3.1 Biological molecules Flashcards
What are monomers?
Give three examples
small molecular units from which larger molecules are made
(Monosaccharides, amino acids and nucleotides
What are polymers?
Give three examples
Molecules made from a large number of molecules joined together
(Carbohydrates, proteins, nucleic acids)
What is a condensation reaction?
joining two molecules together with the formation of a chemical bond and a water molecule
(Forming a disaccharide or polysaccharide)
What is a hydrolysis reaction?
breaks a chemical bond between two molecules and involves the use of a water molecule
What is the bond formed during a condensation reaction?
a GLYCOSIDIC bond
What are monosaccharides?
Give three examples
monomers from which larger carbohydrates are made
(Glucose, galactose, fructose)
What are disaccharides?
formed via the condensation of two monosaccharides
What are the three main disaccharides and what are they made from?
Maltose (2 glucose molecules)
Sucrose (1 glucose and 1 fructose)
Lactose (1 glucose and 1 galactose)
What is an isomer?
SAME molecular formula but the atoms are connected in a different way
What are the two isomers of glucose?
Alpha glucose (OH at bottom)
Beta glucose (OH at top)
What are polysaccharides and give three examples?
condensation of many (2+) glucose units
-Glycogen and starch are made of a-glucose
-cellulose is made of** b-glucose**
Give the structure and function of starch
Structure: amylose and amylopectin
Function: Main energy storage material in plants
* Insoluble so has no impact on water potential
* Compact so lots can be stored
* Release alpha glucose easily when hydrolysed due to the many branched ends in amylopectin - readily used in respiration
Give the structure and function of glycogen
Structure: alpha glucose joined by 1,4 and 1,6 glycosidic bonds
Function: Main energy storage material in animals
* insoluble so does not impact water potential
* Large so does not diffuse out of cells
* compact so lots can be stored
* more highly branches than starch - more rapidly broken down to form glucose which is important as animals have a higher metabolic rate and therefore respiratory rate than plants
Give the structure and function of cellulose
Structure: long chains of β-glucose joined together by 1,4 glycosidic bonds, many parallel hydrogen cross links for strength (straight and unbranched)
Function: structure in plant cell walls
* high tensile strength means plants can withstand osmotic pressure
How does cellulose get its strength?
Microfibrils- Strong fibres made of long cellulose chains joined parallel by hydrogen bonds
Give the structure of amylose
Unbranched helix-shaped chain with 1,4 glycosidic bonds between α-glucose molecules
* Coiled and compact so good for storage
Give the structure of amylopectin
1,4 glycosidic bonds between α-glucose molecules but also 1,6 glycosidic bonds form between glucose molecules creating a branched molecule
* enzymes can easily reach glycosidic bonds for faster glucose release in respiration
Describe the chemical test for reducing sugars
Benedicts test
* add benedicts to sample
* **heat **in water bath (that has been brought to the boil)
* Positive (Coloured precipitate, varying from green to brick red based on concentration)
Describe the chemical test for non-reducing sugars
- Add dilute Hcl to sample, place in water bath (addition of acid will hydrolyse any glycosidic bonds present in any carbohydrate molecules)
- add sodium hydrogencarbonate (neutralises solution)
- retest with benedicts in water bath
Describe the chemical test for starch
Iodine test
* add iodine dissolved in potassium iodide solution
* Starch present = Orange to blue-black
Potassium iodide is added as iodine is insoluble in water
What are triglycerides?
Energy storage molecule
formed by condensation of one molecule of glycerol and three fatty acids
What type of bond is formed during condensation of triglycerides and phospholipids?
ester bond
What type of bond is formed during condensation of amino acids?
peptide bond
(to form a polypeptide-protein)
What are the properties of a saturated fatty acid R-group?
No double bonds between carbons
(Animal fats)
What are the properties of an unsaturated fatty acid R-group?
1+ double bonds
(Molecule bends so liquid at room temp)
What are the 3 elements which make up lipids ?
carbon, hydrogen and oxygen
Describe the structure and properties of triglycerides
- ** Long hydrocarbon tails** = when triglycerides are oxidised during respiration this causes these bonds to break releasing more energy per gram than carbs or protein
- form insoluble droplets which are hydrophobic = no impact on water potential so can be stored
- low mass to energy ratio = lots of energy in a small volume
- high ratio of hydrogen to oxygen atoms so water is released when oxidised
- Also provides buyoncy and insulation
Fatty acid tails are hydrophobic while glycerol molecules are hydrophillic
What are phospholipids?
Bilayer of cell membranes
one of the fatty acids is replaced by a phosphate containing group
Describe the structure and properties of phospholipids
- Bilayer (Polar phosphate points outwards, non-polar fatty acid points inwards creating a hydrophobic core) = barrier to water soluble molecules
Fatty acid tails are hydrophobic while phoshate group is hydrophillic
Are triglycerides polar or non-polar?
Non-polar (hydrophobic so do not impact water potential)
Are phospholipids polar or non-polar?
Polar phosphate head (but non-polar fatty acid tails)
Describe the chemical test for lipids
* Shake test solution with ethanol
* Add to water and shake
* Cloudy white emulsion shows a positive test
Give the main four uses of lipids
- cell membranes
- energy - twice as much as carbohydrates or protein
- waterproofing - insoluble in water
- insulation - fats are slow conductors of heat and act as electrical insulators around the mylein sheath
- protection around delicate organs
What are amino acids?
See diagram via link
monomers from which proteins are made
http://www.a-levelnotes.co.uk/uploads/9/6/0/2/96027112/published/52-amino-acid-structure.png?1566484809
How many types of amino acids are there?
20 (only the side chain (R) changes
What type of bond is formed between a condensation reaction of two amino acids?
Peptide bond
How is a peptide bond formed?
hydroxyl (-OH) is lost from the carboxylic group of one amino acid and a hydrogen atom is lost from the amine group of another amino acid
-The remaining **carbon and nitrogen **atoms then bond
What are dipeptides?
Formed by the condensation of two amino acids
What are polypeptides?
Formed by the condensation of many amino acids
What is a functional protein?
may contain one or more polypeptides
(These include haemoglobin, insulin, enzymes)
Describe the primary structure of proteins
specific sequence of amino acids in a polypeptide chain (DNA arranges order of amino acids in the primary structure)
Amino acids are joined by COVALENT PEPTIDE bonds
Describe the secondary structure of proteins
Hydrogen bonds form between the amino acids, causing them to coil/fold
weak negatively charged nitrogen and oxygen atoms interact with the weak positively charged hydrogen atoms
What is the alpha helix?
amino acids COIL, forming hydrogen bonds between every fourth peptide bond
Type of secondary structure
What is the beta pleated sheet?
amino acids FOLD, 2 parts of chain are parallel so hydrogen bonds form between peptide bonds
Type of secondary structure
Describe the tertiary structure of proteins
Further coiling/folding so more bonds form (between the R groups)
Describe the role of hydrogen bonds in tertiary proteins
Where do they form ?
form between strongly polar (Hydrophillic) R groups
-Weakest but most common bond
R groups
Describe the role of ionic bonds in tertiary protein structure
form between positively charged amine and negatively charged** carboxylic acid** R groups
-Stronger than hydrogen bonds but uncommon
CHARGED R groups
Describe the role of disulfide bridges in tertiary protein structure
form strong covalent bonds between cysteine amino acid R groups
-The sulfurs bond
-These are strong but infrequent and help to stabalise the protein
Describe the chemical test for proteins
Biurets
* Treat sample with sodium or potassium hydroxide to make it alkaline
* add biurets
* Colour should change from blue to lilac if protein is present
(Must be at least TWO peptide bonds, amino acids of dipeptides will give a positive result)
Give five functions of proteins
- Enzymes
- Antibodies
- Transport proteins
- Structural proteins
- Hormones
Describe the structure and function of enzymes
Structure: tight folding and spherical shape
-Soluble so have roles in metabolism and protein synthesis
Describe the structure and function of Antibodies
Structure: Two short and two long polypeptide chains bonded together
-Used in immune response
Describe the structure and function of transport proteins
Structure: Hydrophobic and hydrophillic amino acids so protein folds and forms a channel
-Means it can transport ions and molecules across membranes
Describe the structure and function of structural proteins
Structure: Parallel polypeptide chains with cross links
-Used in karatin and collagen
How does the structure of globular proteins link to their function ?
Give some examples of globular proteins
They are compact, spherical (stabilised by bonds) and soluble (Hydrophobic R groups face in while hydrophillic R groups face out)
Function (Functional) = solubility means they can easily be transported across cell membranes for metabolic reactions
Eg. enzymes, haemoglobin, immunoglobins, insulin
How does the structure of fibrous proteins link to their function ?
Give some examples
Long chain of amino acids in a repetitive sequence which are coiled/folded, several polypeptide chains are joined by hydrogen bonds to form fibres/sheets
Function (structural):
Fibres = provide strengh (eg keratin)
Sheets = provide flexability (eg collagen)
-generally insoluble (external R-groups are non-polar, aka hydrophobic)
Keratin (hair and nails) , Collagen (connective tissue)
Define enzyme
tertiary structure enzymes which act as biological catalysts to increase rate of chemical reactions
Describe how the structure of enzymes relates to their function
- They have a** specific active site** (due to folding in the tertiary structure)
- Which will bind to the complementary substrate
- To form an enzyme substrate complex
How do enzymes speed up chemical reactions ?
they lower the activation energy
* Method 1 = enzyme holds substrate molecules close, reducing repulsion so they bind more easily
* Method 2 = enzyme in the active site puts strain on the bonds so they break down faster
What is the lock and key model of enzyme action ?
Enzyme active site has a fixed shape which is complementary to the substrate
What is the induced fit model of enzyme action ?
- substrate is almost complementary
- active site is induced to mould around the substate
- enzyme-substate complex puts strain on bonds in the substrate
- lowering the activation energy
*Describe the effect of temperature **on enzyme action, up to the optimum point
- As temperature increases
- The **kinetic energy **of the enzyme and substrate molecules increases
- so there are more collisions
- which means more enzyme substrate complexes form between enzyme and substrate
- highest rate of reaction is the** optimum point**
Describe the **effect of temperature **on enzyme action, if it gets too high
- At the optimum point kinetic energy is greatest so molecules collide with the enzyme more often
- The **vibrations **can cause the hydrogen, ionic and disulphide bonds in the tertiary structure to break
- This changes the shape of the active site
- So it is no longer complementary to the substrate
- so enzyme substrate complex cannot form, enzyme has been denatured
Describe the effect of pH on enzyme action
changing pH can impact the enzyme action in two ways:
* extreme pH breaks the hydrogen,ionic and disulphide bonds in the tertiary structure causing the active site to change shape
* can **affect the charges **on the amino acid in the active site, so the substrate can no longer attach
Describe the effect of **enzyme concentration **on enzyme action
- as enzyme concentration increases
- there will be more **successful collisions **between the active sites and the substrates
- so more enzyme substrate complexes form, increasing rate of reaction
- eventually** rate will plateau, **as all the substrates have been used up (Maximum enzyme substrate complexes)
Describe the effect of substrate concentration on enzyme action
- as substrate concentration increases
- there will be more successful collisions between the active site and the substrate
- so more **enzyme substrate complexes **form, increasing rate of reaction
- At the saturation point all the active sites are full, so rate plateau’s and increasing substrate further has no impact (Maximum enzyme substrate complexes)
Explain why changing one amino acid in the primary structure of a protein could prevent it from functioning ?
Exam question
- Primary structure is the sequence of amino acids in a polypeptide chain
- If amino acid changes hydrogen bonds form ina different place so it folds differently in the secondary structure
- Ionic and disulfide bonds will then form in different places which changes the shape of the tertiary structure
- This changes the shape of the active site
- So it is no longer complementary to the substrate and won’t form an enzyme-substrate complex
Why might changing certain amino acids in the active site prevent the enzyme functioning ?
Exam question
- This will alter the shape of the active site so enzyme substrate complexes cannot form
- Amino acids in the active site will be unable to form bonds with the substate
Define catabolic reaction
break down of complex molecules into simpler products
Define anabolic reaction
building of more complex molecules from simpler ones
Define inhibitor
a molecule which binds to something on the enzyme, preventing it from functioning
Describe what would happen to rate of reaction if you increased the concentration of a **competitive inhibitor **
What is the impact of increasing substrate concentration ?
- These have the same shape as the substrate
- So bind to the active site
- which stops the substrate binding, decreasing rate of reaction
(inhibitor is not permenently bound so when it leave another molecule can take its place)
MORE SUBSTRATE = can out complete the inhibitor so rate of reaction will increase
What would happen to the rate of reaction if you increased the concentration of a non-competitive inhibitor ?
What is the impact of increasing substrate concentration ?
- Not the same shape as the substrate
- So they bind to the enzyme away from the active site
- This causes the active site to change shape
- so substrate molecules no longer bind, decreasing rate of reaction
MORE SUBSTRATE = no impact as substrates and inhibitors are not competing for the active site
What do DNA and RNA have in common ?
They are important information-carrying molecules which are both involved in protein synthesis
What is the function of DNA ?
holds the genetic information, and codes for the sequence of amino acids in the primary structure of a protein
What is the function of RNA ?
**transfers genetic information **from DNA to the ribosomes
What are the monomers of DNA and RNA ?
What are the components of this structure ?
nucleotides which are made from:
* Pentose sugar
* Phosphate group
* Nitrogenous base
How are the components in a nuceotide joined ?
joined via condensation reactions to form ester bonds, this forms a single nucleotide
Describe the components of a DNA nucleotide
- **Deoxyribose **sugar
- Phosphate group
- Base (Adenine, Thymine, Cytosine, guanine)
Describe the components of an RNA nucleotide
- Ribose sugar
- Phosphate group
- Bases (Adenine, uracil, cytosine and guanine)
Describe how two nucleotides join, and what type of bond forms ?
they join via a condensation reaction between the **deoxyribose sugar and phosphate **forming a polynucleotide
* Forms a phosphodieser bond (Phosphate and two ester bonds)
Phosphodieser bonds are strong and covalent, which ensures the DNA is not broken down
What is the sugar-phosphate backbone ?
chain of alternating phosphates and pentose sugars, joined by phosphodieser bonds (comprised of two ester bonds and a phosphate)
Describe the structure of DNA
Double helix made of **two polynucleotide chains **which are ANTIPARALLEL and held by** hydrogen bond**s between complementary base pairs
What does antiparallel mean in terms of DNA structure ?
Chains run in opposite directions due to the opposite orientation of the sugar molecule (antiparallel - allows the hydrogen bonds to form between complementary base pairs)
- 5’ and 3’ refers to the carbon no. on the pentose suga, **one strand runs in the 5’ to 3’ direction, the other strand runs in the 3’ to 5’ direction **
- This makes the DNA more stable and also helps with complementary base pairing
How many bonds form between each of the complementary base pairs ?
Thymine - Adenine = 2 bonds
Cytosine - Guanine = 3 bonds
Describe the structure of an RNA molecule
- single polynucleotide chain
- much shorter
Give 5 ways that the structure of DNA is adapted to its function
- Stable - 3 hydrogen bonds between C-G give it stability (Passed bet. generations without much change) - Base pairs are within the helical structure so are protected
- Two strands - can seperate during DNA replication, one strand is used as a template
- Large molecule - lots of genetic info can be stored
- **Base pairing is complementary **- DNA can replicate and transfer info as mRNA (allows identical copies to be made)
- **Weak hydrogen bonds **- allows easy separation during DNA replication
Why did many scientists doubt that DNA carried the genetic code ?
its relative simplicity
Why is semi-conservative replication positive in cells ?
it ensures genetic continuity
Define semi-conservative replication ?
each parent strand in the DNA double helix acts as a template for the synthesis of a new, complementary strand.
In the daughter DNA one strand is from the parental DNA and one strand is newly synthesised
What is the first stage of DNA replication ?
DNA helicase breaks the hydrogen bonds between the complementary base pairs, between the two strands of the double helix
- This causes the double helix to unwind
What is the second stage of DNA replication ?
-Separated parental strands act as templates
- Free DNA nucleotides are attracted to their complementary base pairs on the template strands
What is the third stage of DNA replication ?
DNA polymerase catalyses the joining together of** adjacent nucleotides** via a condensation reaction
- This forms phosphodiester bonds and creates the phosphate-sugar backbone
Why is DNA helicase important in DNA replication ?
- DNA helicase** breaks the hydrogen bonds** between the two strands in a DNA double helix
- This creates two template strands which can form** complementary base pairs** with free nucleotides
Why is DNA polymerase important in DNA replication ?
to join together adjacent nucleotides
What word describes the direction of DNA strands, and why does DNA polymerase only move in one direction ?
Antiparallel - Strands run in opposite directions, one is 3’ and one is 5’
- The active site of DNA polymerase is only complementary to the 3’ end
- Enzyme moves in a 3’ to 5’ direction, which means the new strand is made in a 5’ to 3’ direction
- As the strands are anti-parallel, polymerase on one template moves in the opposite direction to the other
What is the fourth stage of DNA replication ?
-Winding enzyme winds the daughter polynucleotides to** form two double helices**
-Two daughter DNA molecules are **genetically identical **to the parent DNA and contain:
* One strand of the parental DNA
* One newly synthesised strand
What is the difference between conservative replication and semi-conservative replication ?
- Semi-conservative - One original strand and one newly synthesised DNA strand
- Conservative - Original DNA remains intact and newly synthesised DNA join together
Give the stages of the semi-conservative replication experiment ?
- Bacteria are grown in heavy nitrogen (Bacteria incorporate the nitrogen isotopes to make nitrogenous bases)
- Sample of bacteria from heavy nitrogen is added to** light nitrogen** and left for one round of replication - Sample is taken and spun in centrifuge
- DNA is allowed to replicate for two more generations
Give the results of meselson and Stahl’s experiment
- First generation -** All DNA contains one strand of heavy and one strand of light** (DNA settles in the middle)
- Second generation - Some new strands now just contain 14 N
- Third generation - Most of the strands now just contain 14 N
- This shows replication is semi-conservative as one parent strand is always conserved and there is always a newly synthesised strand made from only light nitrogen
What is ATP ?
Adenosine Tri Phosphate
-Immediate source of energy for biological processes (Metabolic reactions must have a constant supply of ATP)
Describe the structure of ATP ?
- Ribose (pentose sugar)
- Adenine nitrogenous base
- Three inorganic phosphate groups
ATP is a nuceotide derivative
How is ATP made ?
What enzyme is the process catalysed by ?
-Re-synthesised in a condensation reaction between ADP and Pi
-This occurs during respiration and photosynthesis
-Catalysed by ATP synthase
This does require a small amount of ATP to create the bond
How is energy released from ATP ?
What enzyme is the process catalysed by?
-ATP is broken down into ADP and P1 in a hydrolysis reaction
-Breaking a bond between the phosphate groups releases a small amount of energy to the surroundings
-Catalysed by ATP hydrolase
- As only one bond has to be hydrolysed to release energy, ATP is an immediate energy source
What two other processes is ATP hydrolysis useful for ?
Give some examples of where they occur
- Can be coupled with other energy requiring reactions so energy released can be used directly instead of being lost
- Inorganic phosphate released can be bonded to another compound (Phosphorylation) which makes the compound more reactive
- Hydrolysis is coupled with muscle contraction and active transport (both require energy)
-Phosphorylation happens to glucose at the start of respiration (glycolysis)
Give the five properties of ATP which make it a better source of immediate energy in cells compared to glucose
- ATP releases energy in a small amount - means less is wasted and cells don’t overheat
- Only **one bond has to be hydrolysed **to energy release is immediate - Glucose needs several bonds to be broken
- ATP is small and soluble - can easily be transported around the cell to provide energy (This one is the same as glucose)
- ATP can transfer energy to another molecule - transferring one of its phosphate groups
- ** ATP cannot leave the cell** - the cell always has its own supply of ATP (glucose can leave so the cell can run out)
In what two places is ATP synthesised ?
mitochondria and chloroplasts
Give four places where ATP is used ?
- Activation of molecules - Phosphorylation lowers the activation energy
- **Metabolism **- building macromolecules (starch and polypeptides)
- Movement - muscle contraction
-
Active transport - changes the shape of carrier proteins in plasma membranes, allowing the movement of molecules against the concentration gradient
* Secretion - formation of lysomes
Describe the** structure of water**
-Water is a dipolar molecule
-It is electrically neutral but the charge is uneavenly distributed due to the fast the oxygen atom is slightly negative and the** hydrogen is slightly positive**
-This means hydrogen bonds can form between the oxygen and hydrogen of neighbouring molecules
Give some examples of when water is used as a metabolite
-Breaks down complex molecules in hydrolysis
-One of the raw materials in photosynthesis
Why does water make a good solvent ?
Give some examples
Dipolar **
-Slight positive charge** will attract any negative ions in solutes, and slight negative charge will attract any positive ions
(These molecules that dissolve are polar - charged, water cannot dissolve non-polar molecules)
-This means the compound is fully surrounded so can be split up and dissolved
Why does water have a** high specific heat capacity ?**
Why is this useful ?
Give some examples
-There are many** hydrogen bonds can absorb a lot of energy so a lot more energy is needed to separate them** (So lots of energy is needed to raise the temperature)
- Useful as itstemperature remains relatively stable ** (acts as a buffer against temperature changes in the environment)
- Uses: a suitable habitat for aquatic organisms, and the water inside organisms helps them maintain a constant internal body temperature **- means enzymes will not denature
Why does water have a** high latent heat of vaporisation ?**
Why is this useful ?
Give some examples
- Many** hydrogen bonds** which need a** lot of energy to break** and convert water from its liquid state to a gaseous state
- Means water provides a cooling effect
- Uses: When humans sweat large amounts of heat energy from the skin is tranferred to the water to evaporate it, which removes lots of heat and **cools **the organism
(similar impact during transpiration in plants)
Why does water have strong cohesion ?
Why is this useful/give examples here?
- Water molecules are dipolar, and the hydrogen bonds cause them to stick together
- Allows** columns of water to move up the xylem **- easier to draw up a column than individual molecules
- Provides surface tension to water - allows small organisms to move and live on water
What are inorganic ions ?
* No carbon
* Occur in solutions in the cytoplasm and bodily fluids
* Concentrations can fluctuate
What is the function of iron ions ?
- They can bind to oxygen so are a key component in haemoglobin
What is the function of hydrogen ions?
- Concentration determines pH
- This is important for enzyme activity as changes in PH can impact the tertiary structure of the protein
What is the function of** sodium ions** ?
- Used for the** transport of glucose and amino acids **across cell membranes (Co-transport)
- Also needed for** transmission of nerve impulses**
What is the function of phosphate ions ?
- Attach to other molecules to form** phosphate groups (Part of RNA, DNA)**
- Bonds between phosphate groups store energy in ATP
- Found in phospholipids (Bilayer in cell membranes
