Summary for the course Basic Cell and Molecular Biology. This course is given in the first year of Biology at the Rijksuniversiteit Groningen. The summary is made from the book Molecular Biology of the Cell.
Summary Molecular Biology of the Cell 2 (book) (WBFA007-04)
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Basic Cell and Molecular Biology (WBBY00105)
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Basic Cell and Molecular Biology
Book - Molecular Biology of The Cell
Chapter 1: Cells and Genomes
Cell biology = the study of the structure, function, and behavior of cells.
The whole of biology is thus a counterpoint between two themes: astonishing variety in
individual particulars; astonishing constancy in fundamental mechanisms.
The universal features of cells on earth
Each species is different, and each reproduces itself faithfully, yielding progeny that belong to
the same species: the parent organism hands down information specifying, in extraordinary
detail, the characteristics that the offspring shall have.
Life employs the free energy to drive a hugely complex system of chemical processes that are
specified by hereditary information.
All cells store their hereditary information in the same linear chemical code: DNA
All living cells on Earth store their hereditary information in the form of double-stranded
molecules of DNA - long, unbranched, pair polymer chains, formed always of the same four
types of monomers.
Monomers = chemical compound known as nucleotides → A,T,C,G. They are strung together
in a long linear sequence that encodes the genetic information.
All cells replicate their hereditary information by templated polymerization
Each monomer in a single DNA strand - that is, each nucleotide - consists of two parts: a sugar
(deoxyribose) with a phosphate group attached to it, and a base, which may be either adenine
(A), guanine (G), cytosine (C), or thymine (T). A binds to T, and C binds to G.
Each sugar is linked to the next via the phosphate group, creating a polymer chain composed of
a repetitive sugar-phosphate backbone with a series of bases protruding from it.
The two strands twist around each other, forming a DNA double helix.
DNA replication = the bonds between the base pairs are weak compared with the
sugar-phosphate links, and this allows the two DNA strands to be pulled apart without breakage
of their backbones. Each strand then can serve as a template for the synthesis of a new DNA
strand complementary to itself.
DNA is the information store for heredity, and templated polymerization i s the way in which this
information is copied throughout the living world.
All cells transcribe portions of their hereditary information into the same intermediary
form: RNA
,Transcription = segments of the DNA sequence(genes) are used as templates for the
synthesis of shorter molecules of the closely related polymer ribonucleic acid (RNA), that then
translate into a protein.
In RNA, the backbone is formed of a slightly different sugar from that of DNA - ribose instead of
deoxyribose - and one of the four bases is slightly different - uracil (U) instead of thymine (T).
During transcription, the RNA monomers are lined up and selected for polymerization on a
template strand of DNA. The outcome is a polymer molecule whose sequence of nucleotides
represents a portion of the cell’s genetic information.
Messenger RNA (mRNA) = guide the synthesis of proteins according to the genetic instructions
stored in the DNA.
Being single-stranded, their backbone is flexible, so that the polymer chain can bend back on
itself to allow one part of the molecule to form weak bonds with another part of the same
molecule.
All cells use proteins as catalysts
Proteins = long unbranched polymer chains, formed by stringing together monomeric building
blocks drawn from a standard repertoire that is the same for all living cells.
Polypeptide = each amino acid is built around the same core structure through which it can be
linked in a standard way to any other acid in the set; attached to this core is a side group that
give each amino acid a distinctive chemical character.
Enzymes = by folding into a precise three-dimensional form with reactive sites on its surface,
these amino-acid polymers can bind with high specificity to other molecules and can act as
enzymes to catalyze reactions that make or break covalent bonds.
Each protein molecule performs a specific function according to its own genetically specified
sequence of amino acids.
All cells translate RNA into protein in the same way
The information in the sequence of a messenger RNA molecule is read out in groups of three
nucleotides at a time: each triplet of nucleotides, or codon, specifies (codes for) a single amino
acid in a corresponding protein.
This genetic code i s read out by a special class of small RNA molecules, the transfer RNAs
(tRNAs). Each type of tRNA becomes attached at one end to a specific amino acid, and
displays at its other end a specific sequence of three nucleotides - anticodon - that enables it to
recognize, through base-pairing, a particular codon in mRNA.
Ribosome = large multimolecular machine composed of both protein and ribosomal RNA.
Each protein is encoded by a specific gene
Special sequences in the DNA serve as punctuation, defining where the information for each
protein begin and end. And individual segments of the long DNA sequences are transcribed into
separate mRNA molecules, coding for different proteins.
RNA molecules transcribed from the same DNA segment can often be processed in more than
one way, so it gives rise to a set of alternative versions of a protein, especially in more complex
cells.
, Gene = the 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.
In all cells, the expression of individual genes is regulated: instead of manufacturing its full
repertoire of possible proteins at full tilt all the time, the cell adjusts the rate of transcription and
translation of different genes independently, according to need.
Stretches of regulatory DNA are interspersed among the segments that code for protein, and
these noncoding regions bind to special protein molecules that control the local rate of
transcription.
Genome = the totality of its genetic information as embodied in its complete DNA sequence.
All cells function as biochemical factories dealing with the same basic molecular building
blocks
Because all cells make DNA, RNA and protein, all cells have to contain and manipulate a
similar collection of small molecules.
ATP = adenosine triphosphate, a building block for the synthesis of DNA and RNA, but also a
carrier of the free energy that is needed to drive a huge number of chemical reactions in the cell.
All cells are enclosed in a plasma membrane across which nutrients and waste materials
must pass
Another universal feature is that each cell is enclosed by a membrane.
Plasma membrane = this container acts as a 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.
The molecules that form a membrane, have the simple physicochemical property of being
amphiphilic - that is, consisting of one part that is hydrophobic and another part that is
hydrophilic. Amphiphilic molecules of appropriate shape, such as the phospholipid molecules
that comprise most of the plasma membrane, spontaneously aggregate in water to create a
bilayer that forms small closed vesicles.
Membrane transport proteins = determines which molecules enter the cell, and the catalytic
proteins inside the cell determine the reactions that those molecules undergo.
The diversity of genomes and the tree of life
Cells can be powered by a variety of free-energy sources
Organotrophic = organisms that get their energy by feeding on other living thing or the organic
chemicals they produce.
Other organisms derive their energy directly from the nonliving world. These primary energy
converters fall into two classes:
1. Phototropic = those that harvest the energy of sunlight
2. Lithotrophic = those that capture their energy from energy-rich systems of inorganic
chemicals in the environment (rocks)
Phototrophic organisms have changed the whole chemistry of our environment: the oxygen in
the Earth’s atmosphere is a by-product of their biosynthetic activities. Some lithotrophs get
energy from aerobic reactions, which use molecular oxygen from the environment; since
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