Chapter 3 Biological molecules Flashcards
water is a liquid between ____ and ____
0 and 100 degrees
water has a very high specific heat capacity of
4200 J/Kg (^-1) degrees C (^-1)
water has a very high latent heat of ______ and ______ - _____
vaporisation
fusion
2260 Jg(-1)
ice (solid water) is ___ ___ than liquid water. Highest density at ____
less dense
4 degrees
water has a very high ____ _______
surface tension
water has strong ____ to surfaces
adhesion
water has low _____ but not too low
viscosity
water is the _______ __________
universal solvent
water has a high ________ of ______ _______ - _______
transmission
visible light
colourless
why is water liquid between 0-100 and what does this allow?
hydrogen bonds make molecules stick together
this allows life to exist
why does water have a high SHC and what does this allow?
energy goes into breaking bonds between the molecules rather than raising the temp
thermostable
what is good about water having a high specific heat of evaporation?
water evaporation is a heat losing mechanism
why is water more dense at 4 degrees and what is the benefit?
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
cold water is more dense than warm water as less __ so…
KE, so water molecules are closer together
adhesion causes?
capillary action
cohesion and adhesion causes ?
movement of water in xylem vessles
water viscosity?
- is low to allow water to act as a transport medium
- flow -> fish, whales can swim
water is a universal solvent - reason, benefit?
water surrounds ions hydration shell
- metabolic reactions occur in solution
high transmission of light - benefits?
- algae photosynthesis
- aquatic organisms to see, hunt
what is the type of bond between monosaccharides in a polysaccharide?
- glycosidic
what is the type of bond between amino acids in a polypeptide?
- peptide bonds
what is the type of bond between glycerol and 3 fatty acids in a lipid?
- ester
what is the type of bond between nucleotides in polynucleotides?
- Phosphodiester
carbs are made of?
CHO
lipids are made of?
CHO
Proteins are made of?
CHONS
Polynucleotides are made of?
CHONP
What is the general formula of a sugar unit?
Cn H (2n) On
glucose + glucose ->
matose
glucose + fructose ->
sucrose
glucose + galactose ->
lactose
maltose has a what bond?
alpha 1,4 glycosidic bond
starch is made of (2 substances)?
amylose, amylopectin
starch is the way that ___ store glucose
plants
how is amylose formed?
- the alpha 1,4 glycosdic bonds are not straight
- this means that as more alpha glucose molecules are added, the chain forms a helix
- 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
amylopectin formation?
- branches can form of the amylose chain
- these are formed from alpha 1,6 glycosidic bonding
why is amylopectin an even more effective storage molecule than amylose?
bc it has many ends to add/ remove glucose from
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
animals store glucose as ____ in
glycogen, muscle and liver cells
glycogen is made of glucose molecules joined together with what bonds?
1,4 glycosidic bonds - very similar to amylopectin in structure
glycogen has many more _____ in the molecule than ___
branches, amylopectin
the branches in glycogen are caused by a what bond?
1,6 glycosidic
glycogen ???????
glucose joined by 1,4
branches caused by 1,6
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
how can you tell whether it’s alpha or beta glucose ?
alpha - 3 up
beta - both 3 and 1 up
what is cellulose a polymer of?
BETA glucose
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
why is cellulose straight?
- chains of beta glucose are straight - not helical - these form cellulose molecule
formation of cellulose fibres?
cellulose molecules align, and are stabilized by H bonds forming fibrils and then fibres .
plant cell walls?
the cellulose cell wall of plant cells is made of cellulose FIBRES giving it mechanical strength
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
structure of triglycerides - monounsaturated definition?
1 double bond
structure of triglycerides - polyunsaturated definition?
> 1 double bond
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
if fatty acids pack tightly together ?
high mp, solid at room temp - FATS
if fatty acids pack loosely?
lo M.p - liquid at room temp - oils
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
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
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.
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
tertiary structure definition?
the overall 3D structure of a protein molecule is determined by the interactions of R groups
what are the 5 interactions in the tertiary structure?
- Di-sulphide bonds - between sulphur atoms of Cysteine R groups
- Ionic bonds - between oppositely charged R groups
- Hydrogen bonds
- Hydrophobic
- Hydrophillic
hydrophobic interactions …
Hydrophobic r groups orientate away from water - often on the inside of a protein molecule
hydrophilic interactions…
Hydrophilic R groups orientate towards water - often on the outside of protein molecules
What are disulphide bonds?
strong covalent bonds between sulphur atoms of Cysteine R groups
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
Globular proteins examples?
- Haemoglobin, insulin, enzyme-catalase
Fibrous proteins examples?
- Collagen, Keratin, Elastin
primary structure - globular vs. fibrous
globular - very precise, non repeating, always same length
fibrous - repeating sequence of AAs, varying in length
solubility in water - globular vs fibrous
- globular = soluble
- fibrous = insoluble
function - globular vs fibrous
- globular = metabolically active
- fibrous = metabolically inactive + structural
conjugated definition?
protein joined to a prosthetic group (non-protein)
calcium ion ?
Ca (^2+)
ammonium ion ?
NH four plus
5 CATIONS need to know?
- Calcium
- Sodium
- Potassium
- Hydrogen
- Ammonium
5 ANIONS need to know?
- Nitrate
- Hydrogen Carbonate
- Chloride
- Phosphate
- Hydroxide
hydrogen carbonate formula
HCO three (^-)
phosphate formula?
PO four (^3-)
Chromatography ?
- A separation technique used to separate mixtures of SIMILAR substances e.g pigments, AAS ect
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
what is adsorption?
Adsorption is the sticking of a particle to a surface
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
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.
Rf value equation?
distance of the spot/ compound from origin/ distance of solvent front from origin
what is a biosensor?
Sensors that use biological components to determine the presence and concentration of molecules
3 components of biosensors are?
- Molecular recognition
- Transduction
- Display
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
transduction?
- A transducer picks up the recognition and produces a signal, for example releasing a coloured molecule or producing an electric current
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
examples of biosensors?
pregnancy test, blood glucose monitor, forensic profile
test for protiens?
Buiret reagent, add a few drops
- stays blue if no protien
- if present, goes purple, lilac, mauve
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)
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
test for starch ?
- iodine, add a few drops
- stays yellow/ brown if none
- turns blue/ black if there
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
limitation of biological tests and solution - 1 Ambiguous
- 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
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
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
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
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
why is the same colour light not used?
all of the light would be transmited and the graphwould just be a straight line
how is a colorimeter calibrated?
- using a ‘blank’
- this is a sol with usually 100% transmission e.g pure water
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
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
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.
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
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
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
ions in solution are called an?
electrolyte
what is a polar molecule?
they have regions of negativity and regions of positivity
why does water have a ‘skin’ of surface tension?
the water molecules are more strongle cohesive to each other than they are to air
ratio for elements in carbohydrates?
C (^x)H(^2)O(y)
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
proteins without prosthetic groups are called?
simple proteins
why are fibrous proteins insoluble?
due to the presence of a high proportion of amino acids with hydrophobic R groups in their primary structures
what is a polymer ?
long chain that is composed of many individual monomers that have been bonded together in a repeatung pattern
LIPIDS ARE _____ NOT ____
macromolcules, not polymers
water is liquid at room temp due to ____ & ______
polar nature, strength of H bonds
cohesion =
attraction between molecules of same type
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
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
monosaccharide def
are single sugar monomers. They are the simplest carbohydrates
what is an isomer?
molecules that have the same chemical formula but have a different arrangement of atoms in space
where is maltose foound?
- germinating seeds as more complex carbs are broken down for energy
where is sucrose found?
transported in the phloem to provide sugars for other parts of the plant
where is lactose found?
in mammalian milk to provide energy for infant mammals
polysaccharides are not ……
sweet tasting or easily soluble, so not sugars
what is an amyloplast?
stores starch, ‘starch grain’
why are cell walls so strong?
cellulose macro fibrils wrap around plant cells in multiple layer at diff angles
why do lipids not dissolve in water?
they are non- polar molecules
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
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
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
why are the fatty acid tails hydrophobic?
they are non-polar, non-charged
what is a hydrophilic molecule??
is a molecule that is attracted to water due to having a charge
what is a hydrophobic molecule?
molecule that is repelled by water due to not having a charge
in a phospholipid bilayer, why are the hydrophobic tails never exposed
the phospholipids can move paste each other which keeps the membrane fluid
cell membrane roles?
- control of substance entry/ exit
- electrical insulation
- creates a barrier to charged molecules
- partially permeable
why are globular proteins soluble?
- hydrophilic R groups on outside
what is a globular protein?
- a protein with a spherical shape that is soluble in water . Typically have metabolic roles
what is a fibrous protein
very long, strong, insoluble protein which often has a structural role in organisms
reducting sugars are?
ALL monosaccharides, most disaccharides
