The Nature of Life. Some properties of life. Copyright 2005 Pearson Education, Inc. publishing as Benjamin Cummings

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1 The Nature of Life Some properties of life opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings

2 Life Displays rder opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings

3 Life Uses Energy opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings

4 Energy flows through an ecosystem Usually entering as sunlight and exiting as heat Sunlight Ecosystem Producers (plants and other photosynthetic organisms) eat hemical energy onsumers (including animals) Figure 1.4 opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings eat

5 A loser Look at ells The cell Is the lowest level of organization that can perform all activities required for life all enclosed by a membrane all use DNA as genetic information Figure 1.5 opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings 25 µm

6 uter membrane and cell surface ELL ytoplasm Nucleu s Figure 1.10 opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings

7 arbon-based Life Essential elements Include carbon, hydrogen, oxygen, and nitrogen Make up 96% of living matter A few other elements Make up the remaining 4% of living matter opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings

arbon is Special The backbone of biological molecules All living organisms are made up of chemicals based mostly on this one element --> organic chemistry The

8 arbon is Special The backbone of biological molecules All living organisms are made up of chemicals based mostly on this one element --> organic chemistry The bonding versatility of carbon allows it to form many diverse molecules, varying in length and shape opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings

9 Molecular omponents of ells arbohydrates food energy, sugars and starches structure (cellulose) Lipids/fats an store energy Major ingredient in cell membranes Proteins Work-horses of cells opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings

10 Proteins Proteins have many roles inside the cell Some serve as structural elements Enzymes serve as catalysts to biochemical reactions in cell Built from amino acids organic molecules possessing both amino group [N bonded to 2 and 1 ] and carboxyl group [] Differ in their properties due to differing side chains, called R groups opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings

Enzymes Are a type of protein that acts as a catalyst, speeding up chemical reactions 1 Active site is available for a molecule of substrate, the reactant on which the enzyme acts.

11 Enzymes Are a type of protein that acts as a catalyst, speeding up chemical reactions 1 Active site is available for a molecule of substrate, the reactant on which the enzyme acts. Substrate (sucrose) 2 Substrate binds to enzyme. Glucose Enzyme (sucrase) 2 Fructose 4 Products are released. Figure 5.16 opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings 3 Substrate is converted to products.

12 Proteins Proteins have many roles inside the cell Some serve as structural elements Enzymes serve as catalysts to biochemical reactions in cell Built from amino acids organic molecules possessing both amino group [N bonded to 2 and 1 ] and carboxyl group [] Differ in their properties due to differing side chains, called R groups opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings

13 Amino Acid Monomers 20 different amino acids make up proteins 3 3 3N + 3 3N+ Glycine (Gly) 3N + Alanine (Ala) 2 3N + Valine (Val) N Leucine (Leu) + Isoleucine (Ile) Nonpolar 3 2 S N 2 2 3N+ 2 3N+ Methionine (Met) 3N+ Phenylalanine (Phe) Figure 5.17 opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings N Tryptophan (Trp) Proline (Pro)

Polar 2 3N + 3N+ Serine (Ser) 2 3N+ 2 3N + 2 3N + Electrically charged 3N+ N3+ 2 2 2 2 2 2 2 2 3N + 2 3N+ Aspartic acid (Asp) Glutamine (Gln) N2 3N Asparagine (Asn) 2 + Basic 2 Acidic Tyrosine

14 Polar 2 3N + 3N+ Serine (Ser) 2 3N+ 2 3N + 2 3N + Electrically charged 3N+ N N + 2 3N+ Aspartic acid (Asp) Glutamine (Gln) N2 3N Asparagine (Asn) 2 + Basic 2 Acidic Tyrosine (Tyr) ysteine (ys) Threonine (Thr) N2 S 3 N2 Glutamic acid (Glu) opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings N2+ Lysine (Lys) 3N+ 2 N 2 3N+ 2 N+ Arginine (Arg) istidine (is)

15 Nucleic Acids Nucleic acids store and transmit hereditary information Genes Are the units of inheritance Program amino acid sequences Are made of nucleic acids There are two types of nucleic acids Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA) opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings

DNA Stores Information Set of operating instructions for cell directs RNA synthesis and protein synthesis through RNA Way of passing down information through generations DNA 1 Synthesis of mrna in

16 DNA Stores Information Set of operating instructions for cell directs RNA synthesis and protein synthesis through RNA Way of passing down information through generations DNA 1 Synthesis of mrna in the nucleus mrna NULEUS YTPLASM mrna 2 Movement of mrna into cytoplasm via nuclear pore 3 Figure 5.25 opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings Ribosome Synthesis of protein Polypeptide Amino acids

17 The DNA Double elix ellular DNA molecules ave two 'zipper edges' that spiral around an imaginary axis Form a double helix backbone The base sequence of 'zipper teeth' Adenine (A), guanine (G), thymine (T), cytosine () unique for each gene The bases in DNA form bonds in a complementary fashion (A with T only, with G only) opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings

The DNA double helix onsists of two anti-parallel nucleotide strands 5 end 3 end Sugar-phosphate backbone Base pair (joined by hydrogen bonding) ld strands A 3

18 The DNA double helix onsists of two anti-parallel nucleotide strands 5 end 3 end Sugar-phosphate backbone Base pair (joined by hydrogen bonding) ld strands A 3 end Nucleotide about to be added to a new strand 5 end 3 end Figure end opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings New strands 3 end

19 Nucleus DNA ell A Nucleotide T A T A G T A G T A Figure 1.7 (a) DNA double helix. This model shows each atom in a segment of DNA.Made up of two long chains of building blocks called nucleotides, a DNA molecule takes the three-dimensional form of a double helix. opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings (b) Single strand of DNA. These geometric shapes and letters are simple symbols for the nucleotides in a small section of one chain of a DNA molecule. Genetic information is encoded in specific sequences of the four types of nucleotides (their names are abbreviated here as A, T,, and G).

20 DNA replication 'unzipping' of two strands to make new, complementary strand opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings

The Book of DNA Level Base pair odon Gene Bacterium uman Atoms Bits 10 100 10,000 10,000,000 3,000,000,000 opyright 2005 Pearson

21 The Book of DNA Level Base pair odon Gene Bacterium uman Atoms Bits ,000 10,000,000 3,000,000,000 opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings ,000,000 6,000,000,000 Language analog Letter Word Sentence Short book Encyclopedia

22 The Genetic ode Uses a four letter alphabet with specific pairing rules ontains redundancy because 4 x 4 x 4 codons could specify 64 amino acids Does not require perfect fidelity in copying because of cross-checking elsewhere Extends to the huge information content of 3 billion base pairs and 25,000 genes (in humans) opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings

23 The Genetic ode opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings

24 Now... The Modern Tree of Life Maps evolution via the gradual deviation of the base pair sequences in DNA or RNA Shows relationships between species Does not depend on identifying or recognizing distinct species True diversity of life found almost entirely within microscopic realm WRK IN PRGRESS! opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings

25 The Modern Tree of Life opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings

26 The Three Domains of Life At the highest level, life is classified into three domains Bacteria Archaea Eukarya The species concept is tricky. Its normally defined by the ability to reproduce (and by a similar appearance) but many organisms can clone or reproduce asexually, and microbes don t look very different from each other. opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings

Life s three domains 4 µm Bacteria are the most diverse and widespread prokaryotes and are now divided among multiple kingdoms. Each of the rod-shaped structures in this photo is a bacterial cell.

27 Life s three domains 4 µm Bacteria are the most diverse and widespread prokaryotes and are now divided among multiple kingdoms. Each of the rod-shaped structures in this photo is a bacterial cell. DMAIN ARAEA Figure 1.15 Many of the prokaryotes known 0.5 µm as archaea live in Earth s extreme environments, such as salty lakes and boiling hot springs. Domain Archaea includes multiple kingdoms. The photo shows a colony composed of many cells. Protists (multiple kingdoms) 100 µm are unicellular eukaryotes and their relatively simple multicellular relatives.pictured here is an assortment of protists inhabiting pond water. Scientists are currently debating how to split the protists into several kingdoms that better represent evolution and diversity. Kingdom Plantae consists of multicellula eukaryotes that carry out photosynthesis, the conversion of light energy to food. Kindom Fungi is defined in part by the nutritional mode of its members, such as this mushroom, which absorb nutrientsafter decomposing organic material. Kindom Animalia consists of multicellular eukaryotes that ingest other organisms. opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings

28 Domain Bacteria and domain Archaea onsist of prokaryotes, cells without nuclei Domain Eukarya, the eukaryotes Includes the various protist kingdoms and the kingdoms Plantae, Fungi, and Animalia Simple, single-celled organisms or microbes dominate life on Earth: 5000x more mass in ocean microbes than all humans combined opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings

29 ells and Energy We know cells are the ingredients of life... And that they carry the instructions for life... But how do they MAKE LIFE? Light energy ESYSTEM ells need: Materials Photosynthesis in chloroplasts ellular respirationin mitochondria rganic + 2 molecules Energy ATP powers most cellular work Figure 9.2 opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings eat energy

30 ATP ells can build incredible variety of molecules from limited set of starting materials --> due to enzyme variety and... ATP! Used to store and release energy for nearly all chemical manufacturing nce produced, can be used to provide energy for any cellular reaction opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings

31 ATP ompletely recyclable! opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings

32 ategorizing Life by arbon and Energy Metabolism comes down to needing primary raw material of life carbon and energy arbon sources Eating = heterotroph Environment = autotroph Energy sources Sunlight = photo(synthesis) rganic compounds (food) = chemo Neither = inorganic chemicals w/o from environment opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings

ategorizing Life by arbon and Energy Liquid water is the final ingredient in metabolism Allows organics to float within cell --> readily available for chemical reactions Medium of

33 ategorizing Life by arbon and Energy Liquid water is the final ingredient in metabolism Allows organics to float within cell --> readily available for chemical reactions Medium of transport for chemicals to and within cells, way to transport waste away Ingredient in many metabolic reactions within cells opyright 2005 Pearson Education, Inc. publishing as Benjamin ummings

Bioinformatics. ONE Introduction to Biology. Sami Khuri Department of Computer Science San José State University Biology/CS 123A Fall 2012

Bioinformatics. ONE Introduction to Biology. Sami Khuri Department of Computer Science San José State University Biology/CS 123A Fall 2012 Bioinformatics ONE Introduction to Biology Sami Khuri Department of Computer Science San José State University Biology/CS 123A Fall 2012 Biology Review DNA RNA Proteins Central Dogma Transcription Translation