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Flashcards in Molecular Biology Deck (58)
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What is organic chemistry?

The study of the properties and structures of organic compounds


What is an organic compound? (2)

1. Organic compound: A compound that contains carbon and is found in living things
2. All organic compounds have carbon backbones, however not all carbon compounds are organic (Ex: CO2, urea)


What are the important properties of carbon? (4)

1. Carbon-carbon bonds are strong and stable due to their covalent bond
2. As a result, carbon can form an almost infinite number of compounds include long carbon chains.
3. No other element can bond like this
4. Therefore, carbon forms the basis of organic life due to its ability to form large and complex molecules via covalent bonding


Define metabolism

The web of all enzyme-catalyzed reactions in a cell or organism


Define anabolism

The synthesis of complex molecules from simpler units, it requires energy (formation of macromolecules from monomers)


Define catabolism

The breakdown of complex molecules into simpler units, it releases energy (formation of monomers from macromolecules)


What is the difference between condensation and hydrolysis reactions? (3)

1. Carbon compounds can be formed using condensation, or broken using hydrolysis:
2. Condensation makes bond, releases water and is an anabolic reaction
3. Hydrolysis breaks bond, requires water, and is a catabolic reaction


What was the theory of vitalism and how was it disproved? (2)

1. Vitalism was a belief that organic molecules can only be synthesized by living things
2. However, in 1800 urea was produced from inorganic chemicals (ammonium cyanate) proving organic molecules don’t have to be synthesized by living things.


Describe how water is structured (3)

1. Water (H2O) is composed of two hydrogen atoms covalently bonded to an oxygen atom
2. The bond formed between the oxygen and hydrogen are referred to as a polar (unequal share of electrons) covalent bond
3. The oxygen atom is slightly negative (δ-) while the hydrogen atoms are slightly positive (δ+) therefore the slightly charged regions of the water molecule can attract other polar or charged compounds and gives water special properties


What is cohesion? (4)

1. An attraction between molecules of the same type
2. This property occurs in water as a result of its polarity and its ability to form hydrogen bonds
3. Even though hydrogen bonds are weak the large number of bonds present in water can give cohesive forces strength
4. E.g: Surface tension allows some organisms to rest or move on top of water’s surface


What is adhesion? (4)

1. An attraction between two unlike molecules
2. This property occurs between water and other molecules as a result of waters polarity and its ability to form hydrogen bonds
3. Individual hydrogen bonds are weak, but large number of bonds gives adhesive forces strength. Therefore, water molecules tend to stick to other molecules that are charged or polar just like cohesion
4. Example: Water moves up the stems of plants because in addition to being attracted to itself (cohesion) it is also attracted to the side of the stem (adhesion). Water is so highly attracted to the sides of the stem that it pulls itself up against the force of gravity without any energy input from the plant - transpiration stream.


What are the solvent properties of water? (2)

1. Water can dissolve any substance that contains charged particles (ions) or electronegative atoms (polarity)
2. This occurs because the polar attraction of large quantities of water can sufficiently weaken intramolecular forces and result in the dissociation of the atoms


What are the thermal properties of water?

1. Water has a high specific heat capacity - able to absorb a lot of energy before changing states e.g. sweat and cells
2. This enables:
o Aquatic organisms who can’t survive extreme temperature changes
o Plants who have openings in their leaves called stomata to let vaporizing water out in order to cool down the left


What are the differences in the thermal properties between methane and water? (3)

1. The differences in thermal properties between water and methane arise from differences in polarity between the molecules
2. While Water is polar and can form intermolecular hydrogen bonds which increases the amount of energy to break it, methane is non-polar and can only form weak dispersion forces between its molecules
3. This means water absorbs more heat before changing state and so:
o Boiling point of water is greater than methane
o Melting point of water is greater than methane
o Latent heat of vaporization of water is greater than methane


Why is methane comparable to water? (2)

1. Comparable size and weight (H2O = 18 dalton ; CH4 = 16 dalton)
2. Comparable valence structures (both have tetrahedral orbital formations, but water is bent due to unbonded electron pairs)


Explain the use of water as a coolant in sweat

1. The change of water from liquid to vapour (evaporation) requires an input of energy
2. This energy comes from the surface of the skin when it is hot, therefore when the sweat evaporates the skin is cooled
3. Because water has a high specific heat capacity, it absorbs a lot of thermal energy before it evaporates
Thus water functions as a highly effective coolant, making it the principal component of sweat


What are the different classes of carbohydrates? (3)

Carbohydrate is another term for sugar. Carbohydrates can be classified into three classes depending on their complexity:
1. Monosaccharides: Monomers of polysaccharides, the simplest carbohydrate e.g glucose, galactose and fructose
2. Disaccharides: A molecule formed by condensation reactions between two monosaccharides e.g maltose, lactose and sucrose
3. Polysaccharides: Polymers with more than 2 molecules linked together in different ways by condensation reactions e.g. glycogen, cellulose and starch.


What is the structure of a fatty acid? (3)

1. Fatty acids consists of a straight chain of an even number of carbon atoms, with hydrogen atoms
2. Fatty acids all have a methyl group (CH3) on one end and a carboxyl group (COOH) at the other end.
3. CH3 -------(CH2)n -------- C =====OOH


What are the three classes of lipids? (3)

1. Phospholipids - they are made from a glycerol bonded to two fatty acids and one phosphate group. They are only partly hydrophobic and form the basis of membranes
2. Steroids all have a similar structure of four fused rings in their molecules. Include cholesterol, progesterone, oestrogen and testosterone
3. Triglycerides are the largest class of lipids and primarily function as a long-term energy storage. They are made from one glycerol bonded to three fatty acids glycerol by condensation reactions. E.g. fats and oils.


Compare the use of carbohydrate and lipids in energy storage

1. Carbohydrates are usually used for short term storage whereas lipids are used for long term storage. 2. Carbohydrates are soluble in water unlike lipids. This makes carbohydrates easy to transport around the body (from and to the store).
3. Carbohydrates are more easily and more rapidly digested so their energy is useful if the body requires energy fast. (aerobic and anaerobic respiration).
4. Since lipids are insoluble they do not have an effect on osmosis which prevents problems within the cells in the body.
5. Lipids also contain more energy per gram than carbohydrates which makes lipids a lighter store compared to a store of carbohydrates equivalent in energy. (Twice as much ATP per gram)


What is BMI? (3)

1. BMI is commonly used as a screening tool to identify potential weight problems
2. BMI=(Weight (in kg))/(Height^2 (in m)) or use of nomogram
3. However, BMI calculations should not solely be used as a diagnostic tool and should be used in conjunction with other measurements. Also BMI values are not a valid indicator for pregnant women


How are blood cholesterol levels regulated? (6)

1. Fats and cholesterol cannot dissolve in blood and are consequently packaged with proteins (to form lipoproteins) for transport:
Low density lipoproteins (LDL) carry cholesterol from the liver to the rest of the body
High density lipoproteins (HDL) scavenge excess cholesterol and carry it back to the liver for disposal
3. Hence LDLs raise blood cholesterol levels while HDLs lower blood cholesterol levels
4. Saturated fats increase LDL levels within the body, raising blood cholesterol levels
5. Trans fats increase LDL levels and decrease HDL levels within the body, significantly raising blood cholesterol levels
6. Unsaturated (cis) fats increase HDL levels within the body, lowering blood cholesterol levels


How do polypeptides differ from one another? (3)

o Their length (number of amino acids)
o Amino acids that are present
o Order of the amino acids - this is what gives each polypeptide its unique properties


What are peptide bonds? (4)

1. Amino acids are linked together in proteins by a special kind of covalent bond known as a peptide bond or amid link
2. Peptide bonds are formed by condensation reactions between the amino group of one amino acid and a carboxyl group of another amino acid
3. A water molecule H2O is also formed
4. Polypeptide chains can be broken down via hydrolysis reactions, which requires water to reverse the process


Outline the 4 levels of protein structure (4)

1. The primary structure refers to the sequence of amino acids in the polypeptide chain. This sequence is unique to that protein, and defines its structure and function
2. The secondary structure of a protein refers to the folding of the polypeptide as a result of hydrogen bonding (Alpha-helix or beta-pleated sheets)
3. The tertiary structure of a protein refers to the twisting and folding of the secondary structure to form a specific 3D shape (held together by interactions between the side chains (The R groups))
4. The quaternary structure of proteins refers to the interactions between polypeptide chains


What is denaturation? (3)

1. A structural change of a protein that results in the loss of its biological properties
2. Due to heat - Heat causes vibrations within protein molecules that break intramolecular bonds and cause the conformation to change. (Irreversible)
3. Due to pH - pH changes causes intramolecular bonds to break


What are enzymes?

Enzymes are (globular) proteins that act as biological catalysts, increasing reaction rates of biological processes without being used up in the process


List some examples of proteins and their functions (8)

Collagen - Used in skin to prevent tearing, in bones to prevent fractures, and ligaments to give tensile strength
Spider silk - Used to make webs for catching prey and lifelines on which spiders suspend themselves. It has very high tensile strength and becomes stronger when stretched
Insulin - Is carried dissolved in blood and binds specifically and reversibly to insulin receptors in the membranes of body cells, causing the cells to absorb glucose and lower glucose concentration
Immunoglobulins - Antibodies that bind to antigens on pathogens
Haemoglobin - A protein found in red blood cells that is responsible for the transport of oxygen
Cytochrome - A group of proteins located in the mitochondria involved in electron transport chain
Rhodopsin - A pigment in the photoreceptor cells of the retina that is responsible for the detection of light
Rubisco - An enzyme involved in the light independent stage of photosynthesis


Explain the differences between the lock and key theory and the induced- fit model (4)

1. Enzymes are extremely particular, and each enzyme only binds with one particular substrate
2. The induced-fit model is based on the lock-and-key model. The lock-and-key model states that the substrate acts as a “key” to the “lock” of the active site
3. The induced-fit model is a theory that says the active site will change shape to enfold a substrate molecule
4. Instead of the active site and substrate being perfect matches, the substrate induces a change of shape in the enzyme


Outline the different factors affecting the enzymes (3)

1. Temperature
Increasing temperature increases enzyme activity since
collisions between substrate and active site happen more frequently due to faster molecular motion at higher temperatures. However, at high temperature the enzymes will become denatured and stop working.
2. pH levels
Increasing pH increases enzyme activity to an optimum point. Increasing pH beyond this optimum point will reduce enzyme activity due to denaturation
3. Concentration
Increasing substrate concentration increases enzyme activity. This is because random collisions between substrate and active site happens more frequently with higher substrate concentrations. However, at high substrate concentrations the active site of the enzyme is saturated therefore raising the substrate concentration has little effect on enzyme activity.