Biological Molecules :). Flashcards
Name some important functions of water?
Reactant Solvent Transports substances Helps with temperature control Habitat
How is water being a reactant useful?
It’s in lots of important chemical reactants including hydrolysis reactions
What’s a solvent?
Something with substances dissolved in it
Where do mort biological reactions take place?
In solution (e.g. Cytoplasm of eukaryotes and prokaryotic cells) so water essential
What causes water be able to transport substances?
It’s liquid and a solvent so materials like glucose and oxygen can be be dissolved and carried around plants and animals
Why does water help with temperate control?
It has a specific heat capacity and a high latent heat of evaporation
How come water can be a habitat?
Helps with temperature control
Solvent
Becomes less dense when freezes so many many organisms can survive and reproduce in it
Molecule of water?
One oxygen (O) joined to two atoms of hydrogen (H2) shared by electrons
Why is the other side of each hydrogen atom left with a slight positive charge?
Shared negative hydrogen electrons pulled towards oxygen atom so other side of hydrogen left slightly positive
What does the unpaired negative electrons in oxygen give it?
A slightly negative charge
Why is water polar?
Has partial negative charge on one side and a partial positive charge on the other.
What do slightly-negatively charged oxygen do to the slightly positively-charged hydrogen atoms of the other water molecules?
Attract them
What’s the attraction called?
Hydrogen bonding and gives water some of its useful properties
What’s specific heat capacity?
The energy needed to raise the temperature of 1g of a substance by 1oC
Why does water have a high heat capacity?
Hydrogen bonds between water molecules absorb a lot of energy so water has a high specific heat capacity so takes s lot of energy to heat up
Why is water a good habitat?
Doesn’t experience rapid temperature changes
Temperate under water likely to be more stable than on land
How much energy to break a hydrogen bond between water molecules?
Lots
Lot of energy used up when water evaporates water property?
High latent heat of evaporation
Why do mammals sweat when hot ?
Waters great at cooling things
Cools surface of the skin
What is cohesion?
Attraction between molecules of same type
Why are water molecules very cohesive?
Polar
What’s does the cohesive of water help?
Water to flow making great for transporting substances. Helps water transported up plant stems in transpiration stream
What are a lot of important substances in biological reactions?
Ionic
What’s ionic?
Made from positively charged atoms or molecules and one negatively-charged atom or molecule
Salt is made from?
A positive sodium ion and a negative chloride ion
What happens because water is polar?
Slightly positive end of water molecule will be attracted to the negative ion and the slightly negative end of water molecule will be attracted to the positive ion they will dissolve
What makes water useful as a solvent in living organisms?
It’s polarity
E.g. Humans important ions can dissolve in water in blood and be transported around the body
What happens to water at low temperature?
Freezes turns from liquid to solid
How far are water molecules held in ice compared to liquid water?
Further
Why does ice float?
water molecules form four hydrogen bonds up other water molecules making a lattice shape making ice less dense than liquid water
Why is water less dense than solid useful to living organisms?
In cold temperatures ice forms insulating layer on top of water- the water doesn’t freeze so organism that live in water don’t freeze and can still move around
What are most carbohydrates?
Polymers
Polymers are?
Molecule made up of monomers bonded together
Monomers make up what?
Carbohydrates called monosaccharides
What is glucose?
A six carbon monosaccharides meaning hexose monosaccharide
Two type of glucose are?
Alpha and beta
What is glucose structure related to?
It’s function as the main energy source in animals and plants
What’s does glucose structure make it?
Soluble
Easily transported
Chemical bonds contain lots of energy
What is ribose?
A monosaccharide with five carbon atoms
Pentose monosaccharide
What are carbohydrates made of?
Carbon
Hydrogen
Oxygen
For every carbon atom in carbohydrate usually how many oxygen and hydrogen are there usually?
2 Hydrogen
1 Oxygen
How are monosaccharides joined together?
By glucosidic bonds
What’s a condensation reaction?
During synthesis, hydrogen atom on one monosaccharide binds to a hydroxyl group on the other releasing a molecule of water
What’s hydrolysis?
Reverse of condensation
Water molecule reacts with glycosidic bond breaking it apart
What happens when two monosaccharides join together?
Disaccharide
Alpha glucose + alpha glucose ->
Maltose
Maltose
Alpha glucose + alpha glucose ->
How other disaccharides made?
In a similar way
Sucrose->
Alpha glucose + fructose
Alpha glucose + fructose
Sucrose->
Lactose
Beta glucose+ galactose->
Beta glucose+ galactose->
Lactose
Polysaccharide is?
When more than two monosaccharides are joined together
What makes amylose
Lots of alpha molecules joined together by glycosidic
Three polysaccharides you need to know about?
Starch
Glucogen
Cellulose
Where do cells get their energy from?
Glucose
How do plants store excess glucose as?
Starch
When a plant needs more glucose for energy?
It breaks down starch to release the glucose
What is starch a mix of?
Two polysaccharides of alpha-glucose amylose and amylopectin
Describe amylose?
Long in branched chain of alpha glucose
Angles of glucosidic bond give it coiled structure like cylinder
Compact
Good for storage
Why is amylose good for storage?
You can fit more into a small space
Describe amylopectin
Long branched chain of alpha glucose
Side branches allow enzymes to break down molecules to get glucosidic bonds easily meaning glucose gets released quickly
Is starch soluble or insoluble?
Insoluble in water so didn’t cause water to enter cells by osmosis which would make then swell
Good for storage
Animals cells get energy from?
Glucose
How do animals store excess glucose?
As glycogen
Glycogen is?
Another polysaccharide of alpha-glucose
Structure of glycogen
Similar to amylopectin except lots more side branches coming off it
Loads of side branches mean stored glucose can be released quicker which is important for energy release
Compact
Cellulose is made of?
Long, in branched chains of beta glucose
What happens when beta-glucose molecules bond?
They form straight cellulose chains
How are cellulose chains linked together?
By hydrogen bonds to form strong fibres called microfibrils
What do strong fibres means for cellulose?
Provide structural support for cells
E.g. In plant cell walls
How much water in a cell?
About 80%
What are triglycerides?
Macromolecules
What are macromolecules ?
Complex molecules with relatively large molecular mass
What do all lipids contain including triglycerides ?
Carbon
Hydrogen
Oxygen
Basic structure of triglyceride?
One molecule of glycerol with three fatty acids attached to it
What do fatty acid molecules have?
Long tails made of hydrocarbons
What is a hydrocarbon?
A compound of atoms containing only carbon and hydrogen atoms
What are these fatty acid tails?
Hydrophobic
What do these tails make lipids?
Insoluble in water
What do all fatty acids have the same and what varies?
Same basic structure
Hydrocarbon tails varies
What are triglycerides synthesised?
By formation of water bond between each fatty acid and glycerol molecule
How is each ester bind of triglycerides formed?
Condensation reaction
Process in which triglycerides formed?
Esterification
When do triglycerides break down?
When esters bonds are broken. Each ester bond broken in hydrolysis reaction
Two types of fatty acids?
Saturated
Unsaturated
Difference between saturated and unsaturated fatty acids?
Hydrocarbon tails
Saturated fatty acids bonds?
Don’t have double bonds between carbon atoms. Fatty acid saturated with hydrogen
Unsaturated fatty acids bonds?
At least one double bond between carbon atoms causing chain to kink
General formula for fatty acid is?
CnH(2n+1)COOH
What are phospholipids?
Macromolecules
What are phospholipids like?
Similar to triglycerides except one of fatty acid molecules replaced by phosphate group
Phosphate group and fatty acid tail (phospholipids)?
Phosphate group is hydrophilic
Fatty acid hydrophobic
What are triglycerides used for plant and animals?
Mainly Energy store molecule
What do some bacteria use triglycerides for?
To store both both energy and carbon (mycobacterium tuberculosis does it)
Two reasons why triglycerides are good for storage?
Insoluble
Long hydrocarbon tails of fatty acid contain lots of chemical energy
Long hydrocarbon tails of fatty acid contain lots of chemical energy explain?
Load of energy released when broken down because of tails lipids contain twice as much energy per gram as carbohydrate
Explain insoluble for good storage triglyceride?
Don’t cause water to enter cells by osmosis which would make them swell.
Triglycerides bundle together as insoluble droplets in cells because?
Fatty acid tails are hydrophobic
Tails face onwards shielding themselves from water with glycerol heads
Where are phospholipids found?
Cell membrane of all eukaryotes and prokaryotes
Phospholipids make up?
Phospholipid bilayer
Cell membrane control what?
Enters and leaves a cell
Phospholipids heads are?
Hydrophilic
Phospholipid tails are?
Hydrophobic
Phospholipid bilayer?
Form double layer with heads facing outwards towards water on either side
Centre of bilayer is hydrophobic so?
Water-soluble substances can’t easily pass through
Membranes act as barrier to those substances
Cholesterol is?
Another type of lipid
Cholesterol structure
Hydrocarbon ring structure attached to hydrocarbon tail. Ring structure has polar hydroxyl group attached to fit in between phospholipid molecules in membrane
Cholesterol size and shape?
Small
Flattened shape
Allows cholesterol to fit between phospholipid molecules in membrane
What to cholesterol bind to?
Hydrophobic tails of phospholipids causing them to pack closer together helping membrane less fluid and more rigid
Proteins are?
Polymers
Amino acids are?
Monomers
Dipeptide is?
Two amino acids joining together
Polypeptide is?
More than 2 amino acids join together
Proteins made of?
One of more polypeptides
Amino acids have the same?
General structure
General structure amino acid
Carboxyl group and amino group attached to carbon atom
Difference between amino acids is?
Variable group they contain
All amino acids contain?
Carbon
Hydrogen
Nitrogen
What do some amino acids contain?
Sulphur
How are amino acids linked together?
By peptide bonds to form dipeptides and polypeptides in condensation reaction
Reverse reaction does what?
Adds molecules of water to break peptide bond hydrolysis reaction
Proteins levels?
Primary
Secondary
Tertiary
Quaternary
Primary structure
Sequence of amino acids in polypeptide chain
Different proteins have different sequences of amino acids in primary structure. Change in one amino acid may change whole protein structure.
Secondary structure
Polypeptide chain doesn’t stay flat or straight
Hydrogen bonds form nearby amino acids in chain makes alpha helix or beta pleated sheet
Tertiary structure
Coiled or folded chain of Amino acids coiled and foiled further
More bonds between different parts of polypeptide chain.
Tertiary structure is last for what proteins?
Ones made from single polypeptide chain
Quaternary structure
Several different polypeptide chains held by bond. Way in which there are held together
Haemoglobin quaternary structure?
Made of four polypeptide chains bonded together
Proteins made from what is quaternary the final 3D structure?
Proteins made from more than one polypeptide chain
Computer modelling can create?
:3D interactive images of proteins
Handy for investigating different levels of structure in protein molecules
Primary structure bonds?
Peptide bonds
Secondary structure bonds?
Hydrogen bonds
Tertiary structure bonds?
Ionic
Disulfide bonds
Hydrophobic and hydrophilic interactions
Hydrogen atoms
Ionic bonds in tertiary?
Attraction between negatively-charged R groups and positively-charged R groups on different parts of the molecule
Disulfide bonds tertiary?
Whenever two molecules of amino acids cysteine come close together, the sulfur atom in one cysteine bond to sulfur in other cysteine forming disulfate bond
Hydrophobic and hydrophilic interactions tertiary?
When hydrophobic R groups are close in protein tend to clump together.
Means hydrophilic R group more likely to be pushed to outside affects how protein folds up in final structure
Hydrogen bond tertiary structure?
Weak bonds form slightly positively-charged hydrogen atoms in some R groups and slightly negatively-charged atoms in other R group on polypeptide chain
Quaternary structure bonds?
Determined by tertiary structure of individual polypeptide chains being bonded together. Can be influenced by all tertiary bonds
Gobular shape?
Round and compact
Hydrophilic R groups on amino acids tend to be pushed outside of the molecule on gobular protein why?
Hydrophobic and hydrophilic interactions in proteins tertiary structure
Gobular proteins insoluble or soluble?
Soluble so easily transported in fluids
Name three functions of gobular proteins in living organisms?
Haemoglobin
Insulin
Amylase
Haemoglobin function
Carries blood around body in red blood cell
Haemoglobin cool stuff
Known as conjugated protein as protein with prosthetic group
Each of four polypeptide chains in haemoglobin has prosthetic group (haem). Haem group contains iron which oxygen binds to.
Insulin is?
Hormone secreted by pancreas
Insulin function
Helps regulate blood glucose level
Why is insulin’s solubility important?
Can be transported in blood to tissues where insulin molecule consists of 2 polypeptide chains held together by disulfide bonds
Amylase is?
Enzyme that catalyses breakdown of starch in digestive system
Amylase structure?
Made of single chain of amino acids
Secondary structure both alpha-helix and beta-pleated sheets section.
What are most enzymes?
Gobular
Fibrous proteins are?
Insoluble and strong
Structural protein
Unreactive
Name 3 fibrous proteins?
Collagen
Keratin
Elastin
Collagen found where?
Found in animal connective tissues like bones, skin and muscle
Collagen describe
Strong molecule
Minerals can bind to protein to increase rigidity in bone
Keratin found
External structures of animals
Skin, hair, nails, feathers and horns
Keratin describe
Either flexible or hard and tough
Elastin found
Elastic connective tissue
Skin, large mood vessels and some ligaments
Elastin describe
Elastic so allows tissue to return to original shape after stretched
Ion is
Atom that has electric charge
Cation
Positive charge ion
Anion
Negative charge ion
Inorganic ion doesn’t contain
Carbon
Inorganic ions really important in
Biological processes
Calcium symbol
Ca2+
Calcium function 4
Transmission of nerve impulses
Release of insulin from pancreas
Cofactor for many enzymes
Bone formation
Sodium symbol
Na+
Sodium function
Generate nerve impulses for muscle contraction and regulating fluid balance in body
Potassium symbol
K+
Potassium function
Generate nerve impulse for muscle contractions and regulating fluid balance in body
Activated essential enzymes needed for photosynthesis in plant cells
Hydrogen symbol
H+
Hydrogen function
Affects pH of substances
Important for photosynthesis in thylakoid membranes in chloroplasts
Ammonium symbol
NH+
Ammonium functions
Absorbed by soil by plants
Important source of nitrogen
Nitrate
NO3 -
Nitrate function
Absorbed from soil by plants
Important source of nitrogen
Hydrogencarbonate symbol
HCO3 -
Hydrogencarbonate function
Acts as buffer helps maintain pH of blood
Chloride symbol
Cl-
Chloride function
Involved in chloride shift helping to maintain pH of blood during gas exchange
Acts as cofactor for amylase
Involved in some nerve impulses
Phosphate symbol
PO4 3-
Phosphate function
Involved in photosynthesis and respiration
Needed for synthesis of many biology molecules
Hydroxide function
Affects pH of substance
OH-
Hydroxide
What is sugar the general term for?
Monosaccharides and disaccharides
Two categories of sugar?
Reducing or non-reducing
The Benedict’s test for what?
Sugars it differs depending on type of sugar you are testing for
What do reducing sugar include?
All monosaccharides (glucose…) and some disaccharides (maltose, lactose…)
Steps of reducing sugar Benedict’s?
Add Benedict’s reagent (blue) to sample and heat in water bath that’s been brought to boil. If tests positive coloured precipitate will form.
Reducing sugars concentration Benedict’s?
The higher the concentration the further the colour change goes
You can compare amounts of reducing sugar in different solutions. More accurate version is to filter solution and weigh out precipitate
If Benedict’s reducing sugars test fails?
If reducing sugars test is negative there could still be non-reducing sugars present
How to test for non-reducing sugars?
Break them down into monosaccharides
Get new sample add dilute HCL, careful heat in water bath, then neutralise with sodium hydrogencarbonate
Do Benedict’s test
What happens if tests for reducing or non-reducing test is positive?
Form coloured precipitate (brick red)
If stays blue doesn’t contain any sugar
Test for glucose
Using test strips coated in reagent
Strips dipped in test solution if colour change glucose present
Colour change compared to chart to give indication of concentration of glucose present.
Test for glucose use?
Testing persons urine for glucose to test for diabetes
Starch test
Iodine test
Add iodine dissolved in potassium iodide solution to test sample
If starch present
Sample changes from browny-orange to dark blue-black colour
If no starch
Stays browny-orange
Protein test
Biuret test
Test solution needs to alkaline so add few drops of sodium hydroxide solution
Add copper II sulfate solution
Protein present
Solution turns purple
No protein present
Stay blue
Lipid test
Emulsion test
Shake test substance with ethanol for about a minute then pour solution into water
Lipid present
Turn milky
More noticeable if there is more
No lipid
Solution stay clear
Colorimeter used for?
Determine concentration of glucose solution
colorimeter 1
Use Benedict’s reagent and colorimeter to get quanta tube estimate of how much glucose (other reducing sugar) is in solution
Colorimetry is
Device that measures strength of coloured solution of how much light passes through it
What does colorimetry measure?
Absorbance. The more concentrated the colour of the solution the higher the absorbance is.
How is it easiest to measure the reducing sugar levels?
Measure concentration of blue Benedict’s solution that’s left after test (the paper the solution the more glucose there was) higher glucose concentration the lower the absorbance of the solution
Initial step of using colorimetry for glucose solution?
Make up several glucose solutions of different known concentration
Can do this using serial dilution technique
How do you make 5 serial dilutions with dilution factor of 2 starting with initial glucose concentration of 40mM?
Step 1
Line up 5 test tubes in a rack
How do you make 5 serial dilutions with dilution factor of 2 starting with initial glucose concentration of 40mM?
Step 2
Add 10cm3 of initial 40mM of solution glucose solution to first test tube and 5cm3 of distilled water to other four test tubes
How do you make 5 serial dilutions with dilution factor of 2 starting with initial glucose concentration of 40mM?
Step 3
Using pipette draw 5cm3 of solution from first test tube add distilled water in second test tube and mix solution throughly. You now have 10cm3 of solution half as concentrated as solution that’s half as concentrated as solution (20mM)
How do you make 5 serial dilutions with dilution factor of 2 starting with initial glucose concentration of 40mM?
Step 4
Repeat process three more times to create solutions of 10mM, 5mM, 2.5mM
What do you need to make the calibration curve?
Glucose solutions
How do you make a calibration curve?
Step 1
Do Benedict’s test on each solution plus negative control of pure water. Use same amount of Benedict’s in each case
How do you make a calibration curve?
Step 2
Remove any precipitate either leave for 24 hours so precipitate settles out or centrifuge them
How do you make a calibration curve?
Step 3
Use colorimeter (with red filter) to measure absorbance of Benedict’s solution remaining in each tube
How do you make a calibration curve?
Step 4
Use results to make calibration curve showing absorbance against glucose concentration
What can you do with this calibration curve?
Test Unknown solution in same way as known concentrations and use calibration curve to find its concentration
What’s a biosensor?
A device that uses biological molecules such as an enzymes to detect a chemical
How does a biosensor work?
Biological molecule produced signal which is converted to electrical signal by transducer (part of biosensor). Electrical signal processed and use to work out other information
Example of biosensor?
Glucose biosensors
What is a glucose biosensor used for?
To determine the concentration of glucose in a solution
How does a glucose biosensor work?
By using enzyme glucose oxidase and electrodes. The enzyme catalyses oxidation of glucose at electrodes creating charge which is converted to electrical signal by electrodes (transducer). Electrical signal processed to electrical out initial glucose concentration
What is chromatography used for?
To separate stuff in mixture once separated can often identify components
Give an example of use of chromatography?
Used to separate and identify biological molecules e.g. Amino acids, carbohydrates, vitamins and nucleic acids
Two types of chromatography you need to know about?
Paper and thin-layer chromatography
Two phases in basic set up of chromatography?
Mobile and stationary
Mobile phase
Where molecules can move
In paper and thin-later chromatography mobile phase is liquid solvent e.g. Ethanol or water
Stationary phase
Where molecules can’t move
Paper chromatography stationary phase is chromatography paper
Thin-layer chromatography stationary phase is thin layer of solid e.g. Silica gel on a glass or plastic plate
Basic principles of chromatography
Mobile phase moves through or over stationary phase
Components in mixture spend different amounts of time in mobile and stationary phase
Components spend longer in mobile phase travel faster or further
Time spend in different phases is what separates components of mixture
Paper chromatography step 1
Draw pencil line near bottom of chromatography paper and put concentrated spot of mixture of amino acids in it. Best if carefully roll paper into cylinder with spot on outside so stand up.
Paper chromatography step 2
Add small amount of prepared solvent to beaker and dip the bottom of paper into it not the spot. Should be done in fume cupboard. Cover lid to stop solvent evaporating
Prepared solvent paper chromatography will be?
Mixture of butan-1-ol, glacial ethanoic acid and water used for amino acids
Paper chromatography step 3
As solvent spreads up paper, different amino acids move with it at different rates so separate out.
Paper chromatography step 4
When solvent nearly reached top take paper out and Mark solvent front with pencil. Then leave paper to dry out before you analyse it.
Paper chromatography step 5
Amino acids aren’t coloured meaning you won’t be able to see them on paper. Before you can analyse them you have to spray paper with ninhydrin solution to turn amino acids purple. Should be done in fume cupboard and gloves should be worn.
Paper chromatography step 6
Use Rf value to identify separated molecules
What is Rf value?
Rate of distance travelled by spot to distance travelled by solvent
How to calculate Rf value?
Rf of amino acid= (distance traveled by spot)/ (distance travelled by solvent).
What do measure once you have measured how far the spot has travelled?
Measure from point of origin to vertical centre of the spot
How do you use the Rf values once calculated?
Looking them up in database or table of known values
