Define a Bronsted-Lowry acid

A

A proton donor

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11
Q

Define a Bronsted-Lowry base

A

A proton acceptor

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12
Q

How is basicity most commonly measured?

A

Using the pKa of a conjugate acid

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13
Q

Finish the sentence: the less acidic the conjugate acid…

A

the more stable it is, the lower the Ka, the higher the pKa, and therefore the more basic the original base

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14
Q

What does pKa tell you?

A

The pH at which the molecule is 50% protonated

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15
Q

What is the difference between an L-amino acid and a D-amino acid?

A

L-amino acids rotate plane polarised light to the left, and D-amino acids rotate plane polarised light to the right

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16
Q

Define amphoteric

A

Can react as either an acid or a base

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17
Q

Define isoelectric point (pl)

A

the pH at which the amino acid exists largely in an overall neutral, Zwitterionic form

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18
Q

How to calculate the pl for neutral amino acids?

A

The average of the two pKa values

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19
Q

How to calculate the pl for acidic amino acids?

A

The average of the two lower pKa values

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20
Q

How to calculate the pl for basic amino acids?

A

The average of the two higher pKa values

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21
Q

Define peptide

A

Chain of amino acids

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22
Q

What does ‘write N-terminus to C-terminus’ mean?

A

The amine group is on the left of the chain and the carboxyl group is on the right of the chain

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23
Q

How do amides form?

A

Condensation reaction between amines and carboxylic acids

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24
Q

How do we control where a reaction between amino acids occur?

A

Using protecting groups or the automated process which involves beads

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25
Q

How do we calculate the isoelectric point for peptides?

A
  1. Write out pKas from highest to lowest
  2. Choose a pH below the lowest and calculate the charge
  3. Choose a pH between the first and second lowest and calculate the charge
  4. Repeat
  5. pl is the average of the pKas either side of q=0
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26
Q

What is the primary structure of a protein?

A

The amino acid sequence

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27
Q

What are the two main secondary structures?

A

Alpha helix, beta sheet

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28
Q

What are the tertiary and quaternary structure?

A

Tertiary - multiple alpha helices/beta pleated sheets
Quaternary - multiple tertiary structures

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29
Q

What holds alpha helices and beta pleated sheets together?

A

hydrogen bonds

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30
Q

How long does it take to return to the same point in an alpha helix?

A

Every 7 amino acids

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31
Q

What is a beta pleated sheet?

A

Long, straight chains which stack next to each other and are held together by hydrogen bonding

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32
Q

What are the four less common secondary structures?

A

Beta turn, 310 helix, triple helix, random coil

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33
Q

What is the purpose of disulphide bridges in the tertiary structure?

A

Bring two peptide fragments together

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34
Q

What is the process for making protein crystals?

A
  1. Protein in water with non-solvent placed as drop on lid
  2. Non-solvent in well/flask
  3. Water evaporates from drop
  4. Protein crystals form
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35
Q

Why is NMR good for determining protein structure?

A
  • More native conditions
  • No need for crystallisation
  • Less precise conditions
  • Less automated
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36
Q

Why is cryo-EM good for determining protein structure?

A
  • More native conditions
  • No need for crystallisation
  • Lower resolution
  • Relies on previous models
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37
Q

How does gel electrophoresis help determine protein structure?

A

Mass/charge ratio is used and movement will depend on protein charge (pKa and pl)

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38
Q

give examples of globular proteins

A

antibodies, membrane channels, enzymes

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39
Q

give examples of fibrous proteins

A

collagen, silk

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40
Q

what is the difference between globular and fibrous proteins?

A

fibrous proteins create very long structures which provide structural integrity, whereas globular proteins are individual units and perform more chemical tasks

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41
Q

define antigen

A

a foreign substance that enters the body, such as bacteria, fungi, allergens, venom, and toxins

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42
Q

define antibody

A

a protein produced by your immune system to attack and fight off antigens

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43
Q

what are membrane proteins?

A

proteins that can transport chemicals and information across biological barriers

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44
Q

what are enzymes?

A

the body’s catalysts - agents that speed up reactions without being consumed

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45
Q

describe the process of an enzyme working

A
  1. substrates enter active site
  2. substrates are held in active site by weak interactions, forming an enzyme-substrate complex
  3. enzyme can lower activation energy and speed up a reaction
  4. substrates are converted to products
  5. products are released
  6. active site is available for two new substrate molecules
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46
Q

what is chymotrypsin?

A

an enzyme that is used in the small intestine to break down proteins into individual amino acids

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47
Q

what is a competitive inhibitor?

A

they resemble the desired substrate and can be bound to the active site, preventing the desired substrate from binding and a reaction occurring

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48
Q

what is a non-competitive inhibitor?

A

they bind to another place on the enzyme which alters its structure and prevents binding

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49
Q

how many hydrogen bonds are between A and T?

A

two

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50
Q

how many hydrogen bonds are between G and C?

A

3

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51
Q

what is deoxyribose?

A

ribose without the OH group bonded to carbon 2

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52
Q

what do the different carbons attach/bond to on deoxyribose to form DNA?

A

the OH groups on carbons 3 and 5 attach to a phosphate, and the OH group on carbon 1 attaches to the nucleobase

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53
Q

define nucleoside

A

base with sugar attached

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54
Q

define nucleotide

A

base with sugar and phosphate attached

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55
Q

why is DNA an antiparallel duplex?

A

as when going down the DNA strand we go 5’ to 3’, and when doing up on the other side we go 5’ to 3’ meaning they are opposites of one another

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56
Q

why is DNA with a higher GC content more stable?

A

as GC has three double bonds compared to AT which has 2

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57
Q

define hybridization

A

the process in which two complementary single-stranded DNA and/or RNA molecules bond together to form a double-stranded molecule

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58
Q

How do we find the complementary sequence?

A
  1. split strand into three base units for clarity
  2. write down the complementary bases
  3. reverse the order to give the strand in 5’ to 3’ format
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59
Q

what does the ‘melting temperature’ of DNA mean?

A

when half of the strands are in a random coil single strand state

60
Q

why does DNA have a double helix structure?

A

the negatively charged phosphate groups repel each other, the presence of hydrogen bonds, and stacking of nucleobases through hydrophobic/Van der Waals interactions compacts the duplex vertically

61
Q

where are quadruple helixes found?

A

in telomeres at the end of chromosomes

62
Q

how is a triplex formed?

A

a third strand binds in the major groove

63
Q

what do telomeres do?

A

determine the lifetime of DNA

64
Q

what is the difference between the molecules of RNA and DNA (not the bases)?

A

extra OH group

65
Q

what is the structure of a chromosome?

A

DNA is coiled around proteins called histones to produce nucleosomes, which are further packed to produce chromosomes

66
Q

how many protein units are required for one nucleosome?

A

8

67
Q

Describe the process of transcription (6 marks)

A
  • DNA helicase binds to a complementary start codon on the DNA and breaks hydrogen bonds
  • DNA unwinds forming a template strand
  • Each exposed base binds to a complementary, free floating nucleotide
  • C with G, A with U
  • RNA polymerase moves along the DNA strand, causing the phosphodiester bonds to form between nucleotides
  • This forms pre-mRNA which is then spliced to remove the introns so it can fit through nuclear pores
68
Q

Describe the process of translation (4-6 marks)

A

-mRNA moves out of the nucleus via nuclear pores and attaches to a ribosome
- tRNA carrying amino acids bind their anticodons to the complementary codon on the mRNA
- A second tRNA does the same and the two amino acids form a peptide bond
- The first tRNA molecule moves away
- The process continues and only ends when a stop codon is reached, forming a polypeptide

69
Q

What is are the three stages of the polymerase chain reaction?

A
  1. Separation of the DNA strand - the DNA fragments, primers, and the DNA polymerase are placed in a vessel in the thermocycler at 95 degrees which causes the two strands of DNA fragments to separate due to the breaking of hydrogen bonds
  2. Addition (annealing) of the primers - the mixture is cooled to 55 degrees so the primers can join (anneal) to their complementary bases at the end of the DNA fragment, providing starting sequences for DNA polymerase
  3. Synthesis of DNA - temperature raised to 72 degrees as this is the optimum temperature for DNA polymerase to add complementary nucleotides along each of the separated DNA strands
70
Q

What is the empirical formula for carbohydrates?

A

C(H2O)

71
Q

How are hemiacetals formed?

A

By the reaction of a carbonyl and an alcohol

72
Q

What are glycodies?

A

Small non-sugar molecules attached through anomeric position to a sugar

73
Q

What are the two distinct parts of a fatty acid?

A

The long hydrocarbon chain and a carboxylic acid group

74
Q

Is the hydrocarbon chain in a fatty acid hydrophobic and hydrophilic?

A

Hydrophobic

75
Q

How do fatty acids form esters and amides?

A

The acid group readily reacts with a hydroxyl or an amino group on a second molecule

76
Q

How do fatty acids differ from one another?

A

Length of hydrocarbon chain and number and position of the carbon-carbon double bonds

77
Q

What is the difference between saturated and unsaturated?

A

Saturated has no carbon-carbon double bonds, and unsaturated does

78
Q

What are phospholipids composed of?

A

Two fatty acids, glycerol, and a phosphodiester head

79
Q

What are steroids?

A

A class of lipid with a polycyclic aliphatic carbon skeleton

80
Q

What are the two wider roles of cholesterol?

A

As an intermediate in biosynthesis of other steroids, and in control of membrane fluidity

81
Q

Amphipiles such as phospholipids are subject to two conflicting forces. What are these?

A
  1. The hydrophilic head is attracted to water
  2. The hydrophobic tail repels water and seeks to aggregate with other hydrophobic units
82
Q

What are the different proteins in the membrane?

A

Ion channels, receptors, and transporters

83
Q

Why can individual phospholipids rotate axially or fatty acid tails flex?

A

Because the VdW interactions are very similar for each arrangement

84
Q

Why is fluidity important in the membrane?

A
  • Processes such as exocytosis, endocytosis, membrane trafficking, and membrane synthesis
  • Allows membranes to fuse and molecules to mix
  • Allows even distribution of membrane molecules between daughter cells following cell division
85
Q

What are the factors influencing fluidity and why?

A

Length - shorter, reduced interactions of the hydrocarbon tails so more fluid
Saturation - each double bond in an unsaturated tail creates a small link
Cholesterol - fill the spaces between the neighbouring phospholipid molecules

86
Q

Does fluidity increase or decrease in membranes with increasing cholesterol content?

A

Decreases

87
Q

Why are cellular membranes asymmetric?

A
  1. Two layers of bilayer have different compositions
  2. Different phospholipid/glycolipid inside and outside
  3. Membrane proteins embedded into membrane with a specific orientation
  4. All lipids are synthesised on the cytosolic surface of the endoplasmic reticulum
  5. Lipids in the outer leaflets are transported there by flippases
88
Q

How do local anaesthetics work?

A

Block the conduction of nerve impulses by affecting the influx of ions through transmembrane channels

89
Q

What is the nucleus composed of?

A

DNA, proteins, lipid membrane

90
Q

What is the nucleosome?

A

The basic repeating subunit of chromatin packaged inside the cells nucleus

91
Q

What is chromatin?

A

A mixture of DNA and proteins that form the chromosomes found in the cells of humans and other higher organisms

92
Q

What is topologically associating domain (TAD)?

A

DNA within these domains interact with each other more than in other domains

93
Q

What is the purpose of nuclear pores?

A

They allow proteins in and mRNA and ribosomes out

94
Q

What is the cytoplasm?

A

A viscous liquid that fills the inside of cells

95
Q

What is the cytoplasm made up of?

A

Water, ions, small molecules, and proteins

96
Q

What occurs in the cytoplasm?

A

Metabolism and is the medium for signal transduction

97
Q

What is the purpose of mitochondria?

A

They generate most of the chemical energy needed to power the cells biochemical reactions

98
Q

What is the composition of DNA?

A

Lipids, proteins, DNA, RNA, small molecules

99
Q

What is the endoplasmic reticulum made up of?

A

Lipids, proteins, DNA

100
Q

What roles does the endoplasmic reticulum play?

A

Calcium storage, protein synthesis, and lipid metabolism

101
Q

What is the purpose of the golgi apparatus?

A

Helps process and package lipid molecules, especially proteins designed to be exported to the cell

102
Q

What is the golgi apparatus composed of?

A

Lipids and proteins

103
Q

What is the simple process of the function of the golgi apparatus?

A
  1. Receives proteins from ER in vesicles
  2. Applies post-translational modifications to proteins
  3. Transports them to internal or external vesicles
104
Q

What is the composition of ribosomes?

A

RNA and proteins

105
Q

What is the function of ribosomes?

A

Produce proteins by translating mRNA into polypeptides via tRNA

106
Q

Where are ribosomes found?

A

Cytoplasm, mitochondria, and rough ER

107
Q

What are endosomes and lysosomes made up of?

A

Lipid membrane

108
Q

What is the function of endosomes and lysosomes?

A
  • They bud off from the ER and golgi apparatus to transport or excrete proteins
  • They bud of from the cell membrane to allow the cell to uptake material from outside (endocytosis)
109
Q

Define metabolism

A

Chemical processes that occur within an organism to maintain life

110
Q

What are the three major steps of cellular respiration?

A

Glycolysis, Krebs cycle, Oxidative phosphorylation

111
Q

What is the first stage of glycolysis and what happens during it?

A

Phosphorylation of glucose to glucose phosphate:
Before it can be split into two, glucose must be made more reactive by the addition of two phosphate molecules. These come from the hydrolysis of two ATP molecules to ADP. This provides the energy to activate glucose and lowers the activation energy for the enzyme controlled reactions that follow. Splitting of the phosphorylated glucose:
Each glucose molecule is split into two 3-carbon molecules known as triose phosphate (each 3-carbon molecule has one phosphate attached). Oxidation of triose phosphate:
Hydrogen is removed from each of the two triose phosphate molecules and transferred to a hydrogen carrier molecule known as NAD to form reduced NAD. The production of ATP:
Enzyme controlled reactions convert each triose phosphate into another 3-carbon molecule called pyruvate. In the process, two molecules of ATP are regenerated from ADP.

112
Q

What is the overall yield of one glucose molecule undergoing glycolysis?

A
  • two molecules of ATP (four produced, but two used up in the initial phosphorylation pf glucose)
  • two molecules of reduced NAD
  • two molecules of pyruvate
113
Q

Does glycolysis require oxygen?

A

No - it takes place in the cytoplasm and so does not require oxygen, nor any organelles

114
Q

What happens during the link reaction?

A
  • pyruvate is oxidised to acetate. In this reaction, the 3-carbon pyruvate loses a carbon dioxide molecule and two hydrogens. These are accepted by NAD to form reduced NAD which is later used to produce ATP
  • The 2-carbon acetate combines with a molecule called coenzyme A to produce an enzyme called acetylcoenzyme A
115
Q

What is the equation for the link reaction?

A

pyruvate + NAD + CoA —> acetyl CoA + reduced NAD + carbon dioxide

116
Q

Where does the Krebs cycle occur?

A

The matrix of the mitochondria

117
Q

Briefly summarise the events that occur in the Krebs cycle (3 bullet points)

A
  1. The 2-carbon acetylcoenzyme A from the link reaction combines with a 4-carbon molecule to produce a 6-carbon molecule
  2. In a series of reactions this 6-carbon molecule loses carbon dioxide and hydrogen to give a 4-carbon molecule and a single molecule of ATP produced as a result of substrate-level phosphorylation
  3. The 4-carbon molecule can now combine with a new molecule of acetylcoenzyme A to begin the cycle again
118
Q

What does one glucose molecule produce during the Krebs cycle?
(Pyruvate will be half of this as two pyruvates = one glucose molecule?

A
  • 6 reduced NAD
  • 2 reduced FAD
  • 2 ATP
  • 4 carbon dioxide
119
Q

What are coenzymes?

A

Coenzymes are NOT enzymes. They are molecules that some enzymes require in order to function.

120
Q

Give three examples of coenzymes and what they do

A

All of the following carry hydrogen atoms from one molecule to another:
- NAD, which is important throughout respiration
- FAD, which is important in the Krebs cycle
- NADP, which is important in photosynthesis

121
Q

Where does oxidative phosphorylation occur?

A

In the mitochondria - within the inner folded membrane (cristae) are the enzymes and other proteins involved in oxidative phosphorylation and hence ATP synthesis

122
Q

What does the synthesis of ATP by oxidative phosphorylation involve?

A

The transfer of electrons down a series of electron carrier molecules which together form the electron transfer chain

123
Q

How does the electron transfer chain work?

A
  • The hydrogen atoms produced during glycolysis and the Krebs cycle combine with the coenzymes NAD and FAD
  • The reduced NAD and FAD donate the electrons of the hydrogen atoms they are carrying to the first molecule in the electron transfer chain
  • The electrons pass along a chain of electron transfer molecules in a series of oxidation-reduction reactions. As these flow along the chain, the energy they release causes the active transport of protons across the membrane into the inter-membranal space
  • The protons accumulate here before diffusing back into the matrix through ATP synthase channels in the inner membrane
  • At the end of the chain the electrons combine with these protons and oxygen to form water. Oxygen is therefore the last acceptor of electrons in the chain
124
Q

Define enzyme

A

A class of protein which acts as a catalyst for a biochemical reaction but is not permanently changed in the reaction

125
Q

How do enzymes work?

A

They lower the activation energy required for the molecular reaction to take place

126
Q

What are co-factors?

A

‘Helper molecules’ that assist in biochemical transformations

127
Q

What are the two classifications of co-factors?

A

loosely bound (co-enzymes) and tightly bound (prosthetic groups)

128
Q

What are prosthetic groups?

A

Small inorganic ions, mostly metal ions. Act as activators and/or inhibitors of activity

129
Q

What are co-enzymes?

A

Small, non-protein molecules that catalyse reactions

130
Q

What is competitive inhibition?

A

Inhibitor competes reversibly with substrate for the active site

131
Q

What is uncompetitive inhibition?

A

Inhibitor binds only to the ES complex, leading to EIS intermediates

132
Q

What is non-competitive inhibition?

A

Inhibitor binds non-covalently to sites other than the active site

133
Q

What is irreversible inhibition?

A

Irreversible inhibitors form covalent or very tight bonds with functional groups on the active site

134
Q

In non-competitive inhibition, what is the site called where binding occurs?

A

Allosteric site

135
Q

What are neurotransmitters?

A

chemicals secreted from the presynaptic membrane

136
Q

what are electrical synapses?

A

ions flow directly from one neurone to another via gap-junctions called electrical synapses

137
Q

what stimuli causes the gating of ion channels

A
  1. Voltage gated
  2. Ligand gated (extracellular ligand)
  3. Ligand gated (intracellular ligand)
138
Q

Describe how G-protein-coupled receptors work

A
  1. The ligand binds to the G-protein hosting GDP in the alpha subunit
  2. Binding changes the conformation of the G-protein, releasing GDP
  3. This creates a pocket which binds GDP
  4. Binding of GDP causes another conformational change
  5. This results in the alpha subunit departing separately
139
Q

Describe the process of phosphorylation

A
  1. cAMP activates protein kinase A
  2. Protein kinase A phosphorylates other specific proteins
  3. Phosphorylation changes their conformations and activates them in turn
  4. Each step we can have multiple turn overs resulting in huge signal amplification
140
Q

What are the four ways drugs can interact with receptors?

A

Agonist, antagonist, partial agonist, inverse agonist

141
Q

Define agonist

A

A ligand that binds to and provokes a signal from a receptor via conformational changes to produce the active state

142
Q

Define antagonist

A

A ligand that binds to a receptor and induces no signal. Blocks agonist binding, and hinders conformational switch to active state

143
Q

Define partial agonist

A

Binds and provokes a signal but diminished compared to a full agonist. Binding is suboptimal and conformational switch may not fully engage

144
Q

Define inverse agonist

A

Removed any base-level activity the receptor had in absence of the ligand

145
Q
A

Year 2 - University (6 decks)

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