Module 2 Section 2 - Biological Molecules Flashcards
Smithson
2 biological molecules people often forget about
- nucleic acids
- inorganic ions (don’t contain carbon)
Which charge does the oxygen atom in a water molecule have?
A partial/slightly negative charge.
What charge do the hydrogen atoms in a water molecule have?
A partial/slightly positive charge.
δ+
delta positive - positive charge
Explain why water can form hydrogen bonds. [1]
Water molecule is polar/as electrons are pulled closer to the oxygen atom
cohesion
The force of attraction between water molecules which makes them stick to each other
adhesion meaning
two different molecules stick together (e.g. water and a surface)
Describe the process of adhesion in plants.
When water molecules are attracted to the impermeable walls of xylem tissue.
Adhesion is the force of attraction between water and surfaces it is in contact with. This makes water molecules stick to other things.
Water molecules are attracted to the ____ walls of ____ tissue.
impermeable, xylem
Explain water’s SHC and the benefit of this.
High SHC due to the hydrogen bonds as they absorb lots of energy. This means water doesn’t experience fast temperature changes, so makes it a good habitat - the temperature is less variable than on land.
Explain water’s SLH and the benefit of this.
Takes a lot of energy to break the hydrogen bonds between molecules so a lot of energy is used when water evaporates. This means water is good as a coolant i.e. sweat.
Explain water’s density and the benefit of this.
Water molecules are held further apart in ice than when liquid as the molecules form a regular lattice with gaps (not air) between the molecules, making ice less dense than when liquid.
In cold temperatures, an insulating layer is formed on the top of the body of water, preventing the water beneath from freezing. This conserves the habitat and organisms don’t freeze, allowing them to continue to move around.
Explain water’s polarity and the benefit of this.
The slightly positive end attracts to the negative ion and the slightly negative end attracts to the positive ion. This means the ions become completely surrounded by water molecules, allowing them to dissolve (water is a useful solvent e.g. for transport of ions).
Why is the ability of water to act as a solvent (excluding transport) important for the survival of organisms? (3)
- Organisms can take in ions
- Water is a medium for reactions [1] because it allows ionic compounds to separate [1]
- Water can dilute toxic substances
5 biological functions of water
- solvent
- transport
- habitat
- reactant in chemical reactions
- aids temperature control (coolant)
What does a diagram of ice look like?
Lattice shape
Lots of air space between water molecules
enzyme cofactor
A non-protein inorganic substance that helps an enzyme to function
How is calcium involved in
biological processes? (4)
- helps transmit electrical impulses
- helps release insulin from the pancreas
- acts as a cofactor for many enzymes e.g. blood clots
- important to form bones
BIIC
How is sodium involved in
biological processes? (3)
- helps muscles to contract
- important to produce nerve impulses
- helps to regulate fluid balance (e.g. keeping plant cells turgid)
For all three, sodium works closely with potassium
How is potassium involved in
biological processes? (4)
- helps muscles to contract
- important to produce nerve impulses
- helps to regulate fluid balance (e.g. keeping plant cells turgid)
- activates enzymes for photosynthesis in plant cells
For the top three, potassium works closely with sodium
How is ammonium involved in
biological processes? (1)
Source of nitrogen (used to make amino acids, nucleic acids etc.)
How is hydrogen involved in
biological processes? (2)
- important for respiration reactions in mitochondria & inner membrane and photosynthetic reactions in thylakoid membranes
- affects substances’ pHs
The top function is similar to one of PO43-’s functions
How is nitrogen involved in
biological processes? (1)
Source of nitrogen (used to make amino acids, nucleic acids etc.)
How is hydrogencarbonate involved in
biological processes? (1)
acts as a pH buffer (which resists pH change) to maintain the pH of the blood
Hydrogencarbonate formula
HCO3-
Phosphate formula
PO43-
Ammonium formula
NH4+
How is phosphate involved in
biological processes? (2)
- involved in photosynthetic and respiration reactions
- needed for the synthesis of lots of other biological molecules (e.g. nucleotides & ATP, phospholipids & calcium phosphate - for strong bones)
The top function is similar to one of H+’s functions
How is chloride involved in
biological processes? (3)
- involved in the ‘chloride shift’ to maintain blood pH & charge of red blood cells
- acts as an enzyme cofactor for amylase
- involved in some nerve impulses
How is hydroxide involved in
biological processes? (1)
affects the pH of substances
Name 4 ions that are involved with nerve function.
- Calcium - nerve impulse transmission
- Sodium & potassium - nerve impulse generation
- Chloride
Name 4 ions that are involved with editing the pH.
- Chloride - chloride shift
- Hydrogencarbonate - pH buffer
- Hydroxide
- Hydrogen
hydrolysis meaning
breaking biological polymers into their constituent monomers by using water to break the chemical bonds between them
What elements are found in proteins?
Carbon, hydrogen, oxygen, nitrogen & sulfur
Can glycolipids contain sulfur? What are they made of?
Nope - glycerol (a carbohydrate) and lipid (fatty acids - a hydrocarbon)
Can phospholipids contain sulfur? What are they made of?
Nope - phosphate group, glycerol (a carbohydrate) and lipid (fatty acids - a hydrocarbon)
structural formula
the formula showing how atoms are arranged in a molecule of a compound
It shows double/single bonds etc.
isomer (+ examples)
same empirical formulae, but they have different structural formulae so have different properties
e.g. alpha and beta glucose
Draw ribose.
look online
Draw alpha glucose.
look online
How is beta glucose different to alpha glucose?
The hydroxyl group and hydrogen switch, so the hydroxyl group is on the top
lactose
Disaccharide of (alpha or beta) glucose and galactose
sucrose
Disaccharide of alpha glucose and fructose
maltose
Disaccharide of two alpha-glucose monomers
Disaccharide of alpha glucose and fructose
sucrose
bonding in sucrose
(alpha-) 1, 2-glycosidic bond
Do you flip the galactose molecule when reacting it with glucose?
No - you just shift galactose down so that the hydroxyl groups line up.
Hydrogen bond
A weak bond between hydrogen (with a partial positive charge) and an oxygen atom (with a partial negative charge) from another molecule
What two polymers make up starch (that you know of)?
Amylose and amylopectin
glycogen - what’s it made of?
A polymer of alpha-glucose monomers bonded together with 1-4 glycosidic bonds and lots of 1-6 glycosidic bonds via condensation polymerisation.
amylose - what’s it made of?
Polymer of alpha glucose, 1-4 glycosidic bonds
cellulose - what’s it made of?
beta glucoses - 1-4 glycosidic bonds with some 1-6 glycosidic bonds
every other beta glucose is flipped (mark scheme says rotated but it’s actually flipped like the other side of a piece of paper) 180 degrees
For a visual representation, see https://cognitoedu.org/coursesubtopic/b3-alevel-cie_IERiWhlX
amylopectin - what’s it made of?
Polymer of alpha glucose, 1-4 glycosidic bonds with some 1-6 glycosidic bonds
Microfibril
Lots of cellulose molecules bonded together
How is amylose’s structure related to its function in biology?
Coiled - compact so good for energy storage
How is amylopectin’s structure related to its function in biology?
Branching due to the 1-6 glycosidic bonds means that more glucose molecules can be accessed by enzymes, so glucose can be released faster
How is starch’s structure related to its function in biology?
Amylose and amylopectin are insoluble so don’t affect the osmatic effects on cells
What holds amylose in its coiled structure?
Hydrogen bonds between alpha glucose molecules
Describe and explain how the structure of amylopectin relates to its function. [3 marks]
- Helical/spiral shape so compact/tightly packed abd good for energy storage
- Large /insoluble so no osmotic effect/does not affect water potential
- Branched (with alpha-1,4 and alpha-1,6 glycosidic bonds) so glucose is (easily)
- released for respiration;
- Large/long so cannot leave cell/cross plasma membrane.
function of glucose
acts as an energy store/reserve
How is glycogen’s structure related to its function in biology?
- compact - good for energy storage
- heavily branched due to lots of 1-6 glycosidic bonds - energy can be released even faster
What gives cellulose its structural properties?
linear/unbranched chains (microfibrils) joined together with lots of hydrogen bonds -> high tensile (stretchable) strength molecule -> used in cell walls as a structural carbohydrate
If a question says ‘structure’, talk about the substance’s branchiness
Why is it okay for plants to store glucose as amylose or amylopectin?
It doesn’t matter as much that very few glucose molecules can be accessed by enzymes as plants don’t need as much energy to live (e.g. no movement, thermoregulation etc.)
Are all carbohydrates polar? Explain your answer.
Yes - they all have at least one hydroxyl group
Is amylose more or less soluble than amylopectin?
Amylose is in theory less soluble because there’s less branching so fewer accessible hydroxyl groups (which make a substance soluble).
However, amylose has a relatively low molecular weight, so there is a higher number of -OH groups as a proportion of the number of carbon atoms that make it up, so amylose is comparatively more soluble (although neither components of starch are very soluble).
What elements are lipids made out of?
Carbon, hydrogen and oxygen
Macromolecule meaning and examples
Complex molecules with a large molecular mass
- Proteins
- Carbohydrates
- Lipids
Type of bond between a glycerol molecule and a fatty acid/phosphate group
Ester bond
Describe the breakdown of a triglyceride molecule.
In a hydrolysis reaction, water molecules react with the ester bonds between the fatty acids and glycerol to break them down
process by which triglycerides are formed
esterification
Why are triglycerides good as energy reserves?
They store more energy per gram - the long hydrocarbon tails of the fatty acids contain lots of chemical energy, so a lot of energy is released when they are broken down.
Do unsaturated molecules have a lower or higher melting point than saturated ones? Explain why.
Lower melting points
The double bonds kink the chains, and as they can’t rotate, the layers don’t fit as closely together.
This means (the forces holding the chains together are weaker so) it takes less energy and so a lower temperature to break them out of this structure melt them.
properties of fatty acid tails
Made of hydrocarbons
Hydrophobic - make lipids insoluble in water
fatty acid structure
carboxyl group
C double bond O and single bond OH with a variable hydrocarbon tail R
general formula for a fatty acid
CnH2n+1COOH
A fatty acid is a carboxylic acid
A phosphate group is hydro____.
hydrophilic
Why can’t polar molecules diffuse through the phospholipid bilayer?
They are hydrophilic and slightly charged. The charges are repelled by the hydrophobic tails in the inside of the phospholipid bilayer.
structure of cholesterol
hydroxyl group bonded to hydrocarbon rings bonded to a hydrocarbon tail
therefore it contains only CHO elements
Compare the structures of cholesterol and triglycerides.
The carbon atoms in triglycerides are linear whereas they are arranged in a ring structure in cholesterol
Are triglycerides soluble in water? Explain the function this has in organisms.
Triglycerides are insoluble, so they don’t cause cells to swell by taking in more water by osmosis.
monoglyceride
Glycerol and a single fatty acid
Describe monoglyceride properties and how they can travel through a membrane.
They are non-polar and small enough to cross the membrane by simple diffusion.
phospholipid basic structure
Consider the differences in the things the middle thing is bonded to
Glycerol bonded to a phosphate group and two fatty acids
1 fatty acid is saturated and the other is unsaturated (contains 1+ double bond) so is kinked
phospholipid function
Phospholipids form a bilayer in cell membranes. The centre is made up of the hydrophobic fatty acid tails, acting as a barrier by preventing water soluble substances from passing through.
cholesterol function
Small and flattened shape allows cholesterol to fit in between the phospholipid molecules
At high temps -> cholesterol binds to the phospholipid hydrophobic tails, causing them to pack together more tightly, making the cell membrane less fluid & more rigid
At low temps -> cholesterol prevents the phospholipids from packing too closely together, making the cell membrane more fluid & less rigid
What lipids are insoluble in water?
Triglycerides, phospholipids & cholesterol
What lipids contain glycerol?
Triglycerides & phospholipids
What lipids contain ester bonds?
Triglycerides & phospholipids
Give the chemical elements that make up a lipid.
Carbon, hydrogen and oxygen.
It’s the same as a carbohydrate!
Give the chemical elements that make up a protein.
Carbon, hydrogen, oxygen, nitrogen and sulfur (consider disulphide bridges)
All of the biological molecules in this topc may contain C, H and O !
Give the chemical elements that make up a nucleic acid.
Carbon, hydrogen, oxygen, nitrogen, phosphorous (consider the components of a DNA molecule)
All of the biological molecules in this topc may contain C, H and O !
Animals have more ____ lipid and less ____ lipid.
saturated, unsaturated
What is biuret reagent made of?
It contains an alkali (NaOH) and copper (II) sulfate, among other things
If you aren’t using the reagent, you can use sodium hydroxide solution and then add copper (II) sulfate solution.
Tip for seeing the colour change with biuret reagent
Hold a white tile behind the solution when observing it so you can see the colour change more clearly
Why does biuret reagent work?
It contains an alkali and copper (II) sulfate, which react in the presence of peptide bonds to make the blue-purple colour.
test for starch
Add a few drops of iodine (dissolved) in potassium iodide solution (not just iodine)
Explain why the iodine isn’t just dissolved in water when you test for starch
Iodine isn’t soluble in water
test for lipids
Add ethanol and shake
Add water (or pour into a second test tube containing water) and shake again
What is Benedict’s reagent made of? What effect does this have?
Contains copper (II) sulfate - the Cu2+ ions are what make it blue.
Why does Benedict’s reagent work?
The Cu2+ ions are reduced to form Cu+ ions. These then cause a red copper (I) oxide precipitate to form (so the more Cu2O compounds form, the redder the solution looks)
How do you get Benedict’s reagent to work?
You heat it (not warm)
Limitation of using Benedict’s reagent to measure the concentration of reducing sugars
It’s semi-quantitative
Why should you always use an excess of Benedict’s reagent?
To make sure all the sugar reacts so all the Cu2O compounds form
How can you test for non-reducing sugars?
First you must test to see if it’s NOT a reducing sugar by adding Benedict’s reagent and heating it
- If you get a negative result (i.e. the solution remains a transparent blue):
- Add acid (e.g. dilute HCl) to the solution, heating it in a water bath that’s been brought to the boil
- Add some alkali to neutralise it
- Then do the normal test for reducing sugars with Benedict’s reagent and then heating it
Explain why the test for non-reducing sugars works.
Adding acid and heating the solution breaks the sugar down into monosaccharides, which then react with the Benedict’s reagent to form red copper (I) oxide precipitate
Give an example of an alkali that could be used in the process to test for non-reducing sugars
Sodium hydrogencarbonate
Benedict’s reagent is added to a glucose solution. What filter do you use to measure the absorbance of the solution with a colorimeter?
Red filter
You choose the colour that the resulting pigment is
Benedict’s reagent is added to a glucose solution.
The more concentrated the solution is, the more/less pale the resulting mixture is and the ____ the absorbance of red light after testing with Benedict’s reagent.
higher
less pale
lower
A student measured the concentration of sucrose in the leaves of a holly bush by testing the mixture formed by grinding a leaf with Benedict’s reagent.
Explain why the student’s method is invalid.
- They only used one leaf (it could have been atypical)
- Other sugars may be present in the lead sample, which they could not distinguish by doing a non-reducing / reducing sugar test.
Describe how you would perform a serial dilution.
- Measure 3cm3 of pure water with a measuring cylinder and pour into all (e.g. four) of your test tubes
- Measure 3cm3 of your stock solution with a syringe and add it into one test tube - this first test tube now has half the concentration of the stock solution
- Shake the test tube so it mixes thoroughly
- Measure 3cm3 of this test tube’s solution with a syringe and add it into the second test tube - this test tube now has half the concentration of the first one
- Repeat the two steps above above for the rest of the test tubes
- Measure and remove 3cm3 of the final test tube’s solution
The five serial dilutions have a dilutor factor of 2.
Describe how you would prepare a solution to measure the absorbance with a colorimeter.
- Do a Benedict’s test on the solutions (this is specifically for the glucose concentration practical)
- Remove any precipitates that have formed (e.g. using a centrifuge or leaving to settle for 24 hours)
Describe how you would measure the absorbance of solutions with known glucose concentrations with Benedict’s reagent and use this to measure the concentration in an unknown sample. [4 marks]
- Produce serial dilutions for known concentrations
- Pour some distilled water using blank into a cuvette so that it’s approzimtely 3/4 full
- Turn the colorimeter on and allow it to stabilise for five minutes. Set it to red light (red filter)
- Place the cuvette into the colorimeter
- Calibrate (zero) the colorimeter
- Remove the cuvette. Get a clean cuvette and use a clean pipette to transfer some of the first test tube’s solution into it
- Wipe away any moisture on the outside of the cuvette and gently tap the cuvette to remove any air bubbles
- Place the cuvette into the colorimeter and record the solution’s absorbance
- Repeat the two steps above for the rest of your solutions
- Plot a calibration curve
- Use the calibration curve to determine the unknown concentration
calibration curve
A curve that shows the relationship between two variables, so it can be used to read off the value of an unknown sample
dipeptide
A molecule formed from two amino acids bonded together with a peptide bond
disulfide bridge/bond
Covalent bond formed between two sulfur atoms in two cysteine amino acids
peptide bond
Bond formed between amino acids (the carboxyl group of one amino acid to the amine group of another) to form a di/polypeptide
What elements specificially is a peptide bond made of?
It’s the bond between the carboxyl group of one amino acid and the amine group of another. It’s between the C double bond O with the N H; the bond between the carbon & nitrogen
What forms a peptide bond?
C single bonded to N
primary structure
Sequence of amino acids in a polypeptide chain
bonds involved with primary structure
Peptide bonds
secondary structure
Twisted or coiled peptide chains
A protein’s secondary structure is formed from either ____ or ____ of protein chains.
folds, coils
bonds involved with secondary structure
hydrogen bonds between the polar NH and C double bond O bonds (amine and carboxyl groups)
two types of secondary structure that you need to know
alpha-helix
beta-pleated sheets
tertiary structure
R groups interact to form a unique, specific 3D shape/structure
bonds involved with tertiary structure
ionic bonds, disulfide bonds, hydrogen bonds, hydrophobic & hydrophilic interactions
What bonds are broken when proteins are heated to high temperatures?
Ionic bonds, hydrogen bonds, hydrophobic & hydrophilic interactions
How do tertiary structures differ?
- They depend on the interactions between the R groups
- They depend on where the R groups are located (not sure?)
Where are hydrophilic R groups found?
Sticking out of the protein as they are more likely to be pushed to the outside
amino acid side chain
variable R group
How can ionic bonds be broken?
High temperatures or changes in pH -> link to enzymes denaturing
How can hydrophobic/hydrophilic interactions be broken?
High temperatures or changes in pH -> link to enzymes denaturing
disulfide bonds are relatively ____. Briefly explain why.
strong - not broken by temperature or pH changes
quaternary structure
Multiple polypeptides bonded together
bonds involved with quaternary structure
disulfide bridges, hydrogen bonds, ionic bonds, hydrophobic and hydrophilic interactions
Can be influenced by all the bonds that make up the tertiary structure as the quaternary structure is usually determined by the tertiary structure
Proteins must have a quaternary structure. T/F and why?
False - not all proteins have a quaternary structure. Proteins made from one polypeptide chain don’t have a quaternary structure; their tertiary structure forms their 3D shape
“What is most remarkable to consider is that a hemoglobin molecule is made up of two α chains and two β chains, each consisting of about 150 amino acids, for a total of about 600 amino acids in the whole protein.”
What is meant by the α chains and β chains?
There are two pairs of identical protein chains - nothing to do with alpha helices and beta pleated sheets
There can be α and β subunits in the quaternary structure
globular protein
A protein that is compact, round and soluble
fibrous protein
A strong, insoluble, rope-shaped (long) protein
A strong, insoluble, rope-shaped (long) protein
fibrous protein
Explain the solubilities of globular and fibrous proteins.
There are hydrophilic and hydrophobic R groups in globular proteins, so there are hydrophilic-hydrophobic interactions in their tertiary structure; the polar hydrophilic R groups are pushed outwards. This means water molecules can surround the hydrophilic R groups and so allowing the globular proteins to dissolve.
Fibrous proteins are insoluble as the hydrophobic R groups aren’t folded away from the external environment.
Give three types of functions of globular proteins, and an example for each.
- Enzymes e.g. amylase
- Messenger proteins e.g. insulin
- Transport proteins e.g. haemoglobin
Give three examples of fibrous proteins.
- Collagen
- Keratin
- Elastin
What is the effect of globular proteins’ structure?
Hint: think about their solubility
The hydrophilic-hydrophobic interactions means glubular proteins are soluble, so they can easily be transported around in fluids e.g. the blood.
prosthetic group
A non-protein compound that is bound to an enzyme and acts as a cofactor to proteins (attaches to proteins to help them function)
conjugated protein
globular protein with a (non-protein) prosthetic group
How is haemoglobin’s structure related to its function?
- It’s a conjugated protein with four prosthetic groups (haems)
- These groups contain iron, which allows oxygen to bind to the red blood cell
How is amylase’s structure related to its function? (2/3)
- Main point = soluble (due to hydrophilic R groups) so can be transported in the blood
- It’s made of a single amino acid chain, having a secondary structure with both alpha-helices and beta-pleated sheets.
- Its round shape can be changed to form an active site complementary to the substrate
Unsure how point 2 relates to its function & if point 3 would get marks
How is insulin’s structure related to its function? (2)
- It’s soluble, allowing it to dissolve in the blood to be transported to the places (muscle tissue and liver) where it acts.
- It’s made of two polypeptide chains held together by disulfide bridges. Holding this shape is important as this allows insulin to bind to receptors
How is collagen’s structure related to its function? (2)
Collagen is very strong so forms animal connective tissues (like in bone, skin and muscle) as it provides tensile strength.
Collagen is also insoluble and stable.
-> provides structual support
Minerals can bind to collagen to increase its rigidity
Where is collagen found?
Animal connective tissues like in bone, skin and muscle
How is keratin’s structure related to its function? (2) (+ where is it found?)
- Found in animal external surfaces
- Can be flexible (like in skin or hair) or hard & tough (like in nails)
How is elastin’s structure related to its function? (2) (+ where is it found?)
Elastic so can return to its original shape after being stretched, so is found in connective tissues, elastic, like in skin or big blood vessels – high content in arteries
Most enzymes are ____ proteins.
globular
State one function of haemoglobin.
To transport oxygen (ignore bind)
carboxylic acid formula + number of hydrogen atoms
CnH2n+1COOH
number of hydrogen atoms = 2(no. carbons - 1) + 1 [+ 1 in the COOH] =
What type of bonds within the tertiary structure of an enzyme will break at high temperatures?
Hydrogen and ionic bonds (and also hydrophobic/hydrophilic interactions)
Where are pigments found in a plant cell specifically?
Thylakoid membranes in the chloroplasts
3 advantages of TLC over paper chromatography.
- the mobile phase moves more quickly through the stationary phase
- the mobile phase moves more evenly through the stationary phase
- there is a range of absorbencies for the stationary phase ?
Why is it important that an organic solvent is used for TLC with photosynthetic pigments?
Organic solvents are non-polar. The photosynthetic pigments are non-polar & lipophilic, so they dissolve in the solvent - they wouldn’t dissolve in polar solvents like water because they are hydrophobic.
Why can using sand when grinding a leaf be helpful?
The sand can help you extract more of the pigments.
Explain why it is important to let the spot dry in chromatography between repeated applications of the sample.
Explain why it’s important to mark the solvent front in TLC immediately?
The solvent used can evaporate quickly, so very soon you won’t know where the solvent is.
safety precautions takes for the TLC practical
How many bonds can water form with its neighbours?
Four
A student carries out the four food tests on samples from a beaker of starch and amylase. What would the results be for each of the tests if the reaction was still occuring?
Iodine: positive (still some starch remaining)
Benedict’s: positive (some reducing sugar present)
Biuret: positive (enzyme)
Emulsion: negative (no lipids formed)
Find a diagram to show the arrangement of elements in fructose. Number the carbons, explaining how you get to your answer.
Carbon 1 is the one bonded to two hydrogens and a hydroxyl group - carbon 1 should have multiple bonds to oxygen.
Then you number the carbons in a clockwise order around the ring.
Further explanation: https://chemistry.stackexchange.com/questions/43546/carbon-numbering-in-carbohydrates
What makes a compound soluble in water?
Having hydroxyl groups
Where can hydrogen bonds form in the secondary structure of a protein?
The hydrogen bonds form with the carbonyl (CO) or amino (NH) groups of backbone
Two solutes have similar Rf values in paper chromatography. Suggest and explain a modification to the method that would distinguish which solute is in an unknown sample. [2]
2 methods - try and give both.
Either:
* Use a longer strip of chromatography paper - gives a higher resolution
* Use a different solvent where the solutes have very different Rf values - they can then be more easily distinguished
