Chapter 3 Biological molecules Flashcards
(142 cards)
1
Q
water is a liquid between ____ and ____
A
0 and 100 degrees
2
Q
water has a very high specific heat capacity of
A
4200 J/Kg (^-1) degrees C (^-1)
3
Q
water has a very high latent heat of ______ and ______ - _____
A
vaporisation
fusion
2260 Jg(-1)
4
Q
ice (solid water) is ___ ___ than liquid water. Highest density at ____
A
less dense
4 degrees
5
Q
water has a very high ____ _______
A
surface tension
6
Q
water has strong ____ to surfaces
A
adhesion
7
Q
water has low _____ but not too low
A
viscosity
8
Q
water is the _______ __________
A
universal solvent
9
Q
water has a high ________ of ______ _______ - _______
A
transmission
visible light
colourless
10
Q
why is water liquid between 0-100 and what does this allow?
A
hydrogen bonds make molecules stick together
this allows life to exist
11
Q
why does water have a high SHC and what does this allow?
A
energy goes into breaking bonds between the molecules rather than raising the temp
thermostable
12
Q
what is good about water having a high specific heat of evaporation?
A
water evaporation is a heat losing mechanism
13
Q
why is water more dense at 4 degrees and what is the benefit?
A
if it cools down after 4 degrees, water molecules form a lattice and push each other apart due to hydrogen bonds so ice is less dense than water so it floats
- ice floats so water underneath ice is insulated and protects aquatic life
14
Q
cold water is more dense than warm water as less __ so…
A
KE, so water molecules are closer together
15
Q
adhesion causes?
A
capillary action
16
Q
cohesion and adhesion causes ?
A
movement of water in xylem vessles
17
Q
water viscosity?
A
- is low to allow water to act as a transport medium
- flow -> fish, whales can swim
18
Q
water is a universal solvent - reason, benefit?
A
water surrounds ions hydration shell
- metabolic reactions occur in solution
19
Q
high transmission of light - benefits?
A
- algae photosynthesis
- aquatic organisms to see, hunt
20
Q
what is the type of bond between monosaccharides in a polysaccharide?
A
- glycosidic
21
Q
what is the type of bond between amino acids in a polypeptide?
A
- peptide bonds
22
Q
what is the type of bond between glycerol and 3 fatty acids in a lipid?
A
- ester
23
Q
what is the type of bond between nucleotides in polynucleotides?
A
- Phosphodiester
24
Q
carbs are made of?
A
CHO
25
lipids are made of?
CHO
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Proteins are made of?
CHONS
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Polynucleotides are made of?
CHONP
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What is the general formula of a sugar unit?
Cn H (2n) On
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glucose + glucose ->
matose
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glucose + fructose ->
sucrose
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glucose + galactose ->
lactose
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maltose has a what bond?
alpha 1,4 glycosidic bond
33
starch is made of (2 substances)?
amylose, amylopectin
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starch is the way that ___ store glucose
plants
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how is amylose formed?
1. the alpha 1,4 glycosdic bonds are not straight
2. this means that as more alpha glucose molecules are added, the chain forms a helix
3. HYDROGEN bonds form between the delta pos H and delta neg O atom stabilising the amylose molecule stopping it from unravelling. this means the molecule is compact and excellent for storage
36
amylopectin formation?
- branches can form of the amylose chain
| - these are formed from alpha 1,6 glycosidic bonding
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why is amylopectin an even more effective storage molecule than amylose?
bc it has many ends to add/ remove glucose from
38
why is starch a good storage molecule?
- compact
- many ends - easy addition/ removal of glucose by enzymes
- insoluble - so glucose is metabolically active and has no osmotic effect
39
animals store glucose as ____ in
glycogen, muscle and liver cells
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glycogen is made of glucose molecules joined together with what bonds?
1,4 glycosidic bonds - very similar to amylopectin in structure
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glycogen has many more _____ in the molecule than ___
branches, amylopectin
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the branches in glycogen are caused by a what bond?
1,6 glycosidic
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glycogen ???????
glucose joined by 1,4
| branches caused by 1,6
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glycogen can be quickly broken down into glucose by....
the enzyme glycogen phosphorylase,which is activated by the hormone glucagon which is secreted by the pancreas in response to low blood glucose
45
how can you tell whether it's alpha or beta glucose ?
alpha - 3 up
| beta - both 3 and 1 up
46
what is cellulose a polymer of?
BETA glucose
47
in cellulose?
- the OH group on Carbon 1 is above the ring
| - this means that for glycosidic bonds to form every other beta molecule must 'flip' 180 degrees to align Oh groups
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why is cellulose straight?
- chains of beta glucose are straight - not helical - these form cellulose molecule
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formation of cellulose fibres?
cellulose molecules align, and are stabilized by H bonds forming fibrils and then fibres .
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plant cell walls?
the cellulose cell wall of plant cells is made of cellulose FIBRES giving it mechanical strength
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humans can't break beta 1,4 glycosidic bc....
the digestive system lacks cellulase so cellulose forms dietary fibres and gives 'bulk' to the food we eat
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structure of triglycerides - monounsaturated definition?
1 double bond
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structure of triglycerides - polyunsaturated definition?
> 1 double bond
54
what is the omega naming method?
OMEGA IS THE LAST LETTER OF THE GREEK ALPHABET. Count from the last carbon to carboxyl group. Omega 3 is the last carbon from the end and the first double bond is between the 3rd and 4th carbons
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if fatty acids pack tightly together ?
high mp, solid at room temp - FATS
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if fatty acids pack loosely?
lo M.p - liquid at room temp - oils
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functions of triglycerides?
- very conc store of energy
- adipose tissue is a very heavy effective insulator - fact used by animals on cold envir
- fats stores in adipose tissue can store unlimited amounts
- waterproofing
- electrical insulation of neurones
- mechanical protection of vital organs
- buoyancy for aquatic animals
58
primary structure definition?
the specific sequence of amino acids in a protein. Determined by the sequence of bases in the DNA (gene) that codes for the specific protien
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secondary structure definition?
(2 prime)
- determined by interactions between the peptide bonds .
- The delta positive H atoms and the delta negative O atoms within the peptide bonds form H bonds with each other.
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the H bonds form 2 secondary structures?
- Alpha helix - formed by H bonds between every 4th peptide bon
- Beta pleated sheet - formed by h bonds that can be distant from each other on the chain
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tertiary structure definition?
the overall 3D structure of a protein molecule is determined by the interactions of R groups
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what are the 5 interactions in the tertiary structure?
1. Di-sulphide bonds - between sulphur atoms of Cysteine R groups
2. Ionic bonds - between oppositely charged R groups
3. Hydrogen bonds
4. Hydrophobic
5. Hydrophillic
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hydrophobic interactions ...
Hydrophobic r groups orientate away from water - often on the inside of a protein molecule
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hydrophilic interactions...
Hydrophilic R groups orientate towards water - often on the outside of protein molecules
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What are disulphide bonds?
strong covalent bonds between sulphur atoms of Cysteine R groups
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Quaternary structure ?
- some proteins have more than 1 polypeptide chain . these interact and fold together to form the overall 3D structure of the protein molecule
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Globular proteins examples?
- Haemoglobin, insulin, enzyme-catalase
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Fibrous proteins examples?
- Collagen, Keratin, Elastin
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primary structure - globular vs. fibrous
globular - very precise, non repeating, always same length
| fibrous - repeating sequence of AAs, varying in length
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solubility in water - globular vs fibrous
- globular = soluble
| - fibrous = insoluble
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function - globular vs fibrous
- globular = metabolically active
| - fibrous = metabolically inactive + structural
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conjugated definition?
protein joined to a prosthetic group (non-protein)
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calcium ion ?
Ca (^2+)
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ammonium ion ?
NH four plus
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5 CATIONS need to know?
- Calcium
- Sodium
- Potassium
- Hydrogen
- Ammonium
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5 ANIONS need to know?
- Nitrate
- Hydrogen Carbonate
- Chloride
- Phosphate
- Hydroxide
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hydrogen carbonate formula
HCO three (^-)
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phosphate formula?
PO four (^3-)
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Chromatography ?
- A separation technique used to separate mixtures of SIMILAR substances e.g pigments, AAS ect
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principles of chromatography - stationary phase
- doesn't move e.g. paper, T;LC - thin layer chromatography , ect...
- separating molecules ADBORB to the stationary phase with different levels of ADSORPTION
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what is adsorption?
Adsorption is the sticking of a particle to a surface
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principles of chromatography -mobile phase?
- moves with the seperating molecules - a solvent e.g. water, organic solvents
- separating molecules DISSOLVE in the mobile phase with different levels of solubility
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molecules are separated according to their
ADSORPTION to the stationary phase and their SOLUBILITY in the mobile phase
The more soluble a pigment, the better it will dissolve and so the further it will move up the TLC strip, but the greater the adsorption, the less it will move up the strip.
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Rf value equation?
distance of the spot/ compound from origin/ distance of solvent front from origin
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what is a biosensor?
Sensors that use biological components to determine the presence and concentration of molecules
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3 components of biosensors are?
- Molecular recognition
- Transduction
- Display
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Molecular recognition ?
- the molecule being sensed - the analyte - is recognised
- this could be an enzyme catalysed reaction, binding to a receptor like an antibody molecule, or binding to a single stranded length of DNA - a way of recognising specific DNA sequences
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transduction?
- A transducer picks up the recognition and produces a signal, for example releasing a coloured molecule or producing an electric current
89
display?
- the signal produced by the transducer is turned into smthg which can be detected by humans, e.g a coloured line or digital readout
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examples of biosensors?
pregnancy test, blood glucose monitor, forensic profile
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test for protiens?
Buiret reagent, add a few drops
- stays blue if no protien
- if present, goes purple, lilac, mauve
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test for reducing sugars?
- Bendict's reagent or Reagent test strips - Clinistixs
- Add a few drops, heat at 80 degrees for 5 mins
- stays transparent blue if none
- if present, brick red precipitate (green, yellow, orange, brick red depend on conc)
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test for non reducing sugars -sucrose ?
- Benedict's reagent
- do Benedict's test - get NEGATIVE RESULT
- NEW SAMPLE, ass hcl heat @ 80 degrees 5 mins,
- cool ,neutralise with NaOH,
- do another benedicts - POSITIVE RESULT
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test for starch ?
- iodine, add a few drops
- stays yellow/ brown if none
- turns blue/ black if there
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test for lipids?
- ethanol and water
- add equal vol of ethanol and shake. decant into water
- neg = no emulsion layer
- pos = milky white emulsion layer
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limitation of biological tests and solution - 1 Ambiguous
1. Ambiguous/ inconclusive/ difficult to see + result for some tests - e.g. emulsion test on something that is already milky
- improvement: alternative test with clear result e.g Sudan III
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limitation of biological tests and solution - 2. subjective result
subjective results - based on opinion
| Improvement: instruments that give digital quantitative results e.g. COLORIMETER, GLUCOSE BIOSENSOR
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limitation of biological tests and solution - 3. presence
some tests only indicate presence not concentration- Buiret test/ Iodine test
Improv: use an altenative method - colorimeter, glucose biosensor
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explain use of centrifuge?
instead of using filter paper to remove suspension (so light can get thru and colorimeter can be used), the centrifuge spins the test tube so suspension settles at bottom of solution
100
what colour light is used in a colorimeter ?
the opp/ complementary colour to the colours of solution being used bc this light would be easily absorbed and so the difference in how conc a solution is can be seen
101
why is the same colour light not used?
all of the light would be transmited and the graphwould just be a straight line
102
how is a colorimeter calibrated?
- using a 'blank'
| - this is a sol with usually 100% transmission e.g pure water
103
globular proteins - haemoglobin?
structure:
- conjugated with Haem prosthetic group
- many regions of alpha helix
- 4 sub-units - 2 alpha, 2 beta
- iron centre
function: - to bind to O to transport it to respiring cells and to deliver O to respiring cells
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globular proteins - insulin
structure;
- soluble
- need to have precise shapes as hormones, also have to fit into specific receptors on cell surface membranes to have their effects
Function: - Involved in the regulation of blood glucose conc & transported in the blood stream
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globular proteins - catalase
- enzyme
- Quaternary protein containing 4 prosthetic haem groups
structure : The presence of iron II ions in the haem groups allow catalase to interact with hydrogen peroxide and speed up its breakdown. H peroxide is damaging to cells and catalase doesn't let it build up.
106
fibrous proteins - collagen
func: mechanically strong = doesn't stretch
- Quaternary structure, 3 helical chains
- repeating sequence of AAs
- ends of molecules are staggered
func: - structural proteins/ insoluble in water
- major component of skin, bone, tendons, cartilage
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fibrous proteins - keratin
struc: - group of fibrous proteins
- has large proportion of cysteine -> many strong disulphide bonds -> areong, inflexible, insoluble material
- degree of disulphide bonds determines flexibility
func: present in hair skin, nails, hair has fewer disulphide bonds than nails, so more flexible
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fibrous protiens - elastin
structure - Quaternary protein made of many stretchy molecules called tropoelastin
func: found in elastic fibres, which are present in the walls of blood vessels and in alveoli of lungs
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ions in solution are called an?
electrolyte
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what is a polar molecule?
they have regions of negativity and regions of positivity
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why does water have a 'skin' of surface tension?
the water molecules are more strongle cohesive to each other than they are to air
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ratio for elements in carbohydrates?
C (^x)H(^2)O(y)
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why are globular proteins soluble?
Hydrophobic R groups on the amino acids are kept away from the aqueous environnement, hydrophillic R groups are kept on the inside of R groups - meaning proteins are soluble in water
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proteins without prosthetic groups are called?
simple proteins
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why are fibrous proteins insoluble?
due to the presence of a high proportion of amino acids with hydrophobic R groups in their primary structures
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what is a polymer ?
long chain that is composed of many individual monomers that have been bonded together in a repeatung pattern
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LIPIDS ARE _____ NOT ____
macromolcules, not polymers
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water is liquid at room temp due to ____ & ______
polar nature, strength of H bonds
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cohesion =
attraction between molecules of same type
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why does water have a high surface tension?
water molecules at the surface of the water are moreb attracted to each other than they are to molecules in the air
- this uneven attraction pulls molecules inwards towards the water below so the surface of water is placed under tension
- this tension results in a thin 'skin' on top of water surface
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why is water more dense at 4 degrees?
- as it freezes, each molecules forms the max 4 bonds H bonds
- in order to do this, the water molecules need to be more spaced out in a regular geometric structure
- less molecules in a space, less dense
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monosaccharide def
are single sugar monomers. They are the simplest carbohydrates
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what is an isomer?
molecules that have the same chemical formula but have a different arrangement of atoms in space
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where is maltose foound?
- germinating seeds as more complex carbs are broken down for energy
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where is sucrose found?
transported in the phloem to provide sugars for other parts of the plant
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where is lactose found?
in mammalian milk to provide energy for infant mammals
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polysaccharides are not ......
sweet tasting or easily soluble, so not sugars
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what is an amyloplast?
stores starch, 'starch grain'
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why are cell walls so strong?
cellulose macro fibrils wrap around plant cells in multiple layer at diff angles
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why do lipids not dissolve in water?
they are non- polar molecules
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why are some lipids liquids?
- The C double bond in the unsaturated chain causes the fatty acid tails to bend
- this bending pushes the unsaturated triglyceride molecules further apart than the saturated molecules
- spaces between molecules weaken inter molecular forces between the unsaturated triglyceride molecules so they form a liquid at room temp
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to form a PHOSPHOLIPID
the joining of the phosphate group onto the glycerol occurs through a condensation reaction between OH group on phosphoric acid and glycerol
- creates a phosphate ester bond
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why is the phosphate head hydrophillic ?
when the phospholipid is surrounded by water, the H ions dissociate from the phosphoric acid, this forms a phosphate group with a - charge
134
why are the fatty acid tails hydrophobic?
they are non-polar, non-charged
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what is a hydrophilic molecule??
is a molecule that is attracted to water due to having a charge
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what is a hydrophobic molecule?
molecule that is repelled by water due to not having a charge
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in a phospholipid bilayer, why are the hydrophobic tails never exposed
the phospholipids can move paste each other which keeps the membrane fluid
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cell membrane roles?
- control of substance entry/ exit
- electrical insulation
- creates a barrier to charged molecules
- partially permeable
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why are globular proteins soluble?
- hydrophilic R groups on outside
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what is a globular protein?
- a protein with a spherical shape that is soluble in water . Typically have metabolic roles
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what is a fibrous protein
very long, strong, insoluble protein which often has a structural role in organisms
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reducting sugars are?
ALL monosaccharides, most disaccharides
