CH 01 Objectives - Summary Molecular Biology of the Cell PDF

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CELL BIOLOGY LECTURE OBJECTIVES Chapter 1: Cells and Genomes After attending this series of lectures and studying the text, lecture presentations, and notes, the student should be able to: 1.

List and describe 10 universal features of cells. 

Storage of hereditary information in same linear code: DNA o Can be transferred and still interpreted/copied

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Replicate DNA by template polymerization o Synthesized on preexisting strand

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DNA transcribed into same intermediary form: RNA o DNA must also express information (RNA and proteins) o Transcription and Translation o RNA transcripts mass produced 

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Serve as mRNA to guide the synthesis of proteins according to the genetic instructions

Translate RNA into protein in same way o Codon to code for amino acids

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Use proteins as catalysts o 20 types of amino acids o make or break covalent bonds

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Fragment of DNA that corresponds to 1 product= genes o Segment of DNA sequence corresponding to a single protein or set of alternative protein variants or to a single catalytic, regulatory, or structural RNA molecule o Regulatory DNA interspersed

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Require free energy o Consumption of free energy is fundamental to life o Required for propagation of DNA

o Has to be spent on the creation of order 

Biochemical factories- same basic building blocks o Biochemical factories with different small-molecule transactions

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Enclosed in a plasma membrane (container) o Plasma membrane- selective barrier; amphipathic o Self assembly o Membrane transport proteins- transport molecules from one side to the other

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Require at least 250 genes (genome) o Doesn’t have to be huge

2.

Define the following terms as they relate to objective #1 above: replication, templated polymerization, transcription, translation (codon/anticodon), conformation, catalysts, gene, genome, amphipathic, and free energy. 

Replication o DNA monomers (nucleic acids) composed of sugar (deoxyribose) w/ phosphate group and base (AGCT) o Each sugar linked via phosphate group; monomers added to the 3’ end o Two strands split into template strands so one molecule of DNA becomes 2

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Templated Polymerization o Each strand is a template for the new strand; way it is copied o Way in which genetic information is copied throughout the living world

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Transcription o Template polymerization in which segments of DNA are used as templates for the synthesis of shorter molecules of RNA; o Step towards making a protein

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Translation (codon/anticodon) o RNA molecules direct the synthesis of proteins o The small pieces = mRNA which guide synthesis of proteins o Codon- section of protein coded for (GAC); specifies for specific amino acid

o Anticodon- opposite of target for protein (CTG); on the amino acid 

Conformation o Shape/Folding o Functional shape of a protein

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Catalysts o Amino acids in proteins can bind with high specificity to other molecules = enzymes o Direct vast majority of chemical processes in the cell o Speed up reactions by lowering activation energy

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Gene o Sections along the DNA are transcribed into separate mRNA molecules, so different proteins; Each section is a gene o Can be processed in different ways  different end results o Expression of individual genes is regulated (regulatory DNA) o (see above) o codes for a single protein

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Genome o Totality of a cell’s genetic information as embodied in its complete DNA sequence o Dictates nature of the proteins, when and where they are made o Doesn’t have to be huge

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Amphipathic o One part hydrophobic and another part hydrophilic o Heads are hydrophilic and tails are hydrophobic for plasma membrane

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Free Energy o Needed for necessary metabolic actions of cell o Like energy of spring in a trap like in a bond o Released when attached to low energy partner arrangement

o In animal cells, derived from chemical food molecules/ plants from sun 3.

List and describe 4 sources of the vast diversity seen in cells. Include in your description of genetic diversity a discussion of how genome size, complexity and sequence analysis show diversity in cells, and how new genes can be formed from mutations and gene transfer. 

Different Sources of free energy o Organotrophic 

Animal, fungi, bacteria

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Energy from other living things and the organic chemicals they produce

o Phototrophic 

Algae, bacteria, plants

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Energy from sunlight

o Lithotrophic 

Some bacteria and archaebacteria

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Energy from inorganic materials

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Microscopic and live in habitats that humans do not frequent

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Some aerobic and some anaerobic

o There couldn’t be organotrophic organisms without the other two. 

Ability to fix Nitrogen and Carbon Dioxide o Inorganic material conversion so that N and C can be used by organisms 

N used for amino acids and nucleic acids

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C used for organic chemicals.

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Plants typically produce them.

o Atmospheric N2 and CO2 are extremely unreactive, so they must be made available for organisms 

Prokaryotes vs. Eukaryotes o Prokaryotes are diverse within their own group 

Live in independence or small communities

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Spherical, rod, spiral, small; some have flagellum

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Bacteria/Archaea

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Don’t have distinct nuclear compartment 

Phototrophic and lithotrophic

o Eukaryotes

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Animals, plants, fungi

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Distinct membrane-bounded nucleus and organelles

Genetic Diversity o Bacteria, Archaea, or Eukaryotes o Classified based in biochemistry and nutritional requirements 

Classification of 3 domains based on a comparison of the nucleotide sequence of rRNA subunit

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A/B similar in energy conversion 

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Bacteria more similar to A in their metabolism

E/A similar in their central dogma 

Molecular level, A resemble E more for central dogma

o New Genes  Mutations 

Neutral, damaging, advantageous (natural selection) 

3rd nucleotide alteration would make the least difference

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intragenic- existing gene randomly modified

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gene duplication

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DNA segment shuffling- two or more existing genes can break and rejoin to make a hybrid gene from two different genes

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Horizontal transfer- DNA piece transferred from the genome of one cell to that of other (even to other species)

o Gene Transfer 

New genes from preexisting genes

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Organisms transferring genes to another organism (horizontal transfer) 

Ex: bacterial virus T4 to host bacterium

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By error (intragenic mutation)

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Gene duplication

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DNA segment shuffling

o Genome Size and Complexity 

how genome size, complexity and sequence analysis show diversity in cells, and how new genes can be formed from mutations and gene transfer. 

Genome size and complexity of organism are not related

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Humans are so complex because of the enormous amount of regulatory DNA we have o Regulatory DNA are areas designed to enhance and facilitate the transcription of other genes; noncoding regions interspersed and bind to special protein molecules that control the local rate of transcription

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Smaller means faster reproduction

Small size means large ratio of surface area to volume so it maximizes the uptake of nutrients across the plasma membrane 

Why prokaryotes have small genome

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Paralogs- gene duplications giving rise to families of related genes within a single cell; diverged in function; arises from duplications from single cell; homolog

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Homologs- genes similar in sequence; genes related by descent in either way;

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Orthologs- genes in two separate species that derive from the same ancestral gene; homolog; speciation 

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Ex: alpha/beta globin/myoglobin

Gene families arises from speciation; homolog 

Paralogs and orthologs

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Get complicated; hemoglobin, myoglobin, globin

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Repeated rounds to replication with mutations in gene copies so they become specialized with different functions in the same cell

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Multiple variants of primordial gene

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related

Similarities between genomes, similar genes present

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Gene expression 

Monitored and controlled by noncoding DNA

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DNA codes for proteins that regulate other gene activities

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Allows for specialization o Still interdependency between cells to survive

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4.

Mutations can reveal function of gene

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Eukaryotes have larger genomes and rich in regulatory DNA; usually live as solitary cells

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Conserved Sequences- some sequences of DNA have been highly conserved without much mutation

Define the following terms as they relate to objective #3 above: procaryote, eucaryote, fixation (N and CO2), organotrophic, phototrophic, lithotrophic, conserved sequences, homologs, paralogs, orthologs, gene family, gene expression.

see above 5.

Briefly describe the structure and function of 2 unique features of eucaryotes and explain how symbiosis may be involved in their developments. 

Mitochondria o Use oxygen, harness energy from oxidation of molecules to make ATP o Large surface area because of inner membrane o Have their own genome; similar to small bacteria o Symbiosis: developed between aerobic eubacteria and early eukaryotic cell

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Chloroplasts o Photosynthesis to obtain energy and produce water and carbon dioxide o Have own genome o Symbiosis: between photosynthetic bacteria and cells already possessing mitochondria o Stacks within

6.

Describe the use and usefulness of the following organisms as models: E. coli, S. cerevisiae, Arabidopsis thaliana, C. elegans, D. melanogaster, Mus musculus 

E. coli

o Adapts to conditions; differ genetically o Reproduces rapidly o Grows easily in simple nutrient broth o Mechanisms of DNA replication, transcription and translation studied o New gene function can sometimes be determined from a homologous gene in E.coli 

S. cerevisiae o Minimal eukaryote o Easy to grow; budding yeast; nutrients = reproduce cell division or sexually 

Haploid or diploid reproduction

o Tough wall, immobile, possesses mitochondria not chloroplasts o No complications of multicellular development; small genome but suffices o Particular reproduction can be induced o Human homologs of yeast genes studied in yeast mutants 

Arabidopsis thaliana o Plant organism; grown indoors quickly o Quick growth with many offspring and closely related to other flowering plants o Genome completely sequenced

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C. elegans o Nematode; o cell division and cell death; aging model o clockwork precision of development o know every cell that develops; aging model because starvation leads to longer life

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D. melanogaster o Fruit fly o Proof of genes and chromosomes; reproduces quickly; cheap o Genes for development similar in insect and vertebrae

o Aging model Mus musculus o Mouse o Humanized, can put genes in them and see the expression or impact of gene; sue this to determine its function...