Basic cell biology
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Cells and Genomes
The universal features of cells on earth
The smallest form of life is a cell
Most organisms are single cells RNA has a flexible backbone and can thus
Once in their life, multicellular organisms were single cells fold in a way where the sequences of the
mRNA are complementary
Living organisms must consume free energy to create and maintain it’s organization
Comparing cells of all organisms
Common to all cells:
- storage of information in DNA
Different among cells:
- source of energy
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- replication, transcription, translation (DNA, RNA, protein) - diversity in shape and size
- each protein encoded by specific gene - prokaryote or eukaryote
- Proteins are catalysts - number of genes
- enclosed by a membrane (nutrients/waste passes) A
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All cells Replicate Their hereditary Information by nucleotide
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Proteins
H The monomers of proteins are called amino acids . Proteins can act as enzymes to catalyze
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reactions that make or break covalent bonds (involved in many chemical processes in cell). These
reactions take place at the catalytic site if the protein.
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It’s a feedback loop: polynucleotides specify amino sequence of proteins -> proteins catalyze
reactions (including the one where new DNA molecules are synthesized. The cell takes food,
processes it to derive building blocks and energy needed to make more catalysts.
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RNA molecules can be processed in more than one way: acid
1. RNA can set rise to a set of alternative versions of a protein anti codon
2. RNA molecules can have catalytic, regulatory, or structural I
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Regulatory DNA bind to special protein molecules that control the
local rate of transcription.
Important words:
Cell: small, membrane-enclosed units filled with a concentrated aqueous solution of chemicals and endowed with the extraordinary ability to create copies of
themselves by growing and then dividing in two.
Cell biology: the study of the structure, function, and behavior of cells
DNA: long, unbranded, paired polymer chains, formed always of the same four types of monomers (nucleotides: A,T,C,G)
Transcription: segments of the DNA sequence are used as templates for the synthesis of RNA
RNA: ribonucleic acid
Translation: synthesis of polymers -> protein
mRNA: transcripts of DNA (messenger RNA)
Polypeptide: joined amino acids in a particular sequence
Ribosomes: large multimolecular machine composed of both proteins and ribosomal RNA
Gene: region of DNA that is transcribed as a single unit and carries information for a discrete hereditary characteristic:
1) single protein (or set of related proteins
2) single RNA (or set of related RNA’s).
Genome: the totality of its genetic information as embodied in its complete DNA sequence
Regulatory DNA: noncoding regions
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,Free Energy
Free energy from the environment, as well as raw materials, are necessary for a cell to operate. A living cell is a dynamic chemical
system, operating far from chemical equilibrium.
The bonds between molecules need to be held and that costs energy,
↳ Free energy has to be spent on the creation of order
ATP is a carrier of this free energy
Membranes
Each cell is enclosed by a membrane, the plasma membrane
The plasma membrane has an outer layer of phospholipids with an hydrophobic and hydrophilic part. This
can be called amphiphilic
Amphiphilic molecules of appropriate shape can aggregate in water to create a bilayer that forms small
enclosed vesicles.
All cells have specialized proteins embedded in their membrane that transport specific molecules from one
side to the other. (Some proteins can be seen as a family by evolution)
Transport proteins determine which molecules enter the cell, and the catalytic proteins inside the cell
determine the reactions that those molecules undergo
Summary
The individual cell is the minimal self-reproducing unit of living matter, and it consists of a self-replicating collection of catalysts.
Central to this reproduction is the transmission of genetic information to progeny cells. Every cell on our planet stores
its genetic information in the same chemical form—as double-stranded DNA. The cell replicates its information by separating
the paired DNA strands and using each as a template for polymerization to make a new DNA strand with a complemen-
tary sequence of nucleotides. The same strategy of templated polymerization is used to transcribe portions of the information
from DNA into molecules of the closely related polymer, RNA. These RNA molecules in turn guide the synthesis of protein
molecules by the more complex machinery of translation, involving a large multi- (A) molecular machine, the ribosome.
Proteins are the principal catalysts for almost all the chemical reactions in the cell; their other functions include the selective
import and export of small molecules across the plasma membrane that forms the cell’s boundary. The specific function of
each protein depends on its amino acid sequence, which is specified by the nucleotide sequence of a corresponding segment
of the DNA—the gene that codes for that protein. In this way, the genome of the cell determines its chemistry; and the
chemistry of every living cell is fundamentally similar, because it must provide for the synthesis of DNA, RNA, and protein. The
simplest known cells can survive with about 400 genes.
Important words
Plasma membrane: selective barrier that enables the cell to concentrate nutrients gathered from its environment and retain the
products it synthesizes for its own use, while excreting its waste products. Without the membrane a cell could not contain its
chemical integrity.
, The diversity of genomes and the tree of life
Free-Energy sources
Organotrophic organisms feed on other living things or the organic chemicals they produce (animals, fungi, bacteria that live in humans)
Phototropic organisms feed on sunlight -> oxygen (bacteria and plants)
Lithotrophic organisms feed on inorganic nutrients (live inhospitable environments). Some are aerobic (oxygen) and other anaerobic (no
oxygen)
Organotrophic organisms (animals) depend on phototrophic organisms (plants) and phototrophic organisms depend on lithotrophic
organisms
A large amount of energy is required to drive the reactions that use these inorganic molecules to make the organic compounds needed
for further biosynthesis
Prokaryotes and Eukaryotes
Most prokaryotic cells are small and simple in outward appearance. They often have a
tough protective coat, called a cell wall, beneath which a plasma membrane encloses a
single cytoplasmic compartment containing DNA, RNA, proteins, and the many small
molecules needed for life. Their genomes are small, they have genes packed closely
together and minimal quantities of regulatory DNA between them.
Many prokaryotes have a remarkable capacity to take up even nonviral DNA molecules
from their surroundings and thereby capture the genetic information these molecules
carry.
The biochemistry of all organisms has a common origin that was fixed during early
evolution
Three Domains
Genome analysis is the most effective way to determine evolutionary relationships.
The prokaryotes comprised two groups: bacteria and archaea
Archaea are phylogenetically more similar to Eukaryotes than Bacteria are to either
Archaea or Eukaryotes
New Generated from Pre-existing genes
Through endless repetition of mutation and natural selection, organisms evolve
Some Genes evolve Rapidly; others Are highly conserved
Innovation can occur in several ways:
1. Intragenic mutation: an existing gene can be randomly modified by changes in its DNA sequence
2. Gene duplication: an existing gene can be accidentally duplicated so as to create a pair of initially identical
genes within a single cell
3. DNA segment shuffling: two or more existing genes can break and rejoin to make a hybrid gene
consisting of DNA segments that originally belonged to separate genes.
4. Horizontal (intercellular) transfer: a piece of DNA can be transferred from the genome of one cell to
that of another..
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The genes gradually become different in the course of
evolution, but they are likely to continue to have
corresponding functions in the two sister species:
orthodogs, paralogs and homologs
Minimal amount of genes which are necessary for life: 300
Important words
Prokaryotes: Prokaryotes have no distinct nuclear compartment to house their DNA (bacteria/archae)
Eukaryotes: Eukaryotes keep their DNA in a distinct membrane-enclosed intra- cellular compartment called the nucleus (plants, fungi, animals)
Gene families: Repeated rounds of this process of duplication and divergence, over many millions of years, have enabled one gene to give rise
to a family of genes that may all be found within a single genome.
Orthologs: homologous genes with same function in two species
Paralogs: Homologous genes with different functions in same species
Homologs: Genes that are related by descent in either way. It’s a general term used to cover both types of relationship
