Theme 2: Biomolecules & their importance in living cells Flashcards
is lipid hydrophobic or hydrophilic?
hydrophobic
what is hydrophobic?
immiscible with water
what is the body’s fattest organ?
the brain
is the average body fat higher in men or women?
woman 22-25%
men 15-18%
what are the functions of lipids?
• Storage lipids: Triacylglycerols
• Membrane lipids: phospholipids (glycerophospholipids,
sphingomyelin), glycolipids, sterols (cholesterol)
• Other roles, e.g., hormones, intracellular signalling,
enzyme cofactors, pigments
what are fatty acids?
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
what is stearic acid?
(18-carbon with 0
double bonds)
saturated fatty acid
what is oleic acid?
(18-carbon with 1 double
bond at the ninth carbon
from the omega end, w-9)
mono-unsaturated fatty acid
what is linoleic acid?
(18-carbon with 2
double bonds, w-9, w-6)
poly unsaturated fatty acid
what are the effects of double bonds on the conformation of fatty acids?
• 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
what do cis double bonds do?
Cis double bonds introduce a rigid bend and do not permit rotation
what are triglycerides composed of?
Composed of three FA residues each in ester linkage with a single
glycerol
what are adipocytes?
specialised lipid storage cells
what is saponification?
production of natural soaps by boiling triglycerides with NaOH
what are the advantages of TAGs as stored fuels?
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
what do the physical properties of fats depend on?
Consistency depends on 1) chain length,
2) degree of saturation and 3) temperature
why do chain length effect the physical properties of fats?
: FAs with longer chains and fewer double bonds
are less fluid
why does saturation effect the physical properties of fats?
- Saturated FAs (12:0-24:0) are waxy solids
* Unsaturated FAs of same length are oily liquids
name 7 cellular membranes
Plasma membrane, endoplasmic reticulum, Golgi apparatus, mitochondria: inner and outer membranes, nuclear membrane, lysosomal membrane
explain plasma membrane
- 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)
name the components of biological membranes
- lipids
- proteins
- carbohydrates
name 3 types of membrane lipids
Phospholipids
Glycolipids
sterols
name 3 types of phospholipids
Phosphoglycerolipids, glycerophospholipids
• Sphingomyelin
give 2 points on glycolipids
- Overlap with phospholipids
* Includes cerebrosides and gangliosides
what do sterols include?
cholesterol
what are the most abundant lipids in membranes
•Glycerophospholipids
what are •Glycerophospholipids composed of?
- Glycerol joined to two FAs (hydrophobic)
* with a phosphate head group (polar)
what are sphingolipid that is a phospholipid composed of?
Composed of one molecule of sphingosine (or derivative), one fatty acid and a polar head joined in a phosphodiester link
what is the second most abundant lipids in membranes?
Glycosphingolipids
what are Glycosphingolipids composed of?
Composed of one molecule of sphingosine (or derivative), one fatty
acid and a polar head joined in a glycosidic link
what is the X group in Glycosphingolipids
Simple sugar: Cerebrosides
Complex sugar: Gangliosides
what do the 4 human blood groups differ in
oligosaccharides on the
surface of red blood cells
what are the 4 different human blood cells?
A,B,AB,O
what are lipid bilayers?
basis of biological membranes
what does the polar surface of the bilayer contain?
charged groups
where are the hydrophobic tails in lipid bilayers?
interior of the bilayer
describe the Interactions of phospholipids and glycolipids
in aqueous medium
Virtually insoluble in water
They cluster together with hydrophobic tails directed away from
water and hydrophilic groups interacting with the surrounding
water
what are the various lipids in the membrane?
- sphingomyelin
- cerebroside
- ganglioside
- phosphoacylglycerol
- cholesterol
describe Asymmetry in membrane layers
- 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
talk about carbohydates in membranes
• 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
name 3 types of proteins in membranes
- Integral proteins
- Peripheral proteins
- Lipid-anchored proteins
where are integral proteins
inserted into membrane
where are peripheral proteins?
loosely bound to membrane
where are 3. Lipid-anchored proteins?
Covalently attached to lipids in the membrane
give some features of integral proteins
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
talk about peripheral proteins
• bound by electrostatic
interactions
• can be removed by raising
the ionic strength
talk about lipid anchored proteins
• 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
talk about the hydrophillic and hydrophobic regions in integral proteins in membranes
• 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
what is the fluid mosaic model?
- 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
describe the fluidity of the membrane
• 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
what effects membranes fluidity?
- 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 - Lipid composition
• Hydrocarbon chain length
• Degree of saturation of hydrocarbon chains
• Presence of sterols
how does temperature effect the fluidity of the membrane
as the membrane heats up it goes from a firmer gel state to a more fluid state
how does cholesterol affect fluidity?
• Cholesterol stabilizes hydrocarbon tails of FA • At 37oC it restricts the movement of phospholipids • At lower temperatures it impedes packing and solidification
name the different movemements of phospholipids in membranes
- rapid rotational diffusion
- very slow transverse exchange (flip flop)
- rapid lateral diffusion
- rapid flexing of the hydrocarbon chain
what does the flipflop diffusion need
to be catalyzes by flippase
what would be an experiment to show lateral movement of membrane lipids?
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
talk about movement of proteins in membranes
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
what is an experiment to show lateral movement of proteins in menbranes
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
describe lipid rafts
- 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
what are the functions of proteins in the plasma membrane?
- Transport
- Enzyme activity
- Signal transduction
- Intercellular joining
- Cell-cell recognition
- Attachment to cytoskeleton and extracellular matrix
why is there need for transport across mebranes?
Cells need to import raw materials for biosynthesis and to export waste
Need to translocate ions across membranes
what inhibits the transport of ions and polar molecules?
the hydrophobic core of the lipid bilayer impedes
transport of ions and polar molecules
name 3 types of transport in the membrane?
- Simple diffusion
- Facilitated diffusion
- Primary active transport
talk about simple diffusion
• 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
give examples of simple diffusion
Hydrophobic molecules such as hydrocarbons
• Gases such as O2
, CO2
, N2
• Small polar uncharged molecules e.g., ethanol
how are polar and charged molecules moved across the membrane
Transport proteins (transporters or permeases) enable molecules
to cross the membrane without coming in contact with the
lipid bilayer
talk about facilitated diffusion
• 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
talk about active transport
• 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
name the types of active transport
primary
secondary
give a few features of primary active transport
= Uniport
Generally powered by ATP hydrolysis
give a few features of secondary active transport
= Indirect active transport
= Co-transport:
Transport of one molecule is driven by co-transport of another molecule
what does symport mean?
flow is in the same direction
what does antiport mean?
flow is in the opposite direction
what provides energy for co-transport?
Movement of molecule X down its concentration gradient drives
movement of molecule S against its concentration gradient
what are the 2 steps for providing enery for co-transport?
- 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.
name 2 lipids with biological activity
- Cholesterol is the precursor of
• steroid hormones (testosterone, estradiol, cortisol)
• vitamin D - Specific enzymes (phospholipases) degrade phospholipids
to produce signalling molecules
what are the 3 types of phospholipids?
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
what does phospholipid A2 do?
Phospholipase A2 acts in response to certain hormonal signals to
release arachidonic acid from membrane phospholipids
what is arachidonic acid and what does it do?
Arachidonic acid is a precursor for eicosanoids
which are involved in inflammation, fever,
pain, blood clotting
describe IP3 and DAG downstream signalling
• 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
role of DNA
deoxyribonucleic acid
storehouse of genetic information
role of RNA
ribonucleic acid
conveys information to cell
encoded by DNA
template for protein synthesis
what is the central dogma?
‘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
Structure of nucleic acids
• 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
what are the bases made of in nucleotides?
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
Sugars (monosaccharides)
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
what is a base +sugar
base + sugar = nucleoside
e.g. adenine + ribose = adenosine
Phosphates
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)
Nucleotides
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
Nucleic acid structure
• 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
Base pairing
• 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
DNA is a ‘double helix’
- 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
Nucleic acids are polymers of?
nucleotides
Nucleic acids are polymers of nucleotides
Polymer = Polynucleotide •Sugar-phosphate backbone •Linkage = phosphodiester bond •Directionality from 5’ to 3’
Building block = Nucleotide • phosphate • sugar • base
Modest chemical differences in nucleotides
of DNA and RNA
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
Other Forms of DNA
# 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
Denaturation of DNA
- 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
In DNA analysis
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
DNA supercoiling
• 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
Enzymes deal with torsional stress
supercoiling
catalyse addition/of supercoils
e.g bacterial DNA gyrase
Promote the removal of supercoils
Topoisomerases
RNA
• 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
Relative abundance of
RNAs in the cell
rRNA 80%
tRNA 15%
mRNA 2-5%
Other RNA
mRNA
• 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)
rRNA
• 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)
tRNA
= 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)
Ribosomes are RNA/protein machines
dedicated to protein synthesis
in both prokaryotes and
eukaryotes, ribosomes consist
of two subunits, one larger than
the other
small nuclear rna
small
processes initial mRNA to its mature form in eukaryotes
small interfering RNA
small
affects gene expression;used by scientists to knock out a gene being studied.
micro RNA
small
affects gene expression; important in growth and development.
Why are Proteins such important
biomolecules in living cells?
• 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]
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
• 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
Amino acids are interesting molecules in
their own right
• 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
Amino acids – basic structural features
- Central carbon atom, Cα
- Amino group, NH3+
- Carboxyl Group, COO- • Hydrogen atom, H
- Sidechain, R
- Sidechain – unique featureof each individual amino acid
Amino acids – Cα is a Chiral centre
- 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
Slow spontaneous racemization of L and D forms of
amino acids – relevance in Fossil dating (Current)
• 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
Groups on Amino acids that can be
ionized
• 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
Amino acids: pKa
• 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
what is the simplest amino acid?
pKa of Glycine
pKa (COOH, carboxyl) = 2.3
pKa (NH3+, amino) = 9.68
pI (isoelectric point – no charge) = pH 6.02
Essential amino acids
• 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
Amino acid names
– 3 letter code
• 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
Single letter code
• 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
Amino acids – 3 groups
biochemically based
on R-groups
- Hydrophobic – 2 subgroups
- Hydrophilic
- Specialized
Amino acids with Hydrophobic side chains
• Two sub-groups
- Aliphatic
- Leucine
- Isoleucine
- Valine
- Aromatic
- Phenylalanine
- Tyrosine
- Tryptophan
Aromatic amino acids
• 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
Some important amino acid derivatives
• 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)
Some not so good amino acid derivatives
- 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
name the 20 amino acids.
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
Amino acids with Hydrophobic side-chains – relevance to protein structure
• Amino acid side-chains can engage in hydrophobic
interactions – important in protein structure
Amino Acids with Electrically-charged R-groups
• 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
Important interactions of Charged, hydrophilic side-chains
in Protein structure
• 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
