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MODULE 1 Flashcards

1
Q

Carbon

A
  • inherently neutral (uncharged)
  • non-polar/hydrophobic
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2
Q

O, N, P (sometimes S)

A

make compounds
* polar/hydrophilic
* partly (dipoles) or fully charged (i.e. molecules with those atoms/colours will be polar)

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3
Q

Covalent bond

A

holds molecules together

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4
Q

Eukaryote

A

organism has cells with a defined nucleus (can be single celled or multicellular)

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5
Q

Prokaryotic

A

single celled organism without a nucleus

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6
Q

Main molecules types in bio

A
  • Water
  • Carbs
  • Lipids
  • Amino acids
  • Nucelotides
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7
Q

Water…

A
  • Stabilise temp
  • Ice floats (insulate water/floating platforms)
  • Water tensions (H bonding)/capillary action
  • Good solvent for polar molecules
  • Poor solvent of hydrophobic molecules (cell membranes)
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8
Q

Monosaccharides

A

Usually form rings
* Glucose (6 atom ring)
* Fructose
* Galactose
* Ribose (5 atom ring)

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9
Q

Carbs/sugars/saccharides

A

Composed of C,H,O with general formula Cn(H2O)n
* ‘n’ # of carbon atoms
* Lots of O = very polar

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10
Q

Disaccharides

A

2 mono joined together
* Lots of different connections
* Lactose
* Sucrose
* Trehalose (glucose/glucose)

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11
Q

Sugar polymers

A

Long chains of mono
* Starch - Storage
* Chitin - Protection
* Cellulose - Structure

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12
Q

Saturated lipid

A

all single bonds
Liquid typically

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13
Q

Unsaturated lipids

A

one or more double bonds
Solids typically

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14
Q

triglycerols

A

Energy stores
* Adipocyte (fat deposit)

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15
Q

steroids

A

Signalling molecules
Lipid

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16
Q

Phospholipids

A

Form cell membranes
* Mostly H-phobic but with polar end
* Polar parts interact with aq enviro, H-phobic parts cluster together
* Lipid bilayers separate inside + outside cell

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17
Q

amino acids

A

Building blocks of protein

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18
Q

In aq sol. the amino and acid group…

A

Are charged (NH3+ and COO-)
* This is the NORMAL STATE for amino acids in nature

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19
Q

Nucleotides

A
  1. Phosphate group (-ve charge)
  2. Sugar (ribose or deoxyribose)
  3. Nucleobase (A,G,C,T,U)
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20
Q

Mono/di/tri-nucleotides

A

dAMP (mono)
dADP (di)
dATP (tri)

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21
Q

Capillary action

A

ability of liquid to flow in narrow spaces, even against gravity

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22
Q

Purine

A
  • double ring, flat aromatic base (A, G)
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23
Q

Pyrimidine

A
  • single ring flat aromatic base (C, T, U)
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24
Q

5’ to 3’

A

Nucleic acids

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25
Q

N-terminus (or amino terminus) to C-terminus (or carboxy terminus)

A

Proteins

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26
Q

Residues

A

Some of monomer is lost on polymerisation, leaving residue incorporated in the growing chain
* For these molecules, the residue is usually the biggest part

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27
Q

Biopolymer synthesis relies on…

A

dehydration reactions and are anabolic

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28
Q

Common sugar phosphate backbone

A
  • Negative charge on phosphates
  • Hydrophilic (sugars and phosphates)
  • 5’ and 3’ ends
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29
Q

Things in DNA vs. RNA

A

Deoxyribose (DNA)
Ribose (RNA)
Uracil (RNA)
Thymine (DNA)

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30
Q

Electrophoresis

A

Nucleic acids migrate in an electric field because they are charged.
* Distance they migrate dependent on size

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31
Q

<50 amino acid residues

A

NB peptides

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32
Q

> 50 residues

A

protein

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33
Q

Aromatic protein side chains and nucleobases have a characteristic absorbance…

A

~280 nm (proteins) or ~260 nm (bases)

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34
Q

Record spectra

A

A260:A280 PROTEINS
A260:A230 CARBS/PHENOL

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35
Q

C and G complement

A

3 hydrogen bonds
stronger

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36
Q

A and T complement

A

2 hydrogen bonds
A bit weaker

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37
Q

beta DNA

A
  1. Strands run in opposite directions
  2. Flat bases stack on top of one another (reduced A260nm intensity)
  3. Negative phosphates repel each other
  4. Right handed double helix
  5. Major and minor grooves
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38
Q

N-glycosidic bond

A

covalent bond between sugar and base in RNA/DNA

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39
Q

Phosphodiester bond

A

covalent bond between nucleotides in RNA/DNA

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40
Q

Deamination

A

loss of an amine

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41
Q

dsDNA

A

double stranded DNA

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42
Q

ssDNA

A

single stranded DNA

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43
Q

Tm/Melting point

A

when 50% of the molecule is unfolded/separated

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44
Q

Information flow

A

Going from DNA >transcription> RNA >translation> PROTEINS

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45
Q

Genome

A

Complete genetic information
DNA

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46
Q

Transcriptome

A

all the RNA expressed in a cell/tissue at a give time

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47
Q

Proteome

A

all the proteins expressed in a cell/tissue at a give time

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48
Q

Prokaryotes have ____ genomes

A

Small
* Bacteria and archaea have circular chromosomes (plasmids)

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49
Q

Eukaryotes have ____ genomes

A

Big
* Linear chromosomes
* Condensed into chromatin
* Wrapped around histone protein

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50
Q

mRNA

A

message for making proteins
* Often multiple copies made, designed to be used then degraded

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51
Q

MicroRNA and snRNA

A

regulatory roles

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52
Q

Ribosomal RNA & Transfer RNA

A

Important for protein synthesis

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53
Q

role of proteins

A

shape, they form receptors, enzymes, hormones and growth factors, toxins, transporters and antibodies

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54
Q

Epigenetic regulation

A

Expression of some genes is altered by chemical modifications of DNA and proteins but NOT to the DNA sequence itself - epigenetics.
* Can be passed through generations of cells (and individuals)

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55
Q

Start Codon

56
Q

Stop Codons

A
  • UAA
  • UAG
  • UGA
57
Q

OPEN READING FRAME (ORF)

A

start to the stop codon of a gene that encodes the protein/peptide

58
Q

Missense

A

Mistake in the DNA code, one of the DNA base pairs is changed

59
Q

Silent

A

Mutation of the protein-coding region that has no effect on the protein sequence

60
Q

Nonsense

A

Single change in DNA code produces stop codon, prematurely terminates protein synthesis

61
Q

Insertion

A

Addition of one (or more) nucleotide base pairs into the DNA sequence

62
Q

Deletion

A

A piece of DNA is removed from the sequence

63
Q

Point mutation

A

Single amino acid has been changed (can also refer to a small # of bases being modified, added or lost in the nucleotide sequence)

64
Q

Frameshift

A

Insertion or deletion mutation results in a change to a gene’s reading frame

65
Q

Duplication mutation

A

Incorrect copying leads to repeated sequences

66
Q

Redundant/degenerate

A

some amino acids are encoded by more than one codon

67
Q

DNA Polymerases

A
  • Make a DNA copy from template
  • Need primer to start
  • Use deoxynucleotide triphosphates as substrate
68
Q

Semi-conservative

A

each newly generated dsDNA contains one original (the template) and one new strand

69
Q

Topoisomerase enzymes

A

cut strands, allow to unwind and stick back together (religate)

70
Q

Biopolymer synthesis

A
  1. Initiation
  2. Chain elongation
  3. Termination
71
Q

ORI (Origin) Sites

A
  • AT-rich (easier to pull strands apart because less stable)
  • DNA binding proteins open up the site
  • DNA helicase unwinds - replication forks
72
Q

Both original/parental strands are copied at the same time

73
Q

Leading strands

A

Primase makes an RNA primer to begin
* DNA polymerase III makes a DNA copy of the strand in the 5’ -> 3’ direction
* Continuous copying

74
Q

Lagging

A

Primase makes multiple RNA primers
* polymerase synthesises, until it runs into the next primer making Okazaki fragments

75
Q

When the two replication forks come together…

A
  • DNA polymerase I replaces the RNA primer with DNA
  • DNA ligase joins pieces
  • Discontinuous copying
76
Q

Termination

A
  • Joining up the new strands
  • Roughly opposite the origin
77
Q

Eukaryotic DNA Replication

A
  • Multiple origins on each linear chromosome
  • Need to strip off nucleosomes before replication and reform afterwards
  • Special mechanisms (telomerase) for the ends telomeres of the chromosomes
78
Q

Chain elongation

A

main phase of polymerisation

79
Q

ssBP/single stranded binding proteins

A

bind to ssDNA and protect from tangling/reforming dsDNA

80
Q

Supercoiling

A

overwinding DNA

81
Q

RNA Polymerases

A
  • Make an RNA copy from a DNA template
  • DON’T NEED A PRIMER to start
  • Use ribonucleotide triphosphates as substrate
  • Limited proofreading
82
Q

Promoter region

A
  • Upstream 5’ end
  • RNA polymerase binds
  • -10 and -35
83
Q

Transcription factor(s)

A

proteins capable of recognising a specific base sequence

84
Q

Promoter strength

A

Strong binding = more RNA copies made
Weak binding = fewer RNA copies made

85
Q

Transcription Regulation: Repression

A

Protein repressor binds.
* This blocks the binding of the sigma factor/RNApol complex
* no gene expression

86
Q

Transcription Regulation: Accelerators

A

Transcriptional Activator (protein) binds at a specific DNA sequence
* alters the structure of the promoter so the transcription factor can now bind more frequently

87
Q

Transcription bubble

A

local unwinding of DNA for transcription

88
Q

Translation

A

Converts a nucleotide sequence to a protein sequence

89
Q

Peptide bond formation is very thermodynamically ____

A

unfavourable

90
Q

Messenger RNA (mRNA)

A

contains template for protein synthesis/information about which amino acids to add in which order

91
Q

Transfer RNA (tRNA)

A

matches the correct amino acids to the template

92
Q

Ribosomal RNA (rRNA)

A

combines with proteins to form the machinery for protein synthesis/catalyses peptide bond formation

93
Q

Aa-tRNA synthetases

A
  • attach the amino acid to the tRNA
  • Catalyse the activation of amino acids
94
Q

Ribosome

A

E-Site - Used tRNAs move here before exiting
P-Site - For growing protein chain
A-Site - Accepts incoming tRNA-aa

95
Q

The stages of protein synthesis

A
  1. Initiation
  2. Elongation
  3. Termination
96
Q

Prokaryotic VS. Eukaryotic Translation

A

Initiation - different mechanism for finding the start codon, special tRNA but normal Met as first amino acid.
Elongation - same
Termination -
* in EU - a single release factor recognises all three stop codons
* prokaryotes have** 2-3**

97
Q

Peptidyl transferase

A

enzyme component of the ribosome that transfers the activated amino acids from tRNA to the growing peptide chain

98
Q

Primary structure

A

Amino acid sequence

99
Q

Secondary structure

A

Local features allow formation of structure - backbone-backbone hydrogen bonding
* Alpha helix & Beta sheet

100
Q

Tertiary structure

A

Overall 3D arrangement of a polypeptide chain
* Held together by lots of different interactions/bonds

101
Q

Quaternary structure

A

Organisation of subunits (Many but not all proteins have multiple subunits)

102
Q

Hydrophobic effect

A

driving force for protein folding

103
Q

Protein Folding

A
  • Info encoded in amino acid sequence
  • Burial of hydrophobic surfaces/side chains in aqueous solvent
  • Collapse of protein chain/formation of secondary structure
  • Firming up tertiary structure by interactions in protein
104
Q

unfolding proteins

A

Proteins much more easily lose their unique 3-D shape if they are heated

105
Q

α-Helices and B-DNA

A

α-helices are a perfect size to fit into the major groove

106
Q

Single strands of protein can fit in the ____

A

minor groove

107
Q

Beta Strand

A

extended form of protein secondary structure

108
Q

Beta Sheet

A

Assembly of beta strands

109
Q

Beta turn

A

form of protein secondary structure, often formed between beta strands in a beta sheet

110
Q

Energy

A

capacity to do work

111
Q

Potential energy

A
  • stored in chem bonds
112
Q

Kinetic energy

A
  • expressed as movement, heat etc.
113
Q

1st law of thermo

A

Energy can be neither created or destroyed
* Transferred

114
Q

2nd law of thermo

A
  • Entropy of universe is increasing
  • Physical and chemical process favour randomness
  • If you apply energy you can push a state towards order
115
Q

Favourable reaction

A

give out energy/exergonic

116
Q

Unfavourable reaction

A

need energy/endergonic

117
Q

substrate molecules

A

contain more free energy

118
Q

Activation energy/barrier

A

The energy required to initiate a reaction

119
Q

Entropy

A

measure of disorder

120
Q

Equilibrium

A

rates of forward and reverse reactions are the same; concentrations of substrates and products don’t change; overall energies are balanced

121
Q

Kinetics

A

how quickly an event happens; rates

122
Q

Thermodynamics

A

measures and transitions of intrinsic energy

123
Q

Enzymes

A

Use catalysts to lower energy barrier

124
Q

Enzyme process

A
  1. E + S
  2. ES (enzyme-substrate complex)
  3. E’S (Enzyme-Transition state complex
  4. E + P
125
Q

Lock and key model

A

substrate molecules fits directly into the active site

126
Q

Induced-fit model

A

substrate induces a shape change for optimal substrate bonding and activity

127
Q

Selection model

A

enzyme exists in multiple forms in equilibrium, only one of which (A) binds substrate

128
Q

Enzyme regulation

A
  • inhibited by compound that binds to the active site, prevents substrate from binding
  • Or binds outside the active site and stops the motions of the enzymes required for activity
129
Q

Pyrophosphate (PPi)

A

released by hydrolysis of NTPs into NMPs; spontaneously forms phosphates (2Pi); provides energy for unfavourable reactions

130
Q

How do tRNA and aminoacyl RNA synthetases work together to correctly translate an mRNA sequence translated into a protein/peptide sequence?

A

aminoacyl RNA synthetases make sure that the correct amino acid is attached to the correct tRNA

131
Q

Kinetic control

A

relates to the energy required to go beyond the activation barrier

132
Q

Thermodynamic control

A

start or end, how quickly is it going to take place

133
Q

How can the hydrolysis of pyrophosphate drive unfavourable interactions?

A

Coupling reactions so the net energy is gained even though one step is unfavoured
* Driving the reaction in one direction

BIOL1007 (4 decks)

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