1
Q
Anabolism
A
building molecules up
2
Q
catabolism
A
breaking molecules down
3
Q
potential energy=?
A
stored energy
4
Q
what energies are produced by motion
A
gravity, chemical, kinetic
5
Q
what is relative mass measured in
A
daltons
6
Q
do electrons that are held further or closer to the nucelus have more potential energy
A
further
7
Q
what do u call the new 4 orbitals formed when H and O bond in water
A
sp3
8
Q
what are the effects of H bonds in water ( properties )
A
higher boiling point
higher cohesion
higher heat of vaporisation
ice has a more open structure
higher surface tension
higher specific heat
good slovent for polar molecules
good solvent for ionic compounds
the ‘oil drop effect’
9
Q
what is heat of vaporisation
A
energy to convert 1g of water from liquid to gas at 25c
10
Q
what is specific heat
A
amount of heat absorbed or lost in order to alter the temperature of 1g of water by 1c
11
Q
what is the ‘oil drop effect’
A
water molecules next to non-polar ( hydrophobic ) molecules cannot satisfy their Hbond requirements, so they are less stable.
to maximise number of H bonds which can be formed, clustering of non polar molecules
( layers separate - more energetically stable)
12
Q
1 mole of a substance is equivelent to …
A
its molecular mass in grams
13
Q
Kw = ?
A
[H+][OH-]
14
Q
make sure you can still do PH calculations
only of strong acids and bases
A
examples on lecture 2
15
Q
PH calculation
A
-log 10 [H+]
16
Q
what is a sulphydryl functional group
A
-SH
17
Q
what is a disulphide bridge
A
covalently links two cysteines
18
Q
what are phosphates a derivative of
A
phosphoric acid
19
Q
the OH groups of phosphoric acids can be replaces by -OR, what does this result in
A
phosphate esters
20
Q
what forms the rigid C=C bond
A
sp2 hybrid orbital and a p orbital.
the p orbital is a pi bond and a sp2 is a sigma bond
21
Q
what types of sugars are in RNA and DNA
A
RNA ia ribose
DNA is deoxyribose
22
Q
examples of purines
A
adenine
guanine
23
Q
examples of pyrimidines
A
cytosine
thymine
uracil
24
Q
are purines single or double ringed
A
double
25
are pyrimidines single or double ringed
single
26
what are the monomers used in the sythesis of nucelic acid
nucleoside triphosphate
27
what is the residue when nucleoside triphoshpate is added to a growing nucelic acid
pyrophosphate
28
which direction can you only add nucleotides too
3' hydroxyl group
29
what is a phosphodiester link between
the hydroxyl group on carbon-3' of one sugar is joined to phosphate 5' on the next
30
the base sequence is always written in which direction
5' to 3'
31
what did watson and crick do
x ray diffraction patters from DNA fibers
1. the cross patern was typical of a helicalstructure ( the density of the fibers suggested that there were 2 DNA strands in a helix )
2. as the layer line spacing is 1/10 the pattern must be 10 residues per turn
3.the repeat distance was 3.4nm so the helical rise was 0.34nm
32
what functions doproteins carry out
enzymic
transport
structural
movement
signalling
defence
storage
33
how do amino acids side chains vary
size and shape
charge
hydrophilicity / hydrophobicity
chemical reactivity
34
out of l and D isomers, which type get incorperated into proteins
L- isomers
35
explain what a zwitterion is
both positive and negaitive charges ( its ionised )
this only exists in certain PHs which is specific to each amino acids
36
what is pKa
the PH at which an ionisable group is one half charged and onehalf neutral
at a lower PH there will be more protonated form
37
amino acids join together to form proteins via...
peptide bonds
38
what direction is the amino acid sequence of a protein in
N to C
N is from an amine group C is fro a carboxyl group
39
does a peptide bond rotate
no there is no free rotation
the peptide bond has a partial double bond character
the peptide bond is rigid and planar
40
how does a protein rotate
around the bonds on either side of the peptide unit
Ca- C bond is a PSI '
N- Ca is a PHI
these can only twist minimaly
41
why are most combinations of psi and phi angles not allowed
because of steric collisions between side chains and the main polypeptide chain
42
what is the main driving force in protein folding
to attaqin an energetically stable structure
for water soluble proteinsits essential to pack hydrophobic side chains into the interior of the protein to hide tgem from surrounding water molecules. this forms a hydrophobic core
As the main polypeptide chain is hydrophilic because of the polar C=O and N-H groups, the protein must adopt structures which ‘neutralise’ these groups by hydrogen bonding.
43
what direction does the primary structure of a protein go in
N terminal to C terminal
44
what i s the main driving force in proteins to fold
to attain an energetically stable strcuture
45
alpha helices are usually formed from streaches of ............. amino acids.
5 - 40
46
how is the alpha helix held togther
N-H and C=O
are hydrogen bonded to one another along the axis of the helix
Amino group of one amino acids and a carboxylic group of another amino aicd. This is as the helix forms , amino acids get close togther so these groups can form hydorgen bonds
47
continous regions form....
alpha helix
48
why is an alpha helix so abundant
the hydrogen bonds between the aminoacids is a stablising interaction making a stable strcuture which explains its abundance
49
there are .... amino acuds per turn.
each amino acid truns the helix through......
the verticle distance from one amino acid to the next is 0.12nm so the pitch o fthe helix is 0.54nm
3.6
100
50
the c=o group of amino acid n is hydorgenbonded to whcuh N-H group
amino acid n + 4
51
where do the amino acid side chains go in an alhpa helix
they project out of the edge of the helix
alpha helixes are tight turm ( compact) those side chains cant be in the centre of the helix as it would effect stability. therefore the sidechain project out of the helix
52
what does the helical wheel diagrem help us see
you can look at the properties and side chains of amino acids to determine location of alpha helix protein / where it could be in the cell
for example lots of hydrophobic residues could indictae it wont be in an aqeuous environemnt
53
what are beta sheets formed from
non-continuos regions of the polypeptide chain
these regions are calld beta strands
54
hwo do the beta strands bond together
beta strands line up and form hydorgen bonds between c=o groups of one stramd and the N-H group of another
55
if the beta strands all run in the same direction the beta sheets are descibed as .....
paralell
56
if the beta sheets run in opposite directions what is it descirbed as....
anti- paralell
57
descibe a parallel beta sheet
the hydrogen bonds are evenly spaced within the sheet.
the beta strands are in an almost fully extended conformation
58
describe the anti-parallel beta sheet
the anti-paralell sheet has narrowly spaced h bonds pair separalty by a larger gap
the beta strands are in an almsot fully extended conformation
59
why are beta sheets oftern called beta pleated sheets
the alpha carbons lie successivley above and below the plane of the sheet
60
what are the secondary structures of alpha helices and beta sheets linked by
loop regions
a chain of amino acids must link together the non continuous parts of the primary structure to from the beta sheets whether it is parallel or antiparallel
61
loop regions vary in length
what are long loops called
random coils
they are hugjley felxible parts of proteins
62
what are short loop regions which connect anti-parallel beta strands are called...
hairpin loops
beta turns
63
why is proline oftern found in loop regions
its locked ringed structure introduces a kink into the polypeptide chain
64
why i s glycine oftern found in loop regiond
its small side chain enables it to form turns when other amino acids cannot
65
anti- parallel beta strands are usually connect by ...
parallel beta strands are usually conected by ....
hairpin loops
an alpha helix
66
when a helix crosses the beta sheet from one edge to another.
what is this called
ebta - alpha - beta motif
67
what post - translational modifications can happen
alterations to some produce the rare amino acids ( eg, hydroxyproline, hydroxylysine)
sugar/ carbohydrates/ glycans can be added to some amino acids ( asparagine, threoine , serine ) this is called glycosylation - glycoproteins ( N linked , O linked )
lipids can also be added lipoproteins
these various post translational modifications can contribute to secondary structure
68
what is tertiary stucture
three dimentional structure of a protein is produced by the association of the secondary stutcure into compact domains
69
when do disulphide bridges from
the side chain of one cysteine can form a crosslink with the side chain of another which is near to it in space. this crosslin is called a disulphide bridge and is a covalnt bond
70
benefits of disulphide bridges
make protiens more resistanc=t to degration and denaturation
71
revisit lectue 8 for example protein sturctures not sure if you actually need to learn them
72
describe a quaternary structure
the chains, subunits, associate into a multimeric complex which is held togther by electrostatic. hydrogen and van der waals bonds
73
what are the two major classes of proteins
globular
fibrous
74
what is a globular protein
protein chains are arranged in compact domains
- usually actibe components of the cellular machinary
75
what is fibrous proteins
proteins chains are arranged into fibres
- have a structural role
76
what are the 3 main group s of fiborous proteins defined by the seconadry sturtcure
coiled coil - keratin and myosin
beta sheets - eg, amyloid fibers and silks
triple helix - the collagens
77
where is keratin found
durable proteins found in hair , nails and feathers
78
descibe alpha keratin structure
the primary stucture of alpha keratin has a 7 amino acid repeat .
abcdefg which forms an alpha helix
residues a and d are hydrophobic and lie on the same side of the alpha helix b c e f g can be any amino acid
two alpha keratin helices twist around each other associating via the hydrophobic daces of the helices. this foms a coiled coil
he coiled-coil dimer
then lines up with
another to form a
staggered antiparallel
tetramer
The tetramers are the
building blocks of
protofilaments which
then form into
protofibrils which then
form microfibrils
79
how is diagrammatic representation of the tertiary sturcture represented
only the polypeptide
backbone is usually shown drawn as a
thick line or ribbon. The presence of
an -helix is usually indicated by the
inclusion of a SPIRAL or CYLINDER
within the ribbon. -strands are drawn
as thick ARROWS, pointing from the
N-terminal end to the C-terminal.
80
desicbe the strcture of fibroin
long streaches contain a six amino acid repeat ( gly, ser, gly, ala, gly, ala ) n whcuh forms an antiparallel beta sheet
the glycine side chain ( H ) project from one side of the sgeet and those of serine and alanine project from the other
the beta sheet scan stack into an array of layers of contacting gly side chains alternating with layers of ser/ ala side chains
81
features of fibroin
silk is extremely strong as any streaching would requie the breaking of the covalent bonds, yet it is flexible becasuse the beta sheet srae interacting via weak van der waals bonds
82
what is th emost abundant vertbrate protein
collagen
83
where is collagen present
skin, bone, teeth , cartilage
84
desibe the primary structure of collagen
Nearly one-third of the amino acids are glycine. Another 15-30%
are proline or hydroxyproline (Hyp)
The primary amino acid sequence consists of a repeating
tripeptide of Gly-X-Y where X is often Pro and Y is often Hyp
85
describe the secondary strutcuer of collagen
Collagen cannot form an a-helix because of the Pro and Hyp
residues. Instead it forms a ‘loose’ helix with around three
residues per turn
86
descibe the quaternary structure of collagen
Three collagen polypeptides wind around each other
in a rope-like twist to form a TRIPLE HELIX
Every 3rd amino acid passes through the centre of the
triple helix which is so crowded that only Gly can fit
The Pro and Hyp residues confer rigidit
The polypeptide chains form inter-chain hydrogen bonds
The triple-helical trimers can often associate to form large, strong fibres
87
functions of carbohydrates
nucelic acids
recognition
structure
fules
88
what is the basic formula for a carbohydrate
( CH20) n
89
what are the simplest carbohydrtaes
molecules with one aldehyde or ketone group and multiple hydroxyl groups
90
what are the simplest carbohydrates called
monosaccharides
91
what is a monosaccharides with an aldehyde called
aldose
92
what is a monosaccahride with a ketones called
ketosose
93
what optical form are most naturally occuring monosaccharides
D
94
a molecule with n asymetric centres and no plane of symetry has how many isomers
2^ n
95
understand how the aldose series and ketose series works ( lectue 9 )
96
aldehyde + alcohol =
hemiacetal
97
ketone + alcohol =
hemiketal
98
why is it important that aldehydes and ketones both react with alchols
the monosaccharides contain alchol groups, so they can react with themselves ( cyclisation )
these reactions are condensation reactions
99
in solution pentose and hexose do what
cyclise to form rings
100
what is an anomeric carbon
C1 this is where the new bond is fomed
101
can glucose switch between alpha and beta form
yes in solution alpha can dissociate into an open chain form then reform into beta
102
what structure is glusoe predominatly in
ring form
its in an open chain from less than 1 percent of the time
103
the alpha and beta isomers of glucose are called
anomers
104
what is the process called when alpha and beta glucose interconvert via their open chain form
mutarotation
105
for aldose where is the anomeric carbon
always on c1
106
in glucose if the OH group points downward its .....
if it points upwards it ....
alpha
beta
107
what is the ring strutcure of aldohexose known as
pyranose rings
108
for ketose what carbon is always the anomeric carbon
c2
109
what is the proof of mutarotation
Plane polarised light passing through 10cm of a 1g/ml solution of b-D-
glucopyranose is rotated through +18.7 degrees
The a anomer rotates the light through +112 degree
This is called OPTICAL ROTATION
When a pure sample of either anomer is dissolved in water, the specific
rotation changes with time until an equilibrium value of +52.7 degrees
is attained
This corresponds to a mixture of 1/3 a-anomer and 2/3 b-anomer
110
what conformations can pyranose rings adopt
chair and boat conformations
111
what conformations can furanose rings adopt
envelope
112
what dictases chair vs boat
the substituents of the ring e.g. small hydrogen atom or bulky hydroxyl group! These clashes care called steric collisions
113
what alpha and beta isomers called
anomers
114
what are monosaccharides joined together by
glycosidic bonds
115
what does a glycosidic bond form between
anomeric carbon of one sugar and a hydroxyl group on another
116
what are sugars containing a free aldehyde or ketone group called and why
reducing sugars
in solution the open chain forms of aldose amd ketose can reduce indicators such as cu 2+ to cu + ( which produces a red precicpitate)
117
what enzyme are sugars joind together by
glycosytransferases
118
why can carbohydrates achieve great structural diversity
because of the may types of monosaccharides and linkage possible
119
what are a few sugars joined togther kown as
oligosaccharides
120
the oh of monosacchardies can be replaces by other greoups such as...
amino
N-acetyl
phosphate
sulphate
carboxylate
hydorgen
121
what is glycogen broken down by
glycogen phosphorylase
122
what is startch broken down by
amylase
123
what is mannans and what is it broken down by
Various structures, used by bacteria, fungi and plants
Broken down by various enzymes
124
explain glycolysis
A series of reactions in the
cytosol of the cell that:
Convert Glucose (a six
Carbon molecule) into 2x
three carbon molecules
known as PYRUVATE.
In doing so some of the
chemical energy stored in
glucose is released.
Involves multiple steps:
For each molecule of glucose
we create a net total of 2
molecules of ATP
125
what happens to pyruvate in 02
transported to the mitrochondiran
126
what happens to pyruvate before it enters the citric acid cyle
pyruvate is converted to acetyl-coenzyme A.
Before entering the
citric Acid cycle
pyruvate is first
combined with a
sulphur containing
compound known as
coenzyme A
The product of this
reaction is Acetyl-CoA
In eukaryotes this takes
place in the matrix of
the mitochondria.
127
desibe the citic acid cycle
Takes place within the mitochondrial matrix
This cycle oxidises organic “fuel” in the form of Acetyl-CoA (a
derivative of Pyruvate)
This cycle produces 1xATP (GTP), 3xNADH and 1xFADH2 per
turn
The citric acid cycle is typically represented as 8 enzymatic
reactions (steps)
Acetyl-CoA joins the cycle by binding to Oxaloacetate forming
a molecule of citrate
The following 7 steps complete the decomposition of citrate
back into oxaloacetate
And therefore we have ourselves a cycle
The NADH and FADH2 are fed into the electron transport
chains and this is where the majority of ATP is produced.
128
define lipids
Lipids are a diverse group of naturally occor molecules that are soluble in non-polar organic solvents such as chloroform (insoluble or poorly soluble in water)
129
desicbe a fatty acid
simple lipid
building bloc for comlex lipids
source of energy - heart and skeletal muscles prefer fatty acids t glucose
important for human diet
130
general structue of a fatty acid
long chain carboxylic acid
hydrophobic hydrocarbon tail
hydrophillic carboxyl head
131
what does amphiphathic mean
two different chemical characteristics
132
how do you systematically name a fatty acid
1) how many ccarbonds
2) is it saturated
saturated = anoic, monounsaturated = enoic,
polyunsaturated = dienoic (2 x C=C), trienoic (3 x C=C
30 what are the position and type of bond
133
what is an essential fatty acid
Unsaturated fatty acids that animals cannot synthesize
but which are need to synthesize other fatty acids
134
why cant animals sythesis essential fatty acids
Animals do not have enzymes that insert C=C into the
hydrocarbon chain beyond carbon 9
135
symptomsof fatty acid deficiency
Symptoms of fatty acid deficiency include a variety of skin
problems such as eczema
136
what are the 2 classes of essential fatty acids
pmega 3
omega 6
137
complex limids split into what 2 catagories
polar lipids
neutral lipids
138
describe triacylglycerols
neutral lipids
Carboxylic acid triesters of glycerol (a 3C trialcohol)
The main dietary source of fatty acids (in fats and oils)
The storage form of fatty acids
an efficient energy store (much better than carbohydrates)
a major source of biochemical energy
139
what does the properties of triacylglycerols depend on
fatty acid composition
bending in tail of unsaturated fatty acid prevents molecules packing tightly togther- increasing fluidity- lowering melting temoerature
140
do animal fats or vegetable oils have a higher perecnetage of unstaurated fatty acids
vegetable oils
141
desicbe animal fats
Mainly saturated fatty acids
Tightly packed molecules
High melting point
Solid at room temperature
142
descibe vegetable oils
Mainly unsaturated fatty acids
Loosely packed molecules
Low melting point
Liquid at room temperature
143
are naturally occring unsaturated fatty acids usually cis or trans
cis
144
do trans double bonds not cause a bend
yes
so wit more trans double bonds they are more solid at room temeorate
145
what two catagories do polar lipids split into
glycerolipids
sphingolipids
146
what 2 catagories to glycerollipids split into
phophoglycerides
glycosylglycerides
147
desibe a phosphoglyceride
2 fatty acids on a glycerol and a phosphate with an x group attached
148
what name of phosphoglyceride do X group cause
- h
- choline
- ethanolamine
- serine
- inositol
phosphatidic acid
phosphatidylcholine
phosphatidylethanolamine
phosphatidylserine
phosphatidylinositol
149
desibe the phopholipid membrane
Phospholipids have two ends with different affinities for
water (amphipathic)
In water, phospholipids spontaneously form lipid bilayers
These structures cluster the hydrophobic regions toward
the inside and leave the hydrophilic regions exposed to the
water environment
150
the importance of biomembranes
Separate the cell contents from its
surroundings (or divide cell into
compartments, i.e. organelles)
Maintain different (bio)chemical
environments between the inside
and outside of the cell (or
organelles)
selectrivley permeable
151
learn the history of membrane structure
1915- rbc membranes were first isolated and analysed found to contain lipids and proteins
1925- membranes descibed as a bilayer of phospholipids
1935- sandwich model - phopholipid bilayer between two layers of globular proteins
(Two problems:
Membranes differ in
composition & structure
Membrane proteins not
very water soluble )
1972- fluid mosaic model- proteins inserted into the membrane sheltering the hydrophobic regions from water
152
evidnace for the fluid mosaic model
freeze fracture of the membrane
membrane proteins bumps in the two layers
153
descibe membrane fluidity
Phospholipids move laterally very fast, but flip-flopping
is quite rare
A phospholipid can move 2 µm (the length of a
bacterial cell) in 1 sec
Latteraly – along only intracellular or extracellular
Flip-flop – moves from intracellularly to extracellulary
154
how does cholesteol effect fluidity
helps stabalize the moelcule
High temps (e.g. 37º) reduce movement less fluid
Lower temps hinder packing maintain fluidity
So acts as a ‘temperature buffe
155
how does fatty acid saturation effect fluidity
kinks keep the membrane frm packing togther, enhancing membrane fludity
156
do proteins also move in the membrane
yes
latteraly
157
what is the hop diffudion of proteins
protens diffuse 100x slower in natural membranes compared to artificial membranes
proteins are fenced in by the cells actin cytoskeleton but may hop into another area
proteins are blocked in discrete regionso of membranes by cytoskeletons they can hop ober confinment
158
membranes contain a complex mixtue of protenis that can be classified into what 3 main groups
Integral proteins
(transmembrane protein)
Peripheral proteins
(loosely bound via other
proteins)
Lipid-anchored
proteins (covalently
attached to lipids, e.g.
GPI-anchored)
159
what determinds how a protein will associate with a membrane
hydrohphobic and hydrophillic domains
160
desibe membrane carbohydrates
Short, branched oligosaccharide chains of <15 sugar units
Highly diverse (between species, individuals, cells)
Act as identity ‘tags’, e.g. blood groups are due to variation in carbohydrates on the surface of red blood cells
161
carbohydrates that are covalently cound to prroteins are called....
glycoproteins
162
carbohydrates that are covalently bound to lipids are called....
glycolipids
163
membranes have a distinct inside / outisde composition that differ in ...
Lipid composition
Peripheral proteins
attached
Carbohydrates
attached
Integral proteins are
asymmetrical with a
defined orientation
164
major roles of membranes
Compartmentalisation
Cells, organelles (mitochondrion, nucleus,
chloroplast, etc.)
Spatial organisation of biochemical reactions
To provide a selectively permeable barrier
cell to cell recogniton / communication
165
what does the rate of diffusion across a lipid bilayer depend on
size of molecule
relative solubility in oil
166
what is the membrane highly permeable to
Highly permeable to small
non-polar molecules and
small uncharged polar
molecules depending on
size (small > large)
167
what is the membrane highly impermeable to
Highly impermeable to
charged molecules (ions)
and large polar molecules
168
how are ions and large molecules like glucose and amino acids ableto move effciently acros biological membranes
Proteins with a hydrophilic
channel allowing ions or
molecules to diffuse passively
from one side to the other
Proteins that bind and
transport molecules in an
energy requiring process
Transport proteins are usually
quite specific for the substance
transported
169
what allowes cell recogiton
some glycoproteins act as idenification tags that are recognised by receptor proteins in other cells
170
why is the abilty to distnguish one type of cell from another crucial
During embryogenesis for the sorting of cells
into tissues and organs
As the basis for recognition and rejection of
foreign cells by the immune system
BIOL YR1
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