Atomic structure Flashcards
(86 cards)
1
Q
All atoms have a central nucleus.
Positively or negatively charged?
A
Positively charged
2
Q
The nucleus is made up of two types of particle:
A
protons and neutrons.
3
Q
Charge of:
Protons
Neutrons
Electrons
A
Protons - positive
Neutrons - uncharged
Electrons - negative
4
Q
Atomic number: definition?
A
The number of protons in the nucleus is called the atomic number, and ranges from 1 to over 100.
5
Q
Mass number: definition?
A
The combined total of protons and neutrons is known as the mass number.
6
Q
What’s the overall charge on the atom?
A
All atoms have an equal number of protons and electrons, so regardless of the atomic number, the overall charge on the atom will always be zero.
7
Q
Carbon Atomic structure
A
Image 1
8
Q
Phosphorus has 15 protons and ____ neutrons, giving it an atomic number of ____ and a mass number of 31.
A
Phosphorus for example has 15 protons and 16 neutrons, giving it an atomic number of 15 and a mass number of 31.
9
Q
What is an ISOTOPE?
A
Isotopes are the atoms in an element that have the same atomic number but a different atomic mass; that is, the same number of protons and thus identical chemical properties, but different numbers of neutrons and consequently different physical properties. Isotopes can be stable or unstable or radioisotopes.
10
Q
Carbon-14 (14C) is a naturally occurring but rare isotope of carbon that has ____ neutrons instead of six, hence the atomic mass of ____.
A
Carbon-14 (14C) is a naturally occurring but rare isotope of carbon that has eight neutrons instead of six, hence the atomic mass of 14.
11
Q
ATOMIC MASS (or ATOMIC WEIGHT): definition?
A
The atomic mass (or atomic weight) of an element is the average of the mass numbers of an element’s different isotopes, taking into account the proportions in which they occur.
12
Q
RADIOISOTOPE: definition?
A
Isotopes are the atoms in an element that have the same atomic number but a different atomic mass; that is, the same number of protons and thus identical chemical properties, but different numbers of neutrons and consequently different physical properties. Isotopes can be stable or unstable or radioisotopes. In the latter, their nuclei have a special property: they emit energy in the form of ionizing radiation while searching for a more stable configuration.
13
Q
Explain how the electrons are arranged
in a series of electron shells.
A
The electrons that orbit around the nucleus do not do so randomly, but are arranged
in a series of electron shells, radiating out from the nucleus. These layers correspond to different energy levels, with the highest energy levels being located furthest away from the nucleus. Each shell can accommodate a maximum number of electrons, and electrons always fill up the shells starting at the innermost one, that is, the one with the lowest energy level.
In our example, carbon has filled the first shell with two electrons, and occupied four of the eight available spaces on the second.
14
Q
The chemical properties of atoms are determined by …
A
The chemical properties of atoms are determined by the number of electrons in the outermost occupied shell.
15
Q
Is Neon, one of the ‘noble’ gases, reactive or unreative? Why?
A
Neon, one of the ‘noble’ gases, has an atomic number of 10, completely filling the first two shells, and is chemically unreactive or inert. Atoms that do not achieve a similar configuration are unstable, or reactive.
16
Q
Reactions take place between atoms that attempt to achieve stability by attaining a full outer shell. These reactions may involve atoms of the same element or ones of different elements; the result in either case is …
A
… a molecule or an ion.
17
Q
The number of ________ determines the reactivity of an atom.
A
The number of unfilled spaces in the outermost electron shell determines the reactivity of an atom. If most of the spaces in the outermost shell are full, or if most are empty, atoms tend to strive for stability by gaining or losing electrons.
18
Q
MOLE: definition?
A
A mole is the molecular mass of a compound expressed in grams.
19
Q
MOLECULAR MASS: definition?
A
The molecular mass is simply the sum of the atomic mass of all the atoms in a
compound.
20
Q
1 MOLE of NaCl is equal to ____?
Molecular formula = NaCl
Atomic mass of sodium = 22.99
Atomic mass of chlorine = 35.45
A
1 MOLE NaCl = Molecular mass NaCl = 58.44g
21
Q
MOLAR SOLUTION: definition?
A
Molar solution = one mole per litre
This is a solution containing one mole dissolved in a final volume of 1 litre of an appropriate solvent (usually water).
22
Q
A one molar (1 M) solution of sodium chloride therefore contains 58.44 g dissolved in water and made up to 1 litre. A 2 M solution would contain _____ g in a litre.
A
A 2 M solution would contain 116.88 g in a litre.
23
Q
AVOGADRO’S NUMBER?
A
1 mole of one compound contains the same number of molecules as a mole of any other
compound.
This number is called Avogadro’s Number, and is 6.023 × 1023 molecules per mole.
24
Q
Describe the formation of molecules of hydrogen and methane by covalent bonding.
A
Image 2
25
Describe an ion formation (Na+, Cl-)
Na has 11 protons
Cl has 17 protons
Image 3
Ion formation. Sodium achieves stability by losing the lone electron from its outermost shell. The resulting sodium ion Na+ has 11 protons and 10 electrons, hence it carries a single positive charge. Chlorine becomes ionised to chloride (Cl−) when it gains an
electron to complete its outer shell.
The sodium atom has 11 electrons, meaning that the inner two electron shells
are filled and a lone electron occupies the third shell. If it were to lose this last electron, it would have more protons than electrons, and therefore have a net positive charge of one; if this happened, it would become a sodium ion, Na+.
26
Positively charged ions are called _____ and negatively charged ones ______.
Positively charged ions are called cations and negatively charged ones anions.
27
IONIC BOND: definition?
Chemical bond, there is an attractive force between positively and negatively charged
ions.
28
Explain the formation of water.
The goal of stability through a full complement of outer shell electrons may also be achieved by means of sharing one or more pairs of electrons. Consider the formation of water; an oxygen atom, which has two spaces in its outer shell, can achieve a full complement by sharing electrons from two separate hydrogen atoms. This type of bond is a covalent bond.
29
Explain the double bond In the formation of carbon dioxide (CO2).
Sometimes, a pair of atoms share not one but two pairs of electrons (see Figure 2.5).
This involves the formation of a double bond.
In the formation of carbon dioxide, the carbon atom shares two pairs of electrons with each oxygen atom.
Image 4
30
Explain the formation of polar
molecules.
IMAGE 5
In the examples of covalent bonding we’ve looked at so far, the sharing of the electrons
has been equal, but this is not always the case because sometimes the electrons may be drawn closer to one atom than another. This has the effect of making one atom slightly negative and another slightly positive. Molecules like this are called polar
molecules and the bonds are polar bonds. Sometimes a large molecule may have both
polar and non-polar areas.
31
The attraction between polar atoms is called ___________, and can take place
between covalently bonded hydrogen and any electronegative atom, most commonly
oxygen or nitrogen. Hydrogen bonds are much weaker than _______ and __________ bonds.
The attraction between polar atoms is called hydrogen bonding, and can take place between covalently bonded hydrogen and any electronegative atom, most commonly oxygen or nitrogen. Hydrogen bonds are much weaker than either ionic or covalent bonds.
32
Explain why water has such a relatively high boiling point, and why most of the water on the planet is in liquid form.
IMAGE 6
Each water molecule can form hydrogen bonds with others of its kind in four places. In order to break all these bonds, a large input of energy is required.
33
Describe Van der Waals forces.
Another weak form of interaction is brought about by Van der Waals forces, which occur briefly when two non-polar molecules (or parts of molecules) come into very close
contact with one another. Although transient, and generally even weaker than hydrogen bonds, they occur in great numbers in certain macromolecules and play an important role in holding proteins together.
34
Why is water an a highly efficient solvent?
Water is the medium in which most biochemical reactions take place; it is a highly efficient solvent, indeed more substances will dissolve in water than in any other solvent.
Substances held together by ionic bonds tend to dissociate into anions and cations
in water, because as individual solute molecules become surrounded by molecules of water, hydration shells are formed, in which the negatively charged parts of the solute attract the positive region of the water molecule, and the positive parts the negative region. The attractive forces that allow the solute to dissolve are called hydrophilic forces, and substances which are water-soluble are hydrophilic (water-loving).
Other polar substances such as sugars and proteins are also soluble in water by forming hydrophilic interactions.
35
What is hydrophobic bonding?
Molecules such as oils and fats are non-polar, and because of their non-reactivity
with water are termed hydrophobic (‘water-fearing’). If such a molecule is mixed with
water, it will be excluded, as water molecules ‘stick together’. This very exclusion by water can act as a cohesive force among hydrophobic molecules (or hydrophobic areas of large molecules). This is often called hydrophobic bonding, but is not really bonding as such, rather a shared avoidance of water. All living cells have a hydrophilic interior surrounded by a hydrophobic membrane.
36
What is an amphipathic substance?
IMAGE 7
An amphipathic substance is one which is part polar and part non-polar. When
such a substance is mixed with water, micelles are formed. The non-polar parts are excluded by the water and group together, leaving the polar groups pointing outwards into the water, where they are attracted by hydrophilic forces. Detergents exert their action by trapping insoluble grease inside the centre of a micelle, while interaction with water allows them to be rinsed away.
37
Water takes part in many essential metabolic reactions, and its polar nature allows for the breakdown to hydrogen and hydroxyl ions (H+ and OH−), and re-synthesis as water.
Complete the reactions:
A—B + H2O →
A—H + B—OH →
Water acts as a reactant in hydrolysis reactions such as:
A—B + H2O → A—H + B—OH
and as a product in certain synthetic reactions, such as:
A—H + B—OH → A—B + H2O
38
The H+ and OH− ions play an important part in cellular reactions. A solution becomes acid or alkaline if there is an imbalance in the amount of these ions present.
If there is an excess of ______, the solution
becomes acid, whilst if ______ predominates, it becomes alkaline.
If there is an excess of H+, the solution
becomes acid, whilst if OH− predominates, it becomes alkaline.
39
The pH of a solution is an expression of the molar concentration of hydrogen ions:
(write the equation)
pH = −log10[H+]
40
In pure water, hydrogen ions are present at a concentration of ______, thus the pH is
______. This is called neutrality, where the solution is neither acid or alkaline.
In pure water, hydrogen ions are present at a concentration of 10−7M, thus the pH is
7.0. This is called neutrality, where the solution is neither acid or alkaline.
41
At higher concentrations of H+, such as 10−3 M (1 millimolar), the pH value is lower, in this case _____, so acid solutions have a value below 7.
At higher concentrations of H+, such as 10−3 m (1 millimolar), the pH value is lower, in this case 3.0, so acid solutions have a value below 7.
42
Alkaline solutions have a pH above 7. An increase of 10exp4 (10 000)-fold in the [H+] leads to a change of only four points on the pH scale. This is because it is a logarithmic scale; thus a solution of pH 10 is _____ times more alkaline than one of pH 9, and _____ times more alkaline than one of pH 8.
Alkaline solutions have a pH above 7. An increase of 10exp4 (10 000)-fold in the [H+] leads to a change of only four points on the pH scale. This is because it is a logarithmic scale; thus a solution of pH 10 is 10 times more alkaline than one of pH 9, and 100 times more than one of pH 8.
43
The possession of a functional group(s) frequently makes an organic molecule more ________ (polar/non polar) and therefore more soluble in water.
The possession of a functional group(s) frequently makes an organic molecule more polar and therefore more soluble in water.
44
Write the formula of these functional groups:
Hydroxyl
Carbonyl
Carboxyl
Amino
Sulphhydryl
Phosphate
IMAGE 8
45
Many of the most important molecules in biological systems are POLYMERS, that is, large molecules made up of smaller subunits joined together by _______ bonds, and in some cases in a specific order.
Many of the most important molecules in biological systems are polymers, that is, large molecules made up of smaller subunits joined together by covalent bonds, and in some cases in a specific order.
46
Carbohydrates are made up of just three different elements:
carbon, hydrogen and oxygen.
47
The simplest carbohydrates are ___________ or simple sugars. These have the general formula ________.
The simplest carbohydrates are monosaccharides, or simple sugars. These have the general formula (CH2O)n.
48
The suffix -_______ always denotes
a carbohydrate.
The suffix -ose always denotes
a carbohydrate.
49
Monosaccharides may be aldoses or ketoses according to whether they contain an __________ group or a ________ group.
IMAGE 9
Monosaccharides may be aldoses or ketoses according to whether they contain an aldehyde group or a ketone group.
50
Monosaccharides can further be classified on the basis of the number of carbon atoms they contain. The simplest are _______ (three carbons) and the most important biologically are __________ (six carbons).
Monosaccharides can further be classified on the basis of the number of carbon atoms
they contain. The simplest are trioses (three carbons) and the most important biologically are hexoses (six carbons).
51
Monosaccharides are generally crystalline solids which are soluble in water and have
a sweet taste. They all reducing sugars, so called because they are able to reduce alkaline solutions of cupric ions (Cu2+) to ___________.
Monosaccharides are generally crystalline solids which are soluble in water and have
a sweet taste. They all reducing sugars, so called because they are able to reduce alkaline solutions of cupric ions (Cu2+) to cuprous ions (Cu+).
52
What is a DISACHARIDE?
IMAGE 10
A disaccharide is formed when two monosaccharides (which may be of the same type or different), join together with a concomitant loss of a water molecule
53
Further monosaccharides can be added, giving chains of three, four, five or more units. These are termed ____________(a few), and chains with many units are ___________.
Further monosaccharides can be added, giving chains of three, four, five or more units. These are termed oligosaccharides (oligo, a few), and chains with many
units are polysaccharides.
54
The chemical bond joining the monosaccharide units together
is called a ____________ linkage.
The chemical bond joining the monosaccharide units together
is called a glycosidic linkage.
55
The bond between the two glucose molecules that make up _________ is called an α-glycosidic linkage; in lactose, formed from one __________ and one ___________, we have a β-glycosidic linkage. The two bonds are formed in the same way, with the elimination of ________, but they have a different orientation in space. Thus disaccharides bound together by α- and β-glycosidic linkages have a different overall shape and as a result the molecules behave differently in cellular metabolism.
The bond between the two glucose molecules that make up maltose is called an α-glycosidic linkage; in lactose, formed from one glucose and one galactose, we have a β-glycosidic linkage. The two bonds are formed in the same way, with the elimination of water, but they have a different orientation in space. Thus disaccharides bound together by α- and β-glycosidic linkages have a different overall shape and as a result the molecules behave differently in cellular metabolism.
56
Isomers: definition?
Isomers: same formula, different structure
57
There are many structural possibilities for the general formula C6H12O6; describe them.
IMAGE 11
58
How Polysaccharides differ from Monosaccharides?
They differ from monosaccharides in being generally insoluble in water, not tasting sweet and not being able to reduce cupric ions.
59
Sugars are more accurately shown as ring structures. Why?
IMAGE 12
60
The five elements found in most naturally occurring proteins are:
carbon, hydrogen, oxygen, nitrogen and sulphur.
In addition, other elements may be essential components of certain specialised proteins such as haemoglobin (iron) and casein (phosphorus).
61
Describe the Amino acid structure.
IMAGE 13
All amino acids, including the
20 commonly found occurring in proteins, are based on a common structure.
It comprises a central carbon atom (known as the α-carbon) covalently bonded to an amino (NH2) group, a carboxyl (COOH) group and a hydrogen atom.
It is the group attached to the final valency bond of the α-carbon which varies from one
amino acid to another; this is known as the ‘R’-group.
62
All proteins are made up of a collection of ‘building bricks’ called _________________ joined together.
All proteins are made up of a collection of ‘building bricks’ called amino acids joined together.
63
The 20 amino acids found in proteins can be conveniently divided into five groups, on
the basis of the chemical nature of their ‘R’-group.
IMAGE 14
It would be advisable to familiarise yourself with the groupings and examples from each of them.
The groups differentiate on the basis of
a polar/non-polar nature and on the presence or absence of an ionisable ‘R’-group.
Note that one amino acid, proline, falls outside the main groups. This differs from
the others in that it has one of its N—H linkages replaced by an N—C, which forms
part of a cyclic structure. This puts certain conformational constraints upon proteins containing proline residues.
The simplest amino acid is glycine, whose R-group is simply a hydrogen atom. This means that the glycine molecule is symmetrical, with a hydrogen atom on opposite valency bonds. All the other amino acids however, are asymmetrical. The α-carbon acts as what is known as a chiral centre, giving the molecule right or left ‘handedness’. Thus two stereoisomers known as the d- and l-forms are
possible for each of the amino acids except glycine. All the amino acids found in naturally occurring proteins have the l-form; the d-form also occurs in nature but only in certain specific, non-protein contexts.
64
Amino acids are joined together
by means of a _________ bond. This involves the ______ group of one amino acid and the
________ group of another. The formation of a peptide bind is a form of condensation
reaction in which _______ is lost.
Amino acids are joined together
by means of a peptide bond. This involves the -NH2 group of one amino acid and the
-COOH group of another. The formation of a peptide bind is a form of condensation
reaction in which water is lost.
65
Write the abbreviations for
each amino acid.
IMAGE 15
66
Describe the formation of a dipeptide.
IMAGE 16
67
What is the secondary structure of a protein?
IMAGE 17
The secondary structure is due to hydrogen bonding between a carbonyl (-CO) group
and an amido (-NH) group of amino acid residues on the peptide backbone.
The ‘R’ group plays no part in secondary protein structure. Two regular patterns of
folding result from this; the α-helix and the β-pleated sheet.
68
Read this about proteins.
IMAGE 18
69
Describe the Secondary structure in proteins: the α-helix and β-pleated sheet.
IMAGE 19
70
Describe the tertiary structure of a protein.
IMAGE 20
The tertiary structure of a protein is due to interactions between side chains, that is,
R-groups of amino acid residues, resulting in the folding of the molecule to produce a
thermodynamically more favourable structure.
The structure is formed by a variety of
weak, non-covalent forces; these include hydrogen bonding, ionic bonds, hydrophobic interactions, and Van der Waals forces. The strength of these forces diminishes with distance, therefore the formation of a compact structure is encouraged. In addition, the -SH groups on separate cysteine residues can form a covalent -S—S- linkage. This is known as a disulphide bridge and may have the effect of bringing together two cysteine
residues that were far apart in the primary sequence.
71
The protein can be denatured by _________ or __________________________; this causes the tertiary structure to break down and the molecule to unfold, resulting in
a loss of the protein’s biological properties. Cooling, or removal of the chemical agents, will lead to a restoration of both the tertiary structure and biological activity,
showing that both are entirely dependent on the ______________ sequence of amino acids.
The protein can be denatured by heating or treatment with certain chemicals; this causes the tertiary structure to break down and the molecule to unfold, resulting in
a loss of the protein’s biological properties. Cooling, or removal of the chemical agents, will lead to a restoration of both the tertiary structure and biological activity,
showing that both are entirely dependent on the primary sequence of amino acids.
72
Describe the quaternary structure of proteins.
Even the tertiary structure is not always the last level of organisation of a protein, because some are made up of two or more polypeptide chains, each with its own secondary and tertiary structure, combined together to give the quaternary structure. These chains may be identical or different, depending on the protein. Like the tertiary structure, non-covalent forces between R-groups are responsible, the difference being that this time they link amino acid residues on separate chains rather than on the same one.
Such proteins lose their functional properties if dissociated into their constituent units; the quaternary joining is essential for their activity.
Phosphorylase A, an enzyme involved in carbohydrate metabolism, is an example of a protein with a quaternary structure. It has four subunits, which have no catalytic activity unless joined together as a tetramer.
73
Although all proteins are polymers of amino acids existing in various levels of structural complexity as we have seen above, some have additional, non-amino acid components. They may be organic, such as sugars (__________) or lipids (___________) or inorganic, including
metals (______________) or phosphate groups (________________).
These components, which form an integral
part of the protein’s structure, are called _____________ groups.
Although all proteins are polymers of amino acids existing in various levels of structural complexity as we have seen above, some have additional, non-amino acid components. They may be organic, such as sugars (glycoproteins) or lipids (lipoproteins) or inorganic, including
metals (metalloproteins) or phosphate groups (phosphoproteins).
These components, which form an integral
part of the protein’s structure, are called prosthetic groups.
74
What is a Prosthetic group?
A prosthetic group is a
non-polypeptide component
of a protein, such as a metal ion or a carbohydrate.
75
What are nucleic acids?
These are deoxyribonucleic
acid (DNA) and ribonucleic acid (RNA), and both are polymers of smaller molecules called nucleotides. As we shall see, there are important differences both in
the overall structures of RNA and DNA and in the nucleotides they contain.
76
Describe a DNA nucleotide.
IMAGE 21
It has three parts, a five-carbon sugar called deoxyribose, a phosphate group and a base.
This base can be any one of four molecules, these are all based on a cyclic structure containing nitrogen. Two of the bases, cytosine and thymine, have a single
ring and are called pyrimidines. The other two, guanine and adenine, have a double
ring structure; these are the purines. The four bases are often referred to by their initial letter only, thus we have A, C, G and T.
77
The nucleotides join together by means of a ___________________ bond. This links the
phosphate group of one base to an -OH group on the 3-carbon of the deoxyribose
sugar of another. The chain of nucleotides therefore has a free -OH group attached to the 3-carbon (the 3' end) and a free phosphate group attached to the 5-
carbon (the 5' end). This remains the case however long the chain becomes.
The nucleotides join together by means of a phosphodiester bond. This links the
phosphate group of one base to an -OH group on the 3-carbon of the deoxyribose
sugar of another. The chain of nucleotides therefore has a free -OH group attached to the 3-carbon (the 3' end) and a free phosphate group attached to the 5-
carbon (the 5' end). This remains the case however long the chain becomes.
78
How is a chain of DNA made?
IMAGE 22
79
Describe the DNA model of JamesWatson and Francis Crick.
IMAGE 23
The structure of DNA however is not just a single chain of linked nucleotides, but two chains wound around each other to give the double helix.
80
The way in which the bases pair is further
governed by the phenomenon of complementary base pairing.
IMAGE 24
A nucleotide containing thymine will only pair with one containing adenine,
and likewise guanine always pairs with cytosine.
81
What are the two important differences
in the composition of nucleotides of RNA and DNA?
The central sugar molecule is not
deoxyribose, but ribose; these differ only in the possession of an -H atom or an -OH group attached to carbon-2.
Second, although RNA shares three of DNA’s nitrogenous bases (A, C and G), instead of thymine it has uracil. Like
thymine, this pairs specifically with adenine.
The final main difference between RNA and DNA is the fact that RNA generally comprises only a single polynucleotide chain, although this may be subject to secondary and tertiary folding as a result of complementary base pairing within the same strand.
82
Although lipids can be large molecules, they are not regarded as macromolecules.
Why?
Because unlike proteins, polysaccharides and nucleic acids, they are not polymers of a basic subunit. Moreover, lipids do not share any single structural characteristic; they are a diverse group structurally, but have in common the fact that they are insoluble in water, but soluble in a range of organic solvents. This non-polar nature is due to the predominance of covalent bonding, mainly between atoms of carbon and hydrogen.
83
What are fatty acids?
IMAGE 25
Fatty acids are long hydrocarbon chains ending in a carboxyl (-COOH) group. They have the general formula:
CH3—(CH2)n—COOH
where n is usually an even number.
They combine with glycerol according to the basic reaction:
Alcohol + Acid → Ester
84
Describe saturated and unsaturated fatty acids.
IMAGE 26
85
What is the structure of phospholipids?
IMAGE 27
They have a similar structure to triacylglycerols, except that instead of a third fatty acid chain, they have a phosphate group joined to the glycerol, introducing a hydrophilic element to an otherwise hydrophobic molecule. Thus, phospholipids are an example of an amphipathic molecule, with a polar region at one end of the molecule and a non-polar region at the other.
This fact is essential for the formation
of a bilayer when the phospholipid is introduced into an aqueous environment;
the hydrophilic phosphate groups point outwards towards the water, while the hydrophobic hydrocarbon chains ‘hide’ inside.
86
What is the structure of steroids?
IMAGE 28
Steroids have a completely different form, but still share in common the property of hydrophobicity. The four ring planar structure is common to all steroids, with the substitution of different side groups producing great differences in function.
Cholesterol is an important component of many membranes.
