3.1 Biological Molecules Flashcards
What is a monomer ?
The smaller units from which larger molecules are made.
What is a Polymer?
Molecules made from a large number of monomers joined together.
What is a condensation reaction?
Joins two molecules together with the formation of a chemical bond and the elimination of a water molecule
What is a hydrolysis reaction ?
Breaks a chemical bond between two molecules and involves the use of a water molecule.
What is a monosaccharide?
The monomers from which larger carbohydrates are made
What type of bond forms between two monosaccharides during a condensation reaction
Glycosidic bond
What is a disaccharide and how are they formed
Formed by the condensation reaction of two monosaccharides with a glycosidic bond , releasing a water molecule
What is a polysaccharide and how are they formed
Formed by the condensation of many monosaccharides joined together with glycosidic bonds , releasing many water molecules
What does glucose + glucose make
Maltose
What does glucose + galactose make
Lactose
What does glucose + fructose make
Sucrose
What is the test for starch?
1) Small sample of food is placed on a spotting tile
2) Drop of iodine dissolved in potassium iodide solution is added
3) If the food sample turns from orange to blue-black , starch is present
What are the features of starch
- Made from alpha glucose monomer
- 1-4 glycosidic bonds in amylose
- 1-6 glycosidic bonds in amylopectin
- It’s a store of glucose
- It’s found in plant cells (chloroplast)
- Amylose = unbranched helix
- Amylopectin = branched molecule
- Helix can compact to a fit a lot of glucose in small spaces.
- Branched structure increases surface area for rapid hydrolysis back into glucose .
- Insoluble so won’t affect water potential
What are the features of cellulose ?
- Made from beta glucose
- 1-4 glycosidic bonds
- Provides structure and strength for cell wall
- Found in cell wall of plants.
- Long , straight , unbranched chains
- Held in parallel by H+ bonds to form fibrils and micro fibrils
- Many hydrogen bonds provide collective strength
- Insoluble so won’t affect water potential
What are the features of glycogen ?
- Made from alpha glucose
- 1-6 and 1,4 glycosidic bonds
- Store of glucose
- Found in animals in the muscle and liver cells
- A highly branched molecule
- Branched increases surface area for rapid hydrolysis back into glucose for respiration to make ATP for energy release
- Insoluble so won’t affect water potential
What are the two types of lipids .
Phospholipids and triglycerides
What is a saturated bond
Contains Only one single carbon bond
What is an unsaturated bond
Contains double carbon , carbon bonds
What happens to,unsaturated fatty acids
The double bond causes the molecule to bend . Therefore cannot pact closely together so they’re liquid at room temperature
What is the structure of a triglyceride
Three fatty acids combined with a glycerol
Each fatty acid forms an ester bond with glycerol in a condensation reaction
Fatty acid = RCOOH
What are properties of triglycerides relating to its structure
- High ratio of energy storing carbon hydrogen bonds to carbon atoms so is used in respiration to release more energy than the same mass of carbohydrates
- Hydrophobic fatty acids so insoluble in water - so no effect on water potential
What is the structure of a phospholipid ?
One of the fatty acid molecules is replaced by a phosphate containing group
It has 2 fatty acids , one phosphate and one glycerol
Has a hydrophilic head which is attracted to water
Has a hydrophobic tail which orients itself away from water
Polar molecules
What are the properties of phospholipids relating to its structure
Polar - form a bilayer within cell surface membranes -> allowing diffusion of non polar or small substances and restricting movement of polar or larger substances
Hydrophilic phosphate heads is abstracted to water so point to water
Fatty acids tails are hydrophobic - repelled by water so point away from water
What is the test for lipids
1) take a completely dry test tube
2) to 2cm^3 of the sample being tested , add 5c ^3 of ethanol
3) shake the tube thoroughly to dissolve any lipid in the sample
4) Add 5cm^3 of water and shake gently
5) A milky - white emulsion indicates presence of a lipid
What is an amino acid
Monomers from which proteins are made
What bond forms between 2 amino acids in a condensation reaction
Peptide bonds
How are dipeptides formed
Condensation reaction of two amino acids
How are polypeptides formed
Condensation reaction of many amino acids
What is the primary structure of protein
The sequence of amino acids in a polypeptide chain forms the primary structure of any protein. These are connected by peptide bonds
What is the secondary structure of protein
• folding of polypeptide chain e.g alpha helix / beta pleated sheets
• Due to hydrogen bonding between amino acids
• between NH and C=O group
What is the tertiary structure of proteins
- 3D folding of polypeptide chain
- Due to interactions between amino acid R Groups
- forming hydrogen bonds , ionic bonds and disulfide bridges
What is the quaternary structure of a protein
- More than one polypeptide chain
- Formed by interactions between polypeptides
What is the test for proteins
1) Place a sample of the solution to be tested in a test tube and add an equal volume of sodium hydroxide solution at room temperature
2) Add a few drops of Buiret reagent to the sample
3) A purple or,lilac coloration indicates presence of a protein
If no change , solution remains blue
What is the test for reducing sugars
1) Add 2cm^3 of the food sample to be tested in a test tube , if it’s not in a liquid grind it up in water
2) Add an equal volume of Benedict’s reagent
3) Heat up mixture in a gently boiling water bath for 5 minutes
positive result = red ppt
What is the test for non reducing sugars
(sucrose)
1) if solution doesn’t change colour (blue ) , add another 2cm^3 of food sample to 2cm^3 of HCl and place in a boiling water bath for 5 mins
2) Slowly add some sodium hydrogen carbonate solution to the condensation test tube to neutralize the acid
3) retest resulting solution with Benedict’s reagent and in a boiling water bath for 5 mins
4) if non reducing sugar was present , solution should turn into red ppt
give 3 common examples of a monosaccharide
glucose , fructose , galactose
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
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 each known conc
4) plot calibration curve - conc 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 conc associated with unknown samples absorbance
describe how triglycerides form
- 1 glycerol molecule and 3 fatty acids
- 3 condensation reactions
- removing 3 water molecules
- forming 3 ester bonds
describe / draw general structure of an amino acid
- COOH = carboxyl group
- R = side chain group
- H2N = amine group
how many amino acids are common in all organisms and how do they vary
20 amino acids differ only in their R group
describe how amino acids join together
- condensation reaction
- removing a water molecule
- between carboxyl group of one amine group of another
- forming a peptide bond
How do enzymes act as a biological catalyst
- Each enzyme lowers activation energy of reaction it catalyses
- To speed up rate of reaction
describe the induced fit model of enzyme action
1) substrate bonds to active site of enzymes
2) causing active site to change shape so its complementary to its substrate
3) so enzyme - substrate complex forms
4) causing bonds in substrate to bend lowering activation energy
describe how models of enzyme action have changed over time
Initially lock and key model
- 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
- Active side is complementary to 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 an enzyme conc increases , rate of reaction increased
• enzyme conc = 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
• substrate concentration = limiting factor ( all substrate 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 substrate to occupy all active sites )
- more enzyme - substrate complexed form
• at a certain point rate of reaction stops increasing
- enzyme concentration = limiting factor
- as all active sites occupied
Describe and explain the effect of temperature on the rate of enzyme controlled reactions
- As temp increases to optimum , rate of reaction increases
• more kinetic energy
• more enzyme substrate complexes form - As temp exceeds optimum , rate of reaction decrease
• enzymes denature and tertiary structure and active site changes shape
• as hydrogen / ionic bonds break
• 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 and 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 concentration of competitive inhibitors on the rate of enzyme controlled reactions
• as conc of competitive inhibitor increases , rate of reaction decreases
- similar shape to substrate
- blocks active site
- so substrates can’t bind
- so fewer enzyme - substrate complexes form
• Increasing substrate conc reduces effect of inhibitors
describe and explain the effect of concentration of non competitive inhibitors on the rate of enzyme controlled reactions
• as conc of non competitive inhibitor increases , rate of reaction decreases
- bonds to site other than the active site ( allosteric)
- changes enzyme tertiary structure / active site shape
- so active site no longer complementary to substrate
- so substrate can’t bind
- so fewer enzyme substrate 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 and rna in all living cells
DNA - holds genetic information which codes for polypeptides
RNA - transfers genetic information from DNA to ribosomes
name the two types of molecule from which a ribosome is made
RNA
Proteins
describe the differences between dnn nucleotides and an rna nucleotides
Dna :
pentose sugar is deoxyribose
base can be thymine
Rna :
pentose sugar is 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 a deoxyribose / ribose of another
- forming phosphodiester bonds
why did many scientists initially doubt that dna carried the genetic code
the relative simplicity of DNA
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 and thymine and guanine and cytosine
- double helix
describe the structure of mrna
- polymer of nucleotides ( polynucleotide )
- each nucleotide formed from ribose , a phosphate group and a nitrogen containing organic base
- bases are uracil , adenine, cytosine and guanine
- phosphodiester bonds join adjacent nucleotides
- single helix
compare and contrast the structure of DNA and mrna
DNA :
- pentose sugar is deoxyribose
- has the base thymine
- double helix
- long
- has hydrogen bonds
mRNA:
pentose sugar is ribose
has the base uracil
single stranded
shorter
does not have hydrogen bonds
suggest how the structure of dna relates to its functions
• two strands - both can act as a template for semi conservative replication
• hydrogen bonds between bases are weak - strands can be separated for replication
• complementary base pairings - accurate replication
• many hydrogen bonds between bases - strong molecule
• double helix with sugar phosphate backbone - protects bases / hydrogen bonds
• long molecule - store lots of genetic information
• double helix ( coiled ) - compact
suggest how you can use incomplete information about the frequency of based on dna strands to find the frequency of other bases
1) % of adenine in strand 1 = % of thymine in strand 2
2) % of guanine in strand 1 = % of cytosine in strand 2
Because of specific complementary base pairings between 2 strands
why is semi- conservative replication important
ensures genetic continuity between generations of cells
describe the process of semi - conservative DNA replication
1) DNA helicase breaks hydrogen bonds between complementary bases , unwinding the double helix
2) both strands act as templates
3) free DNA nucleotide attracted to exposed bases and join by specific complementary base pairings
4) hydrogen bonds form between adenine and thymine and guanine and cytosine
5) DNA polymerase joins adjacent nucleotides on new strand by condensation reactions
6) forming phosphodiester bonds
what is 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 of nucleotides on two ends are fifferent
•• DNA polymerase is an enzyme with a specific shaped active site
• So can only binds to substrate with complementary shape
Name the two scientists who proposed models of the chemical structure of DNA and DNA replication
Watson and Crick
Describe the work of medellin and Stahl in validation the watson-crick model of semiconservative DNA replication
1) bacteria grown in medium containing heavy nitrogen (15N) so nitrogen is incorporated into DNA bases
• dna extracted and centrifuged - settled near the bottom as all DNA molecules contain 2 heavy strands
2) Bacteria transferred to medium containing light nitrogen (14N) and allowed to divide once
• DNA extracted and centrifuged - settled in the middle as all DNA molecules contain 1 original heavy and 1 new light strand
3) Bacteria in light nitrogen (14N) allowed to divide again
• DNA extracted and centrifuged - half settled in middle as contains 1 original heavy and 1 new light stand , half settled near top as contains 2 light strands
why are other models such as conservative replication not supported
bands would be in different places
what is ATP
adenosine triphosphate
Describe the structure of ATP
- ribose - bound to a molecule of adenine base and 3 phosphate groups
- nucleotide derivative
Describe how ATP is broken down
• ATP => ADP + Pi
• hydrolysis reaction using a water molecules
• catalysed by ATP hydrolase
Give two ways in which the hydrolysis of ATP is used in cells
- coupled to energy requiring reactions within cells e.g. active transport , protein synthesis
- Inorganic phosphate released can be used to phosphorylate other compounds , making them more reactive
Describe how ATP is resynthesised in cells
- ADP + Pi => ATP
- condensation reaction removing a water molecule
- catalysed by ATP synthase
- during respiration and photosynthesis
Suggest how properties of ATP make it a suitable immediate source of energy for cells
- Release energy in small amounts / little energy lost as heat
- Single reaction / one bond hydrolysed to release energy
- Cannot pass out of cells
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 5 properties of water that are important in biology
• Metabolite :
Used in condensation / hydrolysis / photosynthesis / respiration
• Solvent :
Allows metabolic reactions to occur
Allows transport of substances
• High specific heat capacity :
Buffers change in temperature
- As can gain / lose a lot of heat / energy without changing temperature
Good habitat for aquatic organisms as temperature more stable than land
Helps organisms maintain a constant internal body temperature
• Large latent heat of vaporisation :
Allows effective cooling via evaporation of a small volume
So helps organisms maintain a constant internal body temperature
• Strong cohesion between water molecules:
supports columns of water in tube like transports cells of plants e.g transpiration stream
produces surface tension when water meets air , supporting small organisms
Where are inorganic ions found in the body
In solution in cytoplasm and body fluid , some in high concentration and others in very low concentrations
Describe the role of hydrogen ions
•Maintain pH levels in body - high con = acidic / low pH
• Affects enzyme rate of reaction as can cause enzymes to denature
Describe the role of iron ions
• component of haem group of haemoglobin
• allowing oxygen to bind for transport
Describe the role of sodium ions
1) involved in co transport of glucose / amino acids into cells
2) involved in action potentials in neurons
3) affects water potential of cells / osmosis
Describe the role of phosphate ions
1) component of nucleotides , allowing phosphodiester bonds to form in DNA / RNA
2) component of ATP , allowing energy release
3) phosphorylates other compounds making them more reactive
4) hydrophilic part of phospholipids , allowing a bilayer to form
