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Chemical Components of the Cells
CB3 pp. 39-48, 50-59, 62-63, 78, 119-127, 130, 140-142
CB4 pp. 39-49, 50-59, 62-65, 121-130, 141-144
Figures reproduced from:
1. Alberts et al. Essential Cell Biology. Garland Science.
2. Despopoulos A., Silbernagl S. Color Atlas of Physiology. 5th edition. Thieme, 2003.
Lecture Outline
- atoms and molecules
- chemical bonds
- molecules in cells:
1) carbohydrates
2) nucleic acids
3) lipids
4) proteins
- protein structure and function
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Atoms and Molecules
- atom: nucleus + electrons
- nucleus contains proton(s) and neutron(s)
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Atoms and Molecules (cont.)
- molecule: 2 atoms or more
- molecules are formed by sharing or transfer of electrons
- this produces covalent and ionic bonds, respectively
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Covalent Bonds
- single: 2 electrons shared, allows rotation
- double: 4 electrons shared, does not allow rotation, rigid
- triple: 6 electrons shared, does not allow rotation, rigid and very strong
H2, hydrogen
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(C) ethyne (acetylene)
N2, nitrogen
Sharing of Electrons is Often Unequal
- this produces polar covalent bonds
- polar covalent bonds make water molecules polar
- each water molecule is a dipole
Electron sharing is equal only between atoms of the same kind
carbons in
organic
compounds
H2, hydrogen
O2, oxygen
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Water Molecule Polarity
-
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allows water molecules to form hydrogen bonds with each other (non-covalent
bonds between H and O from different water molecules)
note: hydrogen bonds are formed not only between water molecules, but also
between water and other molecules, and between H and O within other molecules
(e.g. in proteins, see further)
Water Molecule Polarity (cont.)
- consequences:
1) water is liquid at room temperature
2) water creates a solvent shield around charged and polar molecules (ions,
membrane lipid polar heads, proteins). This causes dissociation of molecules with
ionic bonds into ions (NaCl ↔ Na+ + Cl-)
3) water "repulses" non-polar parts of other molecules, forcing them together
(helps hydrophobic interactions)
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Van der Waal's Attraction
- attraction of any atoms to each other
- caused by vibrations of the nucleus within the electron cloud, which creates temporary
dipoles
- plays a role in hydrophobic interactions
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Strength of Chemical Bonds
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Molecules in Cells
- four major families of small molecules
- present as individual molecules, but also as parts of macromolecules
- besides beeing building blocks, can serve as energy source and as signaling
compounds
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Molecules in Cells (cont.)
- macromolecules are often polymers made of monomers
- polymerization = adding monomers to an end of a polymer (condensation reaction);
the reverse is hydrolysis
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Sugars (Carbohydrates)
- simple sugars, monosaccharides (e.g. glucose): energy source and building blocks
- pentose: 5 carbons; hexose: 6 carbons
glucose
hexose
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hexose too !
Isomers
- have the same atom composition, but different spatial position of atoms
- these small differences are recognized by proteins (e.g. by enzymes and
transporters)
D-glucose
L-glucose
optical isomers
(mirror-image pairs)
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Polysaccharides
-
-
when combined by condensation reactions, monosaccharides give disaccharides (e.g.
sucrose), oligosaccharides (3-50 sugar monomers) and polysaccharides (hundreds or
thousands of sugar monomers)
polysaccharides are formed to store the monosaccharides; when needed,
polysaccharides are broken down and monosaccharides are used as energy source
a polysaccharide
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Carbohydrates as Parts of Other Molecules
- monosaccharides in phosphatidylinositol and glycolipids
- oligo- and polysaccharides in glycocalyx (parts of glycosylated proteins and
glycolipids)
- monosaccharides in nucleic acids (see further)
phosphatidylinositol
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Nucleic Acids - DNA, RNA
- polymers made of nucleotide monomers: di-, oligo-, polynucleotides
- DNA (deoxyribonucleic acids) are made of deoxyribonucleotides
- RNA (ribonucleic acids) are made of ribonucleotides
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Sugars in Nucleic Acids
- pentoses (5 carbons, each is given a number with a prime mark)
β
α
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DNA, RNA
- formed by condensation reaction, phosphate group is linking the nucleotides
- polynucleotides have chemical polarity (the ends are functionally different); not to be
mixed up with electrical polarity!
- the next nucleotide is attached to the 3' end of the growing polynucleotide
H2O
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Bases in Nucleic Acids
- 5 types falling in 2 classes
(used in RNA)
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(used in DNA)
Other Nucleotide-Containing Molecules
-
ATP:
1) building block for RNA
2) energy storage
3) source of phosphate groups for protein phosphorylation
- ADP: product of degradation of ATP, re-usable
ATP
(adenosine-5’-triphosphate)
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ADP
(adenosine-5’-diphosphate)
Other Nucleotide-Containing Molecules (cont.)
- cAMP: signaling molecule
cAMP
(cyclic adenosine-3’,5’-monophosphate)
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Lipids
- fatty acids, triacylglycerols, phospholipids, glycolipids, cholesterol, steroids etc
- often long molecules, but not always polymers
- water-insoluble, soluble in organic solvents (for example, in the cell membranes!)
- fatty acids: carboxyl group and hydrocarbon tail
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Fatty Acids
- saturated (all bonds in the tail are single) and unsaturated (some bonds in the tail are
double; rigid, but give ”bended” structures)
- unsaturated and polyunsaturated fatty acids are necessary in cell membranes,
increase the membrane fluidity
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Fatty Acids (cont.)
- stored as triacylglycerols (esters with glycerol)
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Triacylglycerols
- animal fat (e.g. butter) mostly contain triacylglycerols with saturated fatty acids: pack
tightly, solid at room temperature
- plant oils contain much more triacylglycerols with unsaturated fatty acids: do not pack
tightly, liquid at room temperature
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Phospholipids, Glycolipids
- components of the membrane lipid bilayer
- some are precursors of signaling molecules (IP3, DAG)
- some serve as docking sites at the membrane for certain proteins (DAG, PIP3)
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phospholipid
phosphatidylinositol
(3,4,5)-trisphosphate (PIP3)
Steroids
- cholesterol: component of the membrane lipid bilayer, and precursor of other
steroids:
1) sex hormones and other steroid hormones
2) bile acids (important in digestive tract)
- vitamins D
cholesterol
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testosterone
(male sex hormone)
vitamin D2
Other Lipids
- polyisoprenoids (polymers of isoprene)
- precursors of vitamins A, E, K, coenzyme Q10 etc (all are lipid-soluble)
retinol (vitamin A)
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vitamin K
Lipids as Parts of Other Molecules
- can be bound to proteins to “anchor” them to membranes
- examples of attaching of the lipids to the proteins: myristoylation, palmitoylation
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Lipids as Parts of Other Molecules
- can be bound to proteins to “anchor” them to membranes
- examples of attaching of the lipids to the proteins: myristoylation, palmitoylation
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Incorrect illustration!
Heads of some phospholipids
are used for docking of
proteins (e.g. PIP3).
Proteins
- polymers made of amino acid monomers
- short proteins can be called di-, tri-, oligo-, polypeptides, or just peptides
- common features of amino acids: α-carbon, amino group, carboxyl group, side chain
- 20 amino acids in proteins (differ by the side chains, see further); several more exist
in cells as intermediates in metabolic reactions
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L- and D- Amino Acid Isomers
- optical isomers: L- and D-, all but glycine (R = H)
- proteins consist exclusively of L-amino acids, but D-amino acids are present in the
body (e.g. D-serine is a neurotransmitter)
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Peptide Bonds
- covalent bonds that are formed between amino acids within proteins (all bonds within
individual amino acids are also covalent)
- form rigid planar structures
- peptide chains have chemical polarity (N-terminus and C-terminus)
peptide bond
amino terminus
of the peptide
(N-terminus,
NH2-terminus)
- the next amino acid is attached at the C-terminus of the growing peptide
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carboxyl terminus
of the peptide
(C-terminus,
COOH-terminus)
Proteins Have Flexible Structures
- despite the rigidity of the peptide bonds, since other bonds allow rotation
amino terminus
of the peptide
(N-terminus,
NH2-terminus)
carboxyl terminus
of the peptide
(C-terminus,
COOH-terminus)
these bonds allow rotation
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Amino Acids
- depending on the side chain, are divided into four families: acidic (negatively charged
side chain), basic (positively charged side chain), uncharged polar, nonpolar
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Amino Acids (cont.)
- acidic (negatively charged side chain)
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Amino Acids (cont.)
- basic (positively charged side chain)
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Amino Acids (cont.)
- uncharged polar
can be glycosylated
(a sugar added)
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can be phosphorylated
(phosphate group added)
Amino Acids (cont.)
- nonpolar (1)
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Amino Acids (cont.)
- nonpolar (2)
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Amino Acids (cont.)
- nonpolar (3)
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Protein Structure
- proteins have primary, secondary, tertiary and quaternary structure
- primary structure: sequence of amino acid residues, atoms connected by covalent
bonds
histidine
NH2 S
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T
cysteine
A
K
P
W
valine
G
C
V COOH
Protein Structure (cont.)
- secondary structure: α-helices
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Protein Structure (cont.)
- secondary structure: β-sheets
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Protein Structure (cont.)
- tertiary structure: the final 3-dimentional structure of an individual peptide chain
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Protein Structure (cont.)
- many proteins have structural and functional domains
- transmembrane domains, catalytic domains, binding domains etc.
domain 2
domain 1
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Protein Structure (cont.)
- quaternary structure: complex of 2 or more peptide chains (protein subunits)
an antibody
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Protein Structure (cont.)
- secondary, tertiary and quaternary structure of proteins form due to interaction
between amino acid side chains and between peptide bonds
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Protein Structure (cont.)
- other bonds stabilizing the higher structure of protein molecules:
stacking interactions
(technically covalent bond, sharing of electrons,
but weak as van der Waals interaction)
disulfide bonds
(covalent bonds)
an antibody
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Protein Conformation
- the final folded structure of a protein
- proteins adopt conformation with the lowest energy
- stable, but not rigid, the protein molecules are always in motion
- can change due to interaction with other molecules (ions, lipids, other proteins etc)
- can change due to phosphorylation (covalent binding of phosphate group)
Ca2+- ATPase
Ca2+- free
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Ca2+- bound
Protein Phosphorylation
- covalent binding of phosphate group to serine, threonine, or tyrosine
- the source of the phosphate groups is ATP
- reversible
- the most common way to regulate the function of proteins
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ATP
Protein Functions
- transporters (transfer molecules through membranes)
- receptors (membrane receptors bind signaling molecules on the outside of cells and
transfer the signal to the inside of the cell; cytoplasmic receptors can bind signaling
molecules within the cell)
- attachment proteins (are exposed on the cell surface and bound to a surface, to the
extracellular matrix, or to other cells; e.g. integrins)
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can be an attachment protein
Protein Functions (cont.)
- structural proteins: cytoskeletal proteins, extracellular matrix proteins, scaffolding
proteins (anchors)
Cytoskeletal proteins
can be an extracellular matrix protein
can be an intracellular
scaffolding protein
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Protein Functions (cont.)
- enzymes (catalyze chemical reactions)
within a membrane
within cytosol, or within an organelle, or
outside the cell (like lysozyme below)
lysozyme ,
cleaves polysaccharide chains on the surface of bacteria,
decreasing their attachment ability
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Protein Functions (cont.)
- motor proteins (are able to move along other proteins and thereby to transport
molecules, vesicles, organelles within the cells; to help cell migration, cell division,
active cilia movement, muscle contraction etc)
- antibodies (bind foreign molecules, help to protect the organism from molecular,
bacterial, or viral invasion)
motor protein (vehicle)
a structural protein (road)
an antibody
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