3 - Biological Molecules Flashcards
Generates ATP via chemiosmosis
Slightly negative
Why is ice less dense than liquid water?
The hydrogen bonds between molecules in ice are slightly further apart than the average distance between liquid water molecules
What is an advantage to living organisms of ice being less dense than water?
Ice floats and forms an insulating layer on top of ponds, maintaining a constant temperature for organisms
Why is water a good solvent?
It’s polar so other charged molecules are attracted to it
Why is water’s high specific heat capacity useful for organisms?
It can be used as a coolant, to buffer temperature changes during chemical reactions and to provide a constant temperature for aquatic organisms
Why is water cohesive and adhesive?
Water is cohesive because the hydrogen bonds mean water molecules are attracted to one another. Water is adhesive because it can be attracted to other polar molecules.
Why is it useful to organisms that water is cohesive and adhesive?
Water acts as a good transport medium. These properties also mean that it can move upwards through narrow tubes via capillary action.
What are 3 examples of hexose monosaccharides?
Glucose, fructose, galactose
What is a hexose monosaccharide?
One with 6 carbon
What is a pentose monosaccharide?
One with 5 carbons
What are 2 examples of pentose monosaccharides?
Ribose and deoxyribose
What is the difference between alpha and beta glucose?
The OH group is below Carbon 1 on alpha, and above it on beta
Why is glucose soluble in water?
Because it contains OH groups which make it polar
What is the bond between two monosaccharides called?
Glycosidic bond
What is the disaccharide version of alpha glucose?
Maltose
What is a reaction which creates water called?
A condensation reaction
What is the addition of water to a disaccharide in order to split it into 2 monosaccharides called?
Hydrolysis
What is the test for reducing sugars called?
Benedict’s test
What is Benedict’s Reagant?
An alkaline solution of Copper (II) Sulfate
What colour would blue Benedict’s Reagant change to if reducing sugars are present?
Red
Are all monosaccharides reducing sugars?
Yes
Are most disaccharides reducing or non-reducing sugars?
Non-reducing
Why does Benedict’s Reagant turn red when reducing sugars are present?
Because the blue Cu2+ ions have an electron is added to form brick red Cu+ ions
What is the method for testing for reducing sugars?
- Add 2cm cubed of a food sample (liquid or crushed with water) 2. Add 2cm cubed of Benedict’s Reagant 3. Place the test tube in an 80°C water bath
What is the method for testing for a non-reducing sugars?
- Confirm that the sugar is not a reducing sugar 2. Add 2cm cubed of food sample in liquid form to a test tube 3. Add 2cm cubed of hydrochloric acid 4. Place in 80°C hot water bath for 5 minutes 5. Remove and slowly add sodium hydrogencarbonate until the solution is neutral 6. Re-test the solution using the Benedict’s test
How can you make the Bendict’s Test quantitative?
Use a colorimeter to test the transmission of red light in the solutions. More reducing sugars= more red light
What are 2 examples of biosensors?
Pregnancy test, blood sugar monitor
What is an analyte in a biosensor?
The sample containing the molecule you are testing for
What is the receptor in a biosensor?
The part which interacts with the molecule you are testing for
What is the transducer in a biosensor?
Detects the change in the receptor and provides a response
What does the display in a biosensor do?
Gives a visual representation of the change in the receptor
What colour does iodine change to when starch is present?
Changes to black because iodine molecules become trapped in the helix of the starch
What is the polysaccharide version of beta glucose called?
Cellulose
Which two polysaccharides make up starch?
Amylose and amylopectin
What percentage of starch is amylopectin and what percentage is amylose?
20-30% amylose 70-80% amylopectin
What type of glucose are amylose and amylopectin made up of?
Alpha glucose
What general structure are cellulose molecules?
Long, unbranched chains of beta glucose
Why are cellulose molecules straight?
The bonds between the glucose molecules are straight
What are the strong fibres formed by cellulose chains feld together by hydrogen bonds called?
Microfibrils
Why is cellulose suitable for use in cell walls?
It’s microfibril structure makes it strong enough to provide structural support for cell walls
What are some properties of cellulose?
Strong, insoluble, hard to break down in fibrous form
What is alpha glucose stored as in animals and fungi?
Glycogen
Why is starch used to store glucose?
Because amylose and amylopectin are insoluble so the glucose won’t interfere with osmosis
What is the general structure of amylose?
A tight, unbranched helix
What is the general structure of amylopectin
A long, tight helix structure with branches
Why do amylopectin and amylose’s structures suit their purpose?
Their tight helixes male them compact, and therefore ideal for storage
What is the general structure of Glycogen?
Similar to amylopectin except with many more side branches
Why does glycogen’s structure make it suited to storage?
It is compact like amylopectin because it is coiled. It’s many branches also allow energy to be released quickly, making it suited to more active animals
What are some uses of fat in organisms?
Protection around vital organs, shock absorption, buoyancy in aquatic animals, insulation, making hormones, making up cell membranes and storing energy
What are two types of lipids?
Phospholipids and triglycerides
Are phospolipids polar?
Partially- they have a polar head (The phosphate group) and a non polar tail (the fatty acids)
What is the difference between fats and oils?
Oils are liquid at room temperature, fats are solid
What is the structure of a triglyceride?
A glycerol with three fatty acids (hydrocarbon chains with a carboxyl group) joined to it by glycosidic bonds
Where are triglycerides found in the body?
Adipose tissue and in the bloodstream
Why are triglycerides insoluble in water?
Because of their non-polar tails
What is the structure of a phospholipid?
A glycerol, two fatty acids and a phosphate group
Which carbon do branches occur from in starch and glycogen?
Carbon 6
What is the main use of triglycerides and why?
Energy storage because their hydrocarbon tails contain lots of energy
What is the test for lipids in food?
The emulsion test
What result indicates the presence of lipids when using the emulsion test?
A milky emulsion forming
How would you conduct a test for lipids in a foodstuff?
- Add 2cm cubed of ethanol to either a liquid sample, or add the ethanol to a solid sample, crush it and pipette the ethanol into a separate test tube 2. Add 2cm cubed of water to this ethanol and shake gently 3. Observe the appearance of the test tube contents
Why can ethanol form emulsions?
Because it is not polar
Why do unsaturated fats tend to be liquid rather than solid at room temperature?
Because the double bonds cause a kink in the hydrocarbon chain so the molecules can’t pack together as closely
How many double bonds do monounsaturated alkenes contain?
One double bond only
How many double bonds do polyunsaturated alkenes contain?
Two or more double bonds
What type of alcohol is cholesterol?
A sterol alcohol
Where is cholesterol made?
Mostly the liver and intestines
What are some functions of cholesterol?
Adds stability to the cell membrane, involved in the production of steroid hormones, vitamin D and bile.
What is the structure of cholesterol?
A polar hydroxyl group and 4 carbon rings and a hydrocarbon chain tail, both of which are not polar
What is the structure of an amino acid?
An amine group, a carbon with a hydrogen and an R group (hydrocarbon chain) attached, and a carboxyl group
What is the bond between two amino acids in a dipeptide called?
A peptide bond
Which parts of amino acids bond together to form a dipeptide?
The H of one’s amine group and the OH of the other’s carboxyl group
What is the primary structure of a protein?
The sequence of amino acids in a chain
What is a polypeptide formed of?
Two or more amino acids
What is a protein formed of?
Two or more polypeptides
What is the secondary structure of a protein?
An alpha helix or a beta pleated sheet formed by hydrogen bonds forming between the NH and CO groups in a chain
What are some examples of bonding in a protein’s tertiary structure?
Disulfide bridge, hydrogen bonds between R groups and ionic bonding between oppositely charged R groups folding into its final shape
How are hydrophobic and hydrophilic R groups arranged in the tertiary and quaternary structure of proteins?
Hydrophobic groups on the inside, hydrophilic groups pushed to outside
What forms the quaternary structure of a protein?
The association of two or more individual proteins called subunits. The interactions are the same in the tertiary structure
What is a conjugated protein?
A protein which contains a non-protein group called a prosthetic group as part of its quaternary structure
What is the structure of a globular protein?
Compact and round in shape
What is a simple protein?
One without a prosthetic group
What is it called when a prosthetic group is key to a protein’s function?
A cofactor
What are 3 examples of conjugated proteins
Haemoglobin (contains 4 iron haem groups), lipoproteins (contain a lipid), glycoproteins (contain a carbohydrate)
What is the structure of haemoglobin?
4 polypeptide chains (2 alpha, 2 beta), each of which carry a haem group. The haem groups have Fe2+ resent in the haem group this allowing them to transport oxygen around the body
What is the structure and function of catalase
4 haem prosthetic groups with the presence of iron 2 allowing it to interact with hydrogen peroxide and speed up its breakdown
What is the general structure of a fibrous protein?
Very repetitive primary structures leading to long, strong, organised, rope-like structres which are not folded into a 3D shape
Why are fibrous proteins insoluble?
Because they have many hydrophobic R groups in their component amino acids
What is the structure and function of keratin?
It is a fibrous protein. It has a lot of sulphur containing amino acids this mean there is lots of disulphide bridge in the tertiary structure the amount of disulphide bridges is what determines the flexibility.
Why is the structure and function of Elastin?
It is a fibrous protein. It’s quaternary structure consists of many stretchy molecules called tropoelastin. Found in the walls of blood vessels, alveoli for flexibility
What is the structure and function of collagen?
Is a fibrous protein. Made of three polypeptides wound together in a long string rope like structure it has flexibility
How can non-essential amino acids be synthesised?
By changing the R groups of essential amino acids
Solvent
A fluid into which chemicals dissolve to make a solution
Solute
A component in a solution, dissolved in the solvent.
Solution
A solute dissolved in a solvent
What is an aqueous solution?
One in which water is the solvent
Chromatography
A technique used to separate mixtures of molecules. Relies on the movement of a gas or liquid through a medium
Stationary phase
The medium (which does not move) through which the solvent moves in chromatography.
Mobile phase
The liquid/gas and solvent moving through the stationary phase
Mobile phase of paper chromatography
Any suitable liquid solvent
Why do different chemicals move at different rates in paper chromatography?
Because they have different affinities to the solvent and different properties
What is an Rf value?
The ratio of how far a chemical moved in paper chromatography compared to the maximum distance travelled by the solvent
How do we work out what a substance is using paper chromatography?
Compare it’s Rf value to that of known substances
What is the qualitative test for proteins called?
The Biuret test
How do you conduct the Biuret test for proteins?
Add 2cm cubed of Biuret’s reagant to a liquid food sample
What is a positive test in the Biuret Test?
The solution turning from blue to purple
What does ATP stand for?
Adenosine triphosphate
What are the 3 components in an ATP molecule?
- Adenine base (nitrogenous) 2. Ribose monosaccharide (in the middle) 3. Three phosphoryl groups
What are the three main types of activity which cells require energy for?
- Synthesis 2. Transport (i.e. pumping ions or molecules across a membrane via active transport) 3. Movement (i.e. of protein fibres in muscle cells which cause muscle contraction)
How does ATP release energy?
Although a small amount of energy is needed to break the relatively weak bond holding the last phosphate group onto an ATP molecule, the large amount of energy released when this liberated phosphate undergoes other reactions involving bond formation offsets this
What is ATP an example of? (DNA is also one)
A nucleotide (although ATP is phosphorylated)
How much energy does hydrolysing ATP to release a phosphate group release?
30.6 kJ/mol
How much energy does hydrolysing AMP to release a phosphate group release?
14.2 kJ/mol
What is a Pi molecule?
A phosphoryl group
Why is ATP a poor long-term energy store?
Because it is unstable
Why is ATP a good immediate energy compound?
It releases a small, manageable amount of energy?
How do we get a phosphoryl group to detach from an ATP molecule?
By hydrolysing it
How can glucose be made more reactive?
By phosphorylysing it to create Glucose-6-Phosphate (G6P), which is a more reactive molecule than glucose. ATP allows this.
What are 5 useful properties of ATP?
- Small, so moves easily in/out of and within cells 2. Water soluble (energy-requiring processes occur in aqueous environments) 3. Easily regenerated (can be recharged with energy) 4. Releases energy in small, manageable amounts, so energy isn’t wasted as heat 5. Energy in bonds with phosphate molecules in large enough amount to be useful, but not so large that energy wasted as heat
How much energy does hydrolysing ATP or ADP to release a phosphate group release?
30.6 kJ/mol
Which elements do nucleotides contain?
Carbon, hydrogen, nitrogen, oxygen and phosphorous
What are the two types of nucleic acid?
DNA and RNA
What is a nucleic acid?
A large monomer made up of many nucleotide monomers linked in a chain
What are the 3 components of DNA and RNA?
- Phosphoryl group 2. Pentose monosaccharide (Deoxyribose in DNA, Ribose in RNA) 3. An organic, nitrogenous base (ATGC in DNA, AUGC in RNA)
How are the components in a nucleic acid monomer joined?
By strong covalent bonds formed via condensation reaction
What is the difference between ribose and deoxyribose?
Deoxyribose has 1 less oxygen (4, not 5)
What part of a nucleic acid is acidic?
The phosphoryl group, which is also negatively charged (PO4²⁻)
How is a polynucleotide formed?
When the phosphoryl group (5th carbon of sugar, aka 5’) of one nucleotide and OH group of the 3rd carbon of the adjacent nucleotide’s pentose monosaccharide attach via a condensation reaction
What is the bond between 2 nucleotides called?
Phosphopdiester bond
What is the part of a nucleic acid other than the bases called?
Sugar-phosphate backbone
What way does each strand of DNA run?
From 3’ to 5’
What does it mean that the strands in DNA are antiparallel?
The sugar-phosphate backbone of each strand run in opposite directions
What bonds attract the base pairs of DNA to each other?
Hydrogen bonds
How many hydrogen bonds are there between A and T/U bases?
2
How many hydrogen bonds are there between G and C bases?
3
Which bases are purine?
Adenine and Guanine
What are the full names of A,T,G,C and U?
Adenine, thymine, guanine, cytosine, uracil
What is the difference between pyrimidine and purine molecules?
Purines have double carbon ring structures, pyrimidines have single carbon ring structures
Which bases are pyrimidine?
Thymine, Cytosine and Uracil
What is the difference between the bases of DNA and RNA?
DNA has Thymine, RNA has Uracil
How do purine and pyrimidine molecules fit together?
In a complementary fashion
What does complementary base pairing in DNA ensure about the relative amounts of ATGC?
There is exactly the same amount of Adenine and Thymine, and likewise for Guanine and Cytosine
Which enzyme catalyses the unwinding and separation of DNA’s two strands?
DNA Helicase
How does the DNA molecule unwind?
DNA Helicase travels along the DNA backbone, catalysing reactions which break the hydrogen bonds between complementary base pairs as it reaches them.
What happens after the DNA strand has been ‘unzipped’ in DNA replication?
Free deoxyribose nucleotides present in the nucleus form hydrogen bonds with their complementary bases.
What does DNA Polymerase do?
Causes a phosphodiester bond to form between unjoined deoxyribose nucleotides which have been attracted to the unzipped strand of DNA
What direction is the only one DNA polymerase works in?
From the 3’ end to the 5’ end of the DNA strand
Why does DNA have to replicate each template strand in opposite directions?
Because DNA polymerase only runs along a strand in one direction, but DNA only unwinds and unzips in one direction
Which strand of DNA is the leading strand, and can therefore undergo continuous replication?
The strand which is unzipped from the 3’ end, as DNA polymerase can replicate it continuously as the strands unzip
What happens to the strand unzipped from the 5’ end in DNA replication?
DNA has to wait until a section has been unzipped, then work back along the strand. This results in DNA being produced in segments called Okizaki Fragements.
What joins Okizaki Fragments together?
DNA Ligase
What is the name of the strand unzipped from the 5’ end, and what type of replication does it undergo?
Called the lagging strand and undergoes discontinuous replication
How does a mutation occur during DNA replication?
Because sequences of bases aren’t always matched exactly, and an incorrect sequence can occur in a copied strand. These errors are random and spontaneous
What is semi-conservative replication of DNA?
The idea that each new DNA molecule contains one parent strand (from the original DNA molecule) and one new strand made up of nucleotides not from the original molecule
What experiment provided evidence for semi-conservative replication?
The Meselson-Stahl experiment
Provide a brief overview of the Meselson-Stahl experiment.
- Bacteria were initially grown in heavy nitrogen (¹⁵N), so all bases in their DNA contained only heavy nitrogen, leaving a band of heavy DNA near the bottom of a test tube 2. Then, bacteria were grown in normal (¹⁴N) nitrogen. The 1st generation of DNA all had a medium weight, as one strand was heavy and one light, so there was a band of DNA near the middle of the test tube. 3. Another generation of bacteria was grown in ¹⁴N nitrogen, producing DNA which was 1/2 lightweight (2 light strands) and 1/2 midweight (1 light 1 heavy), meaning that 2 bands formed in the test tube (1 at the top and 1 in the middle)
What is a gene?
A section of DNA used to encode a protein
What do genes control?
All metabolic processes
What is a gene locus?
The position each gene occupies on a chromosome
What is the proper name for a triplet of three bases?
Codon
What sort of code is the genetic code?
A triplet code with 64 different combinations and a degenerative code
What does it mean that the genetic code is degenerative?
That multiple codons can code for one amino acid
What is the importance of each gene in DNA containing a ‘START’ codon?
It ensures that codons are read ‘in frame’ i.e. in order so that the correct order of amino acids is produced
What is special about the ATG codon?
At the very start of a gene, it is a START codon- afterwards, it just codes for methionine
How many STOP codons are there?
3
What do STOP codons do?
End the chain of amino acids, ensuring that no new amino acids are added to the protein
Why is the genetic code a triplet code?
There are around 20 amino acids regularly used by organisms. If it were a single or double code, it would only have 4 or 16 possibilities, not enough to satisfy the needs of organisms
What is transcription of a gene?
The process by which the DNA sequence in a gene is transcribed onto a piece of messenger RNA
Why is gene transcription used in eukaryotes?
Because the full chromosomal DNA molecule is too large to leave the nucleus via a nuclear pore
What is the first step in gene transcription?
RNA nucleotides in the nucleolus are activated by adding two phosphoryl groups (i.e. adenine to ATP)
What is the second step in gene transcription?
DNA helicase is used to unwind the gene to be copied and break the hydrogen bonds between complementary bases (this can occur in the middle of a DNA strand)
What is the third step in gene transcription?
The activated RNA nucleotides bind using hydrogen bonds to their complementary bases on the template strand
What catalyses the joining of adjacent nucleotides on the RNA strand during gene transcription?
RNA Polymerase
What bonds are formed between adjacent RNA nucleotides by RNA polymerase during gene transcription?
Phosphodiester bonds
What action provides the energy for the joining of adjacent RNA nucleotides during gene transcription?
The removal of the two phosphoryl groups from the nucleotides
What are the 3 types of RNA?
- Messenger RNA 2. Ribosomal RNA 3. Transfer RNA
What is the fourth step in gene transcription?
The mRNA strand is released from the DNA and passes out of the nucleus via a nuclear pore, before binding to a ribosome
Which strand of DNA is the one that is replicated during gene transcription?
The sense/coding strand, which runs from 5’ to 3’
What is another name for the template strand?
Antisense strand
What is an exon?
Part of a gene which codes for a protein
What is an intron?
Part of a gene which doesn’t code for a protein
What does pre-RNA contain in terms of exons and introns?
A mixture of both
What is splicing (of a pre-mRNA molecule to a mature mRNA molecule)?
The removal of introns from the pre-mRNA
How can the same piece of pre-mRNA lead to the production of different proteins?
Because exons can be rearranged or even left out during splicing
What type of mRNA binds to a ribosome?
Mature mRNA
When does gene splicing occur?
Once the pre-mRNA molecule has reached the ribosome
What is DNA translation?
The assembly of polypeptides at ribosomes, dictated by the sequence of codons on the single-stranded mRNA
How do mRNA molecules fit into a ribosome?
Along a groove between the large and small sub units
Where is transfer RNA made?
The nucleus
What is an anticodon on a tRNA molecule?
3 unpaired nucleotides (at the opposite end to the amino acid) which are complementary to the codon being bound to
What shape does a tRNA molecule have?
A hairpin
What is found on a tRNA molecule at the opposite end to the anticodon?
Three exposed bases for an amino acid to bind onto
How many tRNA molecules are there and why?
61, as there is no tRNA molecule for the 3 STOP codons
What is the first step in gene translation?
mRNA molecule binds onto the small subunit of the ribosome by its first 2 codons
What is the second step in gene translation?
A tRNA molecule with the anticodon to the START codon carries methionine into the ribosome and attaches to the mRNA, using ATP to form hydrogen bonds with the codon
What is the maximum amount of codons which can be translated by any one ribosome at once?
Two
What is the third step in gene translation?
Another tRNA molecule brings a different amino acid and binds to the second exposed codon on the mRNA
What is the fourth step in gene translation?
A peptide bond forms between the two amino acids, catalysed by rRNA and the enzyme peptidyl transferase in the small ribosomal subunit
What is the fifth step in gene translation?
The ribosome moves along the mRNA, causing the first tRNA to leave (leaving their amino acid behind), translating codons one by one until a stop codon is reached
Why does gene translation stop once a STOP codon is reached?
There are no tRNA molecules for the 3 STOP codons, so the polypeptide chain is broken
How can protein synthesis be sped up?
Multiple ribosomes can be bound onto the same piece of mRNA
