Biol 111- Molecules of Life Flashcards
1
Q
describe kinetic energy
A
the energy an object has/ gains due to its motion e.g. movement and heat
2
Q
describe potential energy
A
the energy an object possesses due to its position e.g. chemical energy. Molecules such as glucose can be broken down to provide chemical energy.
3
Q
name 3 chemical processes that are classed as both kinetic, potential, and also chemical energy?
A
metabolism, anabolism (synthesis of complex molecules for storage) and catabolism
4
Q
what are thermal and light energies in terms of kinetic energy?
A
kinetic energy if we think of light as particles (ohotons).
5
Q
what is the benefit of systems becoming stable as possible?
A
minimising energy usage and maximising entropy
6
Q
how many essential elements do humans and plants have?
A
humans= 25, plants= 17
7
Q
which 4 elements make up 96% of living matter?
A
carbon, oxygen, hydrogen, nitrogen
8
Q
name 4 other elements that make up the other 4% of living matter, and give examples of where they’re found?
A
phosphorus: mostly in DNA
sulphur: dispulphide bridges
calcium: bones
potassium: nervous system
honourable mention of iron (haemoglobin) and iodine (thyroid gland).
9
Q
what is the definition of an atom?
A
smallest unit of matter which still retains the properties of an element.
10
Q
what is an atomic number?
A
number of protons (therefore number of electrons as well)
11
Q
what is a mass number?
A
number of protons + neutrons
12
Q
what is half-life in more chemical/ physics terms?
A
how long it takes for the element to break down into a non-radioactive, stable state. More unstable- quicker half-life e.g. carbon-12.
13
Q
what is a compound?
A
a substance consisting of 2 or more elements in a fixed ratio e.g. NaCl
14
Q
it is energetically favourable to form a covalent bond between which type of electrons?
A
unpaired, as they can be shared or transferred between atoms
15
Q
when are ionic bonds formed?
A
when two atoms very different in attraction for valence electrons come together, to form a crystal e.g. NaCl.
16
Q
why are more polar bonds stronger and require more energy to break?
A
the partial charges create a stronger electrostatic attraction
17
Q
which forces hold proteins together?
A
van der waal’s forces, very short range
18
Q
how does the idea of sp3 hybridisation explain the shape of molecules and the number of bonds carbon can make?
A
it explains the tetrahedral shape of molecules as without them, carbon should make 2 bonds due to the 2 unpaired electrons in two 2p orbitals, to form, for example, a CH2 molecule (which can’t exist outside a reaction).
if all of the 2s and 2p orbitals combine to form 4 sp3 orbitals, this means carbon can make 4 bonds.
19
Q
name (and explain) the NINE wtf effects of hydrogen bonds in water
A
- higher boiling point (liquid at room temp)
- cohesion
- high heat of vaporisation (sweat cooling)
- ice is less dense than water and can float- molecule forms a crystalline lattice with 4 hydrogen bonds per molecule (instead of the 3 in water), so the molecules are held further apart.
- higher surface tension (pond skaters)
- higher specific heat- water resists temp changes
- good solvent for polar molecules, it can interact with anything else polar
- good solvent for ionic compounds- hydration shells can form around each ion, due to the delta positive and negative values of oxygen and hydrogen
- oil drop effect- water less stable when mixed with non-polar/ hydrophobic molecules as it doesn’t satisfy the H-bonding requirements. To maximise the number of H-bonds formed, the non-polar molecules cluster. Important mechanism with some amino acids.
20
Q
what is a mole?
A
molecular mass in grams of a compound e.g. there is 1 mole of water molecules in 18g water.
21
Q
what is pH?
A
concentration of protons present in an aqueous solution.
22
Q
what is the rewritten equilibrium equation for kW, which takes into account the fact that [H2O] is constant in pure water at a set temp and pressure?
A
kW x [H20] = [H+] [OH-]
23
Q
what does tetravalent mean?
A
can form 4 bonds
24
Q
what are geometric isomers?
A
cis/ trans
25
why are C=C double bonds very rigid?
arrangement of electrons, the sp2 hybrid orbitals (sigma bond) and p orbitals (pi bond) come together to form a double bond
26
what are enantiomers?
optical isomers
27
28
why doesn't DNA degrade easily and RNA does?
due to dna's 2 strands and strong backbone
29
what are the purine bases?
adenine and thymine
30
what are the pyrimidine bases?
cytosine, guanine, uracil
31
what is the structural difference in the sugar in DNA compared to RNA?
in DNA, on the 2’ carbon it is bonded to 2 hydrogens, and 2 carbons. In RNA, the 2’ carbon is bonded to 2 carbons, a hydrogen, and an -OH group. Both have an -OH group on carbon 3.
32
how many rings do purines an pyrimidines have?
Purines= 2-ring structures. Pyrimidines= single ring.
33
what is a nucleoside triphosphate?
a type of nucleotide, with a variable number of phosphate groups
34
draw the structure of a pyrophosphate and explain how they're formed
In nucleotide formation, the phosphate group is always attached via a reaction at the 3’ carbon on the sugar (forms a covalent phosphodiester bond). In this reaction, 2 of the phosphates are ejected, and they are known as a pyrophosphate.
35
why is there a 5' end and a 3' end?
The hydroxyl group on carbon-3’ of one sugar is joined to the hydroxyl group on carbon-5’ of the next by a PHOSPHODIESTER LINK
The polynucleotide chain has a direction. One end will have an unreacted 5’ phosphate and the other (3’) will have an unreacted hydroxyl group. The base sequence is always written in the 5’ to 3’ direction
It is the sequence of bases along the backbone which encodes the genetic information
36
describe the importance of photo 51
Watson and Crick analysed X-ray diffraction patterns from DNA fibres. They deduced that:
The cross pattern was typical of a helical structure (the density of the fibres suggested there were 2 DNA strands in a helix)
As the layer line spacing is 1/10 the pattern repeat there must be 10 residues per turn
The repeat distance was 3.4nm so the helical rise was 0.34nm.
37
how many bonds do a-t form, and c-g?
Adenine and thymine for 2 hydrogen bonds between each other, while cytosine and guanine form 3 bonds. This means it’s slightly harder to break a cytosine-guanine bond.
38
what 7 things can proteins be used to carry out?
ENZYMIC e.g. trypsin
TRANSPORT e.g. haemoglobin
STRUCTURAL e.g. collagen
MOVEMENT e.g. actin
SIGNALLING e.g. insulin
DEFENCE e.g. antibodies
STORAGE e.g. ferritin
39
what 3 ways can side chains in an amino acid differ?
size/ shape, charge, hydrophilicity/ hydrophobicity
40
which optical isomer is incorporated into proteins, and which is the only amino acid without optical isomers and why?
L isomers are incorporated into proteins, instead of D, so they tend to be more stable.
Glycine is the only amino acid with no optical isomer, its side chain is a hydrogen atom.
41
at ph 7, the carboxyl and amino groups of an amino acid are ionised, draw a flowchart to show the general structure of an amino acid at ph 1, and ph 11, and describe the loss or gain of H+ ions.
At a lower pH, with a higher concentration of hydrogen ions, it’s very hard for the COOH group to donate its proton (like a concentration gradient), so it stays neutral, whereas the amino group can easily pick up one of the hydrogens. Works with high pH as well.
42
what is pKa in terms of more amino acids terms?
pKa is the pH at which an ionisable group is one-half charged and one-half neutral
e.g. ethanoic acid, CH3COOH has a pKa of 4.8
So at pH 4.8
50% of the molecules are CH3COOH and
50% of the molecules are CH3COO−.
At lower pH there will be more of the protonated form, CH3COOH.
At higher pH there will be more of the ionised form, CH3COO−.
43
why is the amino acid histidine really cool?
its pKa is approximately the physiological pH (6.8).
usually found in the middle of an enzyme’s active site, making it ideal for forcing and breaking interactions as it can change status at physiological pH’s.
44
what is a peptide unit?
the carbon, nitrogen and peptide bond when a peptide is formed- they are rigid and planar.
45
in what direction are amino acid sequences of proteins always written
N->C direction, so there is a free amino acid and free carboxyl group at each end
46
why is rotation restricted in a peptide bond?
it has partial double bond character, caused by the transfer of pi electrons from one p-orbital to another
47
what is a donation as PSI?
Rotation around C(alpha)-C bond
angle
48
what is a donation as PHI?
Rotation around N-C(alpha) bond
angle
49
why are most combinations of psi and phi angles not allowed?
sterile collisions between the side chains and main polypeptide chain. the shape of the entire protein is determined by the values of the psi and phi angles of each amino acid.
If the side chain is big and large, that restricts the number of angles that can be made.
50
is the folding of proteins random?
no xxxx too many combinations
51
which type of side chains are essential to be on the interior of water soluble proteins?
it is essential to pack hydrophobic side chains into the interior of the protein to ‘hide’ them from the surrounding water molecules. This forms a hydrophobic core (similar process to oil forming droplets in water).
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.
52
why are alpha-helixes very stable?
as it forms the helical structure of around 5-40, the amino groups and carboxyl groups are hydrogen-bonded to another one along the axis.
53
how does the hydrophilicity collapse model aid the polypeptide?
gives overriding precedence to a nonspecific collapse of the polypeptide chain which facilitates subsequent formation of specific secondary and tertiary structure- drives the folding of the chain.
54
how many amino acids are there in an alpha helix per turn?
3.6 amino acids, each amino acid turns the helix through 100°.
55
what is the vertical distance from 1 amino acid to the next and therefore the pitch of the helix (turn length)?
The vertical distance from one amino acid to the next is 0.15nm so the pitch of the helix (turn length) is 0.54nm.
56
where do the side chains of an alpha helix project, and how does it aid the structure?
outwards from the edge of the helix, which is good as some of them can be large and could cause steric collisions.
57
are beta-sheets formed from continuous or non-continuous regions of a polypeptide chains?
non-continuous, they are called beta-strands
58
describe parallel and anti-parallel beta-strands
The b strands line up and form hydrogen bonds between the C=O groups of one strand and the N-H groups of another
If the strands all run in the same direction (remember that proteins have a direction, N C) then the b sheet is described as PARALLEL. If the strands run in opposite directions then it is said to be ANTI-PARALLEL.
59
draw a basic diagram of how beta-sheets look when the strands run parallel
60
draw a basic diagram for how beta sheets look when the beta strands run anti-parallel
61
why are beta sheets called beta pleated sheets?
the Ca carbons lie successively above and below the plane of the sheet
62
what are loop regions?
secondary structures are linked by loop regions. they vary in length- the long ones are called random coils and are very flexible, and the short ones are called hairpin loops or beta-turns.
63
why is proline in loop regions, try and draw structure
its locked ring structure introduces a ‘kink’ into the polypeptide chain
64
why is glycine included in loop regions?
GLYCINE is also often found in loops because its small side chain enables it to form turns when other amino acids could not.
65
draw the formation of a beta-alpha-beta motif
66
what are post-translational modifications?
Proteins are always synthesised using the same set of 20 amino acids
However, they can be modified after synthesis (translation) in various ways
Alterations to some produce the “rare” amino acids – hydroxyproline, hydroxylysine
Sugars/carbohydrates/glycans can be added to some amino acids (asparagine, threonine, 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
67
what is tertiary structure?
For most proteins, the final three-dimensional structure of a protein is produced by the association of the secondary structures into compact domains
68
describe the formation and features of disulphide bridges
The side chain of one CYSTEINE can form a crosslink with the side chain of another which is near to it in space (a covalent bond).
They make proteins more resistant to degrading and denaturing.
When these covalent bonds are formed between cysteine, we treat it as one molecule (cystine).
69
draw the formation of triosephosphate isomerase
70
describe cytochrome b in terms of alpha helices and beta sheets formation
Composed entirely of α-helices. Has a bound iron atom that functions as an electron transporter.
71
what is quaternary structure?
proteins formed from more than one polypeptide chain.
The chains, SUBUNITS, associate into a MULTIMERIC COMPLEX which is held together by electrostatic, hydrogen and van der Waals bonds (and sometimes disulphide bridges).
72
what are homodimers and heterodimers?
Homodimer: same polypeptide chain joined together. Heterodimer: different polypeptide chains joined together.
73
describe the composition of haemoglobin in terms of alpha helices and beta chains
composed of 4 polypeptides: 2 identical alpha chains and 2 identical beta chains
74
write a substantial paragraph detailing the 4 levels of protein structure
The primary structure of a protein is the sequence of amino acids which form the polypeptide chain and the position of any disulphide cross-links. This therefore represents all of the covalent bonds within the protein. Different regions of the polypeptide chain then fold into regular local secondary structures, e.g. -helices and -sheets. Tertiary structure is then formed by the packing of these structural elements into compact globular domains. Some proteins contain several subunits formed from individual polypeptides arranged in a quaternary structure.
75
what is a globular protein?
protein chains arranged in compact domains, usually active things in cellular machinery e.g. killing pathogens, forming DNA, just bringing things one place to another, cutting things, moving things, just generally very involved in the activities of the cell.
76
what is a fibrous protein?
protein chains arranged into fibres, usually have a structural role. much simpler sequence usually in nature, need a repetitive element as they play a structural, skeletal role.
There are three main groups of fibrous proteins defined by the secondary structure:
coiled-coil (e.g. keratin and myosin), b-sheets (e.g. amyloid fibres and silks), triple helix (the collagens)
77
explain what keratin proteins are xxxx
they're a family of mechanically durable proteins in hair, nails, etc. They must be very stable and easy to replace as stuff like hair and nails can damage very easily.
The primary structure of a-keratin has a 7 amino acid repeat, a-b-c-d-e-f-g, which forms an a-helix. Residues a and d are hydrophobic and are on the same side of the alpha-helix: b,c,e,f,g can be anything.
. 2 keratin helices can associate at specific points, where the hydrophobic residues (a + d) are, to form a coiled coil.
78
how do many coiled coil dimers twist to form a strong rope?
The 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
explain the structure and lore of fibroin proteins
they are long silk fibroin stretches containing a 6-amino-acid repeats, (-Gly-Ser-Gly-Ala-Gly-Ala-)n which forms an antiparallel b-sheet.
The glycine side chains (H) project from one side of the sheet and those of serine (CH2OH) and alanine (CH3) project from the other.
80
why is silk extremely strong? (hint: fibroin proteins)
Silk is extremely strong as any stretching would require the breaking of covalent bonds, yet it is flexible because the b-sheets are interacting via weak van der Waals bonds.
The b-sheets can stack into an array with layers of contacting Gly side chains alternating with layers of Ser/Ala side chains.
81
82
describe the structure of collagen
the most abundant vertebrate proteins, which form strong fibres present in skin, bone, teeth, cartilage, etc.
about 1/3 of the amino acids are glycine. another 15-30% are proline and hydroxyproline.
The primary amino acid sequence consists of a repeating tripeptide of Gly-X-Y where X is often Pro and Y is often Hyp.
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.
every 3rd amino acid that goes through the center is Glycine, it can fit because it’s very small. Proline and hydroxyproline add to the rigidity, they interact well with each other and lie mostly on the outside.
83
describe the collagen triple helix
Three collagen polypeptides wind around each other in a rope-like twist to form a TRIPLE HELIX.
every 3rd amino acid that goes through the center is Glycine, it can fit because it’s very small. Proline and hydroxyproline add to the rigidity, they interact well with each other and lie mostly on the outside.
The polypeptide chains form inter-chain hydrogen bonds.
The triple-helical trimers can often associate to form large, strong fibres.
84
name 5 general functions of carbohydrates
1. plants e.g. photosynthesis
2. nucleic acids e.g. ribose, deoxyribose
3. recognition e.g. blood groups
4. structure e.g. cellulose, chitin
5. fuels e.g. glucose to atp
85
give the kind of definition of a carbohydrate
they have the basic formula (CH2O)n 'hydrated carbon" e.g. glucose.
86
what are monosaccharides?
the simplest carbohydrates with 1 aldehyde or ketone, and multiple hydroxyl groups, with usually 3-7 carbon atoms.
87
what is a 3 carbon monosaccharide with an aldehyde group called?
GLYCERALDEHYDE, specifically an aldotriose
88
what is a 3 carbon monosaccharide with a ketone group called?
DIHYDROXYACETONE, specifically ketotriose
89
do most naturally occurring monosaccharides occur in the d-form or the l-form?
D- form of molecule instead of L- because the -OH molecule from the chiral carbon is sat on kinda the right-hand side. The chiral carbon that determines this is the one furthest from the aldehyde group.
90
describe vaguely the aldose series with d-isomers,
The figure shows the D isomers only, i.e. they all have the configuration of D-glyceraldehyde at their furthest asymmetric centre from the aldehyde group.
91
describe the ketose series vaguely
92
chemically, how can monosaccharides react with themselves in the same molecule to become cyclic?
Aldehydes can react with alcohols to form a covalent bond (hemiacetal) so that means a long straight-chain monosaccharide can react with itself at both its ends to become cyclic.
Ketones can also react with alcohols to form hemiketals.
93
what is the name of the rings that aldohexoses/ aldopentoses can form?
pyranose rings e.g. glucose. the proportion in the open chain is way less than 1%.
94
describe the formation of cyclic pyranose rings
The cyclisation forms a new asymmetric carbon at C-1 called the ANOMERIC carbon. Two different configurations can exist, alpha and beta. The alpha / beta isomers are called ANOMERS and, in solution, can interconvert via the open-chain form in a process called MUTAROTATION.
FOR ALDOSES THE ANOMERIC CARBON IS ALWAYS CARBON 1.
btw the hydroxyl group can either sit above or below the plane, which means there are 2 different configurations and different molecules.
95
what kind of cyclic rings do ketohexoses form?
furanose rings
FOR KETOSES THE ANOMERIC CARBON IS ALWAYS CARBON 2.
96
97
name a monosaccharide which can form both furganose and pyranose rings
ribose- it's an aldose, so the anomeric carbon is 1 irrespective of whether a furanose or pyranose ring is formed.
98
how is it decided whether a monosaccharide is alpha or beta e.g. alpha/ beta glucose?
When the hydroxyl group sits below the plane, it is alpha, and when it sits above the plane it is beta (e.g. alpha and beta glucose).
The process of folding and unfolding and stuff is called mutarotation.
99
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 alpha anomer rotates the light through +112 degrees.
THIS IS 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, corresponding to a mix of 1/3 alpha anomer and 2/3 beta anomer.
100
monosaccharide rings are usually drawn flat but they don't actually look like that, which tetrahedral shapes can pyranose and furanose rings adopt? (draw them if can)
pyranose- chair and boat confirmations
furanose- envelope
101
which bond are monosaccharides joined by?
glycosidic bonds
102
what is the difference between alpha and beta forms of a monosaccharide?
the alpha form has the -OH group on the anomeric carbon pointing down, while the beta form has it pointing up
103
in solution, do open-chain forms of aldoses and ketoses reduce or oxidise indicators?
reduce them, such as Cu2+ (cupric ion) to Cu+ (cuprous ion)
R-CHO + 2 Cu2+ + 5 OH- -----> R-COO- + Cu2O + 3 H2O
104
describe the reducing and non-reducing end of carbohydrates, with a diagram if possible
The reducing and non-reducing ends give a sense of structural direction for adding more saccharides on.
105
what is an oligosaccharide?
any short stretch of sugars
106
which enzymes are sugars joined by?
glycosyltransferases
107
describe 10 possible linkage combinations in terms of carbon number and alpha/beta for carbs
alpha(1,1), alpha(1,2), alpha(1,3), alpha(1,4), alpha(1,6).
beta(1,1), beta(1,2), beta(1,3), beta(1,4), beta(1,6).
108
what is a -NHCOCH3 group called when placed in a monosaccharide?
N-acetyl
109
what is a -OPO3(2-)- group called when placed in a monosaccharide?
phosphate
110
what is a -OSO3- group called when placed in a monosaccharide?
sulphate
111
what is a -COO- group called when placed in a monosaccharide?
carboxylate
112
113
draw a diagram showing the formation of galactose beta(1-4) glucose from the 2 monosaccharides
114
describe glycolysis + draw out a flowchart of the process
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.
For each glucose we gain a net total of 2 ATP.
115
describe the link reaction in respiration with a flowchart
Before entering the citric Acid cycle pyruvate is first combined with a sulphur containing compound known as coenzyme A, producing acetyl coenzyme A in the mitochondrial matrix.
116
draw the citric acid cycle in respiration
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.
117
why is it difficult to define lipids?
Difficult to define them based on structure as they’re very diverse, so easier to define them based on characteristics e.g. solubility.
118
what is the definition of lipids?
lipids are a diverse group of naturally-occurring molecules that are soluble in non-polar organic solvents such as chloroform (insoluble or poorly soluble in water)
119
what are the 4 important functions and properties of fatty acids?
1. simple lipids
2. building blocks for complex lipids (e.g. fats and phospholipids)
3. source of energy (ATP) for many tissues. heart + skeletal muscle prefer fatty acids to store glucose.
4. important for diet: essential ones, unsaturated vs saturated fats, trans fats
120
draw the general structure of a fatty acid and describe why they are amphipathic
Hydrophobic hydrocarbon tail is made of repeating CH2- groups, and it terminates with a hydrophilic carboxyl group. In naturally occurring fatty acids, there will usually be an even number of CH2- repeats.
121
give examples of mono- + polyunsaturated fatty acids
mono-: oleic acid
poly-: linoleic acid
122
how many C=C double bonds will polyunsaturated fatty acids have?
usually between like 1 + 4
123
what are the systematic names of linoleic acid and oleic acid?
linoleic: cis, cis-9,12-octadecadienoic acid
oleic: cis-9-octadecanoic acid
124
what are essential fatty acids?
unsaturated fatty acids that animals cannot synthesise but which are needed to synthesise other fatty acids
125
why can animals not synthesise essential fatty acids?
They can’t be synthesised, because animal cells don’t contain desaturase enzymes required to insert C=C double bonds beyond carbon 9, which some important essential fatty acids have.
126
what is a symptom of fatty acid deficiency?
a variety of skin problems including eczema
127
what are the 2 classes of EFAs?
-omega-3 type: alpha-linolenic acid (ALA)
-omega-6 type: linoleic acid (LA)
128
how are plants a source of shorts chain EFAs in the diet?
they possess the enzymes needed for their synthesis e.g. delta 12 + delta 15 desaturases.
129
why are fish oils a good source of longer chain omega 3 fatty acids?
fish accumulate them by eating micro algae
130
what are the 2 sub-categories of complex lipids?
neutral (triacylglycerols) + polar lipids
131
draw the structure of triacylglycerols (triglycerides)
132
what kind of lipids are the main dietary source of fatty acids?
triglycerides
133
which is a better storage form of fatty acids + source of biochemical energy, carbs or triglycerides?
triglycerides
134
do the 3 fatty acids in triglycerides have to be the same?
no
135
what is the difference of triglyceride composition in animal fats vs vegetable oils?
animal fats: larger percentage of saturated fatty acids
vegetable oils: almost all unsaturated fatty acids
136
how does the bend in the tail of unsaturated fatty acids lower melting temp?
prevents the molecules from packing tightly together, increasing fluidity, and lowering melting temp
137
describe the difference in physical structure of triglycerides in animals fats vs vegetable oils with a drawing, and how they affect melting point and state at room temp
138
are naturally occurring unsaturated fatty acids cis or trans, and why?
cis, as trans double bonds don't cause a bend.
triacylglycerols with trans double bonds are more solid at room temp.
trans fats produced by partial hydrogenated of vegetable oils implicated in circulatory disease
139
what are the 2 subsections of polar lipids?
sphingolipids (based on sphingosine).
glycerolipids (based on glycerol)- spilt into glycosylglycerdies and PHOSPHOLIPIDS (phosphoglycerides)
140
draw the structure of a phosphoglyceride
141
what would the name of a phosphoglyceride be if the weird group attached to the phosphate was: hydrogen, choline, ethanol amine, serine, inositol
phosphatidic acid, phosphatidylcholine, phosphatidylethanolamine, phosphatidylserine, phosphatidylinositol
142
draw a phosphatidylcholine
143
describe the importance of bio-membranes (3)
1. separate the cell contents from its surroundings (or divide cell into compartments e.g. organelles)
2. Compartmentalise the cell into discrete and different regions and environments with membrane-bound organelles; this allows processes to happen at their optimum. Avoids competition between chemical pathways for substrates, etc.
3. selective permeability
4. cell-to-cell recognition/ communication
144
explain the history of models of membrane structure
1915- red BC (erythrocyte) membranes analysed + contained lipids and proteins
1925- Gorter + Grendel- phospholipid bilayer
1935- Davson + Danielli- PL bilayer between 2 layers of globular proteins. Problems: membranes differ in composition + structure, and membrane proteins not very water soluble
1972- Singer + Nicolson- fluid mosaic
145
what was the evidence for the fluid mosaic membrane model?
they basically freeze-fractured the membrane + took the bilayer apart with a knife, showing bumps of proteins projecting through the membrane.
146
describe how the movement of phospholipids contributes to membrane fluidity
phospholipids move laterally along its plane very fast, but flip-flopping between inner + outer leaves is quite rare (maybe once a month). A phospholipid can move 2 micrometers (length of bacterial cell) in 1 sec.
147
how is the fluidity of phospholipids annoying in terms of microscopy?
just makes it harder to see them under a microscope fairly obvious idk why this is even here
148
how does cholesterol aid the phospholipid membrane in terms of temperature and stuff?
helps stabilise the membrane.
at higher temps (e.g. 37), reduces movement so its less fluid, and it lower temps hinder packing, which maintains fluidity, so acts as a buffer to the free phospholipid movement, reducing the effects of high and low temperatures.
149
how do unsaturated hydrocarbons enhance membrane fluidity?
the kinks keep the phospholipids from packing together, making it more fluid.
saturated hydrocarbon tails pack together, increasing membrane viscosity.
150
describe protein movement in the phospholipid membrane + the Frye and Edidin experiment and the Akihito Kusumi experiment
they also move laterally, but a lot less and not randomly (hop diffusion modification) due to the cell's actin cytoskeleton.
F+E: (1970)- fusion studies in mouse and human cells labelled with different markers.
AK: (2001)- hop diffusion- proteins diffuse 100x slower in natural membranes compared to artificial membranes. Proteins are fenced-in by the cell's actin cytoskeleton but may hop into another area over the walls.
151
what are the 3 groups that the proteins in the phospholipid bilayer can be classified into?
integral proteins: transmembrane ones- the hydrophobic regions are in the hydrophobic core. Tightly bound to the membrane (the big ones that are on all the diagrams). Need a detergent wash to remove.
peripheral proteins: only lightly attached via other proteins, can just wash off with salt wash.
lipid-anchored proteins: covalently attached to lipids e.g. GPI-anchored
152
how do the proteins in a phospholipid membrane dictate how other proteins associate with the membrane?
the hydrophilic and hydrophobic domains determine this
153
describe carbohydrates located in membranes
short, branched oligosaccharide chains of less than 1 sugar units, highly diverse (between species, individuals, etc).
act as identity tags e.g. blood groups are due to variation in carbohydrates on the surface of red blood cells.
most are covalently bound to proteins (glycoproteins), some to lipids (glycolipids)
154
membranes have distinct inside/ outside faces that differ in:
lipid composition
peripheral proteins attached
carbohydrates attached
integral proteins are asymmetrical with a defined orientation, just randomly embedded in there like sticking out
155
describe selective permeability on the phospholipid membrane
the rate of diffusion across a lipid bilayer depends on size of the molecule + relative solubility in oil (polarity).
highly permeable to small non-polar molecules and small uncharged polar molecules depending on size (small > large).
highly impermeable to charged molecules (ions) and large polar molecules
156
how are ions and large molecules like glucose + amino acids able to move efficiently across biological membranes?
1. proteins with a hydrophilic channel allowing ions or molecules to diffuse passively from one side to the other.
2. proteins that bind + transport molecules in an energy-requiring process
Transport proteins are usually quite specific for the substance transported.
157
how do proteins are carbs in a membrane help with cell-cell recognition/ communication?
some glycoproteins act as identification tags that are recognised by receptor proteins in other cells. the ability to distinguish one type of cell from another is crucial for like embryogenesis for the sorting of cells into tissues + organs, and as the basis for recognition and rejection of foreign cells by the immune system
158
describe the 4 more not really important functions of membrane proteins
1. enzymatic activity- sometimes organised in teams to carry out sequential steps in a metabolic pathway
2. signal transduction- receptors for chemical messengers (signal molecules)
3. intercellular joining- 'gap junctions' or 'tight junctions'
4. attachment to the cytoskeleton and extracellular matrix (ECM)- coordination of extracellular processes with intracellular processes, maintains cell shape and stabilises location of the protein
