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Lecture 2

BIO130H1 Lecture Notes - Lecture 2: Nuclear Membrane, Sulfolobus, Thymidine


Department
Biology
Course Code
BIO130H1
Professor
Kenneth Yip
Lecture
2

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Chapter 1 Introduction to the Cell
THE UNIVERSAL FEATURES OF CELLS ON EARTH
Heredity is central to the definition of life: it distinguishes life from other processes
The single cell is the vehicle for the hereditary information that defines the species
It includes the machinery to gather rat materials from the environment, and to construct out of them a new cell
in its own image, complete with a new copy of hereditary information
All Cells store their hereditary information in the same linear chemical code (DNA)
All cells store their heredity information in double stranded DNA: long unbranched paired polymer chains
All cells replicate their hereditary information by template polymerization
Each nucleotide (monomer) consists of two parts: a deoxyribose sugar with a phosphate group attached and a
base (ATCG)
Each sugar is linked with the next phosphate group creating a polymer chain
DNA is synthesized from a template formed by a pre-existing DNA strand
AT (2 H bonds) and CG (3 H bonds)
Two strands twist to form a double helix
Individual sugar-phosphate units are asymmetric, giving the backbone of the strand a definite directionality or
polarity which guides the molecular processes by which the information in DNA is interpreted and copied in
cells: information is always read in a consistent order
A normal DNA consists of two such complementary strands; the nucleotides within each strand are linked by
strong covalent chemical bonds
Bonds between the base pairs are weaker than the sugar-phosphate links, allowing the 2 DNA strands to be
pulled apart without breaking the backbone
DNA replication occurs at different rates with different controls to start/stop it and different auxiliary molecules
to help it along
Template polymerization is 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)

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In transcription, segments of DNA sequence are used as templates for the synthesis of shorter molecules (RNA)
In translation, many of these RNA direct the synthesis of proteins
RNA: ribose instead of deoxyribose; U instead of T
DNA is fixed and sacrosanct, RNA transcripts are mass-produced and disposable
Transcripts mainly serve as an intermediate: messenger RNA to guide the synthesis of proteins according to DNA
Being single stranded, the polymer chain can bend 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
Protein molecules: long unbranched polymer chains, formed by stringing
together monomeric building blocks drawn from a standard repertoire that is the same
for all living cells
Amino acids: monomers of protein; 20 types; same core structure with side
group that gives each its distinctive chemical character
Polypeptides: created by joining aa in a particular sequence folds into a precise
3D form with reactive sites on its surface
Bind with high specificity too other molecules and act as enzymes to catalyze reactions that make or break
covalent bonds
Proteins also maintain structures, generate movements, sense signals; put the genetic info into action
All cells translate RNA into protein the same way
mRNA read 3 nucleotides at a time (codon); several codons correspond to the same aa
code is read out by transfer RNAs; each tRNA is attached to an aa with the anticodon displayed at the other end
tRNA with the right aa is matched with the mRNA; aa have to be linked to extend the chain; tRNA is released
process is carried out by the ribosome, formed of two chains of RNA called ribosomal RNAs
ribosome latches onto the end of mRNA and then trundles along, capturing tRNA and stitching together the aa
The fragment of genetic information corresponding to one protein is one gene
each segment coding for a different protein -> gene
RNA molecules transcribed can often be processed in more than one way, giving rise to a set of alternative
versions of a protein
A gene is the segment of DNA sequence corresponding to a single protein or set of alternative protein variants
or to a single catalytic or structural RNA molecule for those genes that produce RNA but not protein
The expression of individual genes is regulated
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
Other noncoding DNA define where the information for an individual protein begins and ends
The quantity and organization of the regulatory and noncoding DNA vary widely from organism to organism
Genome: the total of its genetic information as embodied in its complete DNA sequence
Life requires free energy

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For a cell to grow or to make a new cell in its own image, it must take in free energy from the environment, as
well as raw materials
Free energy is required for the propagation of information
All cells function as biochemical factories dealing with the same basic molecular building blocks
All cells have to contain and manipulate a similar collection of small molecules
All cells require ATP as a building block for the synthesis of DNA and RNA
Many of the details of their small molecule transactions differ
Some organisms require only the simplest of nutrients and harness the energy of sunlight to make from these
almost all their own small organic molecules
Others feed on living things and obtain many of their organic molecules ready-made
All cells are enclosed in a plasma membrane across which nutrients and waste materials must pass
Each cell is enclosed by the plasma membrane
Acts as a selective barrier that enables the cell to concentrate nutrients gathered from its environment
Retain the products it synthesizes for its own use, while excreting its waste products
Amphiphilic: one part that is hydrophobic and another that is hydrophilic
Placed in water, aggregate spontaneously to form a bilayer that creates small closed vesicles
Cells produce molecules whose chemical properties cause them to self-assemble into the structures that a cell
needs
All cells have specialized proteins embedded in their membrane that transport
specific molecules from one side to the other
Transport proteins in the membrane largely determine which molecules enter the
cell, and the catalytic proteins inside the cell determine the reactions that those
molecules undergo
A living cell can exist with fewer than 500 genes
The bacterium Mycoplasma genitalium lives as a parasite in mammals with ready-made small molecules
Has about 480 genes
The minimum number of genes for a viable cell in today’s environments is probably not less than 200-300
THE DIVERSITY OF GENOMES AND THE TREE OF LIFE
Darkest depths of the ocean, in hot volcanic mud, in pools beneath the frozen surface of the Antarctic and
buried kilometres deep in the earth’s crust
Microorganisms make up most of the total mass of living matter on our planet
Cells can be powered by a variety of free energy sources
Living organisms obtain their free energy in different ways
Organotrophic: feed on other living things or the organic chemicals they produce
Phototrophic: harvest the energy of sunlight; the O in the atmosphere is a by-product of their activities
Lithotrophic: capture their energy from energy-rich systems of inorganic chemicals in the environment
Organotrophic organisms could not exist without these primary energy converters
Phototropic organisms include many types of bacteria, as well as algae and plants
Lithotrophic organisms are microscopic and live in habitats that humans do not frequent
Some lithotrophs get energy from aerobic reactions, which use molecular oxygen from the environment
Other lithotrophs that live anaerobically, in places with little or no molecular oxygen
Hydrothermal vents: regions where the ocean floor is spreading as new portions of the Earth’s crust form by a
gradual upwelling of material from the Earth’s interior
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