biological molecules Flashcards
What are monomers and polymers
● Monomers- smaller, repeating molecules / units from which larger molecules / polymers are made
● Polymers- molecules made from many (a large number) identical / similar monomer molecules
What happens in a condensation reaction
● 2 molecules join together
● Forming a chemical bond
● Releasing a water molecule
What happens in hydrolysis reactions
● 2 molecules separated
● Breaking a chemical bond
● Using a water molecule
Give examples of polymers and the monomers from which they’re made
Nucleotides —-> polynucleotide (DNA/RNA)
monosaccharide eg glucose —-> polysaccharide eg starch
Amino acid —-> polypeptide (protein)
What are monosaccharides? Give 3 common examples
● Monomers from which larger carbohydrates are made
● Glucose, fructose, galactose
Describe the difference between the structure of α-glucose and β-glucose
● Isomers- same molecular formula but differently arranged atoms
● OH group is below carbon 1 in α-glucose but above carbon 1 in β-glucose
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
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 many water molecules
Describe the basic function and structure of starch and glycogen
- Starch*
Energy store in plant cells
● Polysaccharide of α-glucose
● Some has 1,4-glycosidic bonds so is unbranched (amylose)
● Some has 1,4- and 1,6-glycosidic bonds so is branched (amylopectin)
glucogen Energy store in
animal cell - polysaccharide made of alpha glucose 1,4 and 1,6 glycosidic bonds —
Explain how the structures of starch and glycogen 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)
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 bonds so forms 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
Name 3 reducing sugars
Reducing sugars = monosaccharides, maltose, lactose
Describe the test for reducing sugars
- Add Benedict’s solution (blue) to sample
- Heat in a boiling water bath
- Positive result = green / yellow / orange / red precipitate
Name non-reducing sugars
Sucrose
Describe the test for non-reducing sugars
- Do Benedict’s test (as above) and stays blue / negative
- Heat in a boiling water bath with acid (to hydrolyse into reducing sugars)
- Neutralise with alkali (eg. sodium bicarbonate)
- Heat in a boiling water bath with Benedict’s solution
- 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
1.Make sugar solutions of known concentrations
(eg. dilution series)
2. Heat a set volume of each sample with a set
volume of Benedict’s solution for the same time
3. Use colorimeter to measure absorbance (of
light) of each known concentration
4. Plot calibration curve- concentration on x axis,
absorbance on y axis and draw line of best fit
5. Repeat Benedict’s test with unknown sample and
measure absorbance
6. 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 (this may be saturated or unsaturated)
●-COOH = carboxyl group
Describe the difference between saturated and unsaturated fatty acids
● Saturate- 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 a bend / kink)
Describe how triglycerides form
● 1 glycerol molecule and 3 fatty acids
● 3 condensation reactions
● 3 condensation reactions
● 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 the same mass of carbohydrates
● Hydrophobic / non-polar fatty acids so insoluble in water (clump together as droplets, tails inwards)
○ 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 how the properties of
phospholipids relate to their structure
Function: 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
● 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 result = milky white emulsion
Describe / draw the general
structure of an amino acid
● COOH = carboxyl group
● R = variable side chain / group
● H2N = amine group
Central carbon
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 bond
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 disulfide bridges
Describe the quaternary structure of a protein
● More than one polypeptide chain
● Formed by interactions between polypeptides
(hydrogen bonds, ionic bonds, disulfide bridges)
Describe the test for proteins
- add biuret reagent
- positive test result (purple colour)
How do enzymes act as
biological catalysts?
● Each enzyme lowers activation
energy of reaction it catalyses
● To speed up rate of reaction
Describe the induced-fit model of enzyme actio
- Substrate binds to (not completely complementary) active site of enzyme
- Causing active site to change shape (slightly) so it is complementary to its substrate
- So enzyme-substrate complex forms
- Causing bonds in substrate to bend / distort, lowering activation energy
Describe
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 reaction
● As enzyme concentration increases, rate of reaction increases
○ Enzyme concentration = limiting factor (excess substrate)
○ More enzymes so more available active sites
○ So more enzyme-substrate complexes form
● At a certain point, rate of reaction stops increasing / levels off
○ Substrate concentration = limiting factor (all substrates in use)
Describe and explain the effect of substrate concentration on
the rate of enzyme-controlled reactions
● As substrate concentration increases, rate of reaction increases
○ Substrate concentration = limiting factor (too few substrate
molecules to occupy all active sites)
○ More enzyme-substrate complexes form
● At a certain point, rate of reaction stops increasing / levels off
○ Enzyme concentration = 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 temperature increases to optimum, rate of reaction increases
○ More kinetic energy
○ So more enzyme-substrate complexes form
● As temperature exceeds 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 enzyme-substrate 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 enzyme-substrate complexes form
11
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
○ So fewer enzyme-substrate complexes form
● Increasing substrate concentration 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 substrates can’t bind
○ So fewer enzyme-substrate complexes form
● Increasing substrate concentration has no effect on rate of
reaction as change to active site is permanent
reaction
Describe the basic functions of DNA and RNA in all living cells
DNA
DNA - Holds genetic information which codes for polypeptides (proteins)
RNA - Transfers genetic information from DNA to ribosomes
Name the two types of molecule from which a ribosome is made
RNA and protein
RNA and dna nucleotide
DNA - Phosphate group, deoxyribose sugar, nitrogenous bases - adenine, thymine,guanine, cytosine
RNA - phosphate group - ribose sugar, nitrogenous bases - adenine, uracil, guanine and cytosine
Describe how nucleotides join together to form polynucleotides
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
Suggest
Pentose sugar is deoxyribose vs Pentose sugar is ribose
Has the base thymine vs Has the base uracil
Double stranded / double helix vs Single stranded / single helix
Long (many nucleotides) vs Shorter (fewer nucleotides)
Has hydrogen bonds / base pairing Does not
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)→ compac
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
Semi conservative- each new DNA molecule consists of one original / template strand and one new stran
ATP stands for
Adenosinetriphosphate
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 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
5 properties of water
Metabolite
Solvent
High specific heat capacity
Large latent heat of vaporisation
Strong cohesion between water molecules
Water as a metabolite
Used in condensation / hydrolysis / photosynthesis / respiration
Water as a solvent
- Allows metabolic reactions to occur (faster in solution)
- Allows transport of substances eg. nitrates in xylem, urea in blood
High spc in 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
Water as latent heat
● Allows effective cooling via evaporation of a small volume (eg. sweat)
● So helps organisms maintain a constant internal body temperature
Strong cohesion bet water mol
- Supports columns of water in tube-like transport cells of plants
eg. transpiration stream through xylem in plants - Produces surface tension where water meets air, 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
Role of hydrogen ions
● Maintain pH levels in the body → high concentration = acidic / low pH
● Affects enzyme rate of reaction as can cause enzymes to denature (topic 1.4.2)
Iron ions
(Fe2+)
● Component of haem group of haemoglobin
● Allowing oxygen to bind / associate for transport as oxyhaemoglobin (topic 3.4.1)
Sodium
ions (Na+)
- Involved in co-transport of glucose / amino acids into cells (topic 2.3 / 3.3)
- Involved in action potentials in neurons (topic 6.2)
- Affects water potential of cells / osmosis (topic 2.3)
Phosphate
ions (PO4
3-)
- Component of nucleotides, allowing phosphodiester bonds to form in DNA / RNA
- Component of ATP, allowing energy release
- Phosphorylates other compounds making them more reactive (topic 1.6)
- Hydrophilic part of phospholipids, allowing a bilayer to form (topic 1.3 / 2.3)
Name the two scientists who proposed models of the chemical structure of
DNA and of DNA replication
Watson
Watson and Crick
Describe the work of Meselson and Stahl in validating the Watson-Crick
model of semi-conservative DNA replication
Describe the work of Meselson and Stahl in validating the Watson-Crick
model of semi-conservative DNA replication
1. 2. 3. Bacteria grown in medium containing heavy nitrogen (15N) so
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
ATP stands for
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)→
