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Molecular Flashcards

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1
Q

Define cation

A

If an atom loses electrons to form a bond it now has more protons than electrons so the overall charge of this ion will be positive

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2
Q

Define anion

A

If an atom gains electrons to form a bond it now has more electrons than protons so the overall charge of this ion will be negative

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3
Q

Define ionic bonds

A

Bonds that form between metals and non-metals. They often occur in inorganic compounds (not carbon based).

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4
Q

Define covalent bonds

A

Covalent bonds also involve atoms becoming more stable when their outer shell of electrons become full. However, to achieve this instead of donating/accepting electrons (ionic bonds) atoms will share electrons to achieve a stable configuration.

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5
Q

Define hydrogen bonds

A

A molecule of water consists of 2 hydrogen atoms and 1 oxygen atom.

The oxygen end of the water molecule has a slight negative charge and the hydrogen end has a slight positive charge. The molecule is said to be polar

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6
Q

Why do cells need inorganic compounds?

A

Cells need organic compounds – containing carbon and hydrogen atoms to synthesise essential requirements for cells/tissues or as an energy source

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7
Q

Why do cells need inorganic compounds?

A

Cells also need inorganic compounds such as gases, minerals, phosphates, sodium and chloride ions to form structural components

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8
Q

What is molecular biology

A

Molecules within all living things can be categorised into one of four biochemical groups:
Carbohydrates Lipids Proteins Nucleic Acids

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9
Q

Define metabolism

A

Metabolism - refers to all the chemical reactions that happen within an organism. All living organisms carry out large numbers of different chemical reactions. These reactions are often catalysed by enzymes (a protein).

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10
Q

What is anabolism?

A

Anabolism includes reactions that build up larger molecules from smaller ones. They require energy in the form of ATP because you are forming new bonds.

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11
Q

What is catabolism?

A

Reactions that involve breaking down larger molecules into smaller ones. They are the opposite of anabolic reactions.

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12
Q

What are carbohydrates?

A

These are characterised by their composition - they are compounds of carbon, hydrogen and oxygen. They are built from monosaccharides (simple sugars) and can form mono-, di-, and poly- saccharides.

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13
Q

What is a monosaccharide?

A

Are the simple sugars that are the building blocks for the more complex carbohydrates.

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14
Q

What is a disaccharide?

A

Consist of two joined monosaccharaides. These include maltose, lactose and sucrose.

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15
Q

What are polysaccharides?

A

Large molecules in which hundreds to thousands of monosaccharides are linked together.

Starch consists of many joined glucose molecules and is used in plants as a storage molecule which can be broken down when energy is needed.

Glycogen is a form of energy stored as granules in the cytoplasm of animal cells.

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16
Q

What are proteins?

A

Proteins are composed of one or more chains of amino acids (polypeptides) and are have a specific shape. Some are folded to give this 3D shape (globular protein) whereas others remain linear (fibrous proteins).

Amino acids are held together by a peptide bond to form a polypeptide chain. There are 20 different types of amino acids in the body. All of the amino acids contain CHON, there are 2 amino acids that also contain sulfu

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17
Q

What are the four levels of protein structure?

A

The shape and folding is determined by the specific sequence of amino acids (which in turn is specified by the nucleotide base sequence of the gene that codes for the protein
There are four levels of protein structure – primary, secondary, tertiary and quaternary

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18
Q

What are lipids?

A

Lipids are a broad class of molecule that are non-polar (insoluble in water). Lipids are smaller and simpler than complex carbohydrates. Examples include: steroids, waxes, fatty acids, phospholipids, triglycerides.

They are mainly made of two chemicals - glycerol (a type of alcohol) and fatty acids (long carbon-hydrogen chains that end in a carboxyl group - can be saturated or unsaturated).

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19
Q

What are nucleic acids?

A

Each nucleotide is made up of a simple sugar (R ribose or D deoxyribose), a phosphate and a nitrogenous base.

The bases form a sequence, providing the genetic code for a cell.

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20
Q

What is urea?

A

Urea is a nitrogen containing compound with a relatively simple molecular structure. It is the nitrogen component of urine and this was where it was first discovered in the 1720s.

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21
Q

What links amino acids together?

A

Ribosome.

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22
Q

What are polypeptides?

A

Polypeptides are chains of amino acids that are made by linking together amino acids by condensation reactions. This reaction happens on ribosomes (more detail in genetics).

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23
Q

Where are the instructions to create a specific sequence of amino acids to form a polypeptide contained?

A

Within genes in DNA.

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24
Q

What are globular proteins?

A

To give this globular shape, the polypeptides gradually fold up as they are made to develop the final conformation.

This is stabilised by bonds between the R-groups of the amino acids that have been brought together by the folding.

In globular proteins that are soluble in water, there are hydrophilic R-groups on the outside of the molecule and hydrophobic regions on the inside of the protein.

25
Q

What is the role of fibrous protein?

A

In long fibrous proteins (e.g. collagen) the amino acid sequence prevents folding up and ensures that the chain of amino acids remains in an elongated form.
eg. collagen

26
Q

Define the role of insulin

A

A hormone produced by the B cells in the pancreas that stimulates cells in the body to absorb glucose which lowers the blood concentration of glucose. It also stimulates the liver to create glycogen from the glucose in the blood. Insulin binds to specific receptors on cell membranes that correspond to its shape.

-Globular protein

27
Q

Define the role of rhodopsin

A

One of the pigments in your eye that absorb light and give you vision. It contains a light sensitive retinal molecule (the grey central part below) not made of amino acids. This is surrounded by an opsin polypeptide (blue part). The retinal molecule changes shape as it absorbs a photon of light which then changes the shape of the opsin leading to a nerve impulse being sent to the brain. It is found in rod cells of the retina - detect black/white/shadows.

-Globular protein

28
Q

What is the role of immunoglobulin (antibody)

A

They have a Y-shape and the top of the structure is specific to a particular antigen. This is where binding occurs which disables the pathogen. They are produced by plasma cells (activated B cells) as part of the immune response. Your body can produce a huge range of immunoglobulins, each with a different type of binding site specific to a different antigen.

  • Globular protein
29
Q

What is the role of rhodopsin?

A

One of the pigments in your eye that absorb light and give you vision. It contains a light sensitive retinal molecule (the grey central part below) not made of amino acids. This is surrounded by an opsin polypeptide (blue part). The retinal molecule changes shape as it absorbs a photon of light which then changes the shape of the opsin leading to a nerve impulse being sent to the brain. It is found in rod cells of the retina - detect black/white/shadows.

30
Q

Define the role of collagen

A

Collagen is made of three polypeptides wrapped around each other like a rope. ¼ of all protein in the human body is collagen. It forms a mesh of fibres in skin, ligaments and walls of blood vessels to resist tearing and give strength. It also forms part of the structure of teeth and bones to prevent cracking and fractures.

  • Fibrous protein
31
Q

Define the role of spider silk

A

Spiders produce different types of silk with different functions. Dragline silk (below) is stronger than steel and tougher than Kevlar. It contains regions where the polypeptide forms parallel arrays. Other regions seem like a disordered tangle but when stretched they gradually extend making the silk extensible and very resistant to breaking.

  • Fibrous protein
32
Q

What is denaturation?

A

A permanent change to the overall 3D structure of a protein. The main factors that can cause denaturation are changes to temperature and pH.

33
Q

What are the factors of denaturation?

A

Heat – causes vibrations within protein molecules that break bonds and cause the conformation to change. This is almost always irreversible. E.g. An egg white contains albumin proteins which are soluble, heating an egg causes albumin to change shape and it becomes insoluble (turning the egg white into a white solid)

Every protein has an ideal pH at which its conformation is normal. If the pH is increased or decreased, the protein will denature if the pH has deviated too far from the optimum. pH change causes the intramolecular bonds to break within the protein molecule.

34
Q

What is a proteome?

A

A proteome is all of the proteins produced by a cell, a tissue or an organism.

35
Q

What is a genome?

A

The genome is all of its gene.

The genome of an organism is fixed

36
Q

What is the role of an enzyme?

A

Enzymes are globular proteins that work as biological catalysts.

Enzymes are specific to the substrate they bind to. This property is called enzyme-substrate specificity. Each enzyme can therefore only catalyse one biochemical reaction.

37
Q

What is the catalyst?

A

speed up the rate of chemical reactions by lowering the activation energy without being altered themselves

38
Q

How is lactose free milk made?

A

Lactose free milk is produced by either adding free lactase to the milk or by using lactase that has been immobilised on a surface or in beads of a porous material.

This process can be performed in the laboratory by making alginate beads containing lactase and putting them into milk. The lactose concentration of the milk drops and the glucose concentration rises.

39
Q

What is cohesion?

A

Cohesion refers to the binding together of two molecules of the same type, for instance two water molecules.

Water molecules are cohesive – they stick to each other due to hydrogen bonding.

40
Q

What is found in insulin molecules?

A

Peptide bond

41
Q

Outline the differences for reasons between the proteomes of cells within a multicellular organism

A

All the genome is the same in all the cells of an organism

The genome instructs the production of proteomes/ proteins

The proteome is all the proteins produced by a cell

The protein varies within the function and the conditions of the cell

Turning on and off according to a required function

42
Q

What is adhesion?

A

Hydrogen bonds can form between water and other polar molecules, causing water to stick to them

This property is useful in leaves where water molecules adhere to cellulose molecules in cell walls.

43
Q

What is high specific heat capacity?

A

Hydrogen bonds restrict the motion of water molecules. Energy is needed to break these bonds. As a result the amount of energy needed to raise the temperature of water is relatively large.

To cool down water must lose relatively large amounts of energy (to reform the large number of bonds).

44
Q

What is high latent heat of vaporisation?

A

When a molecule evaporates it separates from other molecules in a liquid and becomes a vapour molecule.

Evaporation therefore has a cooling effect – heat ends up being removed as the molecules evaporate.

Considerable amounts of heat are needed to evaporate water, because hydrogen bonds have to be broken. This makes it a good evaporative coolant.

45
Q

How is the body cooled with sweat?

A

The heat needed for the evaporation of water in sweat is taken from the tissues of the skin, reducing their temperature. Blood therefore flowing through the skin is cooled. This process is called evaporative cooling and is possible because water has a high latent heat of vaporisation.

46
Q

Define high boiling point

A

The boiling point of a substance is the highest temperature that it can reach in a liquid state.

47
Q

Define monosaccharide + give examples

A

Monosaccharides are single ring structures (sugar units) consisting of carbon, hydrogen and oxygen. They can be linked together to make larger molecules.

Glucose, fructose and ribose are all examples of monosaccharides.

48
Q

Define disaccharides + give examples

A

Disaccharides consist of two monosaccharides linked together.

E.g. glucose + glucose = maltose; glucose + fructose = sucrose

49
Q

Define polysaccharide + give examples

A

Polysaccharides consist of many monosaccharides linked together.

E.g. starch, glycogen and cellulose are all polysaccharides of glucose molecules.

50
Q

What is a glycosidic bond?

A

The resulting bond that forms between the monosaccharides

51
Q

Outline the properties of cellulose

A

Cellulose is made by linking together beta glucose molecules. Condensation reactions link carbon atoms 1 and 4 on beta glucose molecules.

Cellulose molecules are unbranched chains of beta glucose, allowing them to form bundles with hydrogen bonds linking the cellulose molecules (called cellulose microfibrils).

They have high tensile strength and are used as the basis of plant cell walls.

52
Q

Define the properties of starch

A

Starch is made by linking together alpha glucose molecules. Like in cellulose, the links are made between the –OH groups on carbons 1 and 4.

The –OH groups in alpha glucose all point downwards so all the glucose molecules in starch can be orientated in the same way.

The consequence of this is that the starch molecule is curved rather than straight.

53
Q

What is the difference between amylose and and amylopectin?

A

In amylose the chain of alpha glucose molecules is unbranched and forms a helix.

In amylopectin the chain is branched so has a more globular shape.

54
Q

What are the properties of glycogen?

A

Glycogen is very similar to the branched form of starch, but there is more branching, making the molecule more compact.

It is stored in the liver and some muscles in humans.

Glycogen has the same function as starch in plants – it acts as a store of energy in cells where large stores of dissolved glucose would cause osmotic problems.

55
Q

What are lipids?

A

Lipids are a diverse group of carbon compounds that are insoluble in water.

56
Q

What is the role of triglcyeride?

A

Triglycerides are one of the main types of lipids. Examples of triglycerides are the fat in adipose tissue in humans, oil in sunflower seeds.

Triglycerides are made by combining three fatty acids with one glycerol.

Each of the fatty acids is linked to glycerol by a condensation reaction (therefore 3 water molecules are produced) and the name of these bonds are ester bonds.

57
Q

Why is glycogen needed as energy stores?

A

Glycogen is the carbohydrate used for short term energy storage in the liver.

This is because glycogen can be broken down to glucose rapidly and then transported easily by the blood to where it is needed. Fats in adipose tissue cannot be mobilised as rapidly.

Glucose can be used either in anaerobic or aerobic cell respiration whereas fats and fatty acids can only be used in aerobic respiration.

58
Q

Why do lipids play an important role as an energy store?

A

The amount of energy released in cell respiration per gram of lipids is double the amount released from a gram of carbohydrates. You therefore can store half the amount of lipids as you would carbohydrates – this reduces body mass.

Lipids also have secondary roles that can’t be performed by carbohydrates i.e. they can act as heat insulators and they also act as shock absorbers (reason for being around some organs).

59
Q

Outline the process of glycolysis

A

Glycolysis occurs in the cytoplasm of cells and does not require oxygen (i.e anaerobic).

Enzymes modify the glucose so that ultimately the 6-carbon glucose is split into two 3-carbon molecules called pyruvate.

TWO ATP molecules are needed to start the process of glycolysis and a total of FOUR ATP molecules are formed.

There is therefore a NET GAIN of TWO ATP molecules per glucose molecule that goes through glycolysis

Biology (7 decks)

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