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Principles Collated Flashcards > Biochemistry > Flashcards

Biochemistry Flashcards

1
Q

Bond strengths in order. Strongest to weakest?

A 
Covalent 
Ionic 
Hydrogen 
Hydrophobic interactions 
VDW's
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2
Q

Oxidation states of carbon?

A 
Alkane (in fats)
Alcohol (in carbs)
Aldehyde 
Carboxylic acid 
Carbon dioxide
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3
Q

4 major classes of biomolecules and what they consist of?

A

Proteins/peptides= amino acids
Lipids= triglycerides, phospholipids, steroids
Nucleic acids= DNA/RNA
Carbs= Mono, di, poly saccharides

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4
Q

Example of monosaccharide?

A

Glucose

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5
Q

Examples of disaccharides?

A

Lactose

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6
Q

Examples of polysaccharides?

A

Cellulose

Glycogen

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7
Q

1st law of thermodynamics?

A

Energy can neither be created nor destroyed

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8
Q

2nd law of thermodynamics?

A

When energy is converted from one form to another some of that energy becomes unavailable to do work

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9
Q

What type of reaction is it if the change in free energy is negative?

A

Exergonic (can occur spontaneously)

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10
Q

What type of reaction is it if delta G is positive?

A

Endergonic (cannot occur spontaneously)

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11
Q

Entropy?

A

Loss of useable energy

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12
Q

Primary protein structure?

A

Sequence of amino acids

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13
Q

Secondary protein structure?

A

Formation of backbone

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14
Q

Tertiary protein structure?

A

3D structure

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15
Q

Quaternary protein structure?

A

Spatial arrangement of multiple subunits

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16
Q

What holds proteins together?

A

Disulphide bonds

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17
Q

5 elements of a cell?

A 
SER
RER
Mitochondria
Golgi apparatus 
Ribosomes
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18
Q

Role of SER?

A

Synthesis of steroid hormones

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19
Q

Role of RER?

A

Synthesizes polypeptides

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20
Q

Role of mitochondria?

A

Powerhouse of cell can multiply independently

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21
Q

Role of golgi apparatus?

A

Receives materials from ER and distributes, also modifies proteins

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22
Q

Role of ribosome?

A

Where RNA is translated into protein

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23
Q

Prokaryote?

A

Microscopic single cell organism that does not have a defined nucleus

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24
Q

Eukaryote?

A

Normal cell with normal nucleus

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25
Q

Structure of DNA?

A 
Nucleoside = base + sugar 
Nucleotide = nucleoside + phosphate
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26
Q

Examples of purines?

A

Adenine and guanine

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27
Q

What is collective term for base A&G?

A

Purines

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28
Q

Collective term for C, T & U?

A

Pyrimidines

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29
Q

Examples of pyramidines?

A

Cytosine
Thymine
Uracil

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30
Q

What direction is DNA replication?

A

Always in 5’->3’ direction

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31
Q

What type of primer is required for DNA repication?

A

RNA primer

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32
Q

DNA replication is catalysed by DNA polymerases. True or false?

A

True

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33
Q

Which strand always has a free 3’ end?

A

Leading strand

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34
Q

What unwinds DNA in DNA replication?

A

DNA helicase

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35
Q

How are okazaki fragments made?

A

Lagging strand is replicated in short fragments

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36
Q

What are the short replicated fragments of the lagging strand in DNA called?

A

Okazaki fragments

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37
Q

What does RNA contain?

A

Stem loop

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38
Q

3 types of RNA?

A

rRNA (ribosomal)
mRNA (messanger)
tRNA (transfer)

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39
Q

Role of rRNA?

A

Combines with proteins to from ribosomes where protein synthesis takes place

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40
Q

Role of tRNA?

A

Carries amino acids to be incorporated into protein

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41
Q

Role of mRNA?

A

Carries genetic information for protein synthesis

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42
Q

How many nucleotides do anticodons consist of?

A

3

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43
Q

How many types of RNA polymerases do

  • prokaryotic cells have
  • Eukaryotic cells have?
A
  • 1 type for pro

- 3 types for eu

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44
Q

Types of RNA polymerase in a eukaryote?

A

Pol i, ii, iii

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45
Q

Which RNA polymerase synthesizes all mRNA?

A

Pol ii

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46
Q

Stages of transcription?

A
  • RNA polymerase binding
  • DNA chain separation
  • Transcription initiation
  • Elongation
  • Termination
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47
Q

What happens in first stage of transcription?

A

RNA polymerase binding

  • Detects initiation sites on DNA
  • Requires transcription factors
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48
Q

What does first stage of transcription require?

A

Transcription factors

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49
Q

2nd stage of transcription?

A

Unwinding of DNA

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50
Q

3rd stage of transcription?

A

Transcription initiation

  • Selection of 1st nucleotide of growing RNA
  • Required additional general transcription factors
51
Q

4th stage of transcirption?

A

Elongation

  • Addition of further nucleotides to RNA chain
  • RNA Synthesized in 5’ -> 3’ direction
52
Q

What direction is RNA synthesized in?

A

5->3

53
Q

5th stage of transcription?

A

Termination

-release of finished RNA

54
Q

What is TFIID?

A

General transcription factor required for Pol ii transcribed genes

55
Q

Difference between exons and introns?

A 
Exons= coding regions 
Introns= non-coding regions
56
Q

What happens to introns before translation?

A

They are transcribed together with exons but then removed by splicing before translation into the protein

57
Q

What do anticodons from tRNA form with codons of mRNA?

How many possible combinations?

A

Base pairs

64

58
Q

Number of possible amino acid types?

A

20

59
Q

What is the start codon in translation?

A

AUG

60
Q

Components of translation?

A
  • Amino acids
  • tRNAs
  • Aminoacyl tRNA synthetases
  • Protein factors
  • ATP/GTP
  • Ribosomes
  • mRNA
61
Q

Stages of Translation?

A

Initiation
Elongation
Termination

62
Q

What happens in initiation of translation?

A
  • GTP provides energy
  • Ribosomal sub-unit binds to 5’ end of mRNA and moves along until it finds start codon
  • Initiator tRNA pairs to start codon
  • Large sub-unit joins assembly and initiator tRNA is locked in P site
63
Q

What happens in elongation stage of translation?

A
  • Elongation factor brings aminoacyl - tRNA to A site
  • GTP
  • Second elongation factor regenerates the 1st to pick up next aminoacyl tRNA
  • Peptidyl transferase catalyses peptide bond formation between the amino acids in P and A site
64
Q

What happens in termination stage of translation?

A
  • Occurs when A site of ribosome encounters a stop codon (UAA, UAG, UGA)
  • Finished protein cleaves off tRNA
65
Q

How many tRNA binding sites and their names?

A

3 sites

E, Aminoacyl (A), Peptidyl (P)

66
Q

What does degenerate mean?

A

Many amino acids have more than one codon

67
Q

What does unambiguous mean?

A

Each codon codes only for one amino acid

68
Q

What does an enzyme do?

A

Speed up the rate at which a reaction reaches equilibrium however does NOT affect position of equilibrium.
-They lower activation energy and stabilise the transition state

69
Q

What are enzymes without a cofactor?

A

Apoenzymes

70
Q

What are holoenzymes?

A

Enzymes with a cofactor

71
Q

Induced fit model?

A

Binding of substrate to active site induces a conformational change in the shape of the enzyme resulting in a complimentary fit

72
Q

What type of reaction do protein kinases carry out?

A

Phosphorylation

73
Q

What is Vmax?

A

Maximal rate of reaction at UNLIMITED substrate concentration

74
Q

What is Km?

A

Michaelis constant = 50% Vmax

75
Q

Which types of graphs are used to show enzyme kinetics and why?

A

Lineweaver Burk Plots

- Instead of hyperboles because it is easier to read Vmax and Km

76
Q

What is Vmax in a lineweaver burk plot?

A

Intersection of the straight line with the Y axis

77
Q

What is Km in a lineweaver burk plot?

A

Lines intersection with the x axis

78
Q

Competitive enzyme inhibition?

A
  • Binds to active site
  • Vmax remains the same
  • Km varies
79
Q

What happens to Vmax in competitive inhibition?

A

Remains the same

KM varies

80
Q

Non-competitive enzyme inhibition?

A

Binds to site other than active site

  • Vmax varies
  • Km stays the same
81
Q

What happens to Vmax in Non-competitive inhibition?

A

Varies

82
Q

Michaelis Menten control shown in a diagram looks like?

A

Like a right angle sort of curve.

Steep and not gradual curve

83
Q

Allosteric regulation in a diagram looks like?

A

Much less curved, gradual rise (sort of a loose S shape)

84
Q

Functions of cholesterol?

A

Present in cell membranes
Component of myelin sheath
Precursor molecule for- steroids, vit D & Bile acids

85
Q

Where are triglycerides present in cell membrane?

A

Lipid bilayer

86
Q

Role of triglycerides?

A

Highly concentrated energy stores

87
Q

Anabolism?

A

Requires energy
reductive
Endergonic

88
Q

Catabolism?

A

Breakdown of molecules to yield energy

Exergonic and oxidative

89
Q

How does glucose get into cell?

A

Via Glucose transporters GLUT by facilitated diffusion

90
Q

What is the initial pathway for conversion of glucose to pyruvate?

A

Glycolysis

91
Q

Net gain per glucose during glycolysis?

A

+ 2 ATP

92
Q

Process of glycolysis?

A 
Glucose
|
Fructose-1,6-biphosphate
|
Triose phosphate x2
|
Pyruvate
93
Q

What phosphorylates glucose in glycolysis?

A

Hexokinase

94
Q

What phosphorylates fructose-6-biphosphate?

A

Phosphofructokinase

95
Q

What converts triose phosphate to pyruvate?

A

Pyruvate kinase

96
Q

How is NAD+ regenerated in glycolysis?

A

Through oxidative metabolism of pyruvate

97
Q

What happens to pyruvate in anaerobic conditions?

A

Alcoholic fermentation

Lactic acid formation in humans

98
Q

What happens to pyruvate in aerobic conditions?

A

Further oxidized in krebs cycle

99
Q

Make up of mitochondria?

A

Inner membrane
Outer membrane
Central matrix (contains enzymes of krebs cycle)
Cristae folds

100
Q

Aerobic metabolism of pyruvate happens where?

A

Mitochondrial matrix

101
Q

What happens in metabolism of pyruvate?

A
  • Converted to acetyl-CoA
    -Condenses with 4C compiund to form 6C citric acid
    -Citric acid is decarboxylated twice (yields CO2 x2)
    -
102
Q

What is the conversion of pyruvate to acetyl-CoA catalyzed by?

A

Pyruvate dehydrogenase complex (PDC)

103
Q

How many oxidation reactions happen in Krebs cycle?

A

4

Yields 3 NADH + H+ and 1 FADH2

104
Q

What compound is recreated in Krebs cycle?

A

Oxaloacetate (4C)

105
Q

Which enzyme involved in the Krebs cycle is NOT in the mitochondrial matrix and were is it?

A

Succinate Dehydrogenase

Integrated into the inner mitochondrial membrane

106
Q

How may pairs of electrons are transferred in NADH+ H+ reaction?

A

3 pairs

and 1 pair in FADH2

107
Q

Products from each acetyl CoA in Krebs cycle?

A

3 NADH + H+
1 FADH2
1 GTP
2 CO2

108
Q

What is the standard redox potential of a substance?

A

Measure of how readily substance donates electrons

109
Q

Phosphoryl transfer potential?

A

Free energy change for ATP hydrolysis

110
Q

Electron transfer potential?

A

Measured by redox potential of a compound

111
Q

What does a negative standard redox potential mean?

A

Reduced form of X has lower affinity for electrons than hydrogen

112
Q

What does a positive standard redox potential mean?

A

Reduced form of X has a higher affinity for electrons than hydrogen

113
Q

What is oxidative phosphorylation?

A

Coupling of respiration to ATP synthesis

114
Q

How many stages of oxidative phosphorylation?

A

2 stages

  • electron transport
  • ATP synthesis
115
Q

What happens in electron transport chain?

A

Electrons passed down from high to low redox potentials and transferred onto O2 to make H20

116
Q

What is coupled in the electron chain transport process?

A

H+ transport from mitochondrial matrix to intermembrane space

117
Q

What are protons attracted to in the ETC?

A

The matrix because the matrix side is more negative, there are more protons in the intermembranous space than in the matrix

118
Q

How to inhibit oxidative phosphorlation?

A

Cyanide, Azide, CO= all inhibit transfer of electrons to O2

No proton gradient formed, no ATP synthesized

119
Q

What happens in Oxidative phosphorylation?

A
  • Electrons from NADH/FADH2 are used to reduced O2 to H20
  • Their energy is used to pump protons from mitochondrial matrix to intermembrane space and hen protons flow back across membrane
  • Energy of proton flow is used to phosphorylate ADP to ATP
120
Q

One glucose molecule yields?

A

30-32 molecules of ATP

121
Q

Amount of NADH + H+ created?

A 
3 in Krebs 
2 in Glycolysis 
2 in link 
= 
10 NADH + H+
122
Q

How many FADH2 produced?

A

2 in krebs

123
Q

Calculations for ATP produced from NADH + H= AND FADH2?

A

10 x 2.5= 25 ATP
2 x 1.5= 3 ATP
=
28 ATP

124
Q

Overall ATP?

A 
28 ATP from NADH/FADH 
2 from glycolysis 
2 from Krebs cycle (GTP)
= 
32 ATP

Principles Collated Flashcards (13 decks)

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