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 reactionsStudent 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

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 moleculesHydrophilic molecules (ions, polar) are solubleHydrophobic molecules (nonpolar) are not soluble

Organic molecules: mostly carbohydrates, lipids, proteins, or nucleic acids.

Fig. 2.1

The Molecules of Cells

Fig. 2.2

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

Monosaccharides join together by glycosidic bond→ disaccharide [dehydration reactions (H2O is removed)]

Oligosaccharides: Polymers, a few sugars

Polysaccharides macromolecules; hundreds or thousands of sugars

Monosaccharides

Fig. 2.3C1 to C41-4 bond

Figure 2.4 Polysaccharides

Glycogen: storage form in animal cells. C1-4

Starch: storage in plant cells.• glucose molecules in α configuration: mostly 1-4, some 1-6

Cellulose structural component of plant cell wall. • glucose in β configuration; (β1→4) – long chains, strong fibers

.

Fig. 2.4

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)

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

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 efficientenergy storage than carbohydrates: yield more thantwice as much energy per weight.

Fig. 2.6 triacylglycerol,triglyceride

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-ethanolaminePhosphatidyl-serinePhosphatidyl-choline

Fig. 2.7

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

Figure 2.8 Structure of glycolipids

Many membranes haveGlycolipids

Glycolipids are Amphipathic:Sugar, fatty acids, no phosphate

[Note: Archaeal membranes are very different: ether linkages between glycerol and hydrocarbon isoprene units; see handout]

Fig. 2.8

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

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

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

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

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

Fig. 2.11

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

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

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

Figure 2.13 Structure of amino acids

Amino acids

• Each has α 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*

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

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 α carboxyl group (C terminus)• Sequence of aa definescharacteristics of protein

Fig. 2.15

Figure 2.17 Protein denaturation and refolding

Unique sequence of amino acids in protein is determined by order of nucleotide bases in gene.

Protein’s 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. 2.17 RNase can renature after denatured

Fig. 2.16 insulin has S-S bond between chains

The Molecules of Cells

Protein structure 4 levels:

Primary structure: sequence of amino acids

Secondary structure: regular arrangement of amino acids within localized regions ( helix, 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.

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 structureQuaternary 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 – 2, 2

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

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

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

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

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, (-helical) with portions exposed on both sides

Carbohydrates on outside proteins

Fig. 2.25**

Figure 2.26 Structure of a β-barrel

• Membrane-spanning portions of transmembrane proteins usually α-helical regions of 20 to 25 nonpolar amino acids

• Some membrane-spanning proteins have β-barrel, folding of β sheets into

barrel-like structure (some bacteria, chloroplasts, mitochondria).

Fig. 2.25, 2.26-helix, -barrel

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

Figure 2.28 Channel and carrier proteins

Transmembrane proteins act as transportersChannel 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

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. 2.29Active transport

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

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

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

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

Proteomics: Large-Scale Analysis of Cell Proteins

Drosophila

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

Fig. 2.33

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?