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Principles Biochemistry Flashcards

Revise over Principles Biochemistry lectures.

1
Q

Name four common reactions seen in the body

A

Phoshophorylation, acylation, carboxylation, esterification

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2
Q

What is an acylation reaction?

A

Addition of a fatty acyl group, usually in the process of adding a fatty acid.

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3
Q

What is the final product of carbon metabolism?

A

Carbon dioxide

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4
Q

Name three lipid biomolecules

A

Triglycerides, phospholipids, steroids

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5
Q

Name three carbohydrate biomolecules

A

mono, di and polysaccharides

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6
Q

What is the equation for a change in free energy?

A

ΔG = ΔH – TΔS

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7
Q

What is an exergonic reaction?

A

Reaction in which the total free energy of the product is less than the total free energy of the reactants. They can occur spontaneously.

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8
Q

What is an endergonic reaction?

A

Reaction in which the total free energy of the product is more than the total free energy of the reactants. They cannot occur spontaneously.

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9
Q

Whats does a ΔG value of near zero mean?

A

Reaction is readily reversible.

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10
Q

What is a coupling reaction?

A

Unfavourable cellular processes (have to proceed in direction of positive ΔG) couple to highly favourable processes to allow the reaction to proceed.

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11
Q

Why is ATP so important in a cell?

A

Universal energy currency. This is because the breakdown of ATP is very favourable so unfavourable reactions need to couple to this in order to proceed. This is why it is needed for so many processes.

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12
Q

Is ATP more of less stable than ADP? Why?

A

Less. Close negative charges cause electrical repulsion. Strain is relieved by removing one to make ADP. This is a high energy bond.

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13
Q

Is ATP concentration low or high in a cell?

A

Low. Cells do not store large amounts of ATP, they just have to regenerate it fast.

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14
Q

What is metabolism?

A

All the reactions taking place in the body

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15
Q

What is catabolism?

A

Breaking down complex molecules into smaller ones

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16
Q

What is anabolism?

A

Synthesising complex molecules from smaller ones. Energy consuming,

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17
Q

Give an example of a catabolic pathway.

A

Glycolysis

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18
Q

In glycolysis, what is the gain of ATP?

A

Two molecules

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19
Q

Give an example of an anabolic pathway

A

Gluconeogenesis

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20
Q

What kind of reactions are used as control points in metabolic pathways?

A

Those close to equilibrium. ΔG close to 0.

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21
Q

Give three facts about water.

A
  1. It is polar. Electrons shared unequally dependant on electronegativity.
  2. It is bent, and forms a dipole
  3. It is tetrahedral in shape
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22
Q

What kind of molecules dissolve in water?

A

Ionic and polar (hyrdophilic)

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23
Q

What is a hydrogen bond?

A

Covalent bond between hydrogen and a more electronegative atom.

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24
Q

What happened to non - polar substances in water?

A

Are hydrophobic and so insoluble.

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25
Q

Give an example of hydrophobic molecules. What happens in water?

A

Hydrocarbons. These are excluded and form two layers; “Oil slick” This is the hydrophobic effect.

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26
Q

What is an amphiphilic molecule? What happens to these in water?

A

A molecule that is both hydrophilic and hydrophobic (hydrophilic head and hydrophobic tail) These form micelles in water

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27
Q

What are the two functions of lipids in the cell membrane?

A

Structural (form lipid bilayer)

Precursors for signalling molecules

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28
Q

What are two functions of proteins in the cell membrane?

A

Confer selectivity, Cell - cell recognition

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29
Q

Describe the structure of an amino acid

A

α-carbon bonded to an amino group, a carboxyl group, a hydrogen and a side chain

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30
Q

What are stereoisomers?

A

Non superimposable, mirror images of these amino acids. D and L formations.

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31
Q

What are the four different classes of amino acids?

A

Non polar, polar, acidic and basic

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32
Q

Give three facts about peptide bonds?

A

Partial double bond character, planar, strong and rigid (important for protein folding)

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33
Q

What are acids?

A

Proton donors

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34
Q

What are bases?

A

Proton acceptors

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35
Q

What is the strength of an acid and how is this measured?

A

How readily it donates protons. Measured by the acid dissociation constant.

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36
Q

What is pH?

A

Measure of amount of protons in a solution

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37
Q

What is the henderson hasselbalch equation and what does it do?

A

pH =pKa + log [A-]/[HA]
It connects the Ka of a weak acid with the solution which it is in. This helps us to calculate the properties of buffer solutions.

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38
Q

What is a buffer solution?

A

A solution which can resist small changes in pH and so control the pH of a reaction mixture.

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39
Q

What is a zwitterion amino acid?

A

One that contains a positive and a negative side group, so overall is neutral.

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40
Q

What is the isoelectric pH? How does this change is zwitterions?

A

The pH at which a molecule has no net charge. In uncharged amino acids there are two pKa values!

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41
Q

Describe the acid - base properties of proteins? How does this act in the body?

A

Amino acid side chains can be ionised. Proteins can act as buffers; for example haemoglobin in blood.

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42
Q

What is the effect on protein of a change in ph?

A

Can lead to ionisation and so changes in structure and function.

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43
Q

What is the primary structure of a protein?

A

Amino acid sequence

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44
Q

What is the secondary structure of a protein?

A

Localised conformation of polypeptide backbone

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45
Q

What is the tertiary structure of a protein? Give two types.

A

3D structure of polypeptide in space, including side chains.

Fibrous and globular.

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46
Q

What is the quaternary structure of a protein? Give an example.

A

The spatial arrangement of polypeptide chains in a protein of multiple subunits. (i.e. has a non protein part) Example would be haemoglobin. This has four subunits (two alpha and two beta chains) and both contain a harm group.

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47
Q

What are the four types of polypeptide chain? Describe them (Remember this only considers backbone)

A
  1. Alpha helix. Rod like, one chain
  2. Beta strands
  3. Beta sheets. Can involve one or more chain in either a parallel or anti parallel direction. Turns between strands. Can also be pleated/zig zagged
  4. Triple helix
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48
Q

Can more than one structure element appear in one protein?

A

Yes. In phosphglycerate kinase there is an alpha helix and parallel beta sheets

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49
Q

Give 4 facts about collagen.

A
  1. Component of bone and connective tissue
  2. Most abundant protein in us.
  3. Insoluble
  4. Three left handed, helical chains twisted to form a right handed superhelix
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50
Q

What is tropocollagen

A

Repeating sequence of X-Y-Gly in all strands
X = any amino acid
Y = proline or hydroxyproline
also contains hydroxylysine
Inter-chain H-bonds (no intra-chain)
involving hydroxylysine and hydroxyproline
Covalent inter- and intra-molecular bonds

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51
Q

Give effects on us due to lack of collagen? Why does this happen?

A

Scurvy (bleeding gums, skin discolouration)

  • The enzyme which hydroxylates proline requires vitamin C.
  • If we are defiant in Vitamin C then there is a reduction in hydroxyproline
  • This results in weakened collagen and so strength of connective tissue.
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52
Q

What is a fibrous protein? Give examples.

A

Polypeptide chains organised parallel along a single axis. Long, strong and insoluble.
- Keratin, Collagen

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53
Q

What is a globular protein? Give examples.

A

Proteins folded into a more or less spherical shape. Soluble, outside parts are polar, contain alpha helix and beta sheets.

  • Myoglobin. This has a harm group which contains an iron ion. It stores oxygen in muscle.
  • Haemoglobin
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54
Q

Give five forces which can stabilise tertiary protein structure.

A
  1. Covalent disulphide bonds
  2. Salt bridges ( electrostatic interactions)
  3. Hydrophobic bonds
  4. Hydrogen bonds
  5. Formation with metal ions
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55
Q

What is the attraction between hydrocarbons known as?

A

Van der waals forces.

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56
Q

What four things can lead to denaturation of protein?

A

Heat
Extremes of pH
Detergents, urea
Thiol agents, reducing agents

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57
Q

What does the DNA nucleotide sequence determine?

A

The amino acid sequence in polypeptide chains.

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58
Q

What are a) nucleosides and

b) nucleotides composed of?

A

a) Base + sugar

b) base + sugar + phosphate

59
Q

What are the four bases present in DNA?

A

Adenine, Guanine, Thymine and Cytosine

60
Q

What are the four bases present in RNA?

A

Adenine, Guanine, Cytosine and Uracil

61
Q

Which are purine bases?

A

Adenosine, Guanine

62
Q

Give an example of a DNA building block and a RNA one,

A

deoxy - adenosinse/cytosine/guanine.thymine- triphosphate

Adenosine triphosphate etc

63
Q

What does a phosphodiester bond join? What is the process called in which this occurs?

A

Free 3’ OH group and a 5’ triphosphate

Polymerisation

64
Q

What end are new nucleotides always added to?

A

Free 3’ end.

65
Q

How many bonds bond adenosine and thymine?

A

2

66
Q

How many bonds bond cytosine and guanine?

A

3

67
Q

What bonds base pairs on the inside?

A

Hydrogen bonds

68
Q

What enzyme catalyses DNA replication? Describe the action of this enzyme.

A

DNA polymerase. It can only add to existing nuclear acids and so cannot start DNA synthesis on its own. It requires an initial RNA primer.

69
Q

Describe the meaning of the term semi - conservative

A

Each new DNA strand is composed of one of the parent, original strands and one brand new strand.

70
Q

How are nucleotides added to the leading strand?

A

Continuously to free 3’ ends. (their will always be a free 3’ end)

71
Q

Describe the two nucleotide strands present in DNA

A

Run in an anti parallel direction. One from 5’ to 3 (leading), and one from 3’ to 5’

72
Q

How is the other strand replicated?

A

In short segments/ozakazi fragments

73
Q

What enzyme unzips DNA?

A

DNA helicase

74
Q

What does primes synthesis do?

A

Synthesis an RNA primer

75
Q

What happens to the other two phosphate bonds that do not form a phosphdiester bond?

A

They leave as pyrophosphate (and energy supply)

76
Q

What proofreading mechanism does DNA polymerase possess?

A

3’ to 5’ exonuclease activity which removes incorrect nucleotide and improves error rate

77
Q

What are the three main classes on RNA and what do these do?

A
  1. rRNA: This combines with proteins to form ribosomes where protein synthesis can take place.
  2. tRNA carries the amino acids to be incorporates into the protein.
  3. mRNA carries the genetic information for protein synthesis
78
Q

What makes RNA?

A

RNA polymerases.

79
Q

What are the five stages of transcription?

A
  1. RNA polymerase binding
    - Involves detection of initiation sites on DNA
    - This requires transcription factors
  2. DNA chain separation
    - Unwinding
  3. Transcription initiation
    - Selection of first nucleotide
  4. Elongation
    Addition of further nucleotides
  5. Termination
    - Release of finished RNA
80
Q

What is TBP? What does it do?

A

TATA box binding protein. It is part of TFIID.

81
Q

What is TFIID?

A

General transcription factor required to introduce kink into DNA. It determines transcriptional start and direction and provides a leading platform for further transcription factors.

82
Q

What are the three different types of RNA polymerase in our cells?

A

Pol 1, Pol 2 and Pol 3

83
Q

What does RNA polymerase do?

A

Binds promoter qequences so that transcription can occur.

84
Q

Fill in the blanks: New RNA sequence is ……… to the template strand and ……. to the coding strand

A
  1. Complementary
  2. Identical
    (but U instead of T)
85
Q

Describe the concept of a transcription bubble?

A

Specific sequence moves along the DNA. DNA in unwound in front of the polymerase and rewound behind it.

86
Q

In which direction is the RNA chain synthesised in?

A

5’ to 3’

87
Q

How is transcription terminated?

A

New rNA makes a stem loop structure and an enzyme cleaves of the RNA and it is released and the polymerase dissociates.

88
Q

What are transcription factors?

A

DNA binding proteins. They can regulate transcription both positively or negatively.

89
Q

Give an example of a family of transcription factors

A

Steroid receptors, located in the cytoplasm of the cell. On binding these move to nucleus and bind to DNA.

90
Q

Give an example of a steroid receptor and how it works.

A

Glucocorticoid receptor. When free steroid enter cells they bind to receptor and active it to translocate to the nucleus and regulate genes.

91
Q

What are coding and non coding regions called?

A

Coding = exons

Non coding = introns

92
Q

What it the removal of introns called?

A

Splicing

93
Q

How many nucleotides do codons and anti codons consist of?

A

Three. With four different nucleotides available there are 64 possible combinations.

94
Q

What two molecules can be used as sources of energy in DNA replication?

A

ATP and GTP

95
Q

What is aminoacyl - tRNA syntetases and what does it do?

A

An enzyme which binds amino acids to their correct tRNA molecules. It is highly specific. The charged RNA then delivers amino acid to elongating polypeptide. Provides energy in the form of ATP.

96
Q

Name the three binding sites present on tRNA

A 
E = Exit
P = Peptidyl
A = Aminoacyl
97
Q

How is the energy for initiation provided?

A

Hydrolyisis of GTP

98
Q

Briefly describe initiation

A
  1. Requires initiation factors
  2. GTP hydrolysed
  3. Small ribosome subunit binds to 5’ end of RNA
  4. Moves along mRNA until AUG (start codon) found.
99
Q

Briefly describe elongation

A
  1. Elongation factor brings the next aminoacyl tRNA to the A site where the anticodon base pairs with the codon
  2. GTP hydrolysed. Elongatin factor released
  3. Second elongation factor regenerates the first to pick up the next aminoacyl tRNA
100
Q

What enzyme catalyses the peptide bond formation between amino acids?

A

Peptidyl transferase

101
Q

When does termination occur?

A

When the A site of the ribosome encounters a stop codon. (UAA, UAG, UGA)

102
Q

What is a point mutation?

A

Change in a single base on DNA.

103
Q

What is a missense mutation?

A

One that results in change of amino acid sequence and can change protein function. Seen in sickle cell anaemia.

104
Q

What is a nonsense mutation?

A

Creates new termination codon and so changes length of protein.

105
Q

What is a silent mutation?

A

No change in sequence or protein function

106
Q

What is a frameshift mutation?

A

Addition.deletion changes whole frame of protein.

107
Q

Chromosomal mutation affect larger portions of genes. What are the four types of chromosomal mutations?

A

Deletions
Duplications
Inversions
Translocations

108
Q

What happens when proteins synthesis is finished? Give three options.

A
  1. Protein is moved to final cellular location
  2. Protein is modifies by adding further functional groups
  3. Degradation. Unwanted or damages proteins much be destroyed.
109
Q

Where do proteins made in free ribosomes go? When are these moved?

A

Cytosol, nucleus, mitochondria.

Moved after translation

110
Q

Where do proteins made in bound ribosomes in the ER go? When are these moved?

A

plasma membrane, ER, Golgi apparatus, secreted

Moved during translation.

111
Q

What is glycosylation?

A

Adding sugars to proteins. Important in trageting and regonniton

112
Q

What happens to proteins in the ER?

A

Folding and assembly, and formation of disulphide bonds.

113
Q

What does an enzyme do?

A

Speeds up the rate at which a reaction reached equilibrium.

114
Q

What is the transitions state in a reaction? What role do enzymes play here?

A

The reaction intermediate species which has the greatest free energy in the reaction. Enzymes bind and stabilise this state. The reduce activation energy by providing alternative reaction pathways.

115
Q

The catalytic activity of many enzymes depends on co factors. What are the two types of co factors/coenzymes?

A

Metal ions, organic molecules

116
Q

What are tightly bound coenzymes called?

A

Prosthetic groups

117
Q

What is an enzyme without a co factor called?

A

Apoenzyme

118
Q

What is an enzyme with a co factor called?

A

Holoenzyme

119
Q

Name three metal ion cofactors

A

Zinc, iron, copper. These stabilise transition states.

120
Q

What does coenzymeA do?

A

Transfers acetly groups

121
Q

What does ATP do as a coenzyme?

A

Transfers phosphate groups

122
Q

Do most vitamins function as co -enzymes?

A

Yes.

123
Q

Describe the induced fit model

A

Binding of the substrate to an active site causes a conformation change in the enzyme, resulting in a complementary fit.

124
Q

What are ioszymes?

A

Isofroms of enzymes. The catalyse the same reaction but have different properties and structural sequence. These are synthesised during different stages of foetal development, present in different tissues and present in different cellular locations.
An example. Haemoglobin changes. In the womb it has a much higher oxygen affinity than in th adult.

125
Q

What is creatine kinase?

A

Dimeric protein which binds to the muscle sarcomere. M form produced in muscle, B form in brain and both in the heart.

126
Q

What is a phosphorylation reaction and what is good about them

A

Addition of a phosphate group by a kinase enzyme (reversible covalent modification) and can inactivate or activate an enzyme.
Kinases are very fast, reversible and found in all cells!

127
Q

What carries out phosphorylation reactions?

A

Kinases are very fast, reversible and found in all cells!

128
Q

What does a phosphatase do?

A

Removes a phosphate group.

129
Q

What are zymogens?

A

Inactive precursors of an enzyme which can be irreversibly transformed into active enzymes through the cleavage of a covalent bond.

130
Q

Give examples of where we see activation by cleavage of a covalent bond:

A

In pancreas:Chymootrysinogen and trypsinogen (INACTIVE) are formed.
In small intestineL enteripeptidase cleaves trypsinogen to trypsin (ACTIVE) which then cleaves chymotrypsinogen to form chymotrypsin (ACTIVE)

131
Q

What does Vmax mean in terms of enzyme kinetics?

A

The maximal rate of reaction a unlimited substrate concentration.

132
Q

What is Km in terms of enzyme kinetics? What are the units of this?

A

The Michaelis constant Km is the substrate concentration at which the reaction rate is half of Vmax. Units are concentration (M)

133
Q

How is initial reaction rate (Vo) determined?

A

tangent at the curve at time 0.

134
Q

What does a low Km in a reaction mean?

A

Enzyme only needs a little substrate to works at half maximal velocity

135
Q

What does a high Km in a reaction mean?

A

Enzyme needs a lot of substrate to work at half maximal velocity

136
Q

What is the michaelis men ten equation and what does it do?

A

V = (Vmax [S]))/(Km + [S])

It describes the rate of catalysis as a function of substrate concentration.

137
Q

What does a competitive inhibitor do?

A

Binds to the active site of a substrate; blocking any more substrate.

138
Q

What does a non-competitive inhibitor do?

A

Binds to another site, changing the shape of the conformation so that substrate cannot fit into its active site.

139
Q

Give five mechanisms of enzyme control and examples.

A
  1. Allosteric control
  2. Regulation of transcription (varies rate of protein synthesis)
  3. Reversible covalent modification (phosphorylation)
  4. Irrerersible covalent modification (proteolytic cleavage)
  5. Degradation of an enzyme
140
Q

What is feedback inhibition?

A

Inhibitions of rate limiting enzymes in a pathway by end products. When these build up they can inhibit the first enzyme in the pathway. Common mechanism of allosteric control.

141
Q

What is co operativity?

A

The influence that the binding of a ligand to one promoter has on the binding of a ligand to another promotor in an oligomeric protein.

142
Q

Give one important example of allosteric regulation. What is this an example of?

A

Biniding of oxygen to haemoglobin. Example of positive co - operatively.

143
Q

How does allosteric action actually work?

A

Each subunit of the enzyme has two conformations (active/relaxed or inactive/tight). Allosteric activators or inhibitors lock the enzyme in one these forms though normally it flits between the two deepening or presence of a substrate.

Biochemistry (3 decks)

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