Biological Molecules Flashcards
How many bonds can a carbon atom form?
4
How many bonds can a nitrogen atom form?
3
How many bonds can an oxygen atom form?
2
How many bonds can hydrogen form?
1
What are calcium ions essential for?
Nerve impulse transmission
Muscle contraction
What are sodium ions essential for?
Nerve impulse transmission
Kidney function
What are potassium ions needed for?
Nerve impulse transmission
Stomata opening
What’s the hydrogen ions needed for?
Catalysis of reactions
PH determination
What are ammonium ions used for?
Production of nitrate ions by bacteria
What are nitrate ions needed for?
Nitrogen supply to plants for amino acid and protein formation
What are hydrogen carbonate ions essential for?
Maintenance of blood pH
What are chloride ions essential for?
Balance positive charge of sodium and potassium ions in cells
What are phosphate ions needed for?
Cell membrane formation
Nucleus acid and ATP formation
Bone formation
What are hydroxide ions needed for?
Catalysis of reactions
What does polar mean?
Has regions of positivity and negativity
Name a polar molecule
Water
What bonds form in polar molecules?
Hydrogen bonds abs they are relatively weak interactions which break and reform.
What are the characteristics of water?
High boiling point
Water less dense as a solid
Cohesive
Why does water have a high boiling point?
Hydrogen bonding means that it takes a lot of energy to break all the hydrogen bonds (so many) and therefore evaporate the liquid
Why is ice less dense than water?
Due to the bonding pattern of hydrogen bonds at a certain temperature. Produces giant rigid and open structure with every oxygen at the centre of a tetrahedral arrangement
Why does water have cohesive properties?
Water molecules attracted to each other due to polarity.
Why is water vital for life?
Acts as a solvent
Very efficient transport medium
Acts as a coolant
Surface tension
Does not change temp very easily
Why can water demonstrate capillary action?
As it shows cohesive and adhesive properties water can be taken up by plants by the force of gravity
What is the general formula of carbohydrates?
Cx(H2O)y
Are glucose molecules polar and soluble in water?
Yes
What type of bond forms between two glucose molecules?
Glycosidic bonds
What does the reaction for the joining of 2 glucose molecules produce?
Maltose and water
What do galactose and glucose form?
Lactose
What do fructose and glucose form?
Sucrose
How is amylose formed?
Alpha glucose molecules joined by 1-4 glycosidic bonds.
What shape is amylose and why?
Amylose forms a helix shape due to the angle of the 1-4 glycosidic bonds which makes the chain twist to form a helix which is further stabilised by hydrogen bonding.
What are the characteristics of amylose?
More compact and less soluble than glucose
How is amylopectin formed?
With 1-4 and 1-6 glycosidic bonds between alpha glucose molecules formed by condensation reactions.
What structure does amylopectin have?
Branched structure because of the 1-6 bonds,l. Branches every 25 glucose subunits.
Why is glycogen better for storage than amylopectin?
It has more branches which makes it more compact and less soluble.
How is glucose released for respiration or other processes?
By hydrolysis reactions catalysed by enzymes.
Structure of cellulose?
Alternate beta glucose molecules turned upside down to form 1-4 glycosidic bonds. Forms a straight chain molecule called cellulose.
How are microfibrils formed?
When cellulose makes hydrogen bonds with each other.
What do microfibrils do?
Join together to form macrofibrils which combine to produce fibres. These fibres are strong and insoluble and are used to make cell walls.
How to carry out a Benedicts test for reducing sugars?
Place the sample to be tested into a boiling tube. ( if it’s not liquid, grind it up or blend it in water)
Add an equal volume of Benedict’a Reagent.
Heat the mixture gently in a boiling water bath for 5 mins.
What results will be seen and why?
Reducing sugars react with copper ions in Benedicts. This results in the addition of electrons to the blue Cu2+ ions, reducing them to red brick Cu+ ions. A red brick precipitate forms indicating a positive result.
What kind of test is the Benedict’s test for reducing sugars?
Qualitative
What is the most common non reducing sugar?
Sucrose
What result will sucrose show on a reducing sugar Benedicts test?
None. The solution will stay blue after warming indicating a negative result.
How can you get sucrose to show a positive result?
Boil sucrose with dilute hydrochloric acid. This will hydrolyse the sucrose into glucose and fructose with are both reducing sugars.
Explain the iodine test for starch?
Mix a few drops of iodine dissolved in potassium iodide solution with a sample.
If the solution changes colour from yellow / brown to purple / black then starch is present.
What can manufactured reagent strips be used for?
Can be used to test for the presence of reducing sugars most commonly glucose
How to work a colorimeter?
Place a filter in the colorimeter.
Calibrate colorimeter using distilled water.
Perform Benedict’s test.
Filter out the precipitate of the resulting solutions.
The % transmission of each glucose solution measured by colorimeter.
Plot calibration curve
Are lipids polar?
No
Are lipids soluble?
No
What is a triglyceride?
One glycerol and 3 fatty acids
What group is glycerol a member of?
Alcohols
What group are fatty acids a member of?
Carboxylic acids, consist of a carboxyl group and a hydrocarbon chain attached
How does a triglyceride form?
The hydroxyl groups (OH) interact forming 3 water molecules and bonds between the fatty acids and glycerol molecule, these are called ester bonds.
What is a saturated fatty acid?
Fatty acid chains that have no double bonds present, all the carbons have already formed all 4 of their bonds and therefore cannot bond with anymore.
What is an unsaturated fatty acid?
A fatty acid with double bonds between some of the carbon atoms.
Why are unsaturated fats kinked or bent in their structure?
The presence of double bonds causes the molecule to kind or bend which means that they cannot pack as closely together. As a result, they’re liquid at room temperature.
What are phospholipids?
Modified triglycerides that contain phosphorus as well as carbon hydrogen and oxygen. Inorganic phosphate ions are found in cytoplasm of every cell. These have extra electrons and are therefore negatively charged.
Which part of the phospholipid is polar?
The head
Which part of phospholipid is non polar?
Tails that mix readily with fat.
Which part of the sterol molecule is hydrophilic?
The hydroxyl group as it is polar.
What are the role of lipids in the body?
Membrane formation and hydrophobic barriers
Hormone production
Electrical insulation for impulse transmission
Waterproofing
What is the role of triglycerides in long term storage?
Thermal insulation to reduce heat loss
Cushioning to protect vital organs
Buoyancy for aquatic animals
How can you test for lipids?
Emulsion test
How do you complete the emulsion test?
First mix the sample with ethanol. Then mix the resulting solution with water and shake. If a white emulsion forms as a layer on top of the solution that indicates the presence of lipids.
When is a peptide bond formed?
A bond formed between the amino acid and when water is produced.
What enzyme catalyses amino acid to polypeptide reaction?
Peptidyl Transferase
What is primary structure of proteins?
The sequencing of amino acids. Only bonds involved are peptide bonds.
What is the secondary structure of proteins?
Oxygen, hydrogen and nitrogen atoms of the basic repeating structure of amino acids interact. Hydrogen bonds can form within chain to form alpha helix.
Polypeptide chains can lie parallel to each other joined by hydrogen bonds, this forms a beta pleated sheet.
What is the tertiary structure of a protein?
The folding of the protein into its final shape. The cooking or folding of sections of proteins brings R groups closer so they can interact. This leads to further folding.
What are the 4 interactions that can occur?
Hydrophilic / Hydrophobic reactions - weak interactions between polar and non polar R groups
Hydrogen Bonds - weakest of the bonds
Ionic Bonds - stronger than hydrogen bonds and form between oppositely charged R groups
Disulphide Bridges - covalent and strongest bonds but only form between R groups that contain sulphur
What is quaternary structure of proteins?
Results from the association of 2 or more individual proteins called subunits. Interactions between subunits are the same as in tertiary structure, except they are between different protein molecules.
What subunits are there in enzymes?
2 identical subunits
What subunits are in hormones?
2 different subunits
Subunits in Haemoglobin?
Four subunits made up of 2 sets of 2 identical subunits
Where are the hydrophilic R groups on a protein?
Outside as they form in an aqueous environment in the cytoplasm.
What reaction is used to break down proteins?
Hydrolysis
Characteristics of Globular proteins?
Compact
Water Soluble
Roughly spherical in shape
Hydrophilic r groups on outside
Example of globular proteins?
Insulin (hormone)
What is a conjugated protein?
Globular proteins that co rain a non protein component called a prosthetic group.
Examples of prosthetic groups are harm groups
Examples of conjugated proteins?
Haemoglobin and Catalase.
What does catalase do?
Presence of iron 2+ ions in prosthetic group allow catalase to interact with hydrogen peroxide and speed up its breakdown
What are characteristics of fibrous proteins?
Long molecules Insoluble Organised structure Form long strong molecules Not folded
Examples of fibrous proteins?
Keratin
Elastin
Collagen
Where is keratin found?
Hair, skin and nails.
Large amounts of surplus containing compound cysteine. = disulphides bridges which makes it strong.
Where is collagen found?
Connective tissue found in tendons, skin, ligaments and the nervous system.
What are the components of a nucleotide?
Pentose Sugar
Phosphate group
Nitrogenous base
How do phosphodiester bonds form?
The phosphate group at the 5th carbon of the pentose sugar of the nucleotide forms a covalent bond with the hydroxyl group on the 3rd carbon of the pentose sugar.
What are the pyramidine bases?
Smaller bases, single carbon ring structure = thymine and cytosine
What are the purines?
Larger bases that contain double carbon ring structures - Adenine and Guanine
What is the difference between ribose and deoxyribose?
Deoxyribose has one less oxygen than ribose
Why does DNA form a double helix?
Two strands held together by hydrogen bonds. Each strand has phosphate group (5’) one end end hydroxyl group (3’) at the other. 2 parallel strands arranged so that they run in opposite directions ( anti parallel)
How many bonds do adenine and thymine form?
2
How many bonds to cytosine and guanine form?
3
How do the chains stay parallel?
Because complementary base pairing means that a small pyrimidine base always binds to a large purine base.
What is semi conservative replications?
DNA helix structure unwinds and separates into 2 strands, hydrogen bonds between strands broken. Free dna nucleotides then pair with complementary bases that are exposed.new nucleotides join to their adjacent nucleotides with phosphodiester bonds.
2 new DNA molecules produced. Each one consists of one old strand and one new strand
What is DNA helicase responsible for?
The unwinding and separating of the 2 strands of the DNA double helix. Travels along the backbone ‘unzipping’ the chains by breaking hydrogen bonds.
What does DNA polymerase do?
Catalyses the formation of phosphodiester bonds between the new free nucleotides.
What is continuous replication?
When the leasing strand (3’) is unzipped. DNA polymerase always moves along the template strand in the same direction. Can only bind to the 3’ end. Can be continuously replicated as it is in the right direction.
What is discontinuous replication?
Other strand unzipped the other way from 5’ end. DNA polymerase has to wait until a strand has been unzipped and then work back along the strand. Therefore DNA is produced in sections ( Okazaki Fragments) which the Have to be joined. Causes lagging
What is the genetic code?
The idea that DNA codes for a sequence of amino acids
What is a codon?
A sequence of 3 bases.
What is the triplet code?
The code in the base sequences
What is a gene?
A section of DNA that contains the complete sequence of bases to code for an entire protein .
How many codons are possible?
64 (4 cubed)
What is a start codon?
Comes at the beginning of a gene, signalling the start of a sequence that codes for a protein. If it is in the middle of a gene, it codes for methionine.
What is a stop codon?
Codons that do not code for Amino Acids, they signal the end of. DNA sequence.
Why is the DNA code degenerate?
Different combinations of bases can code for the same amino acid
Explain Transcription?
RNA polymerase binds to the promoter region on a section of DNA
DNA double helix unwinds due to helicase enzyme being present (unzips dna exposing bases)
(Coding strand runs in 5’ to 3’ direction)
mRNA strand formed is the same 5’ to 3’ as the coding strand.
Free RNA nucleotides align opposite their complementary base partner on template strand
RNA polymerase catalyses formation of phosphodiester bonds joining nucleotides to form mRNA strand
Transcription stops at end of gene which has stop codon on mRNA.
RNA polymerase detaches and the mRNA formed also detaches from dna template. mRNA contains code for protein to be synthesised and leaves via the nuclear pore.
Explain Translation?
The ribosome binds to mRNA and moves along the molecule in 5’ to 3’ direction until it reaches a start codon (AUG)
The first tRNA carrying the amino acid methionine ( matches AUG) is needed in order for translation to get started
mRNA read one codon at a time. Anti codons in tRNA align opposite appropriate codons according to base pairings. Each tRNA specific A.A.
Ribosomes make peptidyl transferase which catalyses formation of peptide bonds between adjacent A.A via condensation reactions
Ribosome moves along mRNA chain synthesising a polypeptide chain until it reaches a stop codon.
At this point translation ceases and polypeptide chain released.
What do cells require energy for?
Synthesis
Transport
Movement
What is an ATP molecule comprised of?
A nitrogenous base (always adenine)
A pentode sugar
3 phosphate groups.
What is the sugar in ATP?
Ribose
How does ATP release Energy?
Hydrolysis reaction -
ATP + H2O. = ADP + Pi + energy
Why is ATP not a good long term energy source?
Because the phosphate bonds are unstable. Fats and Carbohydrates are much better for this
What is phosphorylation?
The reattachment of a phosphate group to an ADP molecule. Condensation reaction.
Why is ADP a good immediate energy source?
Because the Inter conversion of ATP and ADP is happening constantly in all living cells, cells do not need a large energy source.
Properties of ATP?
Small
Water soluble
Releases energy in small quantities( no energy wasted as heat)
Easily Regenerated
Contains bonds between phosphates with intermediate energy.
