2 The Composition of Cells

1
2 The Composition of Cells

• BL 424 Ch. 2 Review Composition of Cells
• Cell biology seeks to understand cellular
  processes
• in terms of chemical, physical reactions
• Student Learning Outcomes
• A. To describe molecular composition of cells
• Carbohydrates, lipids, nucleic acids,
  proteins
• Draw phospholipid structures, sugars, amino acid
• B. To explain structure, function of cell
  membranes
• Lipids as barriers, phospholipid bilayer
• Proteins permit transport of substances
• C. To define Proteomics
• Large-scale analysis of cell proteins

2
The Molecules of Cells

• Water is 70 or more of total cell mass.
• Water is polar H atoms slight charge O slight
  charge
• Water molecules form hydrogen bonds
• with each other, or with other polar
  molecules
• Hydrophilic molecules (ions, polar) are soluble
• Hydrophobic molecules (nonpolar) are not soluble
• Organic molecules
• mostly carbohydrates,
• lipids, proteins,
• or nucleic acids.

Fig. 2.1
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The Molecules of Cells

• 1. Carbohydrates simple sugars, polysaccharides
• Monosaccharides (simple sugars) are major
  nutrients basic formula (CH2O)n
• Glucose (C6H12O6)
• principal source of energy,
• substrate for biosynthesis
• of other macromolecules

Fig. 2.2
4
Monosaccharides
Monosaccharides join together by glycosidic bond?
disaccharide dehydration reactions (H2O is
removed) Oligosaccharides Polymers, a few
sugars Polysaccharides macromolecules hundreds
or thousands of sugars
Fig. 2.3 C1 to C4 a1-4 bond
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Figure 2.4 Polysaccharides

• Glycogen storage form in animal cells. C1-4
• Starch storage in plant cells.
• glucose molecules in a configuration mostly
  a1-4, some 1-6
• Cellulose structural component of plant cell
  wall.
• glucose in ß configuration (ß1?4) long
  chains, strong fibers
• .

Fig. 2.4
6
The Molecules of Cells

• 2. Lipids have three main roles
• Energy storage
• Fats (triglycerides)
• Major components of cell membranes
• Phospholipids, glycolipids,
• Sphingomyelin, cholesterol
• Important in cell signaling
• steroid hormones (estrogen)
• messenger molecules (PIP3)

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Figure 2.5 Structure of fatty acids
Fatty acids are simplest lipids long hydrocarbon
chains (16 or 18 C) with (COO-) at one
end. Hydrocarbon chain is hydrophobic (lot of C,
H) Unsaturated fatty acids one or more double
bonds (kink structure) Saturated fatty acids
no double bonds.
Fig. 2.5
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Figure 2.6 Structure of triacylglycerols
Fatty acids stored as triacylglycerols, or fats
3 fatty acids linked to 3-C glycerol (ester
link) Insoluble in water, accumulate as fat
droplets broken down for energy-yielding
reactions. Fats more efficient energy storage
than carbohydrates yield more than twice as
much energy per weight.
Fig. 2.6 triacylglycerol, triglyceride
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Figure 2.7 Structure of phospholipids (Part 1)

• Phospholipids principal components of cell
  membranes 2 fatty acids joined to polar head
  group
• Glycerol phospholipids
• 2 fatty acids bound to
• C in glycerol.
• 3rd C of glycerol
• bound to PO4 head group
• Common head groups
• Phosphatidyl-ethanolamine
• Phosphatidyl-serine
• Phosphatidyl-choline

Fig. 2.7
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Figure 2.7 Structure of phospholipids (Parts 2-
3)
Phosphatidyl-inositol has sugar inositol is
also signaling molecule Sphingomyelin has
serine, (amino acid) instead of glycerol
Fig. 2.7
Phospholipids are amphipathic hydrophobic
tails, hydrophilic head groups part
water-soluble and part water-insoluble basis for
formation of biological membranes
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Figure 2.8 Structure of glycolipids
Many membranes have Glycolipids Glycolipids are
Amphipathic Sugar, fatty acids, no phosphate

Fig. 2.8
Note Archaeal membranes are very different
ether linkages between glycerol and hydrocarbon
isoprene units see handout
12
Figure 2.9 Cholesterol and steroid hormones
Many cell membranes contain cholesterol 4
hydrocarbon rings strongly hydrophobic, but
-OH group on one end is weakly hydrophilic,
so cholesterol is amphipathic steroid hormones
(e.g., estrogens and testosterone) are
derivatives of cholesterol.
Fig. 2.9
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The Molecules of Cells

• 3. Nucleic acids
• Deoxyribonucleic acid (DNA) is genetic material
• Information specifies proteins via mRNA and
  triplet code
• Ribonucleic acid (RNA)
• Messenger RNA (mRNA) - from DNA to ribosomes
• Ribosomal RNA, transfer RNA for protein
  synthesis.
• RNA can catalyze chemical reactions (ribozymes).
• Two important nucleotides
• Adenosine 5'-triphosphate (ATP), chemical energy
  form
• Cyclic AMP (cAMP), signaling molecule within
  cells

ATP
cAMP
14
The Molecules of Cells

• DNA and RNA polymers of nucleotides (purine and
  pyrimidine bases linked to phosphorylated sugars)
• DNA adenine and guanine
• cytosine and thymine
• RNA has uracil
• in place of thymine

Fig. 2.10
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Figure 2.10 Components of nucleic acids (Part 2)

• Bases linked to sugars are nucleosides.
• RNA has ribose DNA has sugar 2'-deoxyribose
• Nucleotides have one or more phosphate groups
  linked to 5' carbon of sugars
• 5 and 3

Fig. 2.10
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Figure 2.11 Polymerization of nucleotides

• Phosphodiester bonds polymerization between 5'
  phosphate of one nucleotide, 3' hydroxyl of
  another
• Oligonucleotides small polymers of a few
  nucleotides.
• Polynucleotides RNA and DNA, thousands or
  millions

• one end of chain 5' phosphate group
• other end in 3' hydroxyl group
• synthesized in 5' to 3' direction

Fig. 2.11
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Figure 2.12 Complementary pairing between
nucleic acid bases

• DNA - double-stranded molecule, 2 chains.
• Bases on inside joined by H bonds between
  complementary base pairs G-C and A-T (A-U)

• Complementary base pairing ? 1 strand of DNA (or
  RNA) acts as template for synthesis of
  complementary strand.
• Nucleic acids are capable of self-replication
• Information of DNA and RNA directs synthesis of
  proteins, which control most cell activities.

Fig. 2.12
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The Molecules of Cells

• 4. Proteins the most diverse macromolecules.
• Thousands of different proteins direct cell
  activities
• Structural components
• Transport and storage of small molecules (e.g.
  O2)
• Transmit information between cells (protein
  hormones),
• Defense against infection (antibodies)
• Enzymes
• Proteins are polymers of 20 different amino acids
  

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Figure 2.13 Structure of amino acids

• Amino acids
• Each has a carbon bonded to carboxyl group
  (COO-), amino group (NH3), hydrogen, and side
  chain.
• Grouped based on characteristics of side chains
  (side chains confer properties)
• Nonpolar side chains
• Polar side chains
• Side chains with basic groups
• Acidic side chains terminate
• in carboxyl groups

Fig. 2.13
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Figure 2.14 The amino acids
Amino acids grouped based on characteristics of
side chains (Side chains confer properties)
Note Ser, Thr, Tyr have OH group, can get PO4
added
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Figure 2.15 Formation of a peptide bond

• Peptide bonds join amino acids
• Polypeptides are chains of amino acids, hundreds
  or thousands of amino acids in length.
• 1st aa is amino group (N terminus)
• Last aa is a carboxyl group (C terminus)
• Sequence of aa defines
• characteristics of protein

Fig. 2.15
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Figure 2.17 Protein denaturation and refolding

• Unique sequence of amino acids in protein is
  determined by order of nucleotide bases in gene.
• Proteins 3-D structure is critical to its
  function
• shape and function of protein is determined by
  amino acid sequence (primary structure)
• 3-D results from interactions between amino acid
  side chains

Fig. 2.16 insulin has S-S bond between chains
Fig. 2.17 RNase can renature after denatured
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The Molecules of Cells

• Protein structure 4 levels
• Primary structure
• sequence of amino acids
• Secondary structure regular arrangement of amino
  acids within localized regions (a helix, b sheet)
• Tertiary structure interactions between side
  chains of amino acids in different regions of
  primary sequence.
• Quaternary structure interactions between
  different polypeptide chains, in proteins
  composed of more than one polypeptide.

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Figure 2.20 Tertiary structure of ribonuclease,
2.21 quaternary

• Tertiary structure folding of polypeptide chain
  from interactions between side chains in
  different regions.
• results in domains, basic units of tertiary
  structure
• Quaternary structure interactions between
  different polypeptide chains in proteins composed
  of more than one polypeptide

RNase
Tertiary Hydrophobic amino acids in
interior Hydrophilic amino acids on surface,
interact with water.
Hemoglobin 2a, 2b
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A phospholipid bilayer

• B. Cell membranes common structural organization
  phospholipid bilayers with associated proteins.
• Phospholipids spontaneously form bilayers in
  aqueous solutions stable barrier between aqueous
  compartments
• Lipid bilayers behave as 2-dimensional fluids
  individual molecules can rotate and move
  laterally - not flip-flop
• Fluidity determined by temperature, lipid
  composition.

Fig. 2.22
Fig. 2.23
26

• Lipid content of cell membranes varies (Table 1).
• Mammalian plasma membranes mostly 4 major
  phospholipids
• Animal cells also contain glycolipids and
  cholesterol
• Organelle membranes have different composition
• Even different lipids on inner, outer surface
  membrane

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Figure 2.24 Insertion of cholesterol in a
membrane
Ring structure of cholesterol helps determine
membrane fluidity Interactions between
hydrocarbon rings and fatty acid tails makes
membrane more rigid. Cholesterol reduces
interaction between fatty acids, maintains
membrane fluidity at lower temperatures.
Fig. 2.23
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The Structure of Cell Membranes The
lipid-globular protein mosaic model

• Fluid mosaic model of membrane structure (Singer
  Nicolson,1972)
• nonpolar parts of membrane proteins sequestered
  within membrane
• polar groups exposed to aqueous environment

Key experiment 2.2
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Figure 2.25 Fluid mosaic model of membrane
structure

• Integral membrane proteins embedded in lipid
  bilayer.
• Peripheral membrane proteins associated
  indirectly - interact with integral membrane
  proteins.
• Transmembrane proteins
• - integral proteins
• span lipid bilayer,
• (a-helical)
• with portions
• exposed on
• both sides
• Carbohydrates on
• outside proteins

Fig. 2.25
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Figure 2.26 Structure of a ß-barrel

• Membrane-spanning portions of transmembrane
  proteins usually a-helical regions of 20 to 25
  nonpolar amino acids
• Some membrane-spanning proteins have ß-barrel,
  folding of ß sheets into
• barrel-like structure
• (some bacteria,
• chloroplasts, mitochondria).

Fig. 2.25, 2.26 a-helix, b-barrel
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Figure 2.27 Permeability of phospholipid bilayers

• Selective permeability of membranes allows cell
  to control its internal composition.
• Some molecules diffuse across bilayer CO2, O2,
  H2O.
• Ions, larger uncharged molecules such as glucose,
  not diffuse

Fig. 2.27
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Figure 2.28 Channel and carrier proteins

• Transmembrane proteins act as transporters
• Channel proteins open pores across membrane.
• selectively open and close in response to
  extracellular signals
• Carrier proteins
• selectively bind,
• transport specific
• small molecules,
• such as glucose
• conformational changes
• open channels
• Much more in Chapt. 13

Fig. 2.28
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Figure 2.29 Model of active transport
Passive transport molecule movement across
membrane determined by concentration and
electrochemical gradients. Active transport
molecules transported against concentration
gradient coupled to ATP hydrolysis ex. export
of H or Na from cell
Fig. 2.29 Active transport
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C. Proteomics Large-Scale Analysis of Cell
Proteins

• C. Large-scale experimental approaches to
  understand complexities of biological systems.
• Genomics systematic analysis of cell genomes -
• all the DNA of organism
• Proteomics systematic analysis to identify all
  cell proteins, where they are expressed, and
  interactions
• Number of genes expressed in any cell is
  10,000.
• Alternative splicing, protein modifications, ?
  more than 100,000 different proteins
• Look at different tissues, time of development,
  cancer cells
• New tools permit these analyses

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Figure 2.30 Two-dimensional gel electrophoresis

• Two-dimensional gel electrophoresis does
  large-scale separation of cell proteins
• Proteins separated based on charge and size.
• Biased toward the most abundant proteins.

Fig. 2.30
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Figure 2.31 Identification of proteins by mass
spectrometry

• Mass spectrometry identifies excised proteins
• protease cleaves protein into small peptides
  then ionized, analyzed in mass spectrometer
  (determines the mass-to-charge ratio of each
  peptide).
• mass spectrum compared to database of known
  spectra says which peptide.

Fig. 2.31
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Proteomics Large-Scale Analysis of Cell Proteins

• Proteomics goals include locations of proteins in
  cells
• Organelles can be isolated by subcellular
  fractionation
• proteins then analyzed by mass spectrometry
• Yeast strains in which each protein has been
  tagged by fusion with GFP (Fluorescence
  microscopy).

Fig. 2.32
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Proteomics Large-Scale Analysis of Cell Proteins

• Networks (interactome) Protein function requires
  interacting with other proteins in complexes
• Systematic analysis of protein complexes
  important goal
• Isolate proteins under gentle conditions
• so complexes not disrupted.
• Analyze protein complexes
• by mass spec
• Also screen with antibodies for
• co-immuno-precipitation
• Genetic screens for in vivo protein
• interactions use yeast two-hybrid
• technique

Drosophila
Fig. 2.33
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Figure 2.33 A protein interaction map of
Drosophila melanogaster

• Review questions
• What was new material in this section?
• Diagram the structure of a phospholipid and a fat
• Diagram ribose, deoxyribose, numbering Carbons
• 3. What are the major functions of fats and
  phospholipids in cells?
• 6. What experimental evidence showed that the
  primary sequence of amino acids contains the
  information for folding of the protein?
• 8. What are the biological roles of cholesterol?