Biophysics 321, Part 1, comprehensive lecture notes
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University Of Bristol (UOB)
Lecture notes written from the slide provided in lectures, includes diagrams, in-depth explanations and easy-to-view layout. This document contains all the information for the first 5 week of the course.
Section 1: Introduction to biological concepts
Cells:
Cell Types:
The cell is the unit of biological organisation. There are three different lineages of cell, all from a
common ancestor:
• Prokaryotes and Archea: These exist in extremely diverse environments. Both have a length of 3
μm or less.
• Eukaryotes: These types of cells make up all animals, plants and fungi, but most are actually
protists (e.g: Algae). These can range in size from a few μm to mm.
Diagram of a Prokaryotic Cell
Prokaryotic and eukaryotic cells do have some
similarities, they both have cell membranes, contain
cytoplasm, have ribosomes and contain DNA.
However, the DNA of a eukaryotic cell is enclosed
in the nucleus, with prokaryote cells do not possess.
Prokaryotic cells can reproduce asexually and
sexually and mostly divide by binary fission.
Whereas Eukaryotic cells mostly reproduce
sexually and divide via mitosis.
Eukaryotic cells are cells containing membrane-
bound organelles and are the basis for both
unicellular and multicellular organisms. In contrast,
Diagram of a Eukaryotic Cell
prokaryotic cells do not have any
membrane-bound organelles and are
always part of unicellular organisms.
The plasma membrane of a Eukaryotic cell
separates it from its environment and
controls what leaves and enters the cell.
The cytoskeleton is present inside the
cytoplasm, which consists of
microfilaments, microtubules, and fibres to
provide perfect shape to the cell, anchor the
organelles, and stimulate the cell
movement.
The nucleus contains DNA and proteins,
this is where ribosome production takes
place.
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,Measuring Cells
Cells are measured by comparing their size with the size of E.coli. E.Coli
is a prokaryotic cell about 2μm in length.
The E.Coli Ruler
Inside the Cell
Cells contain specialised sub units called organelles, which are compartments in a cell that have
specific functions, they can either be membrane-bound or membrane-less. Each organelle is a
compartment and can have completely different protein and ion composition to compartments
surrounding it.
For example, the mitochondria is an organelle that produces chemical energy and is membrane
bound. Ribosomes are membrane-less organelles that assemble proteins.
The nucleus is an organelle found in the centre of the cell, it makes up 10% of the cell by volume
and contains genetic material (DNA). The DNA is stored in the nucleolus which is surrounded by
the nuclear envelope, which allows messenger RNA diffusion in and out.
The proteins in a cell are produced through a process
known as transcription. An RNA polymerase will attach
to the start of a gene sequence in the DNA and create a
strand of messenger RNA out of free bases in the nucleus.
The order of these free bases are determined by the code of
the DNA.
This messenger RNA then travels out of the nucleus into
the cytoplasm, where it is bound to by ribosomes which
reads its code. These ribosomes create amino acids
corroding to the code and transfer RNA molecules carry
these to the ribosome. The RNA is read 3 bases at a time
which creates a chain of amino acids. This chain then fold
to form the 3-D structure of a protein.
Process of Transcription
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, The concentration of the different proteins produced regulates the cells function. Some proteins
have a function of their own, others regulate the function of other proteins — the cell is a
regulatory network. Each cell in the body contains the same DNA, but it is the —regulation of
protein expression and degradation the causes differences between them.
It is important to remember:
• Genotype - the complete set of an organisms genetic material.
• Phenotype - the set of observable characteristics resulting from the interaction between an
organisms genotype and the environment.
For example, humans and chimpanzees share about 98.7% of their DNA, but the expression of the
in phenotypes is very different.
DNA
Structure of DNA and RNA
A gene is a region of DNA that encodes 'instructions' on
how to form certain organelles. This DNA is found in the
chromosome - long strands of it are wrapped around
histones (proteins), giving chromosomes their typical X
shape.
Both DNA and RNA are nucleic acids and they are almost
identical, however DNA is more stable due to its double
helix shape. A nucleic acid is made of a long chain of
repeating units called nucleotides, which contains a 5-
carbon sugar, a phosphate and a base. There are about 6
billion base pair per cell, with each pari being 3 × 10−10 m A Nucelotide
long.
Calculating how much information can be stored in a cell:
One base pair is equal to about 2 bits of information (0.25 bytes).
The volume occupied by 1 base pair is (3 × 10−10 ) × π × (1 × 10−9)2 = 10−27 m 3
Since the radius of a chromosome is about 2nm.
0.25
This gives a storage density of = 2.5 × 10 26 Bm −3
10−27
To form double stranded DNA, two strands intertwine into a helix, with the sugar-phosphate on the
outside and the bases on the interior of the strand, forming the DNA three-dimensional structure.
All known sugars in nucleic acids are chiral and have a D-stereoisomeric configuration.
Both RNA and DNA contain ribose sugars, with the carbon atoms in the sugars labelled 1’ to 5’.
Ribonucleic acid, or RNA, contains D-ribose and deoxyribonucleic acid, or DNA, contains 2-
deoxy-D-ribose. The only difference between these is that deoxyribose lacks the hydroxyl group on
the 2′ carbon atom.
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