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Eukaryotes

unicellular organisms (such as protozoa) all multi-cellular organisms: animals, plant, fungi.
Multi-cellular organisms typically have many specialised cell types such as: root hair cell, white
blood cell, muscular cell, nerve cell.

cell membrane role - The plasma membrane is the boundary that separates the living cell from
its non-living environment.
Cell-cell recognition
Signal transduction
Enzymatic reactions
Transport across the membrane
Intercellular joining
Attachment to the cytoskeleton and to extracellular matrix
• Water Diffusion
Water diffusion in living Cells: Animal cells shrivel(buzulmek) in hypertonic solutions - as a
result of osmosis (water leaving the cell). break in hypotonic solution - as a result of water
filling up the cell.
Plant hypotonic solution. As water passes through the cell membrane by osmosis, it creates a
turgor pressure that pushes the cell membrane against the wall of the cell which becomes
turgid. This occurs in plant cells, bacteria, fungi and protists that have a cell wall.
Animal cell have to live in isotonic solutions where there is no osmotic pressure or must
continually adjust the intracellular(huceyredaxilli) concentration of solute to maintain
isotonicity
• Osmolarity
Osmotic concentration, known as osmolarity, is the measure of solute concentration, defined as the
number of osmoles of solute per litre of solution.

• Sodium Potassium Pump


The sodium-potassium pump (Na+ , K+ , ATPase) is a vital transmembrane ATPase and needs
ATP to function. It is commonly found in animal cells, where it pumps sodium ions (Na+ ) out of
the cells and potassium ions (K+ ) into the cell against strong concentration gradients. The pump
generates concentration gradients between the cell and the extracellular environment which
are useful and help diffusion (diffusion of glucose for example). For every 3 Na+ ions that are
pumped out, 2 K+ ions are pumped in the cell. The pump creates a potential difference, which is
essential for nerve cells and is essential in adjusting the osmotic pressure.
• Ion Channels
• A species is often defined as a group of genetically similar organisms capable of interbreeding
and producing fertile offspring(mehsuldar nesil).
• Phylogenetic Tree Definition, Its Types
The phylogenetic tree of life is the family tree of all living organisms; it illustrates the degree of
similarity in nucleic acid or protein sequences between organisms. The phylogenetic tree
illustrates how the family might have been derived during evolution.
• Construction Of Phylogenetic Trees
Phenetic approach: e.g. compute the genetic distance (i.e. no. of base pairs of DNA which differ)
between two populations, compare similarities between all populations and cluster onto tree
PHENETIC –Based on overall similarity
Cladistic approach: identifying shared derived feature, use numerous different features to arrange
populations on tree. CLADISTIC –Pathways of evolution by comparing shared derived characters
• Water
Not simply a solvent but critical to biochemistry – actively engages and interacts with biomolecules
Water is a unique substance:
• Very high dipole; very high dielectric constant;
• Very high melting/ boiling point compared to similar substances.
• Readily dissolves ions and many polar substances.
• Readily dissociates (H3O+ /OH- ); forms hydrogen bonds
• Frozen water floats (solid state of water is less dense(sıx) than the liquid state)
Essential for life (as solvent, reaction medium, reactant, transport, turgor pressure …….)
Biological Water? In cytoplasm
• Lipids
Lipids are a broad group of naturally-occurring molecules which includes fats, waxes, sterols, fat-
soluble vitamins (such as vitamins A, D, E and K), monoglycerides, diglycerides, phospholipids, and
others. The functions of lipids include storing energy, signaling, and acting as structural components
of cell membranes.
dissolve weakly in water
they are long-chain hydrocarbons
Steroids are classified as lipids because they are not soluble in water but they have a very different
structure to fatty acids. Steroids are based on a four ring structure:
Cholesterol is an example of a lipid with a steroid structure it plays a role in controlling membrane
fluidity.
Testosterone is a steroid hormone found in mammals, reptiles birds and other vertebrates
Fats and waxes: contain ester linkages
Cholesterol and other steroids: no ester linkages
Main roles:
• Energy storage
• Major component of cell membrane
• Signalling (hormones)
• drugs
• Carbohydrates
Main roles:
- Energy source
- Building block of other compounds

• Protein Denaturation

• Enzyme Structure And Function


• Many enzymes consist of a protein and a non-protein (called the cofactor). Cofactors can be
organic molecules or inorganic ions.
• Enzyme activity is temperature and pH dependent.
• Working Principle Of Enzymes

• Controlling Enzymatic Activity


• In presence of inhibitors, the enzyme activity is reduced.
• A competitive inhibitor occupies the active site and prevents substrates from binding to the
enzyme.
• A non-competitive inhibitor binds to a different part of the enzyme, away from the active site,
but by doing so, changes the shape of the enzyme and affects the function of the active site.
• Reaction Rate

• Michaelis-Menten Equation (2 Plots)

Vmax S 
V
S  K M
Lineweaver Burke plot (1/V versus 1/S)

Vmax S 
V
S  K M
1 S  K M [S ] KM
  
V Vmax S  Vmax S  Vmax S 
1 KM 1 1
 
V Vmax [ S ] Vmax
Hanes Woolf plot ([S]/V versus [S])

Vmax S 
V
S  K M
1 S  K M

V Vmax S 
[ S ] S  K M

V Vmax
[S ] [S ] K M
 
V Vmax Vmax

• Dna Replication

DNA can be replicated by using a strand of DNA as a template

Replication always occurs in the 5’-3’ direction

Any mistakes made during replication will lead to offspring with mutations The mutant will have
different properties (protein expression) than the parent
• Dictionary Of The Genetic Code

• Pathway Types

• Controlling Metabolic Pathways (Example Of Lac Operon Model)


Photosynthesis
• Definition
Photosynthesis is the conversion of solar energy into chemical energy stored in sugar and other
molecules
• Reaction
6CO2+6H2O→C6H12O6 + 6O2
• Purpose
• Mechanism
Two main reactions constitute the pathway of photosynthesis: a light dependent reaction which
is the photolysis of water (the splitting of water) and a light independent process which is the
fixation of carbon from carbon dioxide to sugar (the synthesis of glucose).
• Photolysis Of Water
• Photolysis takes place in the grana of the chloroplasts.
• Electrons in chlorophyll absorb photons and attain high energy levels.
• This energy is then used to split water into oxygen and hydrogen, and produce ATP
• Hydrogen is bound to an acceptor molecule called NADP, forming NADPH
• NADPH is used in carbon fixation

• Calvin Cycle (Carbon Fixation)

1) Carbon fixation
-3 CO2 (1c) molecules join 3 molecules of RuBP (5c) and form 6 molecules of 3PG (3c)
2) Reduction of 3 PG
- 6 ATPs enter the cycle give their 6Pi’s and 6 ADPs exit the cycle
-6 NADPHs enter the cycle give their 6H+ (for reduction process) and 6 NADP+ exit the cycle
-Using Pi’s from ATP and H+’s from NADPH 6 molecules of 3PG become 6 molecules of G3P (3c)
3) Regeneration of RuBP
- One molecule of G3P (3c) exits the cycle to form glucose, other 5 continue the cycle and take part
in regeneration of 3 molecules of RuBP
- Energy for regeneration comes from 3 molecules of ATP entering the cycle, after this 3 ADPs exit
the cycle

• Energy Consumption For Each Part


• Koch’s Postulates
1. The suspected pathogen (virus, microbe, etc) must be found in all creatures suffering from the
diseases (and should not be found in healthy one).
2. The suspected pathogen must be isolated from a sick creature and cultured in the laboratory
to obtain a pure culture.
3. The cultured suspected pathogen must be inoculated to a healthy creature and should cause
the same disease symptoms that were seen in the sick creature.
4. The same suspected pathogen must be re-isolated from the inoculated creature and
identified as being identical to the suspected pathogen.
• Methods Of Microbiology
Growing microorganisms
Microorganisms are grown in culture media, which contain all the nutrients required by
microorganisms to develop and replicate.
Serial dilution method – measuring microbial growth A population of microorganism can be
measured directly using cell counts. High-powered microscopy with haemocytometer slides
allows accurate cell count in a standard volume of culture.
Isolation of pure cultures
• Streak plate method Streaking is a technique used to isolate a pure strain from a single species
of microorganism.
• Enrichment culture An enrichment culture is a culture medium with specific and known
qualities that favour the growth of a particular microorganism.

• Bacterial Growth

Give four differences which might be found between prokaryotic and eukaryotic organisms.
- No nucleus in prokaryotes
- Eukaryotic could be multicellular
- Presence of cell wall in prokaryotes and not animal cells
- No organelles in prokaryotes
The yeasts. unicellular ...live in liquid or moist habitats ..reproduce, by simple cell division (fission) or
by the pinching of small “bud cells” off a parent cell (budding).

What is the basic unit of classification in taxonomy? Who invented the bionomial naming system and
how would a species name be written?
Species; Linne; genus and species name; capital letter only for genus and italics

What alternative method could you have used to construct the phylogenetic tree and what is different
from the cladistic approach?
Phenetic; just based on overall similarities

d) DNA is transcripted into mRNA


a) mRNA is transported to the cytoplasm
c) the mRNA binds to the ribosome
b) tRNA brings the aminoacid from the cytosol
e) tRNA binds to its complementary codon on mRNA
f) the aminoacid is added to the growing polypeptide chain

cell membrane indicating four important components


Phospholipids, glycolipids, transmembrane proteins and cholesterol
c) What would be osmotic pressure of the solution in b) in contact with a pure water solution? 45.8 atm
(2)
Give four examples of where fungi are used in bioengineering processes
Brewing, bread making, mycoprotein/quorn production, pencillin etc

i)The main component of the cell membrane are …PHOSHOLIPIDS………………..


ii) A metabolic pathway involves the step-by-step modification of a substrate molecule to form an end
product. Each step is catalysed by a specific …ENZYME………
iii) …PHOTOSYNTHESIS………….. occurs in chloroplasts, and leads to the formation of sugar from water
and CO2.
iv) The organelle in which pyruvate, the product of…GLYCOLYSIS……….., is broken down to water and …
ATP………… is called the …MITOCHONDRIA…………
The energy that is used as the “currency” in energy requiring reactions in the cell is
called.......ATP.....................

 The primary cell wall is a thin and extensible layer that is formed when the cell is growing. It is
composed of carbohydrates and of soluble proteins.
 The secondary cell wall is a thick layer that is formed inside the primary cell wall, after the cell is
fully grown. Conducting cells in xylem possess a secondary wall that contains lignin, a complex
polymer of aromatic alcohols, which strengthens and waterproofs the wall. The secondary cell
wall is the primary constituent of wood

Parsimony - the preferred tree showing evolutionary relationships between species, molecules, or other
entities is the one that requires the least amount of evolutionary change, that is, maximum parsimony.

Active site is the portion of an enzyme that specifically binds to the substrate.

Archaea is one of the two domains of prokaryotes.

Binary fission is the type of cell division by which prokaryotes reproduce; each dividing daughter cell
receives a copy of the single parental chromosome

Active transport occurs with the help of a specific transport protein and necessitates energy input.
Active transport is the movement of a substance across a biological membrane against its concentration
or electrochemical gradient.

Anabolism is the set of metabolic pathways that request energy to construct macromolecules from
smaller units.
Golgi complex - Organelle for manufacturing, warehousing, and shipping certain cellular products
Polypeptide - long, continuous, and unbranched peptide chain
Carbohydrate is a sugar, which is either a monomer (monosaccharide), a dimer (disaccharide) or a
polymer (polysaccharide).

Carbon fixation is the incorporation of carbon from CO2 into an organic compound by an autotropic
organism (plant or any other photosynthetic organism, or a chemoautotropic bacterium).

Catabolic pathway is a metabolic pathways that releases energy by breaking down complex molecules
into simpler compounds.

Cell cycle is an ordered sequence of events in the life of a dividing eukaryotic cell, composed of the M,
G1, S, and G2 phases.

Chlorophyll a is a green pigment located within the chloroplasts of plants; chlorophyll a can participate
directly in the light reactions, which convert solar energy to chemical energy.

Chloroplast is an organelle found only in plants and photosynthetic protists that absorbs sunlight and
uses it to drive the synthesis of organic compounds from carbon dioxide and water.

Cholesterol is steroid that forms an essential component of an animal cell membranes and acts as a
precursor molecule for the synthesis of other biologically important steroids.

Cell wall is a protective layer external to the plasma membrane in plant cells, bacteria, fungi, and some
protists.

Calvin cycle is the second of two major stages in photosynthesis (following the light reactions), involving
atmospheric CO2 fixation and reduction of the fixed carbon into carbohydrate.

Codon - is a three-nucleotide sequence of mRNA that specifies a particular aminoacid or termination


signal; the basic unit of the genetic code.

Chromosome - is gene-carrying structure found in the nucleus. Each chromosome consists of one very
long DNA molecule.

Cofactor is any non-protein molecule or ion that is required for the proper functioning of an enzyme.

Competitive inhibitor is a substance that reduces the activity of an enzyme by entering the active site in
place of the substrate.

Cyanobacteria is a photosynthetic oxygen-producing bacteria,

Cytoplasm is the entire contents of the cell, and bounded by the plasma membrane.

Denaturation (of protein) is a process in which proteins (or nucleic acids) lose their tertiary structure
and secondary structure by application of some external stress (including heat, solvents, acids or base,
ionic).

Diffusion is the spontaneous tendency of substance to move down its concentration gradient from more
concentrated to a less concentrated area.

Digestion is the process of breaking down food into molecules small enough for the body to absorb.

Domain is a taxonomic category above the kingdom level; the three domains are Archaea, Bacteria, and
Eukarya.

Double helix is the form of native DNA.


Enzymes are a class of proteins serving as catalyst, their function is to change the rate of a reaction
without being consumed by the reaction.

Gene is a discrete unit of hereditary information consisting of a specific nucleotide sequence in DNA (or
in RNA in some viruses)

Koch's postulates are a set of four criteria for determining whether a specific pathogen is the cause of a
disease. Krebs cycle is a chemical cycle involving eight steps that completes the metabolic breakdown of
glucose molecules to carbon dioxide. Krebs cycle occurs in the mitochondrion and is the second mafor
stage in cellular respiration.

Lipid is a family of compounds including fatty acids, glycerides, phospholipids, and steroids that are
insoluble in water.

Metabolism is the totality of an organism's chemical processes, consisting of catabolic and anabolic
pathways.

M phase is the mitotic phase of the cell cycle, which includes mitosis and cytokinesis.

Mitosis is a process of nuclear division in eukaryotic cells conventionally divided into five stages:
prophase, prometaphase, metaphase, anaphase, and telophase. Mitosis conserves chromosome
number by equally allocating replicated chromosomes to each of the daughter nuclei.

Nitrogen fixation is the assimilation of atmospheric nitrogen by certain prokaryotes into nitrogenous
compounds that can be directly used by plants.

Noncompetitive inhibitor is a substance that reduces the activity of an enzymes by binding to a location
remote from the active site, changing its conformation so that it no longer binds to the substrate.

Nucleic acid The nucleic acids acts as carriers of genetic information. Nucleic acids are made from long
chain of subunits called nucleotides. Nucleic acids are of two types DNA and RNA.
Nucleotide is the subunit of the chain that makes nucleic acid.

Okazaki fragment is a short DNA fragment synthetised to form the lagging strand of DNA.

Nucleus is the chromosome containing organelle of a eukaryotic cell.

Osmosis is the diffusion of water across a selectively permeable membrane, which provides a free
passage to water molecules only.

Osmotic pressure is a measure of the tendency of a slotion to take up water when separated from pure
water by a selectively permeable membrane.

Passive transport is the diffusion of a substance across a biological membrane

Phospholipids are molecules that constitute the bilayer of biological membrane, having a polar
hydrophylic head and a non polar hydrophobic tail.

Plasma membrane is the membrane at the boundary of every cell that acts as selective barrier.

Polypeptide is a polymer of many amino acids linked by peptide bonds.

Polysaccharide is a polymer of up to over athousand monosaccharides.

Population is a group of individual of one species that live in a particular area.

Protein is a three-dimensional biopolymer constructed from a set of 20 different monomers called


amino acids.
Primary structure is the first level of protein structure referring to the specific sequence of amino acids
and disulfide bridges.

Secondary structure is the localised repetitive coiling or folding of the polypeptide backbone of a
protein due to hydrogen bond formation between peptide linkages.

Tertiary structure is the three-dimensional shape of a proteins molecules due to interactions of side
chains involving hydrophobic interactions, ionic bonds, hydrogen bonds.

Quaternary structure is the particular shape of a complex, aggregate protein, defined by the
characteristic three-dimensional arrangement of its constituent subunits, each polypeptide.

Ribose is the sugar component of RNA

Ribosome is a cell organelle functioning as the site of proteinsynthesis in the cytoplasm. Consists of
rRNA and proteins molecules.

RNA polymerase is an enzyme that links together the growing chain of ribonucleotides during
transcription.

Selective permeability is a property of biological membranes that allows some substances to cross more
easily than others.

Substrate is the substance on which enzyme works.

Taxonomy is the branch of biology concerned with naming and classifying the diverse forms of life.

Transcription is the synthesis of RNA from a DNA template . Information stored in DNA is transcribed
into RNA.

Transfer RNA (tRNA) is a RNA molecule that functions as an interpreter between nucleic acid code and
protein's amino acid sequence.

Translation is the synthesis of a polypeptide using the genetic information encoded in mRNA molecule.
The information in the RNA is used to synthesise proteins.

Turgid or firm. The walled cells become turgid as a result of the entry of water from a hypotonic
environment.

Turgor pressure is the force directed against a cell wall after the influx of water.

Yeast is a unicellular fungi that lives in liquid or moist habitats, reproducing asby simple cell division or
by budding of a parent cell.

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