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BO201 Molecular and Cellular Biology > Theme 2: Biomolecules & their importance in living cells > Flashcards

Theme 2: Biomolecules & their importance in living cells Flashcards

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1
Q

is lipid hydrophobic or hydrophilic?

A

hydrophobic

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2
Q

what is hydrophobic?

A

immiscible with water

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3
Q

what is the body’s fattest organ?

A

the brain

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4
Q

is the average body fat higher in men or women?

A

woman 22-25%

men 15-18%

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5
Q

what are the functions of lipids?

A

• Storage lipids: Triacylglycerols

• Membrane lipids: phospholipids (glycerophospholipids,
sphingomyelin), glycolipids, sterols (cholesterol)

• Other roles, e.g., hormones, intracellular signalling,
enzyme cofactors, pigments

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6
Q

what are fatty acids?

A

simplest lipids and basis of many complex lipids

• Carboxylic acids with
hydrocarbon chains of 4 to 36 carbons

Can be:
• Fully saturated: contains no
double bonds and are
unbranched
• Unsaturated: contains one or
more double bond
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7
Q

what is stearic acid?

A

(18-carbon with 0
double bonds)
saturated fatty acid

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8
Q

what is oleic acid?

A

(18-carbon with 1 double
bond at the ninth carbon
from the omega end, w-9)
mono-unsaturated fatty acid

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9
Q

what is linoleic acid?

A

(18-carbon with 2
double bonds, w-9, w-6)

poly unsaturated fatty acid

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10
Q

what are the effects of double bonds on the conformation of fatty acids?

A

• Kink in hydrocarbon chain
• Causes disorder in packing against other chains
• This disorder causes greater fluidity in membranes with
cis-double bonds vs
saturated FA chains

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11
Q

what do cis double bonds do?

A

Cis double bonds introduce a rigid bend and do not permit rotation

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12
Q

what are triglycerides composed of?

A

Composed of three FA residues each in ester linkage with a single
glycerol

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13
Q

what are adipocytes?

A

specialised lipid storage cells

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14
Q

what is saponification?

A

production of natural soaps by boiling triglycerides with NaOH

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15
Q

what are the advantages of TAGs as stored fuels?

A

Contain more energy than equal weight of carbohydrate
Oxidation of 1 g TAGs yields >twice the energy of 1 g of carbohydrate

Since TAGs are hydrophobic there is no need for water of hydration,
therefore they are lighter

In some animals TAGs are stored under the skin to provide insulation
Provide energy in hibernating animals
May increase buoyancy in aquatic animals

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16
Q

what do the physical properties of fats depend on?

A

Consistency depends on 1) chain length,

2) degree of saturation and 3) temperature

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17
Q

why do chain length effect the physical properties of fats?

A

: FAs with longer chains and fewer double bonds

are less fluid

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18
Q

why does saturation effect the physical properties of fats?

A
  • Saturated FAs (12:0-24:0) are waxy solids

* Unsaturated FAs of same length are oily liquids

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19
Q

name 7 cellular membranes

A 
Plasma membrane, 
endoplasmic reticulum, 
Golgi apparatus,
mitochondria: inner and outer membranes,
 nuclear membrane,
lysosomal membrane
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20
Q

explain plasma membrane

A
  • Outer boundary of the cell
  • Semi-permeable barrier (selective in what it allows in or out)
  • Maintains cellular structure
  • Means of communication with other cells (protein receptors)
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21
Q

name the components of biological membranes

A
  • lipids
  • proteins
  • carbohydrates
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22
Q

name 3 types of membrane lipids

A

Phospholipids
Glycolipids
sterols

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23
Q

name 3 types of phospholipids

A

Phosphoglycerolipids, glycerophospholipids

• Sphingomyelin

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24
Q

give 2 points on glycolipids

A
  • Overlap with phospholipids

* Includes cerebrosides and gangliosides

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25
Q

what do sterols include?

A

cholesterol

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26
Q

what are the most abundant lipids in membranes

A

•Glycerophospholipids

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27
Q

what are •Glycerophospholipids composed of?

A
  • Glycerol joined to two FAs (hydrophobic)

* with a phosphate head group (polar)

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28
Q

what are sphingolipid that is a phospholipid composed of?

A

Composed of one molecule of sphingosine (or derivative), one fatty acid and a polar head joined in a phosphodiester link

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29
Q

what is the second most abundant lipids in membranes?

A

Glycosphingolipids

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30
Q

what are Glycosphingolipids composed of?

A

Composed of one molecule of sphingosine (or derivative), one fatty
acid and a polar head joined in a glycosidic link

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31
Q

what is the X group in Glycosphingolipids

A

Simple sugar: Cerebrosides

Complex sugar: Gangliosides

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32
Q

what do the 4 human blood groups differ in

A

oligosaccharides on the

surface of red blood cells

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33
Q

what are the 4 different human blood cells?

A

A,B,AB,O

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34
Q

what are lipid bilayers?

A

basis of biological membranes

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35
Q

what does the polar surface of the bilayer contain?

A

charged groups

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36
Q

where are the hydrophobic tails in lipid bilayers?

A

interior of the bilayer

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37
Q

describe the Interactions of phospholipids and glycolipids

in aqueous medium

A

Virtually insoluble in water

They cluster together with hydrophobic tails directed away from
water and hydrophilic groups interacting with the surrounding
water

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38
Q

what are the various lipids in the membrane?

A
  • sphingomyelin
  • cerebroside
  • ganglioside
  • phosphoacylglycerol
  • cholesterol
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39
Q

describe Asymmetry in membrane layers

A
  • Both inner and outer layers of bilayer contain mixtures of lipids
  • Compositions on inside and outside of lipid bilayer is different
  • Asymmetry
  • E.g., phosphatidylserine is only found on inner leaflet of the plasma membrane
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40
Q

talk about carbohydates in membranes

A

• Some oligosaccharides are covalently bound to lipids: glycolipids

• Most oligosaccharides are covalently bound to proteins:
glycoproteins or glycosylated proteins

• Usually branched oligosaccharides with less than 15 sugar units

• Oligosaccharides on the outer plasma membrane vary between
species, cell types and in disease

• Important for cell to cell recognition

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41
Q

name 3 types of proteins in membranes

A
  1. Integral proteins
  2. Peripheral proteins
  3. Lipid-anchored proteins
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42
Q

where are integral proteins

A

inserted into membrane

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43
Q

where are peripheral proteins?

A

loosely bound to membrane

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44
Q

where are 3. Lipid-anchored proteins?

A

Covalently attached to lipids in the membrane

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45
Q

give some features of integral proteins

A

Proteins are dispersed and individually
inserted into the phospholipid bilayer

a transmembrane protein
• bound tightly to the interior of the
membrane
• can be removed by treatment with
detergents or ultrasonification
• removal generally denatures them
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46
Q

talk about peripheral proteins

A

• bound by electrostatic
interactions
• can be removed by raising
the ionic strength

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47
Q

talk about lipid anchored proteins

A 
• Anchored on the membrane through
covalent attachment between lipid and an
amino acid in the protein
• Example: GPI-anchored:
(glycosylphosphatidylinositol) to the C
terminal amino acid of protein
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48
Q

talk about the hydrophillic and hydrophobic regions in integral proteins in membranes

A

• Hydrophilic regions of proteins protrude above and below the lipid
bilayer to be exposed to water

• Hydrophobic regions of proteins are positioned within the interior of the
bilayer – alpha helices

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49
Q

what is the fluid mosaic model?

A
  • Fluid: lateral motion of components in the membrane;
  • proteins, for example, “float” in the membrane and can move along its plane
  • Mosaic: components in the membrane exist side-by-side as separate entities

• i.e., a lipid bilayer with proteins, glycolipids, and sterols such as
cholesterol embedded in it

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50
Q

describe the fluidity of the membrane

A

• Most of the lipids and some of the proteins can drift
randomly in the plane of the membrane
• When membranes are solid the permeability
changes and enzymatic proteins in it may become
inactive

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51
Q

what effects membranes fluidity?

A
  1. Temperature
    As temperature decreases membrane remains fluid until a critical temperature is reached and then the phospholipids settle into a closely packed arrangement and the membrane
    solidifies
  2. Lipid composition
    • Hydrocarbon chain length
    • Degree of saturation of hydrocarbon chains
    • Presence of sterols
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52
Q

how does temperature effect the fluidity of the membrane

A

as the membrane heats up it goes from a firmer gel state to a more fluid state

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53
Q

how does cholesterol affect fluidity?

A 
• Cholesterol stabilizes
hydrocarbon tails of FA
• At 37oC it restricts the
movement of
phospholipids
• At lower temperatures it
impedes packing and
solidification
54
Q

name the different movemements of phospholipids in membranes

A
  • rapid rotational diffusion
  • very slow transverse exchange (flip flop)
  • rapid lateral diffusion
  • rapid flexing of the hydrocarbon chain
55
Q

what does the flipflop diffusion need

A

to be catalyzes by flippase

56
Q

what would be an experiment to show lateral movement of membrane lipids?

A

molecules on a surface are labeled with a flurecent dye

A spot on the surface is bleached by an intense highly focused lazer

as labeled molecules diffeused into the spot the contrast begins to fade

eventually the spot is indistinguishable from the rest of the cell surface

57
Q

talk about movement of proteins in membranes

A

Proteins are larger and move more slowly than lipids

Movement is not always free:
Attachment to cytoskeleton:
- immobilises proteins
- propels proteins linked to motor proteins within the cell

58
Q

what is an experiment to show lateral movement of proteins in menbranes

A

membrane proteins labelled with different fluorescent antibodies

hybrid cell produced by cell diffusion

proteins begin to mix in a few minutes at 37deg

proteins completely mised after 40min

59
Q

describe lipid rafts

A
  • Enriched in cholesterol and sphingolipids
  • 100-200nm in diameter, heterogenous, dynamic
  • Specialised microdomains that compartmentalise cellular processes
  • Lipids tend to be more saturated and tightly packed
  • Certain proteins preferentially locate to lipid rafts
60
Q

what are the functions of proteins in the plasma membrane?

A
  1. Transport
  2. Enzyme activity
  3. Signal transduction
  4. Intercellular joining
  5. Cell-cell recognition
  6. Attachment to cytoskeleton and extracellular matrix
61
Q

why is there need for transport across mebranes?

A

Cells need to import raw materials for biosynthesis and to export waste

Need to translocate ions across membranes

62
Q

what inhibits the transport of ions and polar molecules?

A

the hydrophobic core of the lipid bilayer impedes

transport of ions and polar molecules

63
Q

name 3 types of transport in the membrane?

A
  • Simple diffusion
  • Facilitated diffusion
  • Primary active transport
64
Q

talk about simple diffusion

A

• Does not require a protein carrier
• Is not saturated when there is a high concentration of substrate to
be transported
• Is not energy-dependent
• Does not produce a concentration gradient
• Driven by a concentration gradient

65
Q

give examples of simple diffusion

A

Hydrophobic molecules such as hydrocarbons
• Gases such as O2
, CO2
, N2
• Small polar uncharged molecules e.g., ethanol

66
Q

how are polar and charged molecules moved across the membrane

A

Transport proteins (transporters or permeases) enable molecules
to cross the membrane without coming in contact with the
lipid bilayer

67
Q

talk about facilitated diffusion

A

• Requires a specific transport protein
• Does not produce a concentration gradient
• Substance travels down its concentration
gradient
• It is saturated when there is a high
concentration of substrate to be transported
• Not energy-dependent, but it may require a
stimulus, e.g., binding of specific molecule to
the transporter protein may open a channel:
ligand-gated channel

68
Q

talk about active transport

A

• Requires a transport protein, therefore it is
saturated at high concentration of substrate
• Moves substance against a concentration
gradient to produce a gradient
• Energy-dependent:
Active transport is thermodynamically
unfavourable. Must be coupled to an energygenerating process, e.g., ATP hydrolysis

69
Q

name the types of active transport

A

primary

secondary

70
Q

give a few features of primary active transport

A

= Uniport

Generally powered by ATP hydrolysis

71
Q

give a few features of secondary active transport

A

= Indirect active transport
= Co-transport:
Transport of one molecule is driven by co-transport of another molecule

72
Q

what does symport mean?

A

flow is in the same direction

73
Q

what does antiport mean?

A

flow is in the opposite direction

74
Q

what provides energy for co-transport?

A

Movement of molecule X down its concentration gradient drives
movement of molecule S against its concentration gradient

75
Q

what are the 2 steps for providing enery for co-transport?

A
  1. Ion gradient (X) produced by ATP hydrolysis
2. The flow of the ion (X) down its
concentration gradient is coupled to
movement of a second compound
(S) against its concentration
gradient.
76
Q

name 2 lipids with biological activity

A
  1. Cholesterol is the precursor of
    • steroid hormones (testosterone, estradiol, cortisol)
    • vitamin D
  2. Specific enzymes (phospholipases) degrade phospholipids
    to produce signalling molecules
77
Q

what are the 3 types of phospholipids?

A

Phospholipase A: remove a fatty acid from phospholipids

Phospholipase C: removes the phospho-head group from phospholipids

Phospholipase D: splits one of the phosphodiester bonds in the
head group

78
Q

what does phospholipid A2 do?

A

Phospholipase A2 acts in response to certain hormonal signals to
release arachidonic acid from membrane phospholipids

79
Q

what is arachidonic acid and what does it do?

A

Arachidonic acid is a precursor for eicosanoids
which are involved in inflammation, fever,
pain, blood clotting

80
Q

describe IP3 and DAG downstream signalling

A

• IP3 binds to IP3 receptors on the ER membranes and causes
release of Ca2+ release from the ER into the cytosol
• DAG in the membrane activates protein kinase C

81
Q

role of DNA

A

deoxyribonucleic acid

storehouse of genetic information

82
Q

role of RNA

A

ribonucleic acid
conveys information to cell
encoded by DNA
template for protein synthesis

83
Q

what is the central dogma?

A 
‘Central dogma’
DNA RNA protein
DNA encodes RNA makes protein
Central dogma is too simplistic
but a useful starting point
  • DNA synthesis of mRNA in the nucleus
  • movement of mRNA into the cytoplasm
  • synthesis of protein in ribosome using mRNA
84
Q

Structure of nucleic acids

A 
• Composed of nucleotide building blocks
(polynucleotides)
• 2 types:
– ribonucleic acid (RNA)
– deoxyribonucleic acid (DNA)

Each nucleotide has
• a base
• a sugar and
• one or more phosphate groups

85
Q

what are the bases made of in nucleotides?

A 
Bases are Nitrogen-containing molecules
5 different bases
– Adenine (A)
– Cytosine (C)
– Guanine (G)
– Thymine (T)
– Uracil (U)

A, C, G and U are found in RNA
A, C, G and T are found in DNA

purines: A and G
pyrimidines: C, T and U

86
Q

Sugars (monosaccharides)

A

containing 5 Carbon atoms (pentoses)
• ribose in ribonucleic acid (RNA)
• deoxyribose in deoxyribonucleic acid (DNA)

deoxyribose has a H instead of an OH group
at the 2’ position

87
Q

what is a base +sugar

A

base + sugar = nucleoside

e.g. adenine + ribose = adenosine

88
Q

Phosphates

A

Contain
1 mono
2 di- or
3 tri- phosphate groups

e.g. adenosine monophosphate (AMP)
adenosine diphosphate (ADP)
adenosine triphosphate (ATP)
Also: deoxyadenosine triphosphate (dATP)

89
Q

Nucleotides

A 
NTP = nucleotide triphosphate
dNTP = deoxynucleotide triphosphate
N = any base

• Not only relevant to nucleic acid
structure

e.g.s
– ATP ‘energy currency of the cell’
– FAD, NAD, NADP
Oxidation-reduction reactions in metabolism

90
Q

Nucleic acid structure

A

• Nucleotides are joined to each other
through their phosphate groups
= 3’-5’ phosphodiester linkages

• Nucleic acids have a sugar-phosphate
‘backbone’ with the bases attached to the
sugars

Nucleic acids are directional
i.e. have 5’ and 3’ ends

5’ end/terminus
• free 5’-phosphoryl group
3’ end/terminus
• free 3’-hydroxyl group

91
Q

Base pairing

A

• Bases may interact with each other
via Hydrogen bonds
in a process called base-pairing

• H bonds are individually weak

• Base-pairing is specific
A:T in DNA or A:U in RNA 2 H bonds
And G:C in DNA and RNA 3 H bonds

• Base-pairing occurs between
complementary bases

92
Q

DNA is a ‘double helix’

A
  • Structure discovered by Watson and Crick in 1953
  • consists of 2 DNA chains/strands

• 2 DNA chains are anti-parallel
5’!3’
3’”5’

• 2 strands are held together by base-pairing

• Strands of DNA in the double helix are not identical but are complementary
5’ CCTTGACTTG 3’
3’ GGAACTGAAC 5’

• 2 strands of DNA are coiled around the same
axis to form a right-handed double helix

• approx. 10 base pairs per turn of the double
helix

93
Q

Nucleic acids are polymers of?

A

nucleotides

94
Q

Nucleic acids are polymers of nucleotides

A 
Polymer =
Polynucleotide
•Sugar-phosphate
backbone
•Linkage =
phosphodiester bond
•Directionality
from 5’ to 3’
Building block =
Nucleotide
• phosphate
• sugar
• base
95
Q

Modest chemical differences in nucleotides

of DNA and RNA

A

Bases
DNA= A, C, G, T
RNA =A, C, G, U

Two categories:
Small (pyrimidines)
Large (purines)

Sugars
Both pentoses
Deoxyribose
no 2’ –OH
more stable
Ribose
has 2’ –OH
faster turnover
96
Q

Other Forms of DNA

A 
# B-DNA
# considered the physiological
form
# a right-handed helix, diameter 11Å
# 10 base pairs per turn (34Å) of
the helix
# A-DNA
# a right-handed helix, but thicker than B-DNA
# 11 base pairs per turn of the
helix
# has not been found in vivo
# Z-DNA
# a left-handed double helix
# may play a role in gene
#G-quadruplex
#Planar structure arising in
G-reach regions
#Specialized functions
(replication/recombination)
expression
97
Q

Denaturation of DNA

A
  • Double helix unwinds when DNA is denatured
  • Can be re-formed with slow cooling and annealing
• Denaturation: disruption of 2°
structure
– most commonly by heat
denaturation (melting)
– as strands separate, absorbance
at 260 nm increases
– increase is called hyperchromicity
– midpoint of transition (melting)
curve = Tm
– the higher the % G-C, the higher
the Tm
– renaturation is possible on slow
cooling
98
Q

In DNA analysis

A

Strand denaturation, annealing of complementary
strands is key to almost all DNA analysis techniques:
• DNA sequencing
• Determination of gene copy numbers
• Genome editing (CRISPR/Cas9)
• DNA amplification
• Many others

99
Q

DNA supercoiling

A

• Tertiary structure: the three-dimensional arrangement of all atoms of a
nucleic acid; commonly referred to as supercoiling
• Double helix can be considered to be a 2-stranded, right handed coiled rope
• Can undergo positive/negative supercoiling

100
Q

Enzymes deal with torsional stress

supercoiling

A

catalyse addition/of supercoils
e.g bacterial DNA gyrase
Promote the removal of supercoils
Topoisomerases

101
Q

RNA

A 
• Single stranded nucleic acid
• Can fold back on itself to form
stable regions of base-paired
RNA
e.g. stem-loop structures
Base sequence of all RNA
is determined by DNA
102
Q

Relative abundance of

RNAs in the cell

A

rRNA 80%
tRNA 15%
mRNA 2-5%
Other RNA

103
Q

mRNA

A 
• Messenger RNA, mRNA:
a ribonucleic acid that
carries coded genetic
information from DNA to
ribosomes for the synthesis
of proteins
– present in cells in
relatively small amounts
and very short-lived
– single stranded
– biosynthesis is directed by
information encoded on
DNA
(variable size, directs amino acid sequence in proteins)
104
Q

rRNA

A 
• Ribosomal RNA, rRNA: a
ribonucleic acid structural
component of the
ribosomes, the site of
protein synthesis
– ribosomes consist of 60 to
65% rRNA and 35 to 40%
protein

(several types varying sizes, combines with protein to form ribosomes.the site of protein synthesis)

105
Q

tRNA

A

= Link between sequence of nucleotides in mRNA
and sequence of amino acids in protein
• They read the information on the mRNA
• They carry the correct amino acids to the
ribosome
at least 20 different tRNAs
Cloverleaf structure of tRNA

(small,transfer amino acids to site of protein synthesis)

106
Q

Ribosomes are RNA/protein machines

dedicated to protein synthesis

A

in both prokaryotes and
eukaryotes, ribosomes consist
of two subunits, one larger than
the other

107
Q

small nuclear rna

A

small

processes initial mRNA to its mature form in eukaryotes

108
Q

small interfering RNA

A

small

affects gene expression;used by scientists to knock out a gene being studied.

109
Q

micro RNA

A

small

affects gene expression; important in growth and development.

110
Q

Why are Proteins such important

biomolecules in living cells?

A

• Proteins are the functional representation of the genome (molecular
‘toolbox’ of living cells) • The complement of proteins changes many times throughout the
lifetime of a cell – dynamic
• Why?
• A cell is constantly responding to changes in its local environment,
nutritional status & ‘messages’ received from other cells
• The complement of proteins in an individual cell at any given time is
referred to as the ‘Proteome’ [Proteomics – technology & science
behind understanding the composition of the proteome]

111
Q 
Some Biological Functions of proteins
Enzymes
Information flow in the cell –
Transport
mechanical roles
Structural 
Storage and transport
Signalling and communication
Cell-cell interactions
Specialised functions
A

• Enzymes – Nature’s own biocatalysts
• Information flow in the cell –replication and maintenance of the genome, in transcription and translation (Prof. Santocananle’s lectures)
• Transport of solutes across the cell membrane (e.g. transmembrane
pores) [Prof. Gorman’s lectures]
• Mechanical roles – from separation of chromosomes (mitosis),
movement of flagella, to muscle contraction and movement of cargo in cells
• Structural – cellular shape and support (collagen, tubulin, actin, etc.)
• Storage and transport, e.g. Lipoproteins (bind and transport lipids);
Myoglobin and Haemoglobin (carries O2
and CO2)
• Signalling and communication – hormones, cytokines/chemokines
and receptors for various signals
• Cell-cell interactions
• Specialised functions - Antibodies; lectins

112
Q

Amino acids are interesting molecules in

their own right

A

• Biologically very interesting and important
• Many have functions in living organisms or are used to generate small molecules with important functions (e.g.communication in the nervous system)
• Used in living cells for biosynthesis of other biomolecules,
e.g. hormones, nucleic acids, lipids

113
Q

Amino acids – basic structural features

A
  • Central carbon atom, Cα
  • Amino group, NH3+
  • Carboxyl Group, COO- • Hydrogen atom, H
  • Sidechain, R
  • Sidechain – unique featureof each individual amino acid
114
Q

Amino acids – Cα is a Chiral centre

A
  • Cα is a chiral carbon or chiral centre
  • The mirror images cannot be superimposed • D- and L-enanatiomers
  • L-enantiomers of amino acids - selected by Nature
115
Q

Slow spontaneous racemization of L and D forms of

amino acids – relevance in Fossil dating (Current)

A

• Conversion of the L to D enantiomer of an amino acid occurs by a reaction known as racemization
• It is a very slow reaction, e.g. half-life at 18oC is ~50,000 years for conversion of L-Aspartate to D-Aspartate
• Measurement of the D/L ratio can be used in fossil dating (measuring the increase in the D-enantiomer over time in biological fossil samples, e.g.
tooth enamel)
• Some Bacteria possess enzymes known as racemases which catalyze
the conversion from L- to D-enantiomers (thousands of molecules per second) – each racemase is specific for a particular amino acid

116
Q

Groups on Amino acids that can be

ionized

A

• Carboxyl Group (COOH) ,
loses a proton to become
COO-
• Becomes basic

• Amino group (NH2) gains
a proton to become NH3+
• Becomes acidic

• Some sidechains (Rgroups) also ionize

117
Q

Amino acids: pKa

A 
• Ionization of the carboxyl &
amino groups is affected by pH
• pKa is the pH at which there is
an equilibrium, i.e. half of the
groups are ionized and half
not

pKa (COOH, carboxyl) = 2.3
pKa (NH3+, amino) = 9.68

Ionization of Amino acid groups
over a pH range from pH 0-14

118
Q

what is the simplest amino acid?

A

pKa of Glycine

pKa (COOH, carboxyl) = 2.3
pKa (NH3+, amino) = 9.68

pI (isoelectric point – no charge) = pH 6.02

119
Q

Essential amino acids

A 
• Certain amino acids cannot
be synthesized in Eukaryotic
cells
• Dietary supplementation is
essential
• Supplement form?
• Essential amino acids: Ile,
Phe, Leu, Lys, Met, Thr,
Trp, Val
• In addition, children need:
Arg, Cys, His and Tyr
• Genetic engineering of plants to produce higher
yields of the essential amino acids
120
Q

Amino acid names

– 3 letter code

A 
• In general, the 3 letter code represents the first 3
letters of the name of the amino acid
• Some exceptions – 4 main ones in total! 
• Asparagine – Asn
• Glutamine – Gln
• Tryptophan – Trp
• Isoleucine (Ile) should also
be regarded as an exception
121
Q

Single letter code

A 
• Single or 1 letter code – usually first letter of the amino acid name
• Some exceptions – 9 in total! • Aspartic acid – D
• Glutamic acid – E
• Phenylalanine – F
• Lysine – K
• Asparagine – N
• Glutamine – Q
• Arginine – R
• Tryptophan – W
• Tyrosine – Y
Hint: Phonetics or Mnemonics
F = F(ph)enylalanine
122
Q

Amino acids – 3 groups
biochemically based
on R-groups

A
  • Hydrophobic – 2 subgroups
  • Hydrophilic
  • Specialized
123
Q

Amino acids with Hydrophobic side chains

A

• Two sub-groups

  • Aliphatic
  • Leucine
  • Isoleucine
  • Valine
  • Aromatic
  • Phenylalanine
  • Tyrosine
  • Tryptophan
124
Q

Aromatic amino acids

A 
• Phenylalanine,
Tyrosine and
Tryptophan
• Large, bulky groups
• Some are mildly
hydrophobic (e.g.
Tyrosine) – why?
• Tyrosine &
Tryptophan – absorb
UV light

Property can be used to estimate
protein concentration in biological
samples

125
Q

Some important amino acid derivatives

A

• Some amino acids are precursors of hormones and
neurotransmitters

Examples:
• Tryptophan is used in the body for the production of the
natural ‘happy hormone’ Serotonin (sedative/sleepy or calming
effect)
• Milk proteins have high levels of Trp – glass of milk or cocoa
before bed!
• Tyrosine is made from Phenylalanine in the body
• Tyrosine can be converted further to L-DOPA, Dopamine and
finally the ‘flight or fight’ hormone, Adrenaline (also known as
Epinephrine)

126
Q

Some not so good amino acid derivatives

A
  • Monosodium glutamate (MSG) – a derivative of glutamic acid used as a flavour enhancer in the food sector
  • Can cause a physiological reaction where the person feels ‘flu-like’ (chills, dizziness, headaches, etc)
  • Branched amino acids – used in muscle building protein supplements and drink
127
Q

name the 20 amino acids.

A 
alanine - ala - A 
arginine - arg - R 
asparagine - asn - N 
aspartic acid - asp - D 
cysteine - cys - C 
glutamine - gln - Q 
glutamic acid - glu - E 
glycine - gly - G 
histidine - his - H 
isoleucine - ile - I 
leucine - leu - L 
lysine - lys - K 
methionine - met - M 
phenylalanine - phe - F 
proline - pro - P 
serine - ser - S 
threonine - thr - T 
tryptophan - trp - W 
tyrosine - tyr - Y 
valine - val - V
128
Q

Amino acids with Hydrophobic side-chains – relevance to protein structure

A

• Amino acid side-chains can engage in hydrophobic

interactions – important in protein structure

129
Q

Amino Acids with Electrically-charged R-groups

A 
• Two sub-groups also
• 1
st Sub-group: Charged
(acidic or basic) 
• Acidic (-): Aspartate (Asp, D) and
Glutamate (Glu, E) – extra COOH
in R-group (side-chain) 
• Carboxylic acids – lose H at pH 7
• Basic (+): Arginine (Arg, R) and
Lysine (Lys, K) – extra NH3+ or NH2+ group in R-group 
• Amines - bind H at pH 7
• Arg, guanidino
• Lys, 1^o amine
130
Q

Important interactions of Charged, hydrophilic side-chains

in Protein structure

A

• Asp and Glu – R-group (or sidechain) is COO- at pH 7.0
• Negatively charged (acidic) at pH 7.0
• Arg and Lys: R-group (or sidechain) binds a proton and is
positively charged (basic) at pH 7.0
• Arg: C=NH2
becomes C=NH2+
• Lys: NH2
(amide) becomes NH3+(amine)
• These acidic & basic amino acids form ‘Salt bridges’
(interactions between the opposite charges) in proteins –can stabilize protein structure

BO201 Molecular and Cellular Biology (3 decks)

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