Download Molecular Dynamics Simulations with Applications

Dr. Martin O. Steinhauser
Graduate Lecture
University of Basel
Spring Semester 2014
Molecular Dynamics Simulations
with
Applications in Soft Matter
Handout 15
Big Ideas in Biology and a Self-Quiz
Friday, 9th May 2014
The purpose of this handout is to sumarize for you some of the important ideas in biology that
have to do with the properties of macromolecules – the basic constituents of living cells. Most of the
issues mentioned here were introduced in the lecture, some were not. We also provide here a self-quiz
for your pleasure with which you can test your knowledge and which also covers some issues that
weren‘t expanded on in the lecture. The solutions for this self-quiz are provided as well. Enjoy it!
1
Big Idea in Biology
At the molecular level, biology is based on three-dimensional (3D) interactions of complimentary
molecular surfaces.
1.1
Important Concepts in Biology
• All molecules are 3D objects (2D is just a crude representation).
• The structure of a molecule enables its function. Structure is a combination of the 3D shapes of
the molecules and the chemical identities of the different parts of the domains of the molecule.
• Interaction between molecules happens by shape matching/fitting with the use of chemical
entities in the faces of the interacting molecules. Molecules that seem to differ in very minor
ways (e.g. different carbohydrate linkage) can have drastically different properties.
• All interactions in a cell happen because of a combination of (small) molecular forces.
• Many of the physical properties of water are due to hydrogen bonds. Hydrophillic molecules can
form hydrogen bonds with water, thus becoming part of the network. Hydrophobic molecules
need to “hide“ from water, which is looking to displace them in order to resume the hydrogen
bond network and increase entropy.
• Amphiphatic molecules have both hydrophilic and hydrophobic characteristics. This duality
allows them to form vesicles and membranes.
• Membranes separate inside from outside, making existence of cells possible.
1
2
A Bit of History of Cell Biology in a Nutshell
• 1632 – 1723: Antonie van Leeuwenhoek teaches himself to grind lenses, builds a microscope
and draws protozoa, such as Vorticella from rain water, and bacteria from his own mouth.
• 1665: Robert Hooke uses an early microscope to discover small pores in sections of cork, which
he calls “cells“. Later, he observes cells in living plant tissue.
• 1833: Brown publishes his microscopic observations of orchids, clearly describing the cell nucleus.
• 1839: Theodor Schwann and Matthias Jakob Schleiden elucidate the principle that plants and
animals are made of cells, concluding that cells are a common unit of structure and development,
and thus founding the cell theory. The belief that life forms are able to occur spontaneously
(generatio spontanea) is contradicted by Louis Pasteur (1822 – 1895) (although Francesco Redi
had performed an experiment in 1668 that suggested the same conclusion).
• 1855: Rudolph Virchow states that cells always emerge from cell divisions (omnis cellula ex
cellula).
• 1879: Fleming describes with great clarity chromosome behavior during mitosis in animal cells.
• 1931: Ernst Ruska builds first transmission electron microscope (TEM) at the University of
Berlin. By 1935, he has built an EM with twice the resolution of a light microscope, revealing
previously-unresolvable organelles.
• 1953: Watson and Crick made their first announcement on the double-helix structure for DNA
on February 28. This laid the foundation of modern biology, biochemistry, molecular biology
and molecular genetics.
• 1957: Robertson describes the bilayer structure of the cell membrane, seen for the first time in
the electron microscope.
3
Definition of the Cell
The cell is the structural and functional unit of all known living organisms. It is the smallest unit
of an organism that is classified as living, and is sometimes called the building block of life. Some
organisms, such as most bacteria, are unicellular (consist of a single cell). Other organisms, such as
humans, are multicellular. (Humans have an estimated 100 trillion or 1014 cells; a typical cell size is
10 µm; a typical cell mass is 1 nanogram).
In 1837 before the final cell theory was developed, a Czech Jan Evangelista Purkyně observed
small “granules“ while looking at the plant tissue through a microscope. The word cell comes from
the Latin cellula, meaning, a small room. The descriptive name for the smallest living biological
structure was chosen by Robert Hooke in a book he published in 1665 when he compared the cork
cells he saw through his microscope to the small rooms monks lived in. Figure 1 below shows the
typical cell architecture
The cell theory, first developed in 1839 by Matthias Jakob Schleiden and Theodor Schwann, states
that all organisms are composed of one or more cells. All cells come from preexisting cells. Vital
functions of an organism occur within cells, and all cells contain the hereditary information necessary
for regulating cell functions and for transmitting information to the next generation of cells.
2
Figure 1: Cell architecture. Adopted from Essential Cell Biology by Bray et al, Garland Science,
New York and London 2009.
3
4
A Self-Quiz:
4.1
Label the parts of the cell in Figure 2 below
• golgi apparatus
• lysosome
• mitochondrion
• nucleolus
• nucleus
• plasma membrane
• ribosomes on rough ER
• rough endoplasmatic reticulum
• smooth endoplasmatic reticulum
Figure 2: Parts of the cell.
4.2
Describe briefly how each labeled answer functions
4
5
Label the parts of the eukaryotic cell in Figure 3 below using
the following list
• nucleus
• golgi aparatus
• mitochondrion
• cytoplasm smooth
• ribosomes on rough ER
• free ribosomes
• endoplasmic reticulum
• endoplasmic reticulum
• plasma membrane
Figure 3: Parts of the cell.
5
6
Fill out the gap text
1. How do prokaryotic cells differ from eukaryotic cells? Note the prokaryotic cell is much much
smaller than the eukaryotic cell but they are both drawn in Figure 1 so that you can compare
the internal components.
2. Currently, scientists estimate that life first appeared on approximately _ _ _ _ _ _ _
years ago.
3. A key point in the theory of evolution is: slight variations among individuals significantly
affect the chance that a given individual will survive in its environment and reproduce. These
variations among individuals are due to _ _ _ _ _ _ _ _ _ _ _ _ _ .
4. Surface tension occurs in water because it has _ _ _ _ _ _ _ _ _ _ _ _ _ .
5. The building blocks of DNA are _ _ _ _ _ _ _ _ _ _ _ _ _ .
6. The building blocks of proteins are _ _ _ _ _ _ _ _ _ _ _ _ _ .
7. All cells have a membrane composed of _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _.
8. In the process of glycolysis, cells make energy in the form of _ _ _ _ _ _ _ _ _ _ _ _ _.
9. Oxidation and _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ occur together.
10. What is a gene?
11. The “Central Dogma“ states that information flow in the cell is from DNA to _ _ _ _ _ _ _
to _ _ _ _ _ _ _.
12. Are the genes in your eye cells the same or different than the genes in your gut cells?
13. Are the proteins in your eye cells the same or different than the proteins in your gut cells?
6
7
Self-Quiz Solutions
4.1 and 4.2:
a) golgi apparatus – stores, modifies, and packages proteins.
b) rough endoplasmic reticulum – synthesis and sequestration of proteins that function outside
the cytosol.
c) mitochondrion – energy transformation - cell “power plant“ - ATP synthesis.
d) smooth ER – lipid synthesis, chemical modification of proteins.
e) lysosome – a membrane-bound vesicle with hydrolyzing and digesting enzymes.
f) nucleus – contains cellular DNA – stores most of the cell’s information.
g) ribosomes on the rough endoplasmic reticulum – protein synthesis.
h) nucleolus – a spherical body found within the nucleus, where ribosomal RNA is synthesized.
i) plasma membrane – separates the cell from the environment, regulates traffic of materials in
and out of cell.
5:
I.) plasma membrane
II.) endoplasmic reticulum
III.) Golgi apparatus
IV.) ribosomes on the rough endoplasmic reticulum
V.) cytoplasm
VI.) free ribosomes
VII.) smooth ER
VIII.) mitochondrion
IX.) Nucleus
6:
1. How do prokaryotic cells differ from eukaryotic cells? Prokaryotic cells do not have a nucleus
nor organelles like mitochondria, ER, and Golgi apparatus.
2. Currently, scientist estimate that life first appeared on approximately 4 billion years ago.
3. A key point in the theory of evolution is: slight variations among individuals significantly
affect the chance that a given individual will survive in its environment and reproduce. These
variations among individuals are due to mutations.
4. Surface tension occurs in water because it has hydrogen bonds.
5. The building blocks of DNA are nucleotides.
7
6. The building blocks of proteins are amino acids.
7. All cells have a membrane composed of phospholipids.
8. In the process of glycolysis, cells make energy in the form of ATP.
9. Oxidation and reduction occur together.
10. What is a gene? A segment of DNA that directs the production of a protein or RNA molecule.
11. The “Central Dogma“ states that information flow in the cell is from DNA to RNA to protein.
12. Are the genes in your eye cells the same as the genes in your gut cells? The genes in the two
are the same.
13. Are the proteins in your eye cells the same as the proteins in your gut cells? The proteins in
the two are different.
8