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Biology
Chapter 1 Basics/introduction
There are certain properties (characteristics) of life such as :
-growth and developement,
-homeostase (regulation),
-reproduction,
-consumption of energy,
-response to environment,
-Order
-Evolutionary adaption
Touchstones (Grundprinzipien) of life:
-Organization, Information, Energy and Matter, Interactions, Evolution
Life is structured on different levels, that biologists have defined
-Biosphere: consists all of life
-Eco system: consists of all the living things in a particular area including non living
components such as water, soil, gases, stones..
-Communities: all organisms inhabiting a particular ecosystem (plants animals
bacteries)
-Populations: all individuals of a species
-Organisms: one individual living thing (each tree, dog..)
-Organ(Systems): part of body with particular function
-Tissues: group of cells that have the same job, performing a specialized function
-Cell: smallest organism capeable of all functions of life
-Organelles: functional components/structures in a cell
-Molecules: chemical structure consisting of atoms, with specific function
(zooming in is an approach called reductionism
by zooming out you’ll find emergent properties. To understand these better biologist
complete reductionism with systems biology, analysing the interactions among parts)
Function and structure go hand in hand (correlate) because of natural selection
Gene expression = (Proteinbiosynthese) entire process by which information in a gen
directs the manufacture of a cellular product
DNA → transcription → mRNA → translation → chain of amino acids → protein folding
Energy flows through and chemicals cycle
Organisms interact with each other and their environment on all levels of life. They often
use the ability to self regulate by a mechanism called feedback we distinguish between
Negative feedback: the response reduces the initial stimulus (blood sugar regulation)
Postive feedback: The end product speeds up its own production (clotting of blood)
Three domains of life
Prokaryotic : no nucleus nor membrane enclosed organelles
1-Bacteria
2-Archaea (differ in molecular organization thought to be a intermediate between
Bacteria and Eucaryotes)
3-Eukaryotic : nucleus & membrane enclosed organelles (organized in 4 kingdoms)
-Kingdom Plantae: carry out photosynthesis
-Kingdom Fungi: absorb nutrients from outside their bodies
-Kingdom Animalia: ingest other organisms
-Kingdom Protists: mostly unicellular & simple multicellular relatives
Charles Darwin On the Origin of Species by Means of Natural Selection
-Individuals in Populations vary in their traits
-A Population can produce fare more offspring, than can survive -> competition
-Species suit their environments
Evolution accounts for the Unity in the Diversity of Life (universal genetic language of
DNA ,similar skeletons) and evolutionary adaption (match of organisms to their
environments)
natural selection: mechanism of evolutionary adaption (individuals with traits that suit
their environment have higher chances to survive and reproduce)
hypothesys = explanation on trial, has to be falsifyable, can't be verified but becomes
more and more plauseable after a lot of testing and experiments
inductive reasoning = generalization from a large number of specific observations
the sun always rises in the west or all men are mortal for example
deductive reasoning = top-down-logic, reasoning from one or more statements
(premesis) to reach a logically certain solution. All men are mortal, your are a
man → you are mortal
controlled experiment = experiment with controll group, that only differs in the one
factor the experiment is testing called the independent variable (eg color of a
mouse) the predation is the measured factor called dependent variable
qualitative data = descriptions, not mesureable (colors, smells, appearance, texture..)
quantitative date = measureable, deals with numebrs (length, time, cost, volume, area..)
Ribosome = consits of proteins and large pieces of RNA
Chapter 3 Water and Life
Because of the way a water molecule is built it is a polar molecule with the ability to
form hydrogen bonds. Because of this water has four emergent properties, witch are
very important for life on earth. Hydrogen bonding keeps the molecules close to each
other (cohesion)this is the reason for surface tension and how trees are able to transport
water. Because the molecules are held together by these strong forces a lot of heat is
neccessary to increas the temperature (high heat capacity). This helps to keep
temperatures in areas close to large amounts of water relatively steady. To evaporate a
water molecule has to break all bonds to other molecules with needs a lot of enrgy. This
results in a high (heat of evaporization), helping animals to keep their temperature
steady. When cooled below 4° there is not enough energy in the system to break
hydrogen bonds, which causes the molecules to arrange in the lowest energy
configuration in which each molecule is hydrogen bonded to four partners. This
cristalized configuration is abour 10% less dense than at 4°. Therefore Ice floats on top
of water(highest density at 4°) creating new environments and protecting fishes from
freezing. Because water is polar it alows other polar molecules to be solved in it.
(solvent)
Chapter 4 Carbon (C)
Structural isomers = have the same molecular formule (C5H12 for e.g.) but differ in the
arrangement of their carbon skeletons
cis-trans isomers = due to the inflexebility of double bonds the atoms cannot rotate
around the bond axis if the substituents are on the same side its a cis or z isomer
and if they are on opposite sides its a trans or e isomer
chirality = molecules of identical composition but are non-superposeable mirror images
of each other (Hands) are called chiral.
Enantiomers = isomers that are mirror images of each other due to an asymmetric
carbon (one that is attached to four different atoms )
Chapter 5 Struct and funct of large biological molecules
Dehydration =monomers connect by a reaction in which it sets free water
Hydrolysis = Polimer is disassembled by addition of water
Carbonhydrates = sugars and polymers of sugars
monosaccharides = multiple of H2CO e.g. glucose C6H12O6. Distinction between Ketose
CO DB (Carbonylgroup) within skeleton and Aldose Carbonylgroup at the end
Sugars also vary in skeleton length and spatial arangement (Glucose /Galactose)
Disaccharides = Two monosaccharides joined by a glycosidic linkage
Polysaccharides = up to a few thousand monosaccharides
Starch = Glucose storage as granules in plastids. Two forms Amylose (not branched) and
Amylopectin (somewhat (a little) branched)
Glycogen = Glucose storage for animals mainly in liver and muscle cells like amylopectin
but more extensively branched
Cellulose = never branched; hydrogenbonds with parallel polysaccharides about 80 of
these form a microfibrill; most organisms are unable to digest
Chitin = Also a structural polysaccharides with HNCOCH3 Group on second carbon
Lipids = Group of hydrophobic molecules including fats, waxes,steroids, some vitamins,..
Fatty acid = long carbon skeleton (usually 16-18) with a carboxyl group at one end
Fats = Consiting of Fatty acid and Glycerol (propan-1,2,3-triol)
Fat provides more than twice as much energy per gramm than sugar this means you
have less weight to cary around plus fat protects organs and works as an insulation
Phospholipids = Important for cell membrane
Steroids = obtained from diet and sinthesized in liver fats impact cholesterol level
Protein = proteios (=primary) make up 50% of the cell dry mass are all made up from 20
amino acids connected by peptide bonds there are tens of thousands of proteins each
with its unique function and structure. Proteinstructure can be divided into four
substructures
-Primary structure = sequence of amino acids like letters in a word even slightest
changes can cause the protein to loose its function (sickle-cell)
-Secondary structure = Folding of the amino sequence because of oxygens negative and
hydrogens positive charge
-α-Helix delicate coil held by hydrogen bonding between every fourthamino acid
-β pleated sheet hydrogen bonds between parts of the two parallel segments of the
polypeptide backbone
-Tertiary structure = Overall shape of a polypeptide
-Quaternary structure = overall protein structure (sometimes consisting of more than
one polypeptide together eg. Collagen three α-Helixes interwined or Hemoglobin
including a non peptide componed called hemme with an iron atom that binds oxygen.
Denaturation = Changes in physical or chemical conditions can cause the protein to un/
refold eg. High temperature (egg white) or nopolar solvent where hydrophobic
regions now face outward.
Chaperonins = also chaperone proteins are molecules that assist in the folding process of
proteins eg. In E. Coli a big cylinder protects the aminosequence from harmful
chemical conditions in the plasma so the polypept. Can fold properly there are
also controll mechanisms that check if folding was proper. Misfolding is
associated with diseases like alzheimer parkinsons and mad cow disease
Bioinformatics = tries to predict 3d structure of polypeptides based on their
aminosequence. 3D struct can be determined by X-Ray crystallography and NMR
(nuclear magnetic resonance spectroscopy)
Gene expression = The process by which information from a gene is used in the
synthesis of a functional gene product. (mainly Proteins) DNA->RNA-> Protein
Polynucleotide = phosphodiester linkage (two sugars linked by phosphate group) builtin directionality from 5' to 3' (5'-AGTT-3')
RNA = Ribonucleic acid
mRNA = messenger RNA conveys genetic information from the nucleus to the ribosomes
tRNA = transfer RNA brings amino acids to the ribosome during polypeptidesynthesis
about 80 nucleotides long. baise pairing within RNA leads to functional shape
DNA = deoxyribonucleic acid
Genome = entire sequence of the organisms full complement of DNA
Light microscope = 1674 first living cell visualized; Magnification ~1000x; Resolution
min distance to distinguish two seperate points ~0,2um; Contrast difference
between light and dark areas of an image can be enhanced by dyes etc.
Electron Microscope = 1950s; Resolution in practice ~2nm
Scanning Electron Microscopy = 3D Image of surface
Transmission Electron Microscopy = Through thin section of specimen, internal
structure.
Cell Fractionation = isolate components by centrifugating cells.
smooth ER = Enzymes in ER synthesise lipids including oil steroids (sex-/hormones) and
new plasma phospholipids. Detoxifies drugs usually by adding hydroxyl goups.
Store calcium ions, whose release can trigger secretion of vesicles or contraction
of muscle cells
rough ER = Membrane factory (also phospholipids) production of membrane and
secretory proteins, vesicels bud like bubbles from specialized region called
transitional ER
Identification tags such as phosphate groups added to the golgi products aid in sorting
by acting like zip codes. Vesicles budded from the golci have external molecules on their
membranes that recognize docking sites.
Human liver cell recycles half of its macromolecules each week. Lysosomal storage
diseases lack a functioning hydrolytic enzyme and become engorged with indigestible
material.
Central Vacuole = repository of inorganic ions (K,Cl..) growth by maintaining a suitable
surface to cytosol ratio. Some vacuoles store pigments or even poisonous
compounds to attract or drive away animals
Endosymbiont Theory = Ancestor of Eucariotic cell engulfed an oxygen-using-nonphotosynthetic prokaryotic cell becomming an endosymbiont (cell living within
another cell) merging into a single organism (cell with mitrochondiron) that then
engulfed a photosynthetic prokaryote becomming a chloroplast. Evidence: both
posses double membrane, own ribosomes and DNA and are autonomous (grow
and reproduce) Not static as in pictures but dynamic move, grow, pinch in two
Detoxify by transferring hydrogen from molecules onto O2 forming O2H2 which itself is
poisonous but broken down into water by other enzymes. Can also break down fatty
acids eg. In plants glyoxysomes suply energy until plant can perform photosynthesis.
Cytoskeleton = network of fibers extending throughout the cytoplasm. Also provides
anchorage to organelles & enzymes and help form food vacuoles out of membrane
Flagella and cilia consist both of microtubuli a flagellum has a 9+2 pattern and a cilium a
9+0 pattern both are anchored by a basal body (similar to a centriole in sperms becomes
a centriole) movement of the dyneins proteins is coordinaten and happens on one side of
the circle at a time causing it to bend. In vertebrates many cells contain a single primary
cilium acting as a signal antenna
Microfilaments = build the outher cytoplasm layer called cortex and reinforce the cells
shape. They are responisble for amoeboid movement as well, by extending so called
pseudopodia (greek false foot) Furtehermore they are involved in cytoplasmic streaming
in plant cells as well as muscle contraction in collaboration with myosin filaments.
Intermediate filaments = More permantent fixtures to reinforce shape and anchor
organelles stay even after death and maku up the nuclear lamina
Collagen makes up to 40% of proteins in the human body. Integrins can even influence
activity of genes
Glycoprotein = Proteins covalently bonded to carbohydrates usually short sugars
Plant Cell Walls = 0,1um to several micrometers. Young cell thin flexible primary cell wall
when old hardens them by secreting cellulose and proteins bilding a matrix into the
primary wall or by ading a harder secondary wall cells are connected by plasmodesmata
(desma = bond) that allow communication and exchange of substances between cells.
Amphipathic molecules = have both a hydrophilic and a hydrophobic region
Phospholipids can travel about 2um/s proteins are slower but moving as well though
some are held in place ore clustered together with other proteins of complementary
function. Intregral proteins are usually transmembrane or at least embedded in the lipid
bilayer whereas peripheral proteins are not embedded at all but loosely connected to the
surface of the membrane. Its not only a structural but a functional mosaic as well.
Cell recognition = usually established through binding to glycoproteins or sometimes
glycolipids with carbohydrates of fewer than 15 sugars serving as identification tags it's
crucial to organization of cells into tissues and the immunesystem.
Bigger molecules such as proteins cannot pass through the membrane or transport
proteins. The cell uses Exocytosis, where a vesicle fuses with the membrane and
secretes it's substances (eg. Insulin, neurotransmitter or proteins and cyrbohydrates for
cell walls)
There are three types of Endocytosis Phagocytosis (Cell engulfs a particle by extending
pseudopodia) pinocytosis (cell gulps droplets of extracellular fluid into tiny vesicles) and
receptor-mediated endocytosis(ligands-molecules that bind specifically to a certain
receptor- gather together and a pit forms into a coatet vesicle as in pinocytosis).
Metabolism = totality of an organism's chemical reaction (greek metabole = change).
A methabolic pathway begins with one or more specific molecules which are then in a
series of reactions catalyzed by enzymes converted into one or more products. Are
complex molecules broken down into simpler ones releasing energy it's called catabolic
pathway the other way round anabolic pathway.
First law of thermodynamics = energy cannot be created or destroyed only
transformed
Second law of thermodynamics = every energy transfer or transformation increases
the entropy of the universe. An organism might decrease it's entropy by building
complex molecules out of simpler ones this uses energy though and because some
energy is always lost as heat it will increase the entropy of it's surroundings.
Entropy = a measure of disorder/randomness
A Cell does mainly three kinds of work chemical work (pushing endergonic reactions)
transport work (move substances against concentration gradient) and mechanical work
to do so it uses energy coupling – using an exergonic process to drive an endergonic one.
ATP can be hydrolised forming ADP and HOPO3^2- ΔG =-7.3 kcal/mol (-30,5kj) under
standard conditions. Unter cellular conditions ΔG is about -13kcal/mol.
If an endergonic reaction is coupled with ATP hydrolysis it usually forms a
phosphorylated intermediate that enables the overall process to be exergonic
Enzymes work as catalysts reducing the
activation energy. They are not static but
subtly change their shape and even
change it futher when interacting with the
substrate because of intermoleculare
interactions. When there are enough
substrates to bind to all the enzymes it's
said to be saturated at this point only
adding more enzymes can increase the
rate of converting substrate into products.
Activiti is depending on temperature and
pH because after a certain temp the
enzyme substrate complex is getting torn
apart because of the kinetic energy. Most
Enzymes work best at pH of 6-8 but
digestive enzymes need a pH of 2
Many enzymes require nonprotein
helpers for catalytic activity. These
adjuncts are called cofactors (eg metal atoms) if they are organic they're called
coenzymes (many vitamines are coenzymes or bulding material for coenzymes).
Toxins and Poisons are often irreversible
enzyme inhibitors.
Example
-ATP inhibits several catabolic enzymes
while (feedback inhibition – inhibiting it's
own production) ADP activates them,
speeding up catabolism, producing more
ATP
-Hemoglobin binding one oxygen molecule
increses the affinity of the remaining
binding sites
fermentation = partial degradation of sugar
or other organic fuels without oxygen
aerobic respiration = with oxygen whereas anaerobic means without oxygen
Burning glucose is basically a redox reaction in
witch electons lose potential energy when
bound to a more electronegative atom resulting in a G = -686kcal/mol (2,87kJ)
oxidative phosphorylation accounts for about 90%
of generated ATP a smaller amount is formed by
substrate-level phosphorylation. For each molecule
of glucose the cell forms about 32 molecules of ATP
Glycolysis means sugar splitting: a glucose gets split into two three carbon sugars that
are transformed into pyruvate. The process can be devided into two phases the energy
investment and the energy payoff phase resulting in a net gain of 2 ATPs and 2 NADHs
Each NADH transports 10H+ across the membrane. 4 are needed to generate ATP
therefore each NADH synthesises 2.5 ATP. FADH2 which is lower in energy synthesises
1.5 ATP. Because the inner membrane is impermeable to NADH the electones need to be
shuttled across. Depending on the shuttle this results in either NADH or FADH2.
Furthermore H+ can be used to do other kinds of work reducing the ATP yield. About
34% of the potential chemical energy in glucose is transferred to ATP.
Yeast (a fungus) carries out alcohol
fermentation and is used in brewing baking
and winemaking. Lactic acid fermentation is
used to make yogurt and cheese. Muscle cells
can also use it if they lack oxygen. Excess lacetate is then carried to the liver and
converted back to pyruvate. Obligate anerobes carry out only fermentation whereas
facultative anaerobes can do both. Brain cells can only carry out aerobic oxydation.
Fats and Proteins can be used as fuel for respiration as well. In fact a gram of fat
produces in more than twice as much ATP than a gram of carbohydrate. Amino acids
undergo a process called deamination, where the amino group is removed and later
excreted as ammonia (NH3)
Naturally cellular respiration is regulated by different feedback loops in which certain
enzymes are stimulated or inhibited by substrate or products (AMP derives from ADP)
Autotrophs produce their organic molecules form CO2 an other inorganic materials
they are refered to as producers as well. Plants are photoautotrophs
Heterotrophs use organic molecules produced by other organisms also known as
consumers
Mesophyll = tissue inside of the leaf
mesophylle
cells
contein
multiple
chloroplasts
Photosynthesis uses 12 H2O molecules but forms 6
new ones. The O2 released derives from H20 and
not CO2. The oxygen in water is getting oxydized
and the electrons transferred to the glucose this
process is endergonic. Photosynthesis can be broken down into two stages the light
reaction and the calvin cycle.
Carbon fixation = conversion process from
inorganic carbon ( CO2) to organic
compounds
Pigments = Substances that absorb light
Chlorophyll a is the key pigment b an accessory
pigment and the carotenoids broaden the
absorption spectrum but are also used as
photoprotection by absorbing excessive light
energy that could damage chlorophyll or
interact with oxygen. Carotenoids are also used
for protection in the human eye (eat carrots)
The
light
harvasting
complexes
consist
of
pigments
bound to proteins. The special chlorophyll is special
becuase it is able to transfer an electron to another
molecule. There are two types of photosystems.
Photosystem I and Photosystem II differing in the proteins
associated with the chlorophyll a molecules the one in PS I
absorbing best at 700nm called P700 and the one in PS II called P680 absorbing best at
680nm.
Linear electron flow is shown in the picture some photosynthetic bacteria use cyclic
electron flow where only the PS I is used and the Fd shuttles the electrones to the
cytochrome complex. In this case no NADPH is produced. The pH in the thylakoid space
is about 5 and the stroma about 8.
after 3 CO2 entering the cycle one by one (3cycles), a net output of one GP3 is generated
consuming 9 ATP and 6 NADPH
On a hot day most plants close their stomata limiting access to CO2 and releas of O2 that
is produced, favouring a wastefull process called photorespiration. In C3 plants (first
product of carbon fixation is a three carbon compound) the enzyme Rubisco is capable
of binding a O2 in place of a CO2. The product splits and a two carbon compound leaves
the chloroplast where it is transformed into CO2 by peroxisomes and mitochondria. Can
protect the plant from excess light.
C4 Plants use PEP carboxylase in a first cycle to fix CO2 onto PEP. Because PEP
carboxylase has a high affinitiy for CO2 and no affinity for O2 it will also work under
conditions created by partially closed stomata. The CO2 is then „pumped“ into the Calvin
cycle stabilizing the CO2 concentration to make sure rubisco only adds CO2.
CAM plants close their stomata during the day to minimize water loss and only open
them at night, to store CO2 in organic acids. This process is called crassulacean acid
metabolism (CAM). CO2 is released during the day where it is used to build sugars. The
mechanism is similar to C4 where CO2 is also stored in organic acids first.
Cell communication between yeast and mammal cells is strikingly similar (evidence for
evolution) Endocrine signaling is like a radio station only cells with an antenna receptor
can receive the signal. There are three steps reception, transduction and cellular
response. The receptor usually changes it's shape triggering transduction.
G protein coupled receptors (GPCR) use a G protein, capeable of
binding GTP. Many hormones as well as neurotrasmitters use
GPCRs that vary in their binding sites and different G Proteins
inside the cell. In humans vision, smell and taste depend on
GPCRs and pharmacologists found, that up to 60% of all
medicines exert their effect on G protein pathways. G Proteins are
also GTPprotease enzymes hydrolyzing GTP to GDP after a
certain time becoming inactiv and therefore reuseable.
Receptor tyrosine kinease (RTK) exists as monomers after binding they form dimers that
are activated by adding Phospahte from ATP and can then trigger multiple transduction
pathways, which sets them apart from GPCR. Abnormal RTK function is associated with
many forms of cancer
binding to phospholised tyrosine results in a change of shape of the relay molecules.
Ligand-gated ion channels are important for
the nervous system. In synapses they trigger
the electric signal.
Intracellular Receptors bind to signaling
molecules small or hydrophobic enough to
cross the plasma membrane. It can activate
or act as a transcription factor – a protein
that controls which genes are transcribed
into mRNA
Benefits of multiple step pathways are
amplification of the signal (one relay
molecule can activate numerous others
before being turned inactive again), better
control and coordination
Activation of proteins by phosphoriylation
is a widespread cellular mechanism. Each
activated relay molecule (kinase) is able to
activate the next molecule in the phosphorylation cascade. Protein phosphatases then
remove phospate and deactivate the kinases (enzyme capable of transferring a
phosphate group from ATP to a protein) again.
Not all signal transducting molecules are proteins. Small water soluble molecules or ions
called second messengers are important as well, as many proteins are sensitive to the
concentration of aforementioned, Ca2+ and cAMP being the most important ones.
CAMP concentration can boost 20-fold in a matter of seconds usually activating protein
kinase A. Cholera bacteria inhibit GTP hydrolisys of the G Protein, keeping cAMP levels
high. Thus cells secrete salt into the intestinals in combination with osmosis resulting in
epic diarrhea.
Ca2+ concentration in
extracellular fluid is
often
more
than
10'000 times higher
than in the cytosol
The same hormone can have different effects on different cells, because they contain
different proteins. Therefore enpinephrine might cause liver cells to break down
glycogen while it causes muscle cells to contract. The hormone cannot have the same
effect, because they can only activate protein that are present in the cell.
To increase efficiency of signal transduction
scaffolding proteins are used, because relay proteins
are usually large and would take for ever to find its
substrate.
Signal pathways can also interact with eachother
Apoptosis = programmed cell death. DNA and
Organelles are destroyed, packed up in vesicles and digested by specialized scavenger
(Aasfresser) cells.
Cell cycle mitotic phase when cell
divides and interphase when cell
grows. G1 cell grows. S DNA is
duplicated. G2 Cell grows further.
Mitosis divided into the following
subphases where DNA is divided.
Cytokinesis Cytoplasma is divided and
two cells formed.
In Plant cells Cytokinesis is different. Vesicles transport material into the middle of the
cell forming a cell plate while in animal cells a ring of actin microfilaments associated
with the protein myosin contracts.
During anaphase the chromosome is
thought to be walked along the
microtubule by motor protein.
There are other ways of mitosis in dinoflagellates and some yeasts where the nuclear
envelope remains intact during cell division
While nerve and muscle
cells never divide and
liver cells only do if they
have to for eg because
of injury, skin cells
divide regularly.
The cell cycle is
regulated by two types
of proteins protein
kinases and cyclicns
(named
because
concentration fluctuates
with cyclically)
Kineases depend on
cyclins
to
become
activated and are therefore called cyclin
dependent kinases (Cdks)
Another important checkpoint is G1. If the
cell does not recieve a go ahead signal it
might go into a nondividing state called
G0 phase. Liver cells can be called back.
At the M phase checkpoint the cell can
only continue once all chromosomes are
attached to microtubules, which activates
the enzym separase cleaving the cohesins
that hold the chromatids together.
If the cell lacks an essential nutrient or
growth factor it cannot divide. Most
animal cells depend on anchorage . They
can't divide without being attached to a
substratum. Division can also be inhibited
by density dependent inhibition for eg in Skin cells that only bild a single cell layer.
Benign tumor = have too few genetic and cellular changes to survive at another place.
Malignant tumor = are able to spread to new tissues and impair functions of morgans
cells are also considered transformed cells. Spreading is called metastasis.
Cancer cells are „immortal“ because they do not stop dividing whereas normal cells stop
dividing afer 20-50 times and die. Most drugs inerfere with specific steps in the cell cycle
interferring with normal dividing cells though.
Karyotype = ordered display of all chromosomes
homologous chromosomes = have the same length,
centromere position and staining pattern.
Autosomes = all the other chromosomes exept the X and Y
the sex chromosomes.
Diploid cell = containing two sets of chromosomes a
maternal (mother) and a paternal (father) each consisting
of 23 chromosomes (human 2n = 46)
During metaphase I the arrangement of the homologous chromosome pairs is random.
Generating genetic variation. For a human n=23 2^23 combinations are possible.
Character = A heritable feature that varies among individuals (eg flower color)
trait = each variant of a character such as white or red
true breeding = varieties that over many genera tions of self-pollination produced only
the same variety as the parent plant
hybridization = mating/crossing of two true-breeding carieties
F1 generation = first filial gnerartion (lat for son)
An organism with a pair of identicall alleles for a character is said to be homozygous
one with two different alleles heterozygous
Allele = Alternativ versions of a gene, accounting for vatiations in inherited characters.
An organism's observable traits (appearance) are called its phenotype its genetic
makeup its genotype
Law of dominance (uniformitätsregel) if an organism contains two allels, the dominant
allele determines the organism's phenotype uninfluenced by the recessive allele
Law of segregation (spaltungsregel) Two alleles for a heritable character segregate
(seperate from each other) during gamet formation and end up in different gametes.
Law of independent assortment (unabhängigkeitsregel) two or more genes assort
independently -that is, each pair of alleles segregates independently of each other pair of
alleles -during gamete formation (two alleles → 9:3:3:1 phenotypic ratio)
Because of these laws mendel observed in ~1860 a 3:1 ratio when experimenting with
pea plants that differet in character
Testcross = if we cannot tell if an organism is homo(XX)/heterozgous(Xx) we can cross
it with a homozygous(xx) organism. If theres only one phenotype (Xx) the orgenism was
homozygous if it was heterozgous there would be two phenotypes (Xx/xx) 1:1: ratio
monohybrid = heterozygous for the one particular character being followed in the cross
dihybrid = heterozygous for the two character being followed in the cross
incomplete dominance = neither allele is completly dominant F1 generation has a
phenotype somewhere between those of the parents because neither is dominante the
letter C is used with the allele in superscript e.g. (red(C R CR)&wite(CW CW) → pink(CR CW))
F2 generation splits up in red:pink:white in a 1:2:1 ratio
codominance = two alleles affect the pheontype in separate distingushable ways
meaning if two alleles are present they do not result in an intermediate but both are fully
expressed eg. MN molecules on human blood cells
Level dependance = if a allel is dominant or recessive depends on the level at which we
examine the phenotype. the Tay-sachs disease seems recessive (die when (xx)) the
intermediate pheotype (Xx) at biochemical level is of incompletet dominance because
half of the proteins are working. Thus observed at the molecular level its codominant.
Multiple alleles = multiple alleles for a single gene are possible. blood groups are
determined by three alleles of a single gene coding for different carbohydrates.
Pleitropy = Most genes have multiple phenotypic effects.
Epistasis = The phenotypic expression of a gene
at one locus alters that of a gene at a second
locus. One gene determines color - Black(B) is
dominant to brown (b) - while a second gene
determines wheter or not pigments are
deposited in the furr – Deposition (E) is
dominant to no deposition (e). Therefore a cross
might represent an F1 dihybrid cross we'd
expect to end in a 9:3:3:1 ratio but because (E/e)
is epistatic to (B/b) F2 offspring results in a
9:3:4 ratio.
Quantitative characters = such as Height or
skin color vary in gradations along a continuum
they usually indicate polygenic inheritance =
an additive effect of two or more genes on a
single phenotypic character. E.g. if there are 3
genes with two alleles of which the dominant
form adds 1 unit of darkness there would be 7 possible phenotypes. (diploid → 1-6 darkgenes +1 phenotyp for 0 dark-genes)
carriers = Many diseases are inherited as simple recessive traits. Although heterozygotes
usually are phenotipically normal they may transmit the allele to their offspring
Enviromental Impact = leaves of a tree differ in phenotype
Thomas hHunt Morgan = first to associate a
specific gene with a specific chromosome. In 1907
spent two years breeding fruit flies drosophila
melanogaster to find one with white eyes. Throu
breeding he was then able to find, that the white eye
gene was only present on the X sex chromosom.
Wild Type = phenotype for a character most
commonly observed in natural populations
mutant phenotypes = traits alternativ to the wild
type assumed to originate from mutations
Gender = Mammals have two types of sex chromosomes X&Y short segments are equal
to allow them to pair and behave like homologs during meiosis in the testes. In bees and
ants females are diploid and unfertilized eggs (haploid) develop males. Grasshoppers
have only one type of sex chromosome two → female only one → male. There are a
number of x-linked recessive disorders such as red-green color blindness or Hemophilia.
Barr body = Femal mammals inherit two x chromosomes of which one randomly gets
inactivated by condensing into a barr body thus females are heterozygous for a sex
linked trait eg. Cats with patched furr. Inactication involve dna and histone modification
linked genes = genes located
neach each other on the same
chromosome tend to be
inherited together because
only crossing over could
seperate them which is not
likely. If genes are not linked
the testcross offspring would
be expected to occurr in a
1:1:1:1 ratio and if they are
linked in a 1:1:0:0 ratio the
experiment resulted in a
~5:5:1:1
ratio
because
crossing over can still cause
linked genes to be seperated
recombinant offspring =
have new combinations of
traits of their parents
recombination frequency = 10 recombinants/ 100 total offspring = 10% frequency of
recombination
genetic map = ordered list of the genetic loci along a particular chromosome
linkage map = a genetic map based on recombination frequencies. The further away
two genes are the higher the probability that a crossover will seperate them. Thus the
higher the recombination frequency. The recombination frequency can be at maximum
50%. It does not directly correspont to actual physical distances though. Another
problem is some genes are so far apart recombination is almost certain. these genes are
physically connected but still unlinked because they behave like unlinked genes.
Nondisjunction = when homologous chromosomes do not separate during meiosis I or
sister chromatids in meiosis II. Forming gametes with abnormal chromosome numbers
aneuploidy = A zygote formed from such a gamete has an abnormal number of a
particular chromosome this condition is known as aneuploidy. If it is missing a
chromosome its said to be monosomic if it is present in triplicate its trisomic Down
syndrome also called trisomy 21 is such an example
Polyploid = if an organism contains more tan two complete chromosome sets (3n)
triploid (4n£) tetrapoloid. They usually appear more normal than aneuploids
Klinefelter syndrome = XXY males, abnormaly small testes thus sterile, big boobs pos
Turner syndrome = X0 females, sterile, usually normal intelligence
cri du chat syndrome = specific deletion in chromosome 5, severely disabled, cry that
sounds like mewing of a distressed cat.
Errors in meiosis or damaging agents such
as radiation can cause breakage of
chromosome leading to four types of
alternations in chromosome structure.
Chromosomal translocations have been
implicated in certain cancers including
chronic myelogenous leukemia (CML)
Genomic imprinting = vatiations in the phenotype depending on whether an allele is
inherited from the male or female parent. In mice a growth factor gene is only expressed
from the paternal chromosome. Thus offspring only became dwarf when the mutant
gene came from the father. Methylated (-CH3) genes ar usually inactive inthis case
methylation of cytosine nucleotides activates the expression of the allel.
Extranuclear genes = genes located in mitochondria, chloroplasts and other plastids
contain small DNA molecules. Inherited from the mother
DNA as genetic material = until 1940 proteins where beliefed to be the information
holding material. Griffith found that remains of dead pathogenic (disease causing) mixed
with living nonpathogenic bacterias resulted in a transformation of some of those to
pathogenic ones. Research also showed that bacteriphages injected their DNA into
bacterias while their protein shell remained outside. In1950 Chargaff's rules 1. base
composition of DNA varies between species 2. percentages of A&T (Purines – 2 rings)
and G&C (pyrimidines - single ring)Bases are roughly equal. Through X-ray
christallography they found DNA to be two antiparallel strands forming a double helix
In initial pairing errors occur at a rate of
In initial pairing errors occur at a rate of
10^5 but polymerases proofread each
nucleotide against its templat reducing error
rat to 10^10. Chemical and physical agents
such as X-ray can destroy the DNA and has to
be continously repaird like in the nucleotide excision repair above
telomers = short nucleotide sequence (Human:TTAGGG) that is repeated 100 to 1000
times at each end of the molecule. In combination with specific proteins prevent the
staggered (uneven) ends from activating repair mechanisms and Protects genes from
getting lost. They are thaught to be connected to aging. In germ cells telomerase
enzymes catalyze the lenghtening of telomers to normal lenght.
Each eukaryotic chromosome in humans everages about 1,5x10^8 nucleotide pairs and
is ~4cm long. Therefore it has to be tightly packed. Even during interphase most areas
are in a highly condensed state. This type of chromatin is called heterochromatin
distinguished from the less dense euchromatin. Also the chromosomes seem to be
organised and attached to the nuclear lamina.
Genes code mostly for polypeptides that are or built
together with others proteins. Some genes code for
RNA that is never translated into RNA. In bacterial
cells there is no RNA processing.
Codons = There are only 4 nucleotide bases to specify
20 aminoacids → 4^3 = 64 information is based on a
triplet code. These triplets are called codons
Template strand = For each gene only one of the two
DNA strands is transcribed. It is always the same
strand. For other genes however the opposite strand
may be the one that is always the template.
Polymerase untwists the double helix exposing
about
10-20
nucleotides.
Transcription
progesses at a rate of ~40 nucleotides per
second. Amound of RNA can be increased by
multiple polymerase following each other.
RNA splicing = removal of large portions of RNA that is initially sequenced
Exons = Regions that are expresses usually by being translated into amino acid seqs.
Introns = lay between coding regions called intervening sequences get cut out
Spliceosome = large complex of proteins and small RNAs that remove introns
Ribozymes = RNA molecules that function as enzymes some catalyze its own intron
excision. Because its a single strand it can base-pair with complementary regions in the
same molecule giving it a three-dimensional structur. Some bases contrain functional
goups that can participate in catalysis and hydrogen bonding with other nucleic acids
adds specificity to its activity.
Alternative RNA splicing = a gene can encode more than one polypeptide depending on
which segments are treated as exons
Domains = proteins often ahve a modular architecture consisting of discrete structural
and functional regions called domains. Different exons often code for domains thus they
are kind of like codes for basic units that are combined to build a protein.
tRNA = translator. Single strand of RNA that forms 3 dimensional shape through
hydrogen bonding. Because there are only 45 instead of 61 some tRNAs must be able to
bind to more than one codon.
aminoacyl-tRNA synthetase = match
tRNA and aminoacids. 20 different
synthetases each for a specific amino acid
and its tRNA the resulting aminoacyl tRNA
is also called a charged tRNA.
Ribosome = consist to 2/3 out of ribosomal
RNA (rRNA) giving it function and shape
thus it can be regarded as a ribozyme. The
subunits are assembled in the nucleolus.
Eucariotic ribosomes are slightly different
than bacterial ribosomes alowing certain drugs to affect only those of bacterias.
Ribosomes are identical if bound or free and synthesis always begins in the cytosol on a
free ribosom.
Sometimes polypeptides need post translational modifications befor bilding a functional
protein. (attaching sugars,lipids etc, removing amino acids …)
SRP = signal-recognition particle functions as an escort to bring the ribosome to a
receptor protein.
Point mutations = changes in a single nucleotide pair of a gene responisble for the huge
diversity of genes found among organisms.
Silent mutation = no observable effect on the phenotype.
Missense mutations = little effect on protein
nonsense mutation = change of codon into stop codon effect depends on location of
new stop codon
Insertion and deletions cause a frame shift leading almost certain to nonfunctional
protein.
Mutagens = physical and chemical agents that cause mutations
Gene = A gene is a region of DNA that can be expressed to produce a final functional
product that is either a polypeptide or an RNA molecule.
Repressible operon = usually on but can be inhibited
Corepressor = small molecule that cooperates with a repressor to switch an operon off
inducible operon = usually of but can be induced (stimulated)
inducer = small molecule that inacitvates the repressor
allolactose is an isomer of lactose formed
in small amounts from lactose that enters
the cell. Only if allolactose inactivates the
repressor the enzymes to break down
lactose are synthesised.
Positive gene regulation = E.coli only use
lactose if glucose is scarce. In this case
cAMP accumulates and binds to an
activator CAP (catabolite activator
protein) that then stimulates transcription.
Even if no repressor is bound without CAP
not enough RNA will be synthesised.
Differential gene expression = human cells typically express
at maximum ~20% of their protein coding genes some even less
this is why there are different cell types. Gene expression is
usually regualted at transcription eucariotic cells may have
additional stages where they regulate expression. Histone
acetylation causes nucleosomes to become less dense thus
becomming more accessible for transcription while methylation
has the opposite effect. After DNA replication the daughter
strands get methylated too thus inheriting the methylation
pattern.
epigenetic inheritance = Inheritance of traits transmitted by mechanisms not involving
the nucleotide sequence itself is called.
Transcription factors = RNA polymerase needes their assistance to initiate
transcription. Some are used for alle protein coding genes called general transcription
factors. Few of them bind do DNA most bind to other proteins or the polymerase itself.
Some activators recruit proteins that acetylate histones thus promoting transcription
while some repressors remoce acetyl groups reducing it also called silencing. Specific
transcription factors either activators or repressors influence gene expression.
Enhancer = consists on average of 10 control elements that can bind a specific
transcription factor by combinating the control elements differently there is a great
number of possible enhancers by using less activators. Thus gene expression is
determined by the transcription factors made in a cell.