Biochemistry 214
THEME A: BIO-ELEMENTS TO LIVING CELL
Elements unique to chemical elements in living systems based on properties and availability
C, N, O, H, S and P combine forming organic bio-molecules
16 bio-elements in biological systems of living things:
1. Elements forming covalent bonds - H, C, N, O, P and S [1st tier]
2. Mono-atomic ions - Na+, K+, Cl-, Mg2+ and Ca2+ [2nd tier]
3. Trace elements - Mn, Fe, Co, Cu, Zn, Si, B, Al, Br, I and F [3rd and 4th tier]
Abundance of elements - COVALENT BONDS
1. 1st tier (most abundant): hydrogen H, carbon C, nitrogen N and oxygen O
2. 2nd tier: Na+, K+, Cl-, Mg2+, Ca2+, P and S
3. 3rd tier: Mn, Fe, Co, Cu, Zn
4. 4th tier: Cr, Mo, W, B, Al, Si, F, Br, I
C, N, O and H [1st tier]
▪ Selected on unique properties
▪ Most abundant elements in living organisms form stable covalent bonds
▪ 99% in living systems and 47% in the crust (selected on unique properties)
▪ C, N and O form multiple bonds based on lone pairs/no. electrons in outer orbital
▪ sp3 hybridisation: electrons in outer shell project 4 directions into 4 orbitals (4
electron domains)
o tetrahedral 109.5 degrees - carbon forming 4 covalent bonds
o pyramidal 106.8 degrees - nitrogen forming 3 covalent bonds (1 lone pair)
o angular 104.5 degrees - oxygen forming 2 covalent bonds (2 lone pairs)
▪ Life is C based and not silicon Si (same group but C period 2 and Si period 3): Si-Si too
weak and Si-O (glass) too strong/static. Need flexibility to form and break
▪ C covalent bonds to C not too strong creating sp3 hybridisation = tetrahedral carbon
o Organic compounds
o 3D structures
o Chains, linear, branched and cyclic
o Functional groups bonding with O, N and S
P and S [2nd tier]
▪ Selected on chemical properties
▪ High valence (S = 6, P = 5)
▪ Electronegativity lower than N and O
▪ Forms tetrahedral bonds with oxygen
▪ Bonds unstable in presence of water
▪ P and S are energy carriers therefore bonds act as storage of chemical energy
requiring high energy for formation and released when bonds break
Has a high reactivity as it is unstable, bonds in ATP and bonds via SH of CoASH
, Biochemistry 214
Organic compounds
1. Alcohol: bond to OH
2. Aldehyde: C double bond O and bond to H
3. Ketone: C double bond O and not a bond to H but R
4. Carboxylic acid: C double bond O and bond to OH
5. Thiol (Sulfhydryl): bond to SH
6. Amines primary: bond to NH2
Amines secondary: bond to NH and another R
Amines tertiary: bond to N and 2 R’s
Carboxylic acids exist as carboxylate anions in most biological conditions (pH = 7): negative
charge on the oxygen atom as it loses proton (OH) from dissociation so deprotonated
Amines exist as ammonium ions in most biological conditions: positive charge on nitrogen
atom as proton binds so protonated
Functional groups
Always polar molecules: keto-group
1. Hydroxyl: -OH
2. Acyl: C double bond O and R
3. Carbonyl: C double bond O
Carboxylate: C double bond O and bond to O-
4. Sulfhydryl (Thiol): -SH
5. Amino: -NH2 or -N+H3
6. Phosphate: P double bond O, 2 single bonds to O- with single bond to O
Phosphoryl: P double bond O and 2 single bonds to O-
Mono-atomic ions Na+, K+, Cl-, Mg2+ and Ca2+ [2nd tier]
▪ Selected on availability - not specific properties like maintaining ionic strength
▪ Ionic composition of seawater and intracellular fluid is similar
▪ Charge density of ions determines specific function in cell: relatively non-specific role
▪ Ca2+ acts as secondary messenger in cells
▪ Calcium ion double charged, and potassium ion single charged so Ca has a high
density (deal with size of atom and charge)
Trace elements [3rd and 4th tier]
▪ 3rd: Mn, Fe, Co, Cu and Zn
▪ 4th: B, Al, Si, Br, I, F and Cr
▪ Selected for electronic properties
▪ Fe and Cu form stable ions in 2 oxidation states: Fe2+/Fe3+ and Cu+/Cu2+
▪ Redox reactions suited role of alternating electron donors and electron acceptors
▪ Trace elements rarely used with highly specialised function
, Biochemistry 214
Bio-elements combine in biomolecules and higher cell structures
▪ Primary structure - secondary structure - tertiary structure with heme group -
quaternary structure
▪ Proteins has amino acid in string that winds/folds in specialised 3D structure with
multiple subunits to form the quaternary structure
▪ 31 precursor molecules selected on suitability and availability:
o 20 L-amino acids: proteins
o 5 aromatic N-bases coupled to sugar phosphates: nucleic acids DNA and RNA
o 2 D-sugars (D-glucose and D-ribose): carbohydrates and nucleic acids
o Palmitic acid, oleic acid, glycerol and choline: membranes
SUMMARY
✓ The cell is the unit of life
✓ Living organisms composed of only 16 bio-elements
✓ C, N, O, H, S and P combine to form organic biomolecules
✓ Cells highly structured internally
✓ Cells isolated from environment by plasma membrane
✓ Differences in cell structure define 2 classes of organisms: prokaryotes and
eukaryotes
✓ Endosymbiotic theory: eukaryotes originated from prokaryotes through small
prokaryotic cells being absorbed by larger cells and become incorporated into
specialised organelles such as mitochondria and chloroplasts
✓ Cellular functions are associated with specific cell organelles
✓ Cell shape varies according to their functions
✓ Atomic level has 6 elements forming bulk of cells: H, C, N, O (1st) P and S (2nd)
a. Forms sufficiently strong bonds and bonds can be cleaved
b. All form functional groups
✓ 2 tier Na+, K+, Cl-, Mg2+ and Ca2+ plays relatively non-specific roles
nd
✓ Trace elements (3rd and 4th) IMPORTANT because of redox properties
a. Cu and Zn for respiratory chain and haemoglobin (Fe) and hemocyanin (Cu)
specific function
b. Practical applications in plant fertilizers (nitrate reductase, Mo) and plant
tissue culture
Prokaryotes: bacteria cell
▪ DNA molecule with genetic material coiled up in nucleoid region which shares the
fluid interior of cell (cytoplasm) with ribosomes (synthesise proteins), particles and
dissolved molecules
▪ Cell bounded by plasma membrane outside which is a rigid cell wall and have a
gelatinous outer capsule
▪ Simpler, no internal organelle, no true nucleus (nucleoid) in a separate organelle and
all material is in the same compartment
, Biochemistry 214
▪ Pili project from the surface attaching the cell to other cells/surfaces
▪ Flagella protrusions allow bacteria to swim through liquid environment and feed
▪ Rod-shaped bacillus. Bacteria can be pathogenic
Salmonella rod-shaped gram-negative enterobacteria causing typhoid fever,
paratyphoid fever and food borne illnesses
▪ n Haploid
Eukaryotes: animal cell
▪ Difference structural compartments/organelles surrounded by membranes with
various functions: Golgi complex, endoplasmic reticulum
▪ Nucleus localised in a separate compartment
▪ 2 copies of every gene (2n diploid)
▪ Sexual reproduction
Eukaryotes: plant cells
▪ More rigid with cell wall
▪ Chloroplasts, vacuole, cell wall, plasmodesmata, microtubules different to animal cell
▪ Completes photosynthesis with solar energy to chemical energy
▪ Contains chloroplasts and a vacuole (sac of solvents used for a storage compartment
for dissolved substances/sugars)
THEME A: BIO-ELEMENTS TO LIVING CELL
Elements unique to chemical elements in living systems based on properties and availability
C, N, O, H, S and P combine forming organic bio-molecules
16 bio-elements in biological systems of living things:
1. Elements forming covalent bonds - H, C, N, O, P and S [1st tier]
2. Mono-atomic ions - Na+, K+, Cl-, Mg2+ and Ca2+ [2nd tier]
3. Trace elements - Mn, Fe, Co, Cu, Zn, Si, B, Al, Br, I and F [3rd and 4th tier]
Abundance of elements - COVALENT BONDS
1. 1st tier (most abundant): hydrogen H, carbon C, nitrogen N and oxygen O
2. 2nd tier: Na+, K+, Cl-, Mg2+, Ca2+, P and S
3. 3rd tier: Mn, Fe, Co, Cu, Zn
4. 4th tier: Cr, Mo, W, B, Al, Si, F, Br, I
C, N, O and H [1st tier]
▪ Selected on unique properties
▪ Most abundant elements in living organisms form stable covalent bonds
▪ 99% in living systems and 47% in the crust (selected on unique properties)
▪ C, N and O form multiple bonds based on lone pairs/no. electrons in outer orbital
▪ sp3 hybridisation: electrons in outer shell project 4 directions into 4 orbitals (4
electron domains)
o tetrahedral 109.5 degrees - carbon forming 4 covalent bonds
o pyramidal 106.8 degrees - nitrogen forming 3 covalent bonds (1 lone pair)
o angular 104.5 degrees - oxygen forming 2 covalent bonds (2 lone pairs)
▪ Life is C based and not silicon Si (same group but C period 2 and Si period 3): Si-Si too
weak and Si-O (glass) too strong/static. Need flexibility to form and break
▪ C covalent bonds to C not too strong creating sp3 hybridisation = tetrahedral carbon
o Organic compounds
o 3D structures
o Chains, linear, branched and cyclic
o Functional groups bonding with O, N and S
P and S [2nd tier]
▪ Selected on chemical properties
▪ High valence (S = 6, P = 5)
▪ Electronegativity lower than N and O
▪ Forms tetrahedral bonds with oxygen
▪ Bonds unstable in presence of water
▪ P and S are energy carriers therefore bonds act as storage of chemical energy
requiring high energy for formation and released when bonds break
Has a high reactivity as it is unstable, bonds in ATP and bonds via SH of CoASH
, Biochemistry 214
Organic compounds
1. Alcohol: bond to OH
2. Aldehyde: C double bond O and bond to H
3. Ketone: C double bond O and not a bond to H but R
4. Carboxylic acid: C double bond O and bond to OH
5. Thiol (Sulfhydryl): bond to SH
6. Amines primary: bond to NH2
Amines secondary: bond to NH and another R
Amines tertiary: bond to N and 2 R’s
Carboxylic acids exist as carboxylate anions in most biological conditions (pH = 7): negative
charge on the oxygen atom as it loses proton (OH) from dissociation so deprotonated
Amines exist as ammonium ions in most biological conditions: positive charge on nitrogen
atom as proton binds so protonated
Functional groups
Always polar molecules: keto-group
1. Hydroxyl: -OH
2. Acyl: C double bond O and R
3. Carbonyl: C double bond O
Carboxylate: C double bond O and bond to O-
4. Sulfhydryl (Thiol): -SH
5. Amino: -NH2 or -N+H3
6. Phosphate: P double bond O, 2 single bonds to O- with single bond to O
Phosphoryl: P double bond O and 2 single bonds to O-
Mono-atomic ions Na+, K+, Cl-, Mg2+ and Ca2+ [2nd tier]
▪ Selected on availability - not specific properties like maintaining ionic strength
▪ Ionic composition of seawater and intracellular fluid is similar
▪ Charge density of ions determines specific function in cell: relatively non-specific role
▪ Ca2+ acts as secondary messenger in cells
▪ Calcium ion double charged, and potassium ion single charged so Ca has a high
density (deal with size of atom and charge)
Trace elements [3rd and 4th tier]
▪ 3rd: Mn, Fe, Co, Cu and Zn
▪ 4th: B, Al, Si, Br, I, F and Cr
▪ Selected for electronic properties
▪ Fe and Cu form stable ions in 2 oxidation states: Fe2+/Fe3+ and Cu+/Cu2+
▪ Redox reactions suited role of alternating electron donors and electron acceptors
▪ Trace elements rarely used with highly specialised function
, Biochemistry 214
Bio-elements combine in biomolecules and higher cell structures
▪ Primary structure - secondary structure - tertiary structure with heme group -
quaternary structure
▪ Proteins has amino acid in string that winds/folds in specialised 3D structure with
multiple subunits to form the quaternary structure
▪ 31 precursor molecules selected on suitability and availability:
o 20 L-amino acids: proteins
o 5 aromatic N-bases coupled to sugar phosphates: nucleic acids DNA and RNA
o 2 D-sugars (D-glucose and D-ribose): carbohydrates and nucleic acids
o Palmitic acid, oleic acid, glycerol and choline: membranes
SUMMARY
✓ The cell is the unit of life
✓ Living organisms composed of only 16 bio-elements
✓ C, N, O, H, S and P combine to form organic biomolecules
✓ Cells highly structured internally
✓ Cells isolated from environment by plasma membrane
✓ Differences in cell structure define 2 classes of organisms: prokaryotes and
eukaryotes
✓ Endosymbiotic theory: eukaryotes originated from prokaryotes through small
prokaryotic cells being absorbed by larger cells and become incorporated into
specialised organelles such as mitochondria and chloroplasts
✓ Cellular functions are associated with specific cell organelles
✓ Cell shape varies according to their functions
✓ Atomic level has 6 elements forming bulk of cells: H, C, N, O (1st) P and S (2nd)
a. Forms sufficiently strong bonds and bonds can be cleaved
b. All form functional groups
✓ 2 tier Na+, K+, Cl-, Mg2+ and Ca2+ plays relatively non-specific roles
nd
✓ Trace elements (3rd and 4th) IMPORTANT because of redox properties
a. Cu and Zn for respiratory chain and haemoglobin (Fe) and hemocyanin (Cu)
specific function
b. Practical applications in plant fertilizers (nitrate reductase, Mo) and plant
tissue culture
Prokaryotes: bacteria cell
▪ DNA molecule with genetic material coiled up in nucleoid region which shares the
fluid interior of cell (cytoplasm) with ribosomes (synthesise proteins), particles and
dissolved molecules
▪ Cell bounded by plasma membrane outside which is a rigid cell wall and have a
gelatinous outer capsule
▪ Simpler, no internal organelle, no true nucleus (nucleoid) in a separate organelle and
all material is in the same compartment
, Biochemistry 214
▪ Pili project from the surface attaching the cell to other cells/surfaces
▪ Flagella protrusions allow bacteria to swim through liquid environment and feed
▪ Rod-shaped bacillus. Bacteria can be pathogenic
Salmonella rod-shaped gram-negative enterobacteria causing typhoid fever,
paratyphoid fever and food borne illnesses
▪ n Haploid
Eukaryotes: animal cell
▪ Difference structural compartments/organelles surrounded by membranes with
various functions: Golgi complex, endoplasmic reticulum
▪ Nucleus localised in a separate compartment
▪ 2 copies of every gene (2n diploid)
▪ Sexual reproduction
Eukaryotes: plant cells
▪ More rigid with cell wall
▪ Chloroplasts, vacuole, cell wall, plasmodesmata, microtubules different to animal cell
▪ Completes photosynthesis with solar energy to chemical energy
▪ Contains chloroplasts and a vacuole (sac of solvents used for a storage compartment
for dissolved substances/sugars)
