Biological Molecules Flashcards
What are the 5 main biological molecules?
-carbohydrate
-lipids
-protein
-water
-nucleic acid
What are carbs, proteins and nucleic acids?
Macromolecules which are polymers
Type of reaction to turn. Polymer to a monomer.
Hydrolysis- water required to help break covalent bonds
Type of reaction needed to turn a monomer into a polymer.
Condensation- water is proved during covalent bond formation
Enzymes in cells beak down the bonds
3 main types of carbohydrate:
1) monosaccharides
2)disaccharides
3)polysaccharides
Type of monosaccharides:
Glucose- most abundant monosaccharides in nature and most common in food.
Other types: fructose, galactose, deoxyribose ribose
What are alpha and beta glucose?
They are isomers of glucose. Alpha glucose has hydrogen on the top right.
What are disaccharides ?
Simple sugars that consist of 2 monosaccharides bonded together with a glycosidic bond between carbon 1 and 4.
3 types of disaccharides
1) maltose (glucose + glucose)
2) sucrose (glucose + fructose)
3) lactose (glucose + galactose)
What is a glycosidic bond?
-chemical reaction forming the bond is a condensation reaction
- carbon 1 and 4 bonded
-chemical reaction that breaks the bond is hydrolysis due to need for water
-can be broken by boiling sugar in water + enzyme in cells lower activation energy so it happens in the body
What are polysaccharides?
Polymers of many monosaccharides joined via a glycosidic bond.
Large molecules that are insoluble so are suitable for storage e.g cellulose
When hydrolysed they break down in disaccharides and monosaccharides
An example of a polysaccharide
Starch found in starch grains in plants which is made of 200-100000 alpha glucose (condensation reaction) joined together
Explain the structure of amylose
- alpha glucose monosaccharide (20-30%)
- 1,4 glycosidic bond
-forms a helix held together by hydrogen bonds which keeps it compact - insoluble in water so does not affect osmosis
- helix can trap iodine to form a dark blue complex (starch test)
Explain the structure of amylopectin
- alpha glucose monosaccharide (70%-80%)
- 1,4 glycosidic bond with 1,6 glycosidic bond making side branches
- soluble in hot and cold water
- branching creates more terminal ends to chains allowing faster enzyme breakdown (hydrolysis)
Glycogen
-more highly branched than amylopectin
-important storage molecule
- branching creates more terminal ends to chains allowing faster enzyme breakdown
-stored as a compact glycogen granule
-alpha glucose monosaccharide
- 1,4 glycosidic bond and 1,6 glycosidic bond making side branch
-stored as glycogen as it needs to be accessed quickly branched for easy access.
Explain cellulose structure
-most abundant polysaccharide
- a structural polysaccharide only present in plants fungi and some bacteria
-beta glucose monomers
- 1,4 glycosidic bond
- adjacent beta glucose molecules rotate 180 degrees
-long straight chains
-parallel monomer chains form bigger fibres called myofibrils and macrofibrils.
-numerous hydrogen bonds hold ajacent chains together
-fibres created have a high tensile strength
- bonds can be digested using bacterial enzymes
-found in the cell walls of plants biofilm of some bacteria algae and fungi
What are the 2 types of lipids?
Triglyceride and phospholipid
Explain the structure of triglyceride
Consists of 3 fatty acids bonded to one glycerol molecule
Fatty acids = hydrocarbon with carboxylate acid group
Glycerol = hydroxyl group
Condensation reaction causes the bond to be formed this is between the -OH on the glycerol and -OH on the acid group. Bond formed is called an ester.
What are saturated and unsaturated fatty acids?
Saturated = all available bonds in the fatty acid chain have a hydrogen attached
Unsaturated = has a double bond between a carbon this makes the chain kink in that position this will cause the melting and boiling points to decrease because the fatty acid chains are spaced further apart. (Weaker intermolecular forces)
Explain the structure of a phospholipid
Consists of a glycerol molecule with 2 fatty acids and a phosphate group
- has a phosphate head and 2 fatty acid tails
5 main uses of lipids
- energy source ATP ( oxidised to produce energy)
- energy store
- insulation (slow conductors of heat)
- waterproofing (insoluble in water)
- protection (delicate organs)
- production of cholesterol and steroid hormones
Phospholipids in water
-Insoluble but head is polar and hydrophilic
-Tails are hydrophobic and non-polar
This allows them to arrange in special structures in water
Liposomes micelles and bilayer sheets
Triglycerides in water
-Water is a polar molecule so triglycerides are insoluble in water as they are non polar
- they can be dissolved in organic solvents,alcohol and acetone
Polar Molecules
- contain either oxygen, nitrogen or sulphur
-have dipole charges
Waters properties
-metabolite
- solvent
- high latency heat capacity
-cohesion
-specific heat capacity
-density and compressibility
Water as a metabolite
-Used in many metabolic reactions like hydrolysis and condensation
-Byproduct of metabolic reactions
Water as a solvent
Ionic and polar molecules such as biological molecules need to be dissolved into a polar solvent and water is good for this.
Waters high latent heat capacity
-water has a high latent heat capacity as strength of hydrogen bonds. These bonds require lots of energy to be broken and vaporised.
-Water vaporisation can be used for calling down and uses a lot of heat and carried away sweating
-due to the high heat capacity the organism can call without using too much water or energy so they can survive
Waters cohesion
-attraction between the same type of molecule
-Water has strong cohesion due to the hydrogen bonds
-Enables water to flow and transport for example in the xylem
-Produces surface tension so small organisms walk on water
Specific heat capacity of water
-hi so a lot of energy is needed to change the temperature so water has a constant temperature
-Makes the ocean a thermally stable habitat
Waters density and incompressibility
-max density is 4° when water turns to ice and becomes less dense which floats creating insulation. This is due to molecules being further apart.(ocean habitat)
-Incompressible due to strong intermolecular bonds between molecules
What is an amino acid?
-made of an amine group and carboxylic group
-only r group varies
What is a peptide bond?
-a bond between 2 amino acids to form a polypeptide chain
-condensation reaction that takes place inside ribosomes
-catalysed via specific enzymes and hydrolysed via protease enzymes
What is a protein?
A folded polypeptide chain of which is able to perform a specific function
What is the primary structure of a protein?
-specific order of amino acids which determines final shape of protein
-determined via dna
What is the secondary structure of a protein?
-hydrogen bonds form between positive -NH group and negative -CO
-causes chain to twist and fold into specific shapes
-alpha helix or beta plaited sheet
What is the tertiary structure of a protein?
-overall 3D shape of the protein which is critical to its function
-bonds such as ionic, dulsulphide and hydrogen bonds as well as hydrophobic bonds cause this to happen
What is the quaternary structure of a protein?
-proteins with more the one polypeptide chains
-called subunits the structure shows how these are arranged and shows the position of prosthetics
-prosthetics are non protein structures in a protein helping it to carry out the role
What is a protein called if it contains prosthetics?
Conjugated protein
What is the lock and key model of enzymes?
The shape of an active site is complementary to the substrate
What are enzymes?
-Biological catalysts that speed up the rate of the reaction
-made of protein
-lower activation energy to start a reaction
-biological molecules are held via covalent bonds so usually need enzymes to break them
What is the induced fit model of enzymes?
-active site is not complementary to substrate that it acts on
-charged amino acids in active site hold the substrate in place
-on binding the active site changes shape the change in shape either bends bonds in substrate (catabolic reaction) or forces substrate closer together (anabolic reaction)
-products formed are a different shape to substrate so no longer fit active site and move away from
Temperatures effect on enzyme controlled reactions
higher temperature:
-faster rate of collisions with active site and substrate
-with more energy
-so faster ESC formation
Enzyme will denature and active site changes as bonds break causing a change in the tertiary structure. Although primary structure is not affected denaturation is not reversible.
pH effect on enzyme controlled reactions
The tertiary structure of the enzyme is maintained by hydrogen and ionic bonds therefore pH will affect the active site of an enzyme. Many active sites involved in catalysis are charged of which is changed by the pH as the H+ ions are attracted towards the negatively charged residue
All enzymes have optimum pH this is the H+ concentration that gives their tertiary structure best overall shape to bind to substrate. Usually around 7 the range of which the enzyme will work is narrow.
Concentration effect on enzymes
As concentration increases the reaction rate will increase due to increased collisions between active site and substrate so more esc is formed
Enzyme substrate effect on concentration
The greater concentration of substrate means a higher rate due to increased collisions and Avaliable active sites however the active sites will become a limiting factor and the rate will plateau.
Enzyme concentration effect on enzymes
The increase in enzyme concentration will cause an increase in the rate of reaction up to a specific point as greater avaliable active sites for substrate however the rate plagues as not all active sites are saturated as substrate becomes a limiting factor
Enzyme inhibitors
Reduce the rate of enzymes via acting on an enzyme in a specific way.
Competitive inhibition
Inhibitors have:
-similar shape to substrate
-shape complementary to active site
-occupy active site to form enzyme inhibitors complex so substrate is prevented from occupying the active site so there are less ESC so rate slows
Need greater amounts of substrate to reach higher rates in the presence of the inhibitor
Non Competitive Inhibition
-do not compete with substrate for active site as they have a separate binding point to enzyme called allosteric site.
-when binded it distorts shape of active site
-with enough inhibitors reaction will stop
The greater amount of inhibitors the slower the rate of reaction and the faster the rate will plateau due to quickly running out of active sites
Permanent/non permanent inhibitors
Permanent - enzyme is denatured
Non -permanent - removal of inhibitor leaves enzyme ready for catalysis
General rule - competitive = non-permanent non-competitive = permanent
Structure of DNA
-nucleic acid and polymer
-each monomer is a nucleotide made up of 3 components
-each nucleotide is linked by condensation reaction to form a polynucleotide forming a phosphodiester bond between the phosphate group which is attached to the 5’ carbon forming a covalent bond with the OH group on the 3’ end of the adjacent nucleotide
-two anti parallel strands joined via hydrogen bonds between complementary bases a +t and c+
-holds genetic information
-double stranded and double helix
Components of a DNA nucleotide
Phosphate Deoxyribose and a nitrogenous base
Nitrogenous bases are: adenine,thymine,guanine,cytosine
pyrimidines - cytosine and thymine have 1 carbon ring
purines - adenine and guanine have 2 carbon rings
A and T form 2 hydrogen bonds
C and G form 3 hydrogen bonds
Function of DNA
-stable structure that rarely mutates, increased when more c+g is present as they denature at higher temperatures
-backbone protects bases
-interactive forces between bases (base stacking)
-hydrogen bonds break easily so replication and synthesis can take place
-store genetic information
RNA structure
4 nitrogenous bases - adenine,uracil,guanine,cytosine
Phosphate, ribose, nitrogenous bases
Join via phosphodiester bonds
-shorter than DNA and single stranded
3 types of RNA
mRNA - encodes proteins
- no hydrogen bonding
- linear shape
- longer than tRNA
tRNA - acts as an adaptor between mRNA and amino acid
- hydrogen bonding
- anticodon present (3 exposed bases)
- clover shaped
-amino acid binding site
rRNA - forms ribosomes with protein
-bonded to protein to form ribosome
3 stages of protein synthesis
1) Transcription
2) gene splicing (eukaryotes only)
3) Translation
3 stages of protein synthesis
1) Transcription
2) gene splicing (eukaryotes only)
3) Translation
Stages of Transription
1)DNA unwinds and hydrogen bonding breaks and bases become exposed which is catalysed by DNA helicase (RNA polymerase may bind at this stage)
2)free RNA nucleotides bind to exposed bases on the template strand (make direct copy of coding strand)
3)phosphodiester bonds form between RNA nucleotides and RNA polymerase catalyses this
4) mRNA leaves DNA and DNA reseals
Stages of Gene Splicing
-RNA made directly after transcription is called pre-mRNA
-sections called interons are removed and remaining RNA know as exons are joined to form mature mRNA which is then a code for a specific protein
-mRNA then leaves the nucleus via nuclear pores
Stages of Translation
1)mRNA enters the ribosome small subunit which covers 6 bases (2 codons at a time)
2) the starting codon (always AUG) is needed to begin translation (methionine)
3)complementary tRNA binds to the start codon on the mRNA. This carries the correct amino acid for the start codon
4) Another tRNA anticodon with the corresponding amino acid bonds to the next codon on the mRNA
(only two tRNA can bind to the mRNA in the nucleus at once)
5) Then peptide bond formation occurs between adjacent amino acids (ATP requires for condensation reaction) and makes chemical more reactive - peptidyl transferase catalyses this
6) translocation occurs where tRNA move along with the molecule and a polypeptide chain forms of which then folds into a protein
ATP
-universal energy currency in all living organisms (evidence of evolution)
-produced via aerobic/anaerobic respiration or fermentation
-can release energy to energy requiring reactions in cells by phosphorylation where Pi is given to other molecules making them more reactive (hydrolysis is catalysed by ATP hydrolase)
This forms ADP
-can be re synthesised in a condensation reaction using ATP synthase occurs during photosynthesis (photo phosphorylation) and respiration (oxidative phosphorylation) in plant an animal cells when Pi groups are transferred from donor molecules to ATP (substrate phosphorylation)
Why ATP is good for its role/a suitable energy source for cells:
-release small amount of energy -less waste and damage to cells
-energy is readily available
-releases immediate energy through one reaction of breakage of phosphate bonds, enough for cellular reactions but not be wasted as heat
- makes compounds more reactive by phosphorylation
- can be rapidly resynthesized/regenerated
- cannot leave cells but is small so can move around easily
- water soluble
Why we need ATP-
-metabolic-provides energy for building of macromolecules from basic units
-synthesis - protein
-movement-energy for muscle contraction (fibres to slide and shorten)
-active transport-to change shape of carrier protein
-secretion-to from lysosomes for secretion of products
-activation of molecules - phosphorylation
-transport - ATP synthase
ATP Structure
Nucleotide- Adenine (base) , ribose (Pentose sugar) and 3 phosphate groups
Stages of DNA replication
1) DNA helicase enzymes travel along the DNA backbone which catalysis unwinds the 2 strands and breaks hydrogen bonds between base pairs
2) each strand acts as a template for a new strand
3) DNA polymerase enzyme binds to exposed strands (using RNA primers)
4) free DNA nucleotides bind to exposed bases forming hydrogen bonds and complementary base pairing occurs. (3’ to 5’ direction)
4) base pairings form and phosphodiester bonds form between adjacent nucleotides through a condensation reaction catalysed by DNA polymerase
5) Two DNA molecules are formed each with one old and one new strand of DNA
6) the leading strand undergoes continuous replication but the lagging strand is 5’ to 3’ so DNA polymerase has to wait until DNA is unzipped and work back. This forms Okazaki fragments which are joined via DNA ligase
What is the genetic code?
-Order of bases in the DNA which produce a polypeptide chain
-Also codes for functional RNA
-Each gene codes for one protein
3 Key features of the genetic code
1)universal - triplet code are the for all amino acids in all organisms
2)non-overlapping-each base is only part of one triplet
3)degenerate - there is more thank one triplet codon for each amino acid
Genes
Base sequence of DNA found at a locus on a chromosome
1) amino acid sequence of a polypetide
2) functional RNA
Genetic Variation
-genetic variation within a species allowing for natural selection and evolution to take place
The variation can occur by: a Mutation of meiosis cell division
Mutations
Change to a quantity of DNA or the base sequence
Gene Mutation
-substitutions
-deletions
-insertions
Of a single nucleotide which can occur during DNA Replication and can be corrected by enzymes
Deletion/insertion causes a frameshift causing all triplet codes to follow to be changed which then affects amino acid sequence therefor e the primary structure and tertiary structure making an incorrect protein
Chromosome Mutation
Often occurs in meiosis (anaphase) can result in:
1) chromosome rearrangement (large change)
2) aneuploidy (extra/missing chromosome)
3) polyploidy (extra complete set of chromosomes
4 types of Mutation can occur this way - Deletion, duplication, inversion, translocation
Meiosis
-creates 4 daughter cells that are genetically different
-used to produce gametes
-enables variation in a species
-daughter cells have 23 pairs of chromosomes
-produces hapliod cells
-2 cell divisions
Stages of meiosis
DNA replication
- 2 divisions
Stages of meiosis first division
Prophase I
-The chromosomes condense and homologous chromosomes pair up.
-Centrioles migrate to opposite poles of the cell where each centriole starts forming spindle fibres.
-The nucleolus disappears and the nuclear envelope starts to break down, leaving the chromosomes free in the cytoplasm.
Metaphase I
-Chromosomes line up along the equator of the cell in their homologous pairs (so in humans, 23 pairs line up).
-Each chromosome attaches to the spindle by their centromere.
Anaphase I
-Homologous chromosome pairs are separated and pulled to opposite poles of the cell (chromatids stay joined together).
Telophase I
-The chromosomes reach the opposite poles of the cell where they uncoil.
A nuclear envelope forms around each set of chromosomes and the nucleolus starts to reform.
The cytoplasm divides to form two cells (cytokinesis).
Stages of meiosis second division
Prophase II
-The chromosomes condense and are now visible under a microscope.
-Centrioles migrate to opposite poles of the cell where each centriole starts forming spindle fibres.
-The nucleolus disappears and the nuclear envelope starts to break down.
Metaphase II
-The chromosomes line up at the equator of the cell (so in humans, 23 chromosomes line up).
-Each chromosome attaches to the spindle by their centromere.
Anaphase II
-The centromeres divide and separate each pair of chromatids.
-The spindle fibres contract and shorten to pull the chromatids to opposite poles of the cell.
Telophase II
-The chromatids reach the opposite poles of the cell where they uncoil to become long and thin again.
-A nuclear envelope forms around each set of chromosomes to form two nuclei and the nucleolus starts to reform.
-The cytoplasm divides (cytokinesis) and 4 cells are produced.
Recombination
-occurs during the first division
1)bivalents are created
2)chiasmata form
3)alleles are exchanged between homologous pairs of chromosomes
4)further genetic variation in gametes cells produced during anaphase 2 as chromatids are pulled apart
Gamete calculations
Calculations for the possible number of gamete genotype possible =2n
N = number of homologous pairs present in the parent cell
Number of possible offspring genotype from 2 parents =(2n) ^2
Explain why in DNA replication each new strand is sythnesised in a different direction
- DNA is anti parallel meaning the end of each strand is either 5’ or 3’ and each shape of the nucleotides will be different
- DNA polymerase however only has an active site which is complementary to the 3’ end so due to this the enzyme moves in opposite directions along each strand from the 3’ end to 5’ end
Suggest the role of single stranded DNA fragments
-Act as template strands to create 2 new complementary strands
-determine order of the bases
Suggest the role of the DNA nucleotides
-bond to complementary bases
-form a complimentary strand
Describe how an enzyme can be phosphorylated
By the attachment of phosphate to the enzyme via the transfer on energy via ATP through the hydrolysis of ATP to become ADP and Pi.
Makes enzyme chemicals more reactive
ATP hydrolase
Protein found in DNA chromosome
Histone
Describe how ATP is re synthesised in cells
-condensation reaction between ADP and Pi via ATP Synthase
-happens during photosynthesis and respiration
Give two ways in which the hydrolysis of ATP is used in cells
-to provide energy for specific processes or reactions
-add phosphate to molecules and make them more reactive
Describe how an ATP molecule is formed from its component molecules
- 3 phosphates, ribose sugar, adenine base
-condensation reaction - ATP synthase
