Chapter 3 Biological Molecules Flashcards
How is a water molecule structured?
A water molecules is structured in a ‘V’ shape with one oxygen atom bonded covalently to two hydrogen atoms
O
/ \
H H
What type of molecule is water known as?
Water is known as a polar molecule, this is because it has an uneven distribution of charge due to oxygen being more electronegative than hydrogen. This means that electrons orbit around oxygen more than hydrogen, this unequal share of electrons consequently makes oxygen slightly negative and hydrogen slightly positive. This can be represented with the delta symbol next to the oxygen and hydrogen atoms.
What does waters dipolar nature mean?
Waters dipole nature means that there is an attraction between two different water molecules, this attraction is known as a hydrogen bond (these are weak individually, but in large proportions are very strong) which are represented through dots or lines between the slightly positive hydrogen atom and the slightly negative oxygen atom.
What are some of the principle properties of water?
-Water is polar
-Water is a good solvent, as many ions and covalently bonded polar substances (like glucose) can dissolve in it- this allows chemical reactions to occur within cells as it also acts as a transport medium.
-High specific heat capacity this means water is able to absorb a lot of energy for only a small rise in temperature due to the multiple hydrogen bonds present in water. This is beneficial as it is able to maintain a constant temperature consequently providing a suitable habitat for organisms and enzyme activity. This is also vital for water in the blood plasma because as water passes through active regions of the body, heat energy is absorbed but the temperature remains fairly constant.
-Latent heat of vaporisation, in order for water to evaporate, it must absorb a large amount of energy to break the hydrogen bond. Therefore, this is an advantage for living organisms because only a little water is required to evaporate for the organism to lose a great amount of heat providing a cooling effect.
-Ice is less dense than water because when frozen the hydrogen bonds between the water molecules space out meaning there are more air gaps and allowing ice to float. This is beneficial as it provides a habitat for organisms underneath as well as insulating the underlying water so temperatures remain fairly stable.
-Low viscosity allowing water to flow through small vessels and capillaries
-Cohesive due to hydrogen bonds, this allows water to move through the xylem of plants and through blood vessels in animals. Additionally, this enables surface tension due to hydrogen bonds between the top layer of water molecules allowing insects to float.
-Adhesive as water is able to hydrogen bond to other molecules like cellulose, this allows water to move up through the xylem.
-Translucent which enables water to transmit visible light, so aquatic habitats and organisms are able to survive
What are monosaccharides?
Single units which are used as a primary energy source for fuelling cellular metabolism. For example, glucose and fructose.
All monosaccharides are reducing sugars which means they can participate in reduction reactions.
What is the the structure of the isomer: alpha glucose?
CH2OH
\
H C———————O H
\ / \H \ /
C C
/ \ /OH H \ / \
OH C————————C OH
/ \
H OH
What is the structure of the isomer: Beta glucose?
CH2OH
\
H C———————O OH
\ / \H \ /
C C
/ . /OH H \ / \
OH C———————-C H
/ \
H OH
What is a condensation reaction?
This is when two molecules join to form a larger molecule whilst also releasing water in the process. For example, making bonds between two monosaccharides to form a disaccharide (double sugar molecule joined with a glycosidic bond) as well as producing water
What type of monosaccharide is glucose?
Hexose as it contains 6 carbons
What monosaccharides is the disaccharide lactose made from?
Monosaccharides are: Glucose and Galactose
What monosaccharides is the disaccharide sucrose made from?
Monosaccharides: Glucose and Fructose
What monosaccharides is the disaccharide maltose made from?
Monosaccharide: Glucose and Glucose
What is the chemical test for reducing sugars?
Benedict’s reagent- an alkaline solution of copper(II) sulfate
What is the positive result for reducing sugars?
A brick-red precipitate will be formed after heating as the reducing sugar has reacted with the copper ions in the Benedict’s reagent, resulting in the addition of electrons to the blue Cu2+ ions reducing them to a brick red Cu+ ion.
What is the result of using Benedict’s reagent on non-reducing sugars?
Non-reducing sugars do not react with Benedict’s solution and therefore the solution will remain blue after warming, indicating a negative result. However, if sucrose is first boiled with dilute hydrochloric acid a positive result will be given once warmed with Benedict’s solution. This is because the sucrose has been hydrolysed by the acid to glucose and fructose, both reducing sugars.
What is the test for starch?
The Iodine test is used to test for the presence of starch. A few drops of iodine dissolved in potassium iodide solution are mixed with the sample.
What is a positive result of the starch test?
If the solution changes colour from yellow/brown to purple/black then starch is present.
In the starch test, what is iodine dissolved in?
Potassium iodide
What can reagent strips be used to test for?
Test for the presence of reducing sugars, like glucose.
What is the advantage of using reagent strips?
Due to the colour coded chart, the concentration of the sugar can be determined.
What has to happen when two beta glucose molecules combine together?
One of the Beta glucose units has to flip upside down
What is formed when two glucose molecules react together?
A disaccharide which has a 1-4 glycosidic bond
How is starch structured?
Polymer of glucose, which is made up of long chains of alpha glucose molecules.
What is the function of starch?
Energy storage molecule in plants which can be found in chloroplast and concentrated in insoluble starch granules.
Osmotically inactive
What is starch composed of?
Amylose (25%-30%) and Amylopectin (70%-75%)
How is amylose structured?
Made up of long unbranched chains of alpha glucose molecules joined together by 1-4 glycosidic bonds. Coils are induced by the glycosidic bonds.
How is amylopectin structured?
Made up of long branched chains of alpha glucose molecules joined together by a 1-6 glycosidic bond every 23- 30 glucose units, with the rest connected by alpha 1-4 bonds.
What can amylose and amylopectin be broken down by?
Enzyme amylase which hydrolyses the glycosidic bonds.
How is cellulose structured?
Polysaccharide- a large insoluble molecule composed of beta glucose 1-4 glycosidic bonds held together in a bundle of hydrogen bonded Microtubules and fibres.
What is the function of cellulose?
Structural polysaccharide of plants cell wall which is freely permeable to solutes and solvents.
Great tensile strength.
How is glycogen structured?
Large insoluble molecule composed of highly branched chains of alpha glucose molecules.
What is the function of Glycogen?
Storage polysaccharide found in glycogen granules in liver and muscle cells.
Osmotically inactive
Readily converts back into glucose by the influence of the hormone glucagon.
What is the structure of glucose?
A hexose monosaccharide which is a small soluble molecule.
Osmotically active
What is the function of glucose?
Respiratory substrate which is the only fuel for brain cells.
Building blocks for other molecules like starch, cellulose and glycogen.
What are the three important properties of starch and glycogen?
Compact
Free ends for long branching chains means glucose can be added or removed easily
Insoluble
What does a colorimeter measure?
The absorbance and transmission of light.
If a solution is pale, little light will be absorbed, therefore the transmission value will be high while absorbance will be low.
However, if the solution is deeply coloured, more light will be absorbed, therefore the transmission value is low and absorbance value is high.
What disaccharide is a non-reducing sugar?
Sucrose
What are Lipids composed of?
-Built from fatty acid and a glycerol molecule
What are the different types of lipids?
Triglycerides- fats and oils
Phospholipids
Other lipids like:
-Steroids
-Hormones
-Cholesterol
-Waxes
What is the function of lipids?
The function depends on the structure of the lipid, however typically they are used for:
Energy Storage
Metabolic water source
Membrane structure
Water proofing
Insulation
Hormones
What types of lipids contain fatty acids?
Triglycerides
Phospholipids
Waxes
What types of lipids don’t contain fatty acids?
Steroids and Cholesterol
What is the displayed formula of an ester bond?
O — C
||
O
Where is the ester bond formed within a lipid?
Ester bonds are formed between the fatty acids and the glycerol molecule during a condensation reaction
How are saturated fatty acid structured?
The hydrocarbon chain has only single bonds that are in straight chains.
How are unsaturated fatty acids structured?
Contain some carbon atoms that are double bonded with each other.
This unsaturated nature causes kinks in the straight chains which means the molecules cant be packed closely together.
How is a triglyceride lipid structured?
Three fatty acids attached to a glycerol molecule.
How is a phospholipid structured?
Two Fatty acids attached to a glycerol molecule, one of the fatty acids is replaced by the phosphate group.
The Fatty acids are hydrophobic while the phosphate group is hydrophilic.
How are lipids respired?
1-Hydrolysis of ester bonds in triglycerides
2-Glycerol and fatty acids are completely broken down into H2O and CO2
3-This releases energy which is twice as much as the respiration of carbohydrates and release lots of water that is required by some organisms.
What are the advantages of lipids as a storage molecule?
Not water soluble
Don’t effect the water potential of the cell contents
Can be stored in a compact way
What is the test for lipids?
Ethanol test
1- 2cm^3 of oil is placed into a boiling tube
2-This is then mixed with 2cm^3 distilled water and 2cm^3 ethanol solution
3-A positive test of lipids turns ethanol milky white or cloudy
Explain how the structure of phospholipids allows them to form the bilayer of a plasma membrane
Phospholipids contain a hydrophilic head (the phosphate group) which is attracted to and bonds with the water. They then also contain a hydrophobic tail (the fatty acid) which is repelled by water.
What is the structure of cholesterol?
Small molecule made from 4 carbon based rings, found in all biological membranes.
It’s small, narrow and hydrophobic which allows it to sit in between the hydrophobic tails of the phospholipid bilayer.
What is the function of cholesterol?
Regulates the fluidity and strength of the membrane.
Cholesterol helps reduce the fluidity of membranes at high temperatures and increases fluidity at low temperatures.
Manufactures Vitamin D, Steroid hormones like testosterone and bile
What is Nucleic acid?
Large molecules contained in the nucleus of cells
What are the two types of Nucleic acid?
DNA- Deoxyribonucleic acid
RNA- Ribonucleic acid
What is the importance of Nucleic acid?
Important in the storage and transport of genetic information to make proteins
What elements does Nucleic acid contain?
-Carbon
-Hydrogen
-Oxygen
-Nitrogen
-Phosphorus
Which form long polymer molecules
What is the structure of a DNA nucleotide?
Deoxyribose sugar molecule attached to a base and a phosphate group
The Bases are: Adenine, Cytosine and Thymine, Guanine which are complementary to each other
What is the structure of a RNA nucleotide?
Ribose sugar attached to a base and phosphate group
The bases are: Adenine, Uracil and Guanine and Cytosine which are complementary to each other, however this time the Thymine has been replaced by Uracil.
How is ATP structured?
A ribose sugar which is attached to the Adenine base and three phosphate groups
How does ATP function?
ATP releases energy by breaking off a phosphate group to form ADP.
When a phosphate group is added it can then form ATP again.
What is the bond between two nucleotides known as?
Phosphodiester bond- this is a strong covalent bond.
What groups are the five bases split up into?
Purine and Pyrimidine bases
What are the Purine Bases?
Adenine- A
Guanine- G
How many Carbon rings do Purine bases have?
Contains two carbon rings
What are the Pyramidine Bases?
Uracil- U
Cytosine- C
Thymine- T
How many carbon rings do Pyrimidine bases have?
Contains one carbon ring
What do lipids contain?
Lipids contain Carbon, Hydrogen and Oxygen, however they generally contain more hydrogen and less oxygen
What are the similarities and differences between DNA and RNA?
Similarities- Both DNA and RNA have a phosphate group
They are both made of nucleotides
Have complementary base pairs
Differences
DNA contains the bases ACTG while RNA contains the bases ACUG
DNA has a deoxyribose sugar molecule in the nucleotide while RNA has a ribose sugar molecule in the nucleotide
DNA has a double helix structure, while RNA is a single strand of DNA
DNA is always found in the nucleus, while RNA can move out of the nucleus
What do lipids with a high proportion of unsaturated fatty acids tend to form?
Lipids with a high proportion of unsaturated fatty acids are oils and tend to be a liquid at room temperature.
What do lipid with a high proportion of saturated fatty acids tend to form?
Lipids which have a high percentage of saturated fatty acids are usually solid at room temperature.
What are properties of lipids?
They are insoluble in water as they are generally hydrophobic, however are soluble in organic molecules.
They also don’t form polymers.
Where are unsaturated fatty acids obtained from?
Mainly obtained from plant sources
Describe the process of Semi- Conservative Replication?
Firstly, a DNA molecule will unwind and unzip due to the DNA Helicase which travels along the DNA backbone, catalysing reactions that break the hydrogen bonds between complementary base pairs as it reaches them.
Therefore, this exposes the bases of the polynucleotide chains and each chain will act as a template so a new polynucleotide can be synthesised.
Free nucleotides which have been activated are attracted to to the complementary bases.
The DNA polymerase joins the nucleotides together creating new phosphodiester bonds in a condensation reaction.
Finally, once all the nucleotides are joined to form complete polynucleotide chains. Two identical chains are formed, each chain will containing one template strand and one daughter stand.
How is an amino acid coded for?
A triplet code which is degenerate, this means that each amino acid is coded for by more than one triplet.
What are the characteristics of messenger RNA?
Single stranded molecule
Contains ribose
Contains uracil instead of Thymine.
What is the process of Transcription?
- DNA Helicase enzyme acts on a region of DNA to break the hydrogen bonds between bases.
-RNA Polymerase moves along one of the two DNA strands- template strands
-Free RNA nucleotides are attracted to the exposed complementary bases
-RNA Polymerase will then form the phosphodiester bonds in between the RNA nucleotides.
-As the RNA nucleotides join together the pre- mRNA is formed
-The template strand will then rejoin with the previous DNA strand forming a double helix
-When the RNA Polymerase reaches a stop codon, the chain is terminated and the pre-mRNA detaches.
What is the process of Translation?
In the cytoplasm the mRNA attaches to a ribosome at the ‘start’ codon
tRNA molecules then attach to the ribosome and their anticodons pair up with appropriate codons on the mRNA
The amino acids transported by the tRNA link together as the ribosome moves along the mRNA bringing in 2 tRNA molecules at any one time
An enzyme and ATP are used to join the amino acids with a peptide bond
The ribosome continues to move along the mRNA adding amino acids until all codons have been translated and a stop codon has been reached.
What is tRNA?
Small molecule made of RNA which is single stranded and folded into a clover leaf shape with one end of he chain being slightly longer. The longer section is attached to an amino acid while there are three bases at the opposite end of the tRNA called an anticodon. Each amino acid has a different anticodon.
What elements are found in proteins?
Nitrogen, Oxygen, Hydrogen, Carbon, Sulfur
What is the structure of an amino acid?
H R O
\ | //
N— C— C
/ | \
H H OH
R- variable
Amine group- NH2
Acid group - COOH
How do two amino acids join together?
Join together in a condensation reaction and producing water
H R O H R O
\ | || | | //
N—C—C—N—C—C O H
/ | | \ || |
H H H OH C—N This is the peptide bond formed
+H2O
What are the different protein structures?
Primary, Secondary, Tertiary and Quaternary structures
What are Primary structures?
A sequence of amino acids where hundreds of amino acids link together to form polypeptide chains. The chemical interaction (attraction and repulsion) of individual amino acids helps define the final protein shape.
What are Secondary structures?
There are two common types of secondary structures:
-A helix coil
-Beta pleated sheet
The secondary structure is the shape of the polypeptide chain, most proteins contain a mixture of the two common secondary structures.
What are Tertiary structures?
The way in which the polypeptide chain is folded, the protein folds because of the interactions between ‘R’ groups or side chains on the amino acids.
What are the different types of interactions that occur between R-groups in a tertiary structure?
Disulphide bonds
Ionic bonds
Hydrogen bonds
Hydrophilic/hydrophobic interactions
What are Disulphide bonds?
This is the strongest of bonds which forms a single covalent bond between R- groups that contain sulfur atoms, this also involves disulphide bonds that occur between cysteine ( a sulphur containing amino acid).
Disulphide bonds are important in folding and stability of proteins
They can be broke down by reducing agents .
What are Ionic Bonds?
These are bonds which are stronger than hydrogen bonds and form between oppositely charged R- groups.
What are Hydrogen Bonds?
This is formed between amino acids with strongly polar R groups (H—O, N—H)
Individually the bonds are weak, however collectively they are strong
What are Hydrophobic and Hydrophilic interactions?
Hydrophobic amino acids are more stable and tend to be found inside proteins where water is excluded- Non- polar R groups.
Hydrophilic amino acids tend to be found on the outside of proteins
What is a Quaternary Structure?
This results from the association of two or more individual proteins called sub units, these protein sub units can be identical or different.
What are Globular Proteins?
Globular proteins are roughly spherical, compact and water soluble this is because the hydrophilic R-groups are on the outside of the protein, while the hydrophobic R-groups on the amino acids are kept away from the aqueous environment.
What is insulin?
Hormone involved in the regulation of blood glucose concentration,
Insulin needs to have precise shapes in order to fit into specific receptors on the cell-surface membrane.
Insulin also travels in the bloodstream so needs to be soluble.
What type of protein is insulin?
Globular
What is a Conjugated protein?
These are globular proteins that contain a prosthetic group (this can be lipids, carbohydrates, metal ions or molecules)
What are Haem groups?
Haem groups are a type of prosthetic group containing the Fe^2+ ion
What is Haemoglobin?
Red oxygen carrying pigment found in Red Blood Cells.
They are quaternary proteins formed from four polypeptides: two alpha and two beta subunits, each subunit contains a prosthetic Haem group.
The Fe^2+ ion in the Haem group can combine reversibly with an oxygen molecule enabling haemoglobin to transport oxygen.
What type of protein is Haemoglobin?
Conjugated Protein
What is Catalase?
Catalase is an enzyme which had a quaternary structure containing four Haem prosthetic groups
The presence of the Fe^2+ ion in the prosthetic group allows catalase to interact with hydrogen peroxide and speed up its breakdown.
Why is catalase important?
Important as Hydrogen peroxide is damaging to cells and cell components so catalase ensures that it cannot accumulate.
What type of protein is Catalase?
Conjugated Protein
What are Fibrous Proteins?
Fibrous Proteins are formed from long insoluble molecules due to the presence of a large proportion of amino acids with hydrophobic R-groups.
The amino acid structure is repetitive and organised forming a rope-like structure
What is Keratin?
Found in hair, skin and nails
Contains a large proportion of sulfur containing amino acid cysteine, this results in many strong disulphide bonds forming strong, inflexible and insoluble materials.
What type of protein is Keratin?
Group of Fibrous proteins
What are proteins without prosthetic groups known as?
Simple proteins
What is Elastin?
Quaternary protein made from linking many stretchy molecules called tropelastin to create a large insoluble, cross-linked structure.
This structure allows Elastin to be stretched and recoiled without breaking.
Elation can be found within the skin and walls of blood vessels to give strength and elasticity to the tissues.
What type of protein is Elastin?
Fibrous Protein
What is Collagen?
Connective tissue found in skin, muscles and tendons.
It is made up of three polypeptides chains wound together in a long and strong rope-like structure.
Every third amino acid in the polypeptide chain is glycine which allows the protein molecules to form a triple helix.
What type of protein is Collagen?
Fibrous Protein
What is a negative result of the test for starch?
Iodine will remain yellow-brown
How many hydrogen bonds is the Adenine and Thymine base pair held together by?
Two hydrogen bonds
How many hydrogen bond is the Guanine and Cytosine base pair held together by?
Three hydrogen bonds
What are the important cations?
Calcium ions (Ca2+)
Sodium ions (Na+)
Potassium ions (K+)
Hydrogen ions (H+)
Ammonium ions (NH4+)
What are the important anions?
Nitrate (NO3-)
Hydrogen carbonate (HCO3-)
Chloride (Cl-)
Phosphate (PO4^3-)
Hydroxide (OH-)
What is the role of Calcium ions?
Involved in muscle contraction and nerve impulse transmission
What is the role of Sodium ions?
Involved in co-transport, reabsorption of water in the kidney and nerve impulse transmissions
What is the role of Potassium ions?
Involved in the stomatal opening and nerve impulse transmission
What is the role of hydrogen ions?
Involved in chemiosmosis, pH determination and catalysis of reactions
What is the role of ammonium ions?
Involved in the nitrogen cycle, where by bacteria convert ammonium ions into nitrate ions
What are the roles of Nitrate ions?
Mineral absorbed by plants to provide a source of nitrogen to make amino acids.
What is the role of hydrogen carbonate ions?
Maintains the pH of the blood
What is the role of Chloride ions?
Provide a negative charge to balance the positive sodium and potassium ion in cells
What is the role of Phosphate ions?
Involved in the formation of phospholipids for cell membranes, nucleic acids and ATP formation and in making bones
What are three properties of Fibrous Proteins?
Insoluble in water
Unreactive
Stable/ Strong structure
