Biological Molecules Flashcards
1
Q
What is the difference between organic and inorganic compounds?
A
Organic compounds are the complex, carbon-containing compounds (carbohydrates, fats, proteins, nucleus acids)
Inorganic compounds are simpler and smaller (water, ions, bases)
2
Q
What is a polar molecule?
A
A molecule that carries charge
3
Q
Why is water referred to as being a dipole?
A
Water has 2 areas of opposite charge within its structure
(two positive hydrogen atoms and one negative oxygen atom)
4
Q
What makes water molecules cohesive?
A
Hydrogen bonds form between the positive hydrogens and the negative oxygens of neighbouring water molecules
5
Q
What compound do calcium ions (Ca2+) form in cell walls?
A
Calcium pectate
6
Q
What are iron ions (Fe2+) needed for making?
A
Haemoglobin in the blood, enzymes and cytochromes (electron transfer agents)
7
Q
What is phosphate (PO4 2-) needed for?
A
Making ATP, phospholipids, proteins and nucleus acids
8
Q
What is nitrate (NO3 2-) needed for?
A
Nitrogen from nitrate is needed for making amino acids which are then used to form proteins, such as enzymes, nucleic acids and chlorophyll
9
Q
What compound is Magnesium (Mg2+) used to make?
A
Chlorophyll
10
Q
What is a buffer?
A
A compound that acts in such a way to resist changes in pH (due to adding or removing acid or alkali)
11
Q
Name two buffers
A
Sodium/Potassium hydrogen carbonate
Albumen
12
Q
What elements do carbohydrates contain?
A
Carbon, Hydrogen and Oxygen
13
Q
Name the 3 groups on carbohydrates
A
Monosaccharides, Disaccharides and Polysaccharides
14
Q
What are monosaccharides?
A
The basic carbohydrate monomers. They are classified depending on the number of carbon atoms present in their structure.
Biologically important monosaccharides are triose, pentose and hexose sugars
15
Q
What are isomers? Give an example
A
Isomers are molecules with the same molecular formulae but different structural formulae
Eg: glucose and fructose
16
Q
What is the difference between alpha and beta glucose?
A
The hydroxyl group (-OH) in B-glucose is positioned downwards on the Carbon-1 atom whereas in a-glucose the hydroxyl group (-OH) is positioned upwards on carbon-1
17
Q
What are disaccharides?
A
Double carbohydrates formed from two monosaccharide monomers combined by a condensation reaction. Glycosidic bonds form between the monosaccharides
18
Q
What is a condensation reaction?
A
A condensation reaction involves the removal of water and is the reaction involved when smaller molecules COMBINE to make larger ones
19
Q
What is a hydrolysis reaction?
A
A hydrolysis reaction involves the addition of water and is the reaction involved when larger compounds are BROKEN DOWN into smaller ones
20
Q
What bond is formed between monosaccharide subunits when forming a disaccharide or polysaccharide?
A
A glycosidic bond
Eg: the bond formed when two a-glucose molecules combining is called a 1,4 glycosidic bond.
21
Q
What do the numbers correlate to in a glycosidic bond?
A
The carbon atoms that the bond is formed between
22
Q
What disaccharide is formed when a-glucose and a-glucose combine?
A
Maltose
23
Q
What disaccharide is formed when a-glucose and fructose combine?
A
Sucrose
24
Q
What disaccharide is formed when a-glucose and galactose combine?
A
Lactose
25
What are polysaccharides?
Complex carbohydrate which often form very long chains. They are formed through condensation reactions joining a large number of monomers together. Glycosidic bonds link the monosaccharides to form the long chains
26
What is the polysaccharide starch formed from?
Starch is made from chains of alpha glucose. There are two types of chains, amylose and amylopectin.
27
Describe amylose
Alpha-glucose molecules are linked by 1,4 glycosidic bonds. These chains are coiled to form a spiral. The spirals are held in place by hydrogen bonds. Amylose is an unbranched chain
28
Describe amylopectin
Alpha-glucose is linked by 1,4 glycosidic bonds and also 1,6 glycosidic bonds. These form spirals and side branches. The branches may occur as one branch every ten glucose molecule.
29
What makes starch such a good storage molecule in plants?
• The molecules of both amylose and amylopectin are very **compact**. Therefore a large number of glucose is stored in a small space
• Being **insoluble**, it will not affect the water potential of the cell
• The branched nature of amylopectin creates many **terminal ends** that are **easily hydrolysed**
• The large molecule will not easily pass through the cell membrane
30
What is the carbohydrate glycogen made from?
Long branched chains of alpha glucose with a mixture of 1,4 and 1,6 glycosidic bonds.
Glycogen is **more** branched than starch
31
What makes glycogen a good storage molecule in animals and fungi?
• It is **compact** as the shorter, more branched molecules allows it to be packed into granules
• It is **insoluble** so it will not affect the water potential of the cell
• There are many **terminal ends** for faster **hydrolysis**
32
Where is glycogen found?
Glycogen is found as granules in liver and muscle cells.
33
Where is starch found?
Starch is found as grains in the chloroplasts of plant cells.
34
What is cellulose made from?
Cellulose is made from long, straight chains of **beta-glucose** which are joined by 1,4 glycosidic bonds.
Adjacent chains are held in place by **cross-linkages** of hydrogen bonds
35
Cellulose is structurally important in plant cell walls. Why?
It has **high tensile strength** due to the cross-links formed by hydrogen bonds. It is also strong due to the beta-glucose molecules forming long, straight chains making it a fibrous molecule
36
What elements are lipids made of?
Carbon, Hydrogen and Oxygen
Less oxygen and more hydrogen than carbohydrates
37
What are the main types of lipids?
Triglycerides and phospholipids
Lipids also include waxes and steroids
38
How are triglycerides formed?
They are formed from one glycerol molecule and three fatty acids. These combine by condensation reactions
39
What type of bond is found in triglycerides and where is it found?
**Ester Bonds** which are formed between the hydroxyl (-OH) and carboxyl (-COOH) groups of the 3 fatty acid chains
40
What are the main jobs of triglycerides?
• They act as **energy stores** and release more energy per unit mass than carbohydrates would
• **Insulation** as they are non-conductive.
• The sub-cutaneous fat layer beneath the skin acts to **protect** the major organs
41
How is energy released from triglycerides?
**Hydrolysis** occurs during digestion, breaking the ester bonds and releasing energy
42
What is a saturated fatty acid?
Saturated fatty acids contain the maximum number of hydrogen atoms and therefore have **no C=C double bonds**
43
What is an unsaturated fatty acid?
Unsaturated fatty acids do not have the maximum number of hydrogen atoms and **do contain C=C double bonds**
44
What are polyunsaturated fats?
Polyunsaturated days have more than one C=C double bond
45
What is the difference between fats and oils?
Fats are solid at room temperature and are often made from saturated fatty acids.
Oils are liquid at room temperature and are often made from unsaturated fatty acids
46
Describe the structure of a phospholipid
Phospholipids are made from one glycerol molecule attached to 2 fatty acids and a phosphate molecule.
47
Explain the properties of a phospholipid
The phosphate-glycerol head of the phospholipid is **hydrophilic**, meaning it is attracted to water as it is polar.
The fatty acid tails of the phospholipid are **hydrophobic** and repels water as it is non-polar
48
What is the importance of phospholipids in the body?
They form the **phospholipid bilayer** which is what cell membranes are made from
They are found in the lungs as **surfactant** which prevents the lungs collapsing due to the surface tension of water molecules coating the alveoli
49
What different ways can phospholipids arrange themselves?
On the surface of water they form a **monolayer**
When forming cell membranes they form a **bilayer**
When submerged in water they form **micelles**
50
What elements are proteins made from?
Carbon, Hydrogen, Oxygen, Nitrogen and often sulphur and phosphorus
51
What are the various roles of proteins?
Biochemically important as enzymes, hormones, antibodies and buffers.
Structurally important as membranes, hair, muscle, fibres, nails, bones, connective tissue.
Under the conditions of starvation the body uses proteins for energy
52
What is the monomer of proteins? How many unique types are there
Amino acids, there are 20 different types of amino acid
53
What are proteins composed of? What is their structure
Polymers composed of amino acids.
Amino acid (-NH2) at 1 end + carboxyl group (-COOH) at other end. Different R-group (where sulphur might be)
54
What are long chains of amino acids called?
Polypeptides
55
How are amino acid sub-units combined to form a protein
Amino acids are combined through condensation reactions (the removal of water). **Peptide bonds** form between the OH in the carboxyl (-COOH) group and the H in the amino group (-NH2). This forms long chains of polypeptides which then form a protein.
56
What is the importance of the R group in an amino acid?
The R groups determine the role and properties of the polypeptide.
This includes its solubility, it’s ability to work as a buffer, it’s enzymatic abilities, the bonds it can form etc
57
What is a dipeptide and how is it formed?
A dipeptide is formed when two amino acids combine through condensation reactions and the formation of a peptide bond
58
What is the difference between a polypeptide and a protein?
A polypeptide is formed when up to 100 amino acids combine through condensation reactions to form a long chain.
A protein consists of one or more of these chains which are then folded, branched or cross-linked
59
What does the primary structure of a protein mean?
The primary structure is the sequence of the amino acids which are joined together by peptide bonds
60
What does the secondary structure of a protein mean?
This is the way in which the chain of amino acids folds or turns on itself to make patterns. These folds come from hydrogen bonds forming between the negative (-OH) in the carboxyl group and the positive (-H) in the amino group of the amino acids. These patterns are namely alpha helixes and beta pleated sheets
61
Describe the alpha helices
The alpha helix consist of twists and turns in the chain of amino acids which are held in place by hydrogen bonds at regular intervals, forming a spiral
62
Describe beta pleated sheets
Beta pleated sheets are more rigid and less flexible configurations.
They are formed by the **anti-parallel** chains of adjacent amino acids held in place by hydrogen bonds
63
What does the tertiary structure of a protein mean?
This involves the further folding a secondary protein. This additional folding provides the protein with its unique 3-D shape and a range of bonds between the R-groups of amino acids in the chain.
64
What bonds are present in a tertiary structure of a protein?
Relatively weak **Hydrogen bonds**
**Ionic bonds** are formed between the amino and carboxyl groups. These can be damaged by changes in pH
**Disulphide bonds** are covalent bonds formed between R-groups of sulfur-containing amino acids
**Hydrophobic Interactions** involving the amino acids with hydrophobic R-groups which tend to influence the tertiary structure
65
What does the quaternary structure of a protein mean?
This organisation only exists if there id **more than one polypeptide chain** present. They may contain non-protein **prosthetic groups**
66
What is the importance of non-protein components (prosthetic groups) in a quaternary structure
These are integral in the protein’s function
67
Give examples of conjugated proteins?
A conjugated protein is a protein that contains a prosthetic group.
Glycoproteins, which are important in membrane structure. A carbohydrate is attached to the protein
Haemoglobin, which consists of four polypeptide chains. These are attached to an iron-rich **haem** group
68
What are the two main types of proteins?
Fibrous proteins and globular proteins
69
Describe fibrous proteins
Fibrous proteins consist of polypeptide chains arranged to form long fibres of sheets. The parallel chains are cross-linked to form strong stable molecules. Often have structural function. Fibrous proteins have high tensile strength
70
Describe globular proteins
Globular proteins consist of polypeptide chains folded to give a spherical 3-D shape which is very specific
71
Explain how **collagen** is a fibrous protein
Each collagen molecule consists of three identical polypeptide wound round each other and held together by hydrogen bonds.
72
Where is collagen found?
Collagen is found in tendons that link muscle to bone. Collagen has **high tensile strength** and does not stretch when tension is applied
73
Explain how **Haemoglobin** is a globular AND conjugated protein
Haemoglobin is made from **4 polypeptide chains** (therefore it is quaternary). These chains are tightly folded giving it a **globular** shape. Each polypeptide chain is attached to a **iron-rich haem group** (the prosthetic group). The iron ions in the haem group carry oxygen
74
What is a glycoprotein?
A protein which is attached to a carbohydrate. An example would be mucin which is found in the respiratory tract
75
What is a prion?
Prions are a particular type of protein found in mammals. They are found in the nervous system and it is thought that they are involved in **synaptic transmission**
76
What is the difference between a normal prion protein (PrP or PrPc) and a disease-causing prion (PrPSc)?
The disease-causing prion protein (PrPSc) has a higher proportion of beta pleated sheets (compared to alpha helices)
77
What happens once the disease-causing form of a prion is present in an organism?
It leads to a chain reaction causing the number of other disease-causing prions to increase. Ie the prion protein present progressively becomes more misfolded
78
What are the two key features of disease-causing prion proteins?
That they can **replicate** and that they are **infectious**
79
Is there an incubation period?
The incubation period of a prion disease is between **5 and 20 years**
80
What makes the normal PrP prion protein change into the PrPSc prion?
- The normal prion protein can **spontaneously** adopt the PrPSc form
- May be genetic and a **mutation** in the DNA that codes for prion proteins can be passed from parent to offspring
- Through **eating contaminated food**
81
What examples of prion diseases are there?
• **Scrapie** which affects sheep
• **bovine spongiform encephalopathy (BSE)** which affects cattle
• **variant Creutzfeldt-Jakob disease (vCJD)** which affects humans. This is usually acquired through eating contaminated beef products that contain the PrPSc prion
82
What are the typical effects of prion diseases?
They are **neurodegenerative spongiform** diseases, these **impair brain function**
83
What brain functionality can be effected by a prion disease?
Change in memory and personality,
Impaired co-ordination and behavioural changes
Dementia is common
84
What elements are nucleic acids made from?
Carbon, hydrogen, oxygen, nitrogen and phosphorus
85
What are the building blocks of nucleic acids?
Nucleic acids and formed from **nucleotides** which consist of a phosphate group, a **pentose** sugar and a nitrogenous base. These are combined through condensation reactions
86
What bonds are present between the phosphate group and the pentose sugar? What will this form?
Phosphodiester bonds link each nucleotide together. This will form a polynucleotide
87
Name two important nucleic acids
DNA (deoxyribonucleic acid) and RNA (ribonucleic acid)
88
Name an important nucleotide used in an organism and give its function
ATP (Adenosine Triphosphate) supplies and carries energy in cells
89
What are the nitrogenous bases?
Adenine, Thymine, Guanine, Cytosine
(Uracil is present in RNA)
90
Describe the structure of DNA
DNA is a double helix, composed of two anti-parallel polynucleotide chains joined by hydrogen bonds between their nitrogenous based. The pentose sugar present in DNA is deoxyribose. Phosphate groups are also present, these are linked to the deoxyribose by phosphodiester bonds
91
What is the base pairing in DNA molecules?
Adenine pairs with Thymine (2 hydrogen bonds linking)
Guanine pairs with Cytosine (3 hydrogen bonds linking)
92
How many base pairs are there in a complete turn of a helix?
10 base pairs
93
What is the role of DNA?
DNA is the genetic code of living organisms and is found in all cells (with few exceptions). It regulates the development of living organisms though the control of **protein synthesis**
94
What is a gene?
A sequence of DNA that codes for a polypeptide
95
Describe the structure of RNA
RNA is a single stranded and shorter chain. The nucleotides are linked by phosphodiester bonds but the nitrogenous based are Adenine, **Uracil**, Guanine and Cytosine
96
What are the 3 types of RNA
Messenger RNA, Transfer RNA and Ribosomal RNA
97
What is the role of Messenger RNA?
Carries the code from the DNA in the nucleus to a ribosome in the cytoplasm where protein synthesis takes place
98
What is the role of Transfer RNA?
Carries the amino acids to the mRNA/ribosome where protein synthesis is taking place.
99
What shape is Transfer RNA?
It is a single chain folded into a ‘clover leaf’ shape
100
What is the correlation of Transfer RNA and amino acids?
There are as many different types of tRNA as there are amino acids. Their structure is similar
101
What is the role of Ribosomal RNA?
Made in the nucleolus and forms over half the mass of each ribosome
102
What does DNA Helicase do?
This enzyme causes the DNA double helix to **unzip** by breaking the hydrogen bonds between the bases.
103
What happens after the DNA double helix is ‘unzipped’?
Each strand of DNA becomes an **original template strand**. Free nucleotides join to the template strands in the correct sequence, following base pairing rules. The result is 2 new DNA molecules. One strand in each new molecule is the **original template** and one is a **new** DNA strand
104
What does DNA polymerase do?
DNA polymerase helps the new **complementary** DNA strands to form by **catalysing** the polymerisation of nucleotides to each other via phosphodiester bonds.
105
Why is the process of DNA replicated described as **semi-conservative replication**
Each of the new DNA molecules contains one **original template** strand and one **new** DNA stand
106
Who proved the semi-conservative model?
Meselson and Stahl
107
Who worked out the structure of DNA?
Watson and Crick
108
What did the **conservative** model theory propose?
In this model the original DNA does not unzip but is simply copied to form a new double strand
109
What we’re the radioactive isotopes used in the Meselson-Stahl experiment?
N15 and N14
110
Why were these isotopes used?
Nitrogen is part of DNA’s structure as it is forms the nitrogenous based
111
GENERATION 1 of this experiment shown what after density-gradient centrifugation?
The bacterial DNA was now hybrid DNA. Half was made of N15 and half N14
112
GENERATION 2 of this experiment shown what after density-gradient centrifugation?
The ratio was that 50% of DNA is hybrid N14/15 and 50% was only N14
113
What did GENERATION 3 show?
A ratio of 3:1 for light (N14) to hybrid
114
What properties does water have?
Polar
hydrogen bonds = cohesion
high specific heat
density anomality (ice)
115
What is the importance of water in organisms?
Transport medium (cohesion/adhesion),
chemical reactions (photosynthesis), temp control (buffer),
support (Turgidity),
movement (nastic)
reproduction (fertilisation).
116
State the difference between a Fructose and Glucose molecule
Fructose has a 5 membered ring and glucose has a 6 membered ring, however, both are hexose sugars.
117
State the general formula of a monosaccharide
(C H2 O)n
118
State the general formula of a disaccharide
C12 H22 O11
119
What are the properties of globular proteins?
Compact, helical + roll, into ball, hydrophobic interactions, water-soluble, less stable than fibrous (metabolic role)
120
State the roles of globular proteins
Metabolic role. Enzymes, antibodies + hormones. e.g. haemoglobin.
121
Why would surgical sterilisation of instruments previously used in a surgery of a patient infected with CJD not kill the prions present?
Prions are stable and resistant to temperature and radiation.
122
What is a reducing sugar?
Sugar that can reduce due to free aldehyde group. More easily broken down.
123
What is the role of DNA Ligase?
Joins polynucleotides together.
