Topic 1 Flashcards
what are monomers and polymers?
● Monomers - smaller / repeating molecules from which larger molecules / polymers are made
● Polymer - molecule made up of many identical / similar molecules / monomers
what happens in a condensation reaction?
● 2 molecules join together
● Forming a chemical bond
● Releasing a water molecule
what happens in a hydrolysis reaction?
● 2 molecules separated
● Breaking a chemical bond
● Using a water molecule
what are monosaccharides? give 3 examples
● Monomers from which larger carbohydrates are made
● Glucose, fructose, galactose
describe the difference between the structure of α-glucose and β-glucose
OH group is below carbon 1 in α-glucose
but above carbon 1 in β-glucose
Alpha & beta glucose are isomers →
same molecular formula, differently arranged atoms
what are disaccharides and how are they formed?
● Two monosaccharides joined together with a glycosidic bond
● Formed by a condensation reaction, releasing a water molecule
List 3 common disaccharides & monosaccharides from which they’re made
Disaccharide Monosaccharides
Maltose Glucose + glucose
Sucrose Glucose + fructose
Lactose Glucose + galactose
what are polysaccharides and how are they formed?
● Many monosaccharides joined together with glycosidic bonds
● Formed by many condensation reactions, releasing water molecules
describe the basic function and structure of starch and glycogen
Starch - Energy store in
plant cells
● Polysaccharide of α-glucose
● Amylose - 1,4-glycosidic bonds → unbranched
● Amylopectin - 1,4- and 1,6-glycosidic bonds → branched
Glycogen - Energy store in
animal cells
● Polysaccharide made of α-glucose
● 1,4- and 1,6-glycosidic bonds → branched
explain the structures of starch and relate to their functions
Starch
(amylose)
● Helical → compact for storage in cell
● Large, insoluble polysaccharide molecule → can’t leave cell / cross cell membrane
● Insoluble in water → water potential of cell not affected (no osmotic effect)
Explain how the structures of glycogen relate to their functions
Glycogen (and starch
amylopectin)
● Branched → compact / fit more molecules in small area
● Branched → more ends for faster hydrolysis → release glucose for respiration to
make ATP for energy release
● Large, insoluble polysaccharide molecule → can’t leave cell / cross cell membrane
● Insoluble in water → water potential of cell not affected (no osmotic effect)
Describe the basic function and structure of cellulose
Function
● Provides strength and structural support to plant / algal cell walls
Structure
● Polysaccharide of β-glucose
● 1,4-glycosidic bond → straight, unbranched chains
● Chains linked in parallel by hydrogen bonds forming microfibrils
Explain how the structure of cellulose relates to its function
● Every other β-glucose molecule is inverted in a
long, straight, unbranched chain
● Many hydrogen bonds link parallel strands
(crosslinks) to form microfibrils (strong fibres)
● Hydrogen bonds are strong in high numbers
● So provides strength to plant cell walls
Describe the test for reducing sugars
Reducing sugars = monosaccharides, maltose, lactose
1. Add Benedict’s solution (blue) to sample
2. Heat in a boiling water bath
3. Positive result = green / yellow / orange / red precipitate
Describe the test for non-reducing sugars
Non-reducing sugars = sucrose
1. Do Benedict’s test and stays blue / negative
2. Heat in a boiling water bath with acid (to hydrolyse into reducing sugars)
3. Neutralise with alkali (eg. sodium bicarbonate)
4. Heat in a boiling water bath with Benedict’s solution
5. Positive result = green / yellow / orange / red precipitate
Suggest a method to measure the quantity of sugar in a solution
● Carry out Benedict’s test as above, then filter and dry precipitate
● Find mass / weight
Suggest another method to measure the quantity of sugar in a solution
- Make sugar solutions of known concentrations
(eg. dilution series) - Heat a set volume of each sample with a set
volume of Benedict’s solution for same time - Use colorimeter to measure absorbance (of
light) of each known concentration - Plot calibration curve - concentration on x axis,
absorbance on y axis and draw line of best fit - Repeat Benedict’s test with unknown sample and
measure absorbance - Read off calibration curve to find concentration
associated with unknown sample’s absorbance
Describe the biochemical test for starch
- Add iodine dissolved in potassium iodide (orange / brown) and shake / stir
- Positive result = blue-black
Name two groups of lipid
Triglycerides and phospholipids
Describe the structure of a fatty acid (RCOOH)
● Variable R-group - hydrocarbon chain (saturated or unsaturated)
● -COOH = carboxyl group
Describe the difference between saturated and unsaturated fatty acids
● Saturated: no C=C double bonds in hydrocarbon chain; all carbons fully saturated with hydrogen
● Unsaturated: one or more C=C double bond in hydrocarbon chain (creating bend / kink)
Describe how triglycerides form
● 1 glycerol molecule and 3 fatty acids
● Condensation reaction
● Removing 3 water molecules
● Forming 3 ester bonds
Explain how the properties of triglycerides are related to their structure
Function: energy storage
● High ratio of C-H bonds to carbon atoms in hydrocarbon chain
○ So used in respiration to release more energy than same mass of carbohydrates
● Hydrophobic / non-polar fatty acids so insoluble in water (clump together as droplets)
○ So no effect on water potential of cell (or can be used for waterproofing)
Describe the difference between the structure
of triglycerides and phospholipids
One of the fatty acids of a triglyceride is substituted
by a phosphate-containing group
describe function of phospholipids
form a bilayer in cell membrane, allowing diffusion of lipid-soluble (non-polar) or very small
substances and restricting movement of water-soluble (polar) or larger substances
Describe how the properties of
phospholipids relate to their structure
● Phosphate heads are hydrophilic
○ Attracted to water so point to water (aqueous environment) either side of membrane
● Fatty acid tails are hydrophobic
○ Repelled by water so point away from water / to interior of membrane
Describe the test for lipids
- Add ethanol, shake (to dissolve lipids), then add water
- Positive = milky white emulsion
Describe the general
structure of an amino acid
● COOH = carboxyl group
● R = variable side chain / group
● H2N = amine group
How many amino acids are common in all organisms? How do they vary?
The 20 amino acids that are common in all organisms differ only in their side group (R)
Describe how amino acids join together
● Condensation reaction
● Removing a water molecule
● Between carboxyl / COOH group of one
and amine / NH2 group of another
● Forming a peptide bond
What are dipeptides and polypeptides?
● Dipeptide - 2 amino acids joined together
● Polypeptide - many amino acids joined together
Describe the primary structure of a protein
Sequence of amino acids in a polypeptide chain, joined by peptide bonds
Describe the secondary structure of a protein
● Folding (repeating patterns) of polypeptide chain eg.
alpha helix / beta pleated sheets
● Due to hydrogen bonding between amino acids
● Between NH (group of one amino acid) and C=O (group)
Describe the tertiary structure of a protein
● 3D folding of polypeptide chain
● Due to interactions between amino acid R groups
(dependent on sequence of amino acids)
● Forming hydrogen bonds, ionic bonds and disulphide bridges
Describe the quaternary structure of a protein
● More than one polypeptide chain
● Formed by interactions between polypeptides
(hydrogen bonds, ionic bonds, disulphide bridges)
Describe the test for proteins
- Add biuret reagent (sodium hydroxide + copper (II) sulphate)
- Positive result = purple / lilac colour (negative stays blue) → indicates presence of peptide bonds
How do enzymes act as
biological catalysts?
● Each enzyme lowers activation
energy of reaction it catalyses
● To speed up rate of reaction
How do enzymes act as
biological catalysts?
Enzymes catalyse a wide range of
intracellular and extracellular reactions
that determine structures and functions
from cellular to whole-organism level.
Describe the induced-fit model of enzyme action
- Substrate binds to (not completely complementary) active site of enzyme
- Causing active site to change shape (slightly) so it is complementary to substrate
- So enzyme-substrate complex forms
- Causing bonds in substrate to bend / distort, lowering activation energy
Describe how models of enzyme action have changed over time
● Initially lock and key model (now outdated)
○ Active site a fixed shape, complementary to one substrate
● Now induced-fit model
Explain the specificity of enzymes
● Specific tertiary structure determines shape of active site
○ Dependent on sequence of amino acids (primary structure)
● Active site is complementary to a specific substrate
● Only this substrate can bind to active site, inducing fit and forming an enzyme-substrate complex
Describe and explain the effect of enzyme concentration on
the rate of enzyme-controlled reactions
● As enzyme conc. increases, rate of reaction increases
○ Enzyme conc. = limiting factor (excess substrate)
○ More enzymes so more available active sites
○ So more enzyme-substrate (E-S) complexes form
● At a certain point, rate of reaction stops increasing / levels off
○ Substrate conc. = limiting factor (all substrates in use
Describe and explain the effect of substrate concentration on
the rate of enzyme-controlled reactions
● As substrate conc. increases, rate of reaction increases
○ Substrate conc. = limiting factor (too few enzyme
molecules to occupy all active sites)
○ More E-S complexes form
● At a certain point, rate of reaction stops increasing / levels off
○ Enzyme conc. = limiting factor
○ As all active sites saturated / occupied (at a given time)
Describe and explain the effect of temperature on
the rate of enzyme-controlled reactions
● As temp. increases up to optimum, rate of reaction increases
○ More kinetic energy
○ So more E-S complexes form
● As temp. increases above optimum, rate of reaction decreases
○ Enzymes denature - tertiary structure and active site
change shape
○ As hydrogen / ionic bonds break
○ So active site no longer complementary
○ So fewer E-S complexes form
Describe and explain the effect of pH on
the rate of enzyme-controlled reactions
● As pH increases / decreases above / below an optimum, rate of
reaction decreases
○ Enzymes denature - tertiary structure and active site change shape
○ As hydrogen / ionic bonds break
○ So active site no longer complementary
○ So fewer E-S complexes form
Describe and explain the effect of concentration of competitive inhibitors on the rate of enzyme-controlled reactions
● As concentration of competitive inhibitor increases, rate of
reaction decreases
○ Similar shape to substrate
○ Competes for / binds to / blocks active site
○ So substrates can’t bind and fewer E-S complexes form
● Increasing substrate conc. reduces effect of inhibitors
(dependent on relative concentrations of substrate and inhibitor
Describe and explain the effect of concentration of non-competitive inhibitors on the rate of enzyme-controlled reactions
● As concentration of non-competitive inhibitor increases, rate of
reaction decreases
○ Binds to site other than the active site (allosteric site)
○ Changes enzyme tertiary structure / active site shape
○ So active site no longer complementary to substrate
○ So substrates can’t bind so fewer E-S complexes form
● Increasing substrate conc. has no effect on rate of reaction as
change to active site is permanent
Describe the basic functions of DNA
Holds genetic information which codes for polypeptides (proteins)
Describe the basic functions of RNA
Transfers genetic information from DNA to ribosomes
Name the two types of molecule from which a ribosome is made
RNA and proteins
Describe the differences between a DNA nucleotide and an RNA nucleotide
DNA nucleotide:
pentose sugar = deoxyribose
base can be thymine
RNA nucleotide:
pentose sugar - ribose
base can be uracil
Describe how nucleotides join together to form polynucleotides
● Condensation reactions, removing water molecules
● Between phosphate group of one nucleotide and deoxyribose/ribose of another
● Forming phosphodiester bonds
Why did many scientists initially doubt that DNA carried the genetic code?
The relative simplicity of DNA - chemically simple molecule with few components.
Describe the structure of DNA
● Polymer of nucleotides (polynucleotide)
● Each nucleotide formed from
deoxyribose, a phosphate group and a
nitrogen-containing organic base
● Phosphodiester bonds join adjacent
nucleotides
● 2 polynucleotide chains held together by hydrogen bonds
● Between specific complementary base
pairs - adenine / thymine and cytosine / guanine
● Double helix
Describe the structure of (messenger) RNA
● Polymer of nucleotides (polynucleotide)
● Each nucleotide formed from ribose, a phosphate group and a nitrogen-containing organic base
● Bases - uracil, adenine, cytosine, guanine
● Phosphodiester bonds join adjacent nucleotides
● Single helix
Compare and contrast the structure of DNA and (messenger) RNA
DNA nucleotide RNA nucleotide
deoxyribose ribose
thymine uracil
Double stranded single stranded
double helix Single helix
(many nucleotides) (fewer nucleotides) Has hydrogen bonds Does not
base pairing
Suggest how the structure of DNA relates to its functions
● Two strands → both can act as templates for semi-conservative replication
● Hydrogen bonds between bases are weak → strands can be separated for replication
● Complementary base pairing → accurate replication
● Many hydrogen bonds between bases → stable / strong molecule
● Double helix with sugar phosphate backbone → protects bases / hydrogen bonds
● Long molecule → store lots of genetic information (that codes for polypeptides)
● Double helix (coiled) → compact
Suggest how you can use incomplete information about the frequency of
bases on DNA strands to find the frequency of other bases
- % of adenine in strand 1 = % of thymine in strand 2 (and vice versa)
- % of guanine in strand 1 = % of cytosine in strand 2 (and vice versa)
Because of specific complementary base pairing between 2 strands
Why is semi-conservative replication important?
Ensures genetic continuity between generations of cells.
Describe the process of semi-conservative DNA replication
- DNA helicase breaks hydrogen bonds between complementary bases, unwinding the double helix
- Both strands act as templates
- Free DNA nucleotides attracted to exposed bases and join by specific complementary base pairing
- Hydrogen bonds form between adenine-thymine and guanine-cytosine
- DNA polymerase joins adjacent nucleotides on new strand by condensation reactions
- Forming phosphodiester bonds
what is the meaning of semi-conservative?
each new DNA molecule consists of one original / template strand and one new strand
Use your knowledge of enzyme action to suggest why DNA polymerase
moves in opposite directions along DNA strands
● DNA has antiparallel strands
● So shapes / arrangements of nucleotides on two ends are different
● DNA polymerase is an enzyme with a specific shaped active site
● So can only bind to substrate with complementary shape (phosphate end of developing strand)
Name the two scientists who proposed models of the chemical structure of
DNA and of DNA replication
Watson and Crick
Describe the work of Meselson and Stahl in validating the Watson-Crick
model of semi-conservative DNA replication
- Bacteria grown in medium containing heavy nitrogen (15N) and nitrogen is incorporated into DNA bases
● DNA extracted & centrifuged → settles near bottom, as all
DNA molecules contain 2 ‘heavy’ strands - Bacteria transferred to medium containing light nitrogen (14N) and allowed to divide once
● DNA extracted & centrifuged → settles in middle, as all DNA molecules contain 1 original ‘heavy’ and 1 new ‘light’ strand - Bacteria in light nitrogen (14N) allowed to divide again
● DNA extracted & centrifuged → half settles in middle, as contains 1 original ‘heavy’ and 1 new ‘light’ strand; half settles near top, as contains 2 ‘light’ strands
What is ATP?
Adenosine triphosphate
Describe the structure of ATP
● Ribose bound to a molecule of adenine (base) and 3 phosphate groups
● Nucleotide derivative (modified nucleotide)
Describe how ATP is broken down
● ATP (+ water) → ADP (adenosine diphosphate) + Pi (inorganic phosphate)
● Hydrolysis reaction, using a water molecule
● Catalysed by ATP hydrolase (enzyme)
Give two ways in which the hydrolysis of ATP is used in cells
● Coupled to energy requiring reactions within cells (releases / provides energy)
○ Eg. active transport, protein synthesis
● Inorganic phosphate released can be used to phosphorylate (add phosphate
to) other compounds, making them more reactive
Describe how ATP is resynthesised in cells
● ADP + Pi → ATP (+ water)
● Condensation reaction, removing a water molecule
● Catalysed by ATP synthase (enzyme)
● During respiration and photosynthesis
Suggest how the properties of ATP make it a suitable immediate source of
energy for cells
● Releases energy in (relatively) small amounts / little energy lost as heat
● Single reaction / one bond hydrolysed to release energy (so immediate release)
● Cannot pass out of cell
Explain how hydrogen bonds occur between water molecules
● Water is polar molecule
● Slightly negatively charged oxygen atoms attract slightly positively
charged hydrogen atoms of other water molecules
explain metabolite as a property of water
Used in condensation / hydrolysis / photosynthesis / respiration
explain solvent as a property of water
- Allows metabolic reactions to occur (faster in solution)
- Allows transport of substances eg. nitrates in xylem, urea in blood
explain high SHC as a property of water
● Buffers changes in temperature
● As can gain / lose a lot of heat / energy without changing temperature
1. Good habitat for aquatic organisms as temperature more stable than land
2. Helps organisms maintain a constant internal body temperature
explain high latent heat of vaporisation as a property of water
● Allows effective cooling via evaporation of a small volume (eg. sweat)
● So helps organisms maintain a constant internal body temperature
explain cohesion as a property of water
- Supports columns of water eg. transpiration stream through xylem in plants
- Produces surface tension, supporting small organisms (to walk on water)
Where are inorganic ions found in the body?
In solution in cytoplasm and body fluid, some in high concentrations and others in very low concentrations
Describe the role of hydrogen ions
● Maintain pH levels in the body → high conc. = acidic / low pH
● Affects enzyme rate of reaction as can cause enzymes to denature
Describe the role of irons ions
● Component of haem group of haemoglobin
● Allowing oxygen to bind / associate for transport as oxyhaemoglobin
Describe the role of sodium ions
- Involved in co-transport of glucose / amino acids into cells
- Involved in action potentials in neurons
- Affects water potential of cells / osmosis
Describe the role of phosphate ions
- Component of nucleotides, allowing phosphodiester bonds to form in DNA / RNA
- Component of ATP, allowing energy release
- Phosphorylates other compounds making them more reactive
- Hydrophilic part of phospholipids, allowing a bilayer to form
