Molecules of life (Chapter 3) Flashcards
1
Q
What are the Molecules of life?
A
Molecules of life are metabolic macromolecules that are critical for the functioning of organisms.
2
Q
Why are metabolic macromolecules important?
A
They are commercially attractive substances and are used in genetic engineering.
3
Q
What are the key metabolic processes?
A
- Existence - to provide energy, building material, etc.
- Propagation - to increase the number of microorganisms
(Live long and prosper)
4
Q
What is the relationship between niche and metabolic capabilities?
A
Metabolic capabilities determine the niche in which the microorganisms will be found.
Niche: is a set of conditions where organisms can survive and reproduce.
The niche in which an organism lives resulted in the evolution of key metabolic capabilities.
5
Q
Physiological features of microorganisms determine what?
A
Physiological features of microorganisms determine:
- the conversions that these microorganisms can bring in nature or in a process.
- if the microorganisms are advantageous or disadvantageous for a process.
6
Q
What is important in bioprocesses
A
In Bioprocesses, it is crucial to evaluate how metabolic capabilities and features can be exploited to maximize process performance and product yield.
7
Q
What are physiological features?
A
Dependence on oxygen,
Source of carbon,
Source of energy
8
Q
What are the three classes of molecules of life that the key elements can be subdivided into?
A
Macromolecules,
Macro elements,
Trace elements.
9
Q
List the elements that form part of the macromolecules
A
Carbon, C = 50% oxygen, O = 20% nitrogen, N = 14% hydrogen, H = 8% phosphorous, P = 3% Sulphur, S = 3%
10
Q
List the elements that form part of the macro elements:
A
Magnesium, Mg
Potassium, K
Calcium, Ca
Iron, Fe
11
Q
List the elements that form part of the trace elements
A
Mo, Mn, Co, Ni, Cu, Zn, I, Al, B
12
Q
What are the four major groups of complex organic molecules in life?
A
Carbohydrates
lipids
proteins
Nucleic acids (DNA and RNA)
13
Q
The four major groups of complex organic molecules of life usually consist of:
A
repetitive units such as polymers
14
Q
Which complex organic molecules are responsible for structural functions?
A
Carbohydrates and proteins
15
Q
Which complex organic molecules act as a source of energy?
A
Carbohydrates and lipids
16
Q
Which complex organic molecules act as information storage?
A
Nucleic acids
17
Q
What are the four most important functional groups that form part of the molecules of life?
A
Hydroxyl (-OH)
Carboxyl (-COOH)
Amino (-NH2)
Phosphate (-PO4)
18
Q
What are the features of the functional groups?
A
- All four groups are polar of charged - important for interactions in an aqueous environment
- All four groups are reactive - readily participate in chemical reactions
19
Q
What are phosphate functional groups important for?
A
Phosphate groups
- are important in the role of transferring energy in the cell, and
- act as energy-rich cofactors that promote certain reactions
20
Q
Isomers
A
Have the same chemical composition but a different form.
Several biological molecules are isomers
21
Q
Sugars as isomers
A
The position of a -OH and the presence of an aldehyde or keto group determines the specific sugar and the role/function of that sugar.
22
Q
Stereoisomers
A
Chiral molecules that are enantiomers of each other
non-superimposable/mirror images
or
when molecules are enantiomers - when they have a chiral centre
23
Q
Specific preferences of life in stereoisomers
A
Amino acids always in the L-form
Sugars always in the D-form
24
Q
Diastereomers/diastereoisomers
A
Stereoisomers that are not enantiomers
different configurations at one or more (but not all) of the related stereocentres
Not mirror images
25
Anomers
Diastereoisomers that differ in configuration at the carbon closest to the aldehyde or ketone group. (Carbon 1)
26
What are the most abundant carbohydrates in nature?
Cellulose and hemicellulose (components of wood)
and
starch (general storage source in plants)
27
Carbohydrates are polymers of
Basic six-carbon sugars (hexoses) - C6H12O6
and
five-carbon sugars (pentoses) - C5H10O5
suffix "-ose" implies sugar
28
The ratio of elements is carbohydrate polymers
C:H:O = 1:2:1
29
Name the two forms of sugar
aldoses: contain an aldehyde at the terminal carbon (eg. glucose)
ketoses: contain a ketone at the near-terminal carbon (eg. fructose)
30
D-aldoses
1. all molecules have an aldehyde group
2. as the chain length increases, carbon is added closest to the carbonyl group of the aldehyde.
3. in D-aldoses all the hydroxyl groups closest to the terminal CH2OH groups point to the right.
4. Diastereoisomers (non-superimposable, non-mirror-image isomers) are formed with increasing carbon chain length (the result of adding hydroxide groups to the chain in opposite directions).
31
D-Glyceralaldehyde
or glyceral is a triose monosaccharide with the chemical formula C3H6O3.
It is the simplest of all common aldoses and plays a key role in central metabolic pathways.
32
D-ketoses
1. all molecules have a ketone group
2. as the chain length increases, carbon is added to the closest carbonyl group of the ketone group.
3. In D-ketoses all the hydroxyl groups closest to the terminal CH2OH groups point to the right.
4. Diastereoisomers are formed with increasing carbon chain length.
33
Forms of Hexoses and pentoses
Hexoses are usually in the pyranose form (five carbons and oxygen form the ring structure).
Pentoses are usually in the furanose form (four carbons and oxygen form the ring structure).
Some hexoses can also be in the furanose form - have two carbons that are not included in the ring structure
34
Three different projections of sugar
Fischer, Haworth and Chair projections.
Haworth and Chair projections are more correct since sugars in the aqueous form are more stable in the ring structure.
35
What form are aldoses and ketoses usually written in in metabolic pathways?
Aldoses and ketoses are usually written in pyrosis (or ring) form in metabolic pathways.
e.g. D-glucose is converted to D-glucopyranose
36
D-glucopyranose forms
The hydroxyl group on the anomeric C1 can exist either in the alpha (downwards) or beta-form (upwards). (aBove)
37
Monosaccharides
General sugars are:
hexoses: glucose, fructose, mannose and galactose
pentoses: xylose and arabinose
These sugars appear in the three major carbohydrates/polysaccharides (cellulose, hemicellulose and starch).
Ribose is a basic building block of nucleic acids
Glucose is the primary product of photosynthesis and has a special function in life as the most abundant source of carbon for most life forms.
38
Disaccharides
Glucose + fructose = Sucrose (table sugar)
| galactose + glucose = Lactose (milk sugar)
39
How are disaccharides formed?
most important disaccharides are formed via condensation (dehydration) reactions between monosaccharides.
40
What is the most common form of sugar storage?
Sucrose (common table sugar) is the most common form of storage of sugar in plants (e.g. sugarcane and sugar beet). It is formed form a glucose and fructose molecule and is a disaccharide.
41
Lactose
Lactose is the basic source of carbon and energy in milk and is formed from galactose and glucose.
42
What is pyranoside?
A pyranoside is a pyranose in which the anomeric OH at C(1) has been converted into an -OR group.
43
What is a pyranosyl?
One hydrogen substituted for some substituient.
44
Maltose
alpha-glucose + beta-glucose = maltose
| Building block of starch
45
Cellobiose
beta-glucose + beta-glucose = cellobiose
| Building block of cellulose
46
Cellobiose
beta-glucose + beta-glucose = cellobiose
| Building block of cellulose
47
Difference and similarities between maltose and cellobiose
Both contain two glucose molecules
Maltose has an alpha-1,4-bond while cellobiose has a beta-1,4-bond.
The alpha/beta are determined by the position of the -OH attached to the C(1) of glucose.
48
Most abundant polymers
Cellulose and starch are sugar polymers consisting of glucose monomers linked by glycosidic bonds.
Formed by dehydration reactions. Form glycosidic linkages. (bonds)
Have same chemical formula - but differ drastically.
49
Differences between cellulose and starch
Even though both have the same formula:
alpha-1,4,-bond in starch makes it readily degradable by mammals
beta-1,4-bond in cellulose makes in insoluble and very rigid. (Mammals cannot digest beta-bonds.)
50
Starch's two forms
Starch exists in two forms:
1. Amylose: single chains that represent 20% of starch (alpha-1,4 bonds)
2. Amylopectin - branched chains represent 80% of starch (alpha-1,6 bonds at branches).
51
Glycogen
Has a similar structure to starch and is often referred to as "animal starch" because it is the storage carbohydrate of animals.
52
Amylases
Enzyme used to digest amylose polymers.
1. among the first enzymes to be used on industrial scale
2. Produced by Bacillus spp., Aspergillus spp., saliva
3. Broad range of applications for the breakdown of starch
4. alpha-amylase: cuts amylose chain at random sites
beta-amylase: cuts amylose chain from non-
reducing end to yield maltose units.
gama-amylase or glucoamylase: cuts amylose alpha-
1,6 bonds
53
Cellulases
Enzyme that digests cellulose
1. Major industrial importance
2. Used for degradation of lignocellulose to simple sugars (ethanol, butanol).
3. Mostly produced by fungi, e.g. Trichoderma reesei (wood rot fungus).
54
Why are amylase and cellulase enzymes important?
They catalyze the degradation of polymers into oligomeric (short-chain) or monomeric constituents.
55
How are amylase and cellulase enzymes formed?
They are naturally produced by a wide variety of organisms, but in some instances are also heterologously produced by a recombinant host organism such as S cerevisiae.
In other words: the genes from the natural producer is transferred to another host strain, which then produces the protein coded for by the transferred gene.
56
Lipids
- Lipids are the second largest group of complex organic compounds
- Consist primarily of carbon, hydrogen and oxygen
- Complex lipids can also contain nitrogen and phosphorous
- store 2.5 times more energy per gram than carbohydrates (e.g. starch)
57
The basic component of lipids:
The basic component of lipids is fatty acids.
- hydrocarbon chain with a carboxyl group at the terminus
- fatty acids are non-polar due to the long hydrocarbon chain
- insoluble in water, but soluble in organic solvents such as ether and chloroform.
58
Neutral lipids:
formed by linking three fatty acids to glycerol
| -important storage molecules in animals and plants.
59
Why lipids can store more energy than carbohydrates:
Carbon atoms in glucose have oxidation states of -1, 0 or +1.
In palmitic acid (a fatty acid) ALL BUT ONE carbon have oxidation states of -2 or -3. (This means that the carbon atoms in fatty acids have more electrons around them.)
When electrons move from an atom with a low affinity for electrons (low electronegativity), like carbon, to one with high electronegativity, like oxygen, energy is released.
Thus, when the larger number of electrons around the carbon atoms in fatty acids are transferred to oxygen (when the fatty acids are oxidized), more energy is released than when the same process happens to carbohydrates.
60
Neutral lipids
A large array of fatty acids can be found in neutral lipids.
Neutral lipids predominantly consist of storage triacylglycerols and fatty acid esters.
61
Polar lipids
mainly comprise membrane glycolipids and phospholipids.
62
Saturated fatty acids
No double bonds
particularly found in animals
the maximum amount of hydrogen atoms possible
examples: Palmitic acid and stearic acid
associated with atherosclerosis (deposits of fat in arteries) and consequently heart attacks.
63
Unsaturated fatty acids
Have double bonds
generally found in plant tissue
examples: Oleic acid and Linoleic acid
are healthier in the human diet than saturated fatty acids
64
Describe briefly how lipids are formed:
Simple fats compounded to sugars (glycolipids) or phosphates (phospholipids)
65
Phospholipids
Phospholipids for, the basic unit of cell membranes
66
Fatty acids and the cell membrane:
Fatty acid moieties are non-polar (hydrophobic) and associate with each other to form the lipid by-layer of cell membranes.
-the phospho groups are polar (hydrophilic) and orientate towards the outside to associate with water.
Cell membranes thus form natural seperation between the inside and outside cells and are differentially permeable membranes for the exchange of nutrients and breakdown products.
67
Physical properties of the fatty acid...
Physical properties (solubility, melting point) of the fatty acid are determined by the length and saturation of the hydrocarbon tail.
- Tails cluster (lattice) and form hydration shells to minimize hydrophobic exposure.
- unsaturation disrupts the lattice, allows water to become ordered around tails
- weakening of lattice is increased solubility and lower melting point.
68
Lipids and soap
Fatty acid salts is a key component of soap
Oil/dirt is sequestered inside the lipophilic micelle
Washed away with water
69
Three types of lipids in soaps
Liposome
Micelle
Bilayer sheet
70
Proteins
Fundamental role in structure and function of living cells.
| Different group of macromolecules
71
Roles of protein
1. enzymatic reactions - key to metabolic pathways (enzymes are proteins)
2. immunity
3. transport of molecules
4. movement by flagella or muscle tissue
5. regulation of genes
6. storage of ions (e.g. ferritin in hemoglobin)
72
Amino acids and protein
Proteins are composed of twenty amino acids and thousands of combinations are possible to form different proteins.
73
what do amino acids consist of?
carbon
hydrogen
oxygen and,
nitrogen
74
How are amino acids linked and what do they form?
Amino acids are linked through amine bonds into polypeptide chains.
75
Cysteine
Cysteine is an amino acid that contains thiol (-SH) and can form disulphide bonds through oxidation of the thiol groups.
76
What type of enantiomers are incorporated into proteins?
Only L-enantiomers are incorporated into proteins and these are bases on the position of the amino group.
77
All amino acids have...
all amino acids have an amino- and carboxy terminus with variable side chains (R) that determine/distinguish between the 20 general amino acids.
78
How are amino acids divided?
Amino acids can be divided into groups according to features of the particular side-chain:
non-polar (hydrophobic)
polar (hydrophilic)
ionic (charged)
79
What is the basic structure of an amino acid?
Four groups arranged around a central alpha-carbon.
80
What is the general amino acid structure?
The general amino acid structure is alpha-amino acid.
In other words, the amino group is attached to the alpha-carbon, next to the carboxyl group.
Also attached to the alpha carbon is hydrogen and a side chain (R).
81
The customary form of writing amino acids:
At neutrality, the carboxyl group (pKa =2) loses an electron - wants to make the environment more acidic
and an amino group (pKa = 10) picks one up - wants to make environment more alkaline at neutrality.
(Is a Zwitterion)
82
What is a Zwitterion?
A molecule or ion having separate positively and negatively charged groups, the overall charge is zero.
83
Different amino acids
Each amino acid has a different side group which causes the amino acid to have a different property.
Proteins are made of strings of amino acids - polypeptides. Can alter the function of the protein.
84
What are proteins?
Proteins are polypeptides that form through dehydration reactions between the amino and carboxyl groups of amino acids, forming peptide bonds.
85
Disulfide bonding in proteins
Proteins can contain intramolecular S-S bonds between cysteine residues that provide stability to the protein structure.
86
Hydrophilic and hydrophobic amino acids
Hydrophobic amino acids are normally found on the surface of proteins for interaction with water
Hydrophobic amino acids are inside the protein structure to ensure stability through hydrophobic interactions between different folds of protein.
Property is essential for the correct functioning of the protein also essential for effective interaction with the cell membrane.
87
Four levels of the structural complexity of proteins
1. Primary structure: Sequence of amino acids
2. Secondary structure: Spatial arrangement
3. Tertiary structure: 3D arrangement
4. Quaternary structure: Combination of different polypeptides
88
Explain the primary structural level of complexity of proteins
The primary structure is the sequence in which amino acids are covalently linked.
Different sequence = different primary structure
The sequence determines the protein functionality
89
Explain the secondary structural level of complexity of proteins
The secondary structural level of proteins is the spatial arrangement of the polypeptide chain around a single axis.
alpha-helix (spiral): biological activity
beta-pleated sheet (flat) hydrogen bond arrangement: structural activity
90
What is meant by the tertiary structure level of complexity of proteins?
The tertiary structural level is the 3D arrangement of the primary and secondary structures of the polypeptide
91
What is meant by the quaternary structure level of complexity of proteins?
This is the combination of different polypeptides, each with its own primary, secondary and tertiary structures.
92
How are secondary structures stabilized?
Secondary structures are stabilized by
1. H2-bonds between H of amino and O of carboxyl groups
2. Disulphide bonds from oxidation of thiol groups
3. Ionic bonding between carboxyl and amide groups
4. Hydrocarbon side-chain interactions
93
Sterilisation principles
The tertiary and quaternary structures are positioned to form active sites for enzymes.
If the native structure is disrupted, there is a loss of enzyme activity and a loss of metabolic activity.
In sterilization, if you kill the enzymes/proteins you kill what they are meant to form.
Steam sterilization is the most popular method of sterilization - more easily damaged (denatured) in hydrated form.
94
Downstream processing of proteins
It is important to keep downstream processing in mind when working with proteins, especially if heat is involved.
95
Nucleosides, nucleotides and nucleic acids
Most fundamental and important constituent in living cells.
Involved in:
1. Energy generation and transmission
2. metabolism
3. Repositories and transmitters of genetic information (blueprint of organism)
96
Nucleoside
Most basic building block is aldopentose (ribose) and nitrogenous base at C1.
97
How many bases can be attached to the ribose in nucleosides?
Five different bases can be attached to the ribose in nucleosides.
98
What are purines?
Purines are double ring bases found in nucleosides. There are two: Adenine and guanine.
99
What are pyrimidines?
Cytosine, thymine and uracil are single ring bases in nucleosides called pyrimidines.
100
Thymine
A pyrimidine that is found in DNA only.
101
Uracil
A pyrimidine that is found in RNA only.
102
Adenosine
Adenosine = Adenine + ribose
The nucleoside where adenine is bound to ribose forms the basis of the main energy carrier in the cell namely ATP.
103
Nucleotides
If phosphate moieties are added to the nucleosides you get nucleotides.
(Up to three phosphate groups can be added to the sugar at C5)
104
Nucleic Acids
Polymers of nucleotides joined by phosphodiester bonds
105
DNA
Deoxyribonucleic acid
thymine only found in DNA (is a pyrimidine)
Has deoxyribose as a sugar moiety
106
RNA
Ribonucleic acid
uracil is only found in RNA (is a pyrimidine)
has a ribose sugar
107
How are DNA and RNA formed?
DNA and RNA are formed by polymerase enzymes that link nucleotides to each other.
108
How are DNA and RNA most stable?
DNA is more stable in the double-strand structure
| RNA can exist stably as single-stranded molecules
109
Chromosomes
Supercoiled nucleic acids
