course 1 Flashcards
prebiotic period
formation of basic organic compounds of living systems
(saccharides, lipids, amino acids, nucleotides) via chemical
reactions probably in reducing atmosphere
What are the basic prerequisites for origin of cell?
boundaries against environment → local accumulation of molecules
(open system), it depends on the development of membranes
* development of metabolism (catalytic function of molecules:
proteins,RNA)
* development of autoreproduction capacity & development of an
internal memory system (genetic information: RNA, DNA)
What is the key role of RNA?
it carries information for its own reproduction and
simultaneously it can have a catalytic activity: ribozyme
What were the first cells?
Prokaryotes
Procaryotic cell is original.
Eucaryotic cell is derived from procaryotic cell
How did eukaryotic cells originate from prokaryotic cell?
Development of nucleus and endoplasmic reticulum
* Origin of mitochondria and chloroplasts: endosymbiotic theory
What is the origin of mitochondria?
An ancestral eucaryotic cell is thought
to have engulfed the bacterial ancestor of mitochondria, initiating a symbiotic
relationship.
What is the origin of chloroplasts?
An early eucaryotic cell, already
possessing mitochondria, engulfed a photosynthetic bacterium (a cyanobacterium)
and retained it in symbiosis.
What are the 3 domains of organisms?
bacteria, archea, eucarya
What are protists?
protists are unicellular eukaryotic organisms
What are the groups/ kingdoms of multicellular eukaryotes?
Plants, fungi and animals
What is the job of molecular clock?
By means of molecular clock, we can assess the time point when two
concrete lineages of organisms branched (how they are relative):
phylogenetic tree
What is an essential difference between a prokaryotic and eukaryotic cell?
Procaryotic cell (procaryotes): chromosomal DNA is not bounded
by membrane structure, i.e. the cell has not regular nucleus.
* Eucaryotic cell (eucaryotes): chromosomal DNA is bounded by
membrane structure (nuclear envelope), i.e. the cell has regular
nucleus.
What is the basic structure of prokaryotic cell?
nucleoid (DNA)
* plasmids
* cytoplasm
* plasma membrane
* cell wall
* capsule (outer protective layer in some procaryotes, polysaccharides)
* flagella and pili
What is a nucleoid?
Nucleoid is a region where DNA is located within the cell (chromosome).
It contains one molecule of doublestranded (ds) DNA and proteins and histone like proteins
What are some characteristics of prokaryotic chromosome?
mostly circular, arranged in the form of
loops and attached to plasma membrane.
How many replication origins in prokaryotic cell?
1
The chromosome is attached to plasma membrane by what?
The chromosome
is attached to plasma membrane by replication origin.
What is a plasmid?
Plasmid represents a small circular doublestranded DNA. It involves
genes which are not indispensable for the life of procaryotic cell.
Plasmids are present in the cytoplasm of some procaryotes.
What types of plasmids there are?
F (fertility) plasmids: genes indispensable for conjugation
* R (resistance) plasmids: genes producing resistance to
antibiotics etc.
* Col (colicin) plasmids: genes coding for colicins, which kill other
bacteria
* Degradative plasmids: enable degradation of unusual substances
(e.g. salicylic acid)
* Virulence plasmids: turn bacterium into a pathogen
What are some characteristics of cytoplasm?
Cytoplasm= everything inside the cell surrounded by plasma membrane, nucleoid + plasmids, cytosol
What can be found in the cytosol?
Cytosol contains:
* Ribosomes (70S) and cytoskeleton
It has a gel-like character and most of chemical reactions of the cell
occur here.
What is realized in the cytoplasm?
DNA replication and DNA transcription as well as mRNA translation are
realized in cytoplasm.
How do plasma membranes differ in archaea/ and bacteria and eukarya?
Phospholipids in archaea have branched phytanyl sidechains rather than linear and there is an ether bond instead of an ester bond that connects the lipid to the glycerol.
What is the structure of cell wall?
Most of procaryotic cells have rigid cell wall. Its structure contains polymers of peptidoglycan (murein) in bacteria and
pseudopeptidoglycan (pseudomurein) in archaea
The cell wall of gram-positive bacteria is made up of what?
cell wall is made up of only peptidoglycans
The cell wall of gram-negative bacteria is made up of what?
the cell wall is supplemented with
lipopolysaccharide coat.
What is the difference between eukaryotic and prokaryotic flagellum?
Prokaryotic flagellum is significantly thinner, it is not covered by a membrane, protein
flagellin is present in bacteria as well as archaea
What are essential ways how prokaryotes acquire energy?
Phototrophic organisms (procaryotes and eucaryotes): they acquire
energy from sunlight (photosynthesis)
* Chemotrophic organisms (procaryotes and eucaryotes): they
acquire energy by the oxidation of chemicals
* Lithotrophic organisms (procaryotes): they acquire energy by
the oxidation of inorganic chemicals (H2S, Fe2+
* Organotrophic organisms (procaryotes and eucaryotes): they
acquire energy by the oxidation of organic chemicals
(fermentation, oxidative phosphorylation)
What is the source of carbon for autotrophic organisms?
inorganic
compounds (CO2) represent a source of carbon
What is the source of carbon for heterotrophic organisms?
organic compounds (glucose) represent a source of carbon
What are the differences between archaea and bacteria?
Bacteria:
* chromosomal DNA is not
organized in structures similar
to nucleosomes
* genes without introns
* thymine is present in the tRNA
* RNA polymerase is simple (4
polypeptides)
* fatty acids in membrane lipids
are bound to glycerol by ester
bond
* cell wall from peptidoglycan
Archaea:
* chromosomal DNA is organized
in structures similar to
nucleosomes
* tRNA and rRNA genes contain
introns
* thymine is absent in the tRNA
* RNA polymerase is complex
(more than 8 polypeptides)
* fatty acids in membrane lipids
are bound to glycerol by ether
bond
* cell wall from
pseudopeptidoglycan
Compare prokaryotic and eukaryotic cell
Procaryotic cell:
* 1-10 µm
* 1000 - 4000 genes
* it does not have regular nucleus
* non-mitotic division of
chromosomes
* transcription and translation are
not separated
* 70S ribosomes
* without classical cytoskeleton
* more or less without organelles
Eukaryotic cell:
5-100 µm
10 000 - 30 000 genes
it has a regular nucleus
* mitotic division of chromosomes
* transcription and translation are
separated
* 80S ribosomes
* cytoskeleton
* organelles
Virtually all animal life depends on what for their survival?
Virtually all animal life depends on bacteria for their survival because they possess the genes and enzymes necessary to
synthesize vitamin B12 and provide it through the food chain.
Bacteria as a biomass …….. all plants and animals.
exceeds
What are the molecular characteristics of bacteria?
Bacteria have a primitive chromosome
called a nucleoid – composed of
DNA which is double stranded, circular, and supercoiled.
Proteins (histone like).
Bacterial genes do not have introns.
RNA transcription and protein translation occur in the same compartment (ie. there is no nucleus in bacteria only a nuclear region).
There is no cytoskeleton in bacteria.
Bacteria have ribosomes, each consisting of a small (30S) and a large (50S) subunit.
Division is binary and non-sexual (process known as binary fission).
Describe the bacterial colony growth curve.
Lag phase - bacteriaadapt to growth conditions. They are not dividing.
Log phase(also called logarithmic phase or exponential phase)
bacterial cell number doubling.
Stationary phase - growth reaches a plateau as the number of dying cells equals the number of dividing cells.
Death phase - an exponential decrease in the number of living cell.
What are some characteristics of archaea?
They have a unique biochemistry eg. Ether lipid cell membrane.
They use more sources for energy compared to eukaryotes eg. Ammonia, metal ions, hydrogen gas.
First observed in extreme environments eg. Hot springs, salt lakes etc
They are important for human microbiota in the gut, mouth and skin.
There is no evidence that they can cause a disease
What are some molecular characteristics of archaea?
Archaea have chromatin composed of
DNA (double stranded, circular, supercoiled)
Histones (similar to eukaryotic histones)
Introns are present in the genes encoding tRNA and rRNA.
RNA transcription and protein translation are similar to eukaryotic processes.
There is an actin cytoskeleton in archaea.
Archaea have ribosomes, each consisting of
a small (30S) and a large (50S) subunit.
Archaea reproduce by binary division,
fragmentation or budding.
What is a plasmid?
Plasmid is a circular double stranded DNA molecule. Plasmids often carry genes that benefit the survival of the organism.
Plasmids encode genes for resistance to antibiotics or heavy metals.
Plasmids encode genes for metabolic enzymes involved in nitrogen fixation.
What does a plasmid need to replicate independently?
A stretch of DNA from which replication is initiated/started
known as an origin of replication (Ori).
What are integrative plasmids that can also insert into the host chromosome?
episomes
What is the Griffith‘s experiment (1928) ?
Infection of mice by virulent and non-virulent strains of S. pneumoniae - Identified a ´Transforming Principle´
What is the Avery, McLeod, McCarthy (1944) experiment?:
Griffith experiment repeated but with isolated DNA → identified the ´Transforming Principle´ to be DNA.
What is transduction?
A process whereby foreign DNA is introduced into another cell by a virus.
A virus that infects bacteria is called a bacteriophage.
This leads to genetic recombination in bacteria.
The bacteriophage can transfer DNA from one bacterium to another bacterium
What is a general/non-specific transduction?
a transfer of any part of host DNA (only bacterial genes)
How does general transduction proceed?
1)Bacterium is infected by phage DNA.
2)Phage replicates and bacterial DNA is broken down into pieces.
Sometimes a fragment of bacterial DNA is packaged into phage capsid instead of phage DNA.
3)The donor cell lyses and phage carrying bacterial DNA is released to infect a new host cell.
4)DNA in the new host cell become recombined after infection.
What is specialized/specific transduction?
the transfer of a particular part of host DNA along with viral genes.
What is the result of a specialized transduction?
The recipient cell receives
a new metabolic ability
(from the transferred bacterial genes)
What is conjugation?
The transfer of genetic material between bacterial cells via:
direct cell to cell contact
or
2) a bridge-like connection between two cells.
It is a method of horizontal gene transfer.
It is not sexual reproduction (ie. there is no transfer of gametes).
Transferred DNA is known as a transposon/conjugative plasmid.
The transferred DNA is often beneficial to the recipient.
Benefits may include antibiotic resistance, xenobiotic (chemical) tolerance or the ability to use new metabolites.
What is an operon?
Anoperonis a functional unit of transcription and genetic regulation.
It enables organisms (eg. prokaryotes) to regulate gene expression depending on
the environmental conditions.
What are the 3 basic DNA compartments making up an operon?
1) Promoter – a nucleotide sequence that enables a gene to be transcribed.
The promoter is recognized by RNA polymerase, which then initiates transcription.
2) Operator– a segment ofDNA to which a repressorbinds.
The repressor protein obstructs the RNA polymerase from transcribing the genes.
3) Structural genes – the genes that are regulated within the operon.
What are the 2 operons in prokaryotes?
The Lac (Lactose) operon
The Trp (Tryptophan) operon
How does transcription start?
By binding of of the enzyme RNA polymerase (RNAP)
which binds to thepromoter, immediately upstream of the genes.
What are inducible genes?
They code for catabolic enzymes, produced only in presence of substrate = inductive regulation
What are repressible genes?
genes for anabolic enzymes - negative feedback by product of anabolic pathway = repressive regulation
Basic structure of eukaryotic cell
Nucleus: separated from the cytoplasm by nuclear envelope,
it contains most of cellular DNA
* Cytoplasm: interior of the cell (without the nucleus), most of
metabolic reactions of the cell occur here
* Plasma membrane: it forms outer boundary of the cell
* Cell wall: some eucaryotic cells have rigid cell wall (plants)
* Flagell and cilia: some eucaryotic cells
Nucleus
Nuclear envelope (inner & outer membrane ), it bounds nucleus against rest of the cell, nuclear pores are located in nuclear
envelope
* Nuclear lamina: localized just beneath nuclear envelope (proteins lamins)
* Chromatin: linear chromosomes (nucleosomes: DNA & histones),
DNA encodes genetic information of the cell
* Nucleolus: place of ribosome production, it is not separated from rest of the nucleus by membrane structure
Nucleus is the place for DNA replication (DNA→DNA) and for DNA
transcription (DNA→RNA).
Plasma membrane
Plasma membrane serves as a barrier to outer environment.
Structure of plasma membrane: lipid bilayer, outer and inner layer can
differ as to present lipids
There are various membrane proteins anchored in plasma membrane,
what are their functions?
transport of molecules across plasma
membrane, attachment of the cell, receiving information from
extracellular environment (receptors)
What is plasma membrane involved in?
Plasma membrane is involved in (1) import and export of molecules,
(2) attachment of cells to other cell or to extracellular matrix, (3)
receiving information from the environment and (4) cell movement.
What is the structure of plant cell wall?
cellulose (microfibrils)
hemicellulose (branched polysacharide)
pectin (polysacharide)
What is the purpose of a cell wall?
Cell wall provides the cell with a protection against mechanical damage
and pathogens, forms external skeleton of the cell (and thus skeleton of
whole plant) and mediates cell-cell interaction)
What is the job of flagella and cilia?
Flagella: enable movement of eucaryotic cell
Cilia: enable movement in the vicinity of eurcaryotic cell
What is the structure of eukaryotic flagellum?
it is similar for both
flagellum and cilium, significantly differs from the structure of procaryotic
flagellum (it is significantly more complex), microtubules (9 dublets + 2),
motor protein dynein
Describe cytoplasm: what does it include? What occurs there?
Cytoplasm includes:
* Cytosol which is cytoplasm without membrane-bounded organelles, it has
rather character of a gel than a solution, many fundamental chemical
reactions of the cell occur here
* Membrane-bounded organelles
Cytoplasm is the place for mRNA translation (RNA →protein).
What does the cytosol contain?
Cytosol contains:
* Ribosomes (80S): ribosome is a complex of RNA and protein molecules , ribosome is the place of mRNA translation
* Cytoskeleton:
Three types filaments:
* microtubules (tubulin)
* Intermediate filaments (various proteins: keratins, vimentin, lamins)
* actin filaments (actin)
Cell cortex (mesh-like structure from actin filaments located beneath
plasma membrane)
Cytoskeleton gives the cell its shape, its capacity to move and
transport signal.
What are the two basic types of membrane-bounded organelles also known as complex „cell like“ organelles that contain their own DNA?
Mitochondria: energy production (ATP) by oxidative
phosphorylation
* Chloroplasts (only plants): photosynthesis
What is the structure of mitochondria?
4 different compartments (matrix, inner membrane, outer membrane and intermembrane space)
What is the function of mitochondria?
ATP production
other functions (buffering cytosolic redox potential:
decrease of NADH level in cytosol leads to increased NAD+
level in cytosol for glycolysis; plenty of ATP: citrate from
mitochondria → cytosol for biosynthesis, e. g. fatty acids;
starvation: oxidation of amino acids in mitochondria)
What are simple membrane-bounded organelles?
Endoplasmic reticulum:
* Smooth endoplasmic reticulum
* Rough endoplasmic reticulum
* Golgi apparatus:
* Transport vesicles
Lysosomes
Peroxisomes
Vacuoles
Endoplasmic reticulum
Endoplasmic reticulum: synthesis of lipids, membrane proteins
and synthesis of proteins for export from the cell
Smooth endoplasmic reticulum
Smooth endoplasmic reticulum (without ribosomes): synthesis
of fatty acids and phospholipids, detoxification (hepatocytes)
modification of proteins: glycosylation
Rough endoplasmic reticulum
Rough endoplasmic reticulum (with ribosomes): synthesis of
membráne proteins and organelle proteins and synthesis of
proteins for export
modification of proteins: glycosylation, formation of disulfide
bonds, chaperones
Golgi apparatus
Golgi apparatus: modification and transport of the molecules
produced in the ER
modification of protein: glycosylation, phosphorylation, proteolysis
Transport vesicles
Transport vesicles: material transport within the cell and outside of
the cell
Lysosomes
contain enzymes for degradation (acid hydrolases)
→ degradation of substances, acid pH [FIG.]
lysosomal diseases: insufficient activity of some of hydrolases
leads to the accumulation of substrate
* example: Gaucher syndrome (neurological disorders in children)
Peroxisomes
Peroxisomes: reactions where dangerously reactive hydrogen
peroxide is produced and degraded (oxidases, catalase)
Vacuoles
Vacuoles (only plants): large membrane-bounded vesicles
containing water solutions of substances (ions, saccharides etc.)
DNA transcription and RNA translation in eukaryotic cell
Eucaryotic cell separates DNA transcription from RNA translation:
processing of RNA transcript by splicing before its translation!
What is the size and morphology of eukaryotic cell?
Size of eucaryotic cell: usually 5-100 µm
Generally, eucaryotic cell is bigger than procaryotic cell.
Shape of eucaryotic cell very diverse:
* unicellular eucaryots (protists)
* multicellular eucaryots (connected with cell function in organism):
e.g. lymphocyte, erythrocyte, hepatocyte, muscle cell, epithelial
cell, neuron etc
What is the metabolism like in eukaryotic cells?
Eucaryotes exert lower variability in biochemical capabilities, including
the capability of acquiring energy, than procaryotes.
Essential ways of acquiring energy:
* Phototrophic eucaryotes
* Chemotrophic eucaryotes: only organotrophic eucaryotes (only
procaryotes are lithotrophic)
Source of carbon:
* Autotrophic eucaryotes
* Heterotrophic eucaryotes
Dependence on oxygen:
* Aerobic eucaryotes
* Anaerobic eucaryotes
What are the 4 basic types of tissues?
(1) epithelial tissue, (2)
connective tissue, (3) muscles and (4) nervous tissue
What is osmosis?
passive movement of solvent molecules through a semi permeable membrane
o only water passes (not ions) from an environment of low osmotic pressure to an environment of high osmotic
pressure
What are some strong electrolyte – fully soluble in water?
NaCl -> Na+ + Cl-
Na2SO4 -> 2Na+ + SO42-
KNO3 -> K+ + NO3
NaH2PO4 -> Na+ + H2PO4
What are some insoluble salts?
product of solubility KS
BaSO4 <-> Ba2+ + SO42-
KS = [Ba2+] * [SO42-]
Dissolving or organic substances in water links to what?
Links with polarity – polar molecules will dissolve in water, non-polar will not
- Those forming hydrogen bonds are soluble
Substances that are water soluble
= polar = hydrophilic = lipophobic
Substances that are water in-soluble
= non-polar = hydrophobic = lipophilic
Carboxylic acids how are they polar?
carboxylic acids with a shorter carbon chain (up to 8C) are polar and thus also hydrophilic
o additional chain means that the molecule will be hydrophobic – thus higher fatty acids in blood need to be
transported with the help of transport protein - albumin
What are some substances with amphipathic character?
usually large molecules with one hydrophilic and one hydrophobic part
o soaps and detergents
o e.g. phospholipids – form bilayers -> membranes, micelles, liposomes
What are some hydrophobic substances?
oils in water
o TAG - triacylglycerol
o carry no dipole moment, carry no electrical charge à insoluble in water
o in water lipid droplets will form and float -> droplets come together to minimize their
surface exposure
What is the composition of bodily fluids in intracellular fluid?
intracellular fluid - main cation = K+ = 140mM – smaller hydration shell than Na2+ -> passes membranes easier
o main anion - proteins – large molecules, hold negative charge, cannot escape outside
What is the composition of bodily fluids in extracellular fluid?
extracellular fluid– main cation = Na+ = 140mM
o main anion = Cl- = 100mM
- organic substances -> glucose, amino acids, urea
What is the Arrhenius theory of acids and bases?
acids – substances which release hydrogen cations into aqueous solution
o HNO3 -> H+ + NO3
-
- bases – substances which release hydroxide ions anions OH-
o NaOH -> Na+ + OH- - neutralization – mutual reaction between an acid and a base, production of water and salt
o NaOH + HNO3 -> NaNO3 + H2O
What is the Brönsted theory of acids and bases?
acid - substances (molecules and ions) that donate H+ to another substance
- basic – substances able to accept H+ from another substance
- cleavage/loss of a proton turns the acid into a base
What are some solutions of strong acid and strong bases?
strong electrolytes = fully dissociates
- strong acids -> HCl, HNO3, H2SO4, HClO4
- strong bases -> NaOH, KOH, Ca(OH)2, Ba(OH)2
What are buffers?
solutions that resists pH changes
- mixture of weak acid and its conjugate salt
What is chromatography?
chromatography - liquid, gas -> separation of compounds according to different affinities for mobile and
stationary phase
What is electrophoresis?
electrophoresis – separation of substances by their ability to move in an electric field
Describe liquid chromatography
based on weak bond interactions between the studied substance and the different polar
phases
o mobile phase = nonpolar solvent (acetonitrile, methanol)
o stationary phase = polar molecules (silica gel, octadecyl silica)
- polar substances will attach to stationary phase and non-polar will travel faster
Describe high performance/high pressure liquid chromatography - HPLC
stationary phase – very small granules (2-5 μm) of silica gel, hydrated silica, which is then modified and silicon groups
bind to hydrocarbon chains, forming octadecyl silicone gel
- mobile phase - solvent - acetonitrile, methane
- detector - HPLC can use Mass spectrometry as a detector
- machine construction
Describe thin layer chromatography - TLC (Thin Layer Chromatography)
The stationary phase is either a liquid fixed on the supporting material or a solid absorbed in the form of a thin layer
- Used mainly in the separation of azo dye (benzene nuclei separated by an azo group)
Describe Gas chromatography
mobile phase formed by inert gases (He, N2, Ar)
- analysis of mainly volatile substances - lipids
- capillary column
- detector – Flame ionizing detector (FID)
What is electrophoresis?
fast and effect technique based on the movement of charges particles in an electric field
- isoelectric point – value of pH in solution where a zwitterion stops moving in an electric field (e.g. proteins)
What are saccharides?
sugars which form via photosynthesis in plants
o 6 CO2 + 12 H2O -> C6H12O6 + 6 O2 + 6 H2O
- simplest monosaccharides have 3 carbons (=triose) -> glyceraldehyde
How are monosaccharides classified?
Monosaccharides belong among hydroxyl derivatives and carbonyl compounds
-via functional group - aldose and ketose
o aldose - ribose, glucose, mannose (C2 epimer of glucose), galactose (C4 epimer of glucose)
o ketose - ribulose, fructose
- according to the number of carbon atoms - triose C3, tetrose C4, pentose C5, hexose C6, heptose C7
o pentose - ribose, deoxyribose, ribulose
o hexose - glucose, fructose, galactose, mannose
Presence of what leads to optical activity?
presence of chiral carbon = optical activity
What are enantiomers?
isomers which are mirror images ( L a D enantiomers)
D-isomers occur naturally
What are genetic series of aldoses?
another carbon is inserted between 1. and 2. carbon atom
- epimer – isomers which differ by their OH group orientation
around a carbon
- galactose and glucose – isomers which differ by their OH group
orientation around the 4th carbon
o galactose is a C4 epimer of glucose
- glucose and mannose – isomers which differ by their OH group
orientation around the 2nd carbon
o mannose is a C2 epimer of glucose
What is a ketose?
a dihydroxyacetone that has no chiral carbon (it is still considered a saccharide, even though it cannot be found freely in
nature)
What are 2 storage polysaccharides?
-glycogen – branched polysaccharide (animal)
o formed by the connection of α-1,4-glycosidic bond and branched α-1,6- glycosidic bond
§ branching allows faster breakdown of polysaccharide chains
o polysaccharide in human -> storage of glucose
- starch –amylose and amylopectin
o amylose – only linear chain
o amylopectin – linear chain, sometimes branched
What is an example of a building polysacharide?
cellulose – formed by the connection of glucose by β-1,4- glycosidic bound (which human enzymes cannot breakdown)
o form tube like structures which connect
What are lipids?
Lipids are substances of natural origin
- are not water soluble
- consist of fatty acids and alcohol
- in the body, they are synthesized from acetyl-coenzyme A (acetyl-CoA)
- hydrolyzable lipids have an ester or glycosidic bond
How do we classify lipids?
hydrolysable:
o simple
§ fats – glyceraldehyde + FA
* solid
* liquid -> oils (high number of unsaturated fatty acids)
§ waxes - glyceraldehyde + FA with 16 or more carbons
o compound
§ phospholipids
§ lipoproteins
§ glycolipids
- non-hydrolysable
o steroids – derived from sterane
o terpenes – consists of two or more isoprenoid units
What are fatty acids?
usually even number of carbons
- can form esters with cholesterol
- saturated – only simple bonds, palmitic acid, stearic acid
- unsaturated – double bonds in configuration cis, oleic acid
- polyunsaturated fatty acids – have more than one double bond; linoleic acid, linolenic acid, arachidonic acid
What are triacylglycerols?
they are esters of 3 fatty acids and glycerol
- non-soluble in water
- belong to hydrolysable lipids
- in cells stored in the form of lipid droplets (not bound by a membrane)
- function – storage of energy, source of carbons, heat and electrical isolation
What are steroids?
basic skeleton of steroids is formed by sterane - tetracyclic hydrocarbon
- most important steroid is cholesterol
o important part of biological membrane
o it is a precursor of all steroid hormnes and bile acids
What is a nucleotide and a nucleoside composed of?
nucleotide = nitrogen base + sugar (pentose) + phosphate
nucleoside = nitrogen base + sugar (pentose)
What is the structure of nucleic acids?
N-glyosidic bond – in-between nitrogen base and sugar, binds to the 1st sugar carbon
- Ester bond– in-between sugar ad phosphate, binds to the 5th sugar carbon
- phosphodiester bond – a connection between the 3rd sugar carbon of one nucleotide and 5th sugar carbon of the second
nucleotide
How is nucleic chain orientated?
linear nucleic chains always have a free OH group at one end on 3rd carbon of pentose (3’ end) and at the other end a
free phosphate bound to the 5th carbon of pentose (5’ end)
- synthesis of new chain always occurs in the 5‘ -> 3‘ direction
o this means that new nucleotides bind to the 3’ end
What is the chemical nature of proteins?
Proteins are biopolymers of amino acids. They are macromolecules
How many proteinogenic amino acids are there?
There are 21 proteinogenic AAs
other AAs are formed by a
posttranslational modification
Which amino acids belong to the non-polar group?
Ala,Val, Leu, Ile, Pro, Phe, Trp, Met, they are all hydrophobic since they are non-polar
Which amino acids belong to the polar group?
Gly ,Ser, Thr, Cys, Tyr, Asn, Gln They are all hydrophillic since they are polar
Which amino acids belong to the polar group?
Gly ,Ser, Thr, Cys, Tyr, Asn, Gln They are all hydrophillic since they are polar
Which amino acids belong to the polar group?
Gly ,Ser, Thr, Cys, Tyr, Asn, Gln They are all hydrophillic since they are polar
Which amino acids belong to the acidic group?
Asp and Glu. They are both negatively charged
Which amino acids belong to the basic group?
Lys, Arg, His. They are all positively charged
What are nonproteinogenic amino acids?
ornithine citrulline, L-dihydroxyfenylalanine p
(L-DOPA), β-alanine γ-aminobutyric acid (GABA), taurine
What are some essential amino acids?
1) branched chain AAs (Val, Leu, Ile)
2) aromatic AAs (Phe, Trp)
3) basic AAs (Lys, Arg, His)
4) Thr, Met
What do side chains of amino acids determine?
Side chains of AAs determine final
properties of proteins
What is the isoelectric point?
pH value at which the net
charge of a compound is zero
What do solutions of amino acids belong to?
Solutions of AAs belong among
ampholytes
What do peptides and proteins contain?
contain 2 or more AAs bound by
peptide bond(s)
oligopeptides: 2 – 10 amino acids
polypeptides: > 10 amino acids
proteins: polypeptides of Mr > 10 000
What bonds are formed among amino acids?
peptide bonds
Spacial arrangement and biological function of proteins are dependent on what?
spacial arrangement and biological function
are DEPENDENT
on the amino acid composition
What influences final structure of proteins
side chains of AAs influence a final
structure of proteins
What are the covalent bonds found in proteins?
peptide bond -CO-NH-
disulfide bond -S-S
What are the non-covalent bonds found in proteins?
hydrogen bonds: -H…..O- -H…..N-
hydrophobic interactions: nonpolar side chains
ionic interactions: -COO- /+H3N-
What is the primary structure of proteins?
= order of amino acids
* read: from N- to C- end
* it is coded on a genetic
level
* stabilization:peptide bonds
What is the secondary structure of proteins?
a-helix or B-pleated sheets
= spatial arrangement of the polypeptide chain given by rotation of the planar peptide bonds around α-carbons
stabilization: hydrogen bonds
between –CO- and -NH of the peptide bonds
What are the most common helixes found among proteins?
α-helix (right-handed)
collagen helix (left-handed, steeper)
What is the tertiary structure of proteins?
= spatial arrangement of the secondary
structures (folding of domains)
stabilization: between side chains of AAs
1) hydrogen bonds
2) ionic (electrostatic) interactions
3) hydrophobic interactions
4) disulfide bonds
What does the function of proteins depend on?
a function is related to the spatial structure
IT DEPENDS ON AMINO ACIDS COMPOSITION
How do we classify proteins according to their tertiary structure?
1) globular proteins (spheroproteins)
spheroidal shape both secondary structures are abundant
2) fibrous proteins (scleroproteins) rod-like shape ,one secondary structure predominates
e.g. α-keratin, collagen
What is the quaternary structure of proteins?
= oligomeric structure of a protein (2 or more
subunits = polypeptide chains ~ monomers)
* i.e. the structure is found only in proteins
composed of 2 or more chains (subunits)
* stabilization: noncovalent interactions
* the proteins have an „allosteric effect“
(it can generate cooperative behavior of subunits)
What happens when an allosteric effector binds to one protein subunit?
If an allosteric effector binds to one subunit,
other subunits change their shape
How do we classify proteins?
1) by localization in an organism
intra- / extracellular
2) by function
structural / biological active
3) by shape
globular / fibrous
4) by chemical composition
simple / complex (conjugated) proteins
What do conjugated proteins contain?
conjugated proteins contain polypeptide chain
(= apoprotein) + nonprotein prosthetic group
glycoproteins
metalloproteins
hemoproteins
phosphoproteins
nucleoproteins
What are the physicochemical properties of proteins?
water solubility depends on the structure
* proteins form colloidal solutions
(viscosity, sedimentation, light dispersion)
colloidal-osmotic pressure = onkotic pressure
* proteins can be salting-out of the solution
(~ water sheet removing)
How can proteins be denatured?
heat, whipping, shaking, radiation
strong pH changes, salt of heavy metals,
organic solvents, detergents
Proteins act as what and give a positive reaction with what?
proteins act as antigens formation of
antibodies
proteins give positive reaction with
biuret reagent
Are proteins able to absorb UV radiation?
Proteins strongly absorb UV radiation
Under physiological pH, what charge do proteins have?
under physiological pH
proteins are negatively charged
How can we determine proteins in a laboratory?
chemical reacion of peptide bonds with
biuret reagent - spectrophotometry
* complementary reaction with an antibody
- immunochemistry
* separation in an electric field
- electrophoresis
* denaturation
What are chaperons?
proteins which help correct the arrangement and formation of proteins
o stop the formation of incorrect bonds or connections, some even have the capability to unfold and refold a
protein
o chaperons also include heat shock proteins, which allow proteins to pass though membranes
How is protein structure formed?
Protein function results from its structure.
Folding of protein molecule into relevant 3D structure is determined by
weak noncovalent bonds:
* Electorstatic forces
* Hydrogen bonds
* Van der Waals forces
* Hydrophobic interactions
Disulfide bonds: the stabilize 3D structure of protein molecule
What are basic shapes of protein molecules?
Globular proteins (insulin, actin)
Fibrilar proteins (collagen, elastin)
What are protein families?
They include proteins similar in their structure and function.
Proteins of one protein family are coded by genes of one gene family.
What is the use of functional polymers of proteins?
Capability of protein molecules for self-organizing.
Association into big polymers and the formation of various structures:
* Filaments (actin, elastin)
* Tubules (microtubules)
* Sheets (membrane proteins, protein FtsZ in bacteria – tubulin
homolog)
* Spheres (viral capsids)
What are complexes of various proteins called?
proteasomes
What molecules bind to proteins?
Ligands: ligand binding is highly selective and directly related to the function of protein.
Conformational change due to binding of other molecule leads to change in activity
What are the different types of bound atoms/molecules that bind to proteins?
Binding of ion/atom: Ca 2+ (calmodulin), Fe 3+ (transferrin, IRP-iron regulatory protein)
* Binding of small molecule:
* Glycosylation (binding of saccharide): glycoprotein
* Phosphorylation (binding of phosphate): protein kinase,phosphatase
* Binding of GTP: GTP-binding proteins
* Binding of other small molecules: heme (hemoglobin), retinal (rhodopsin)
* Binding of nonprotein macromolecule: DNA (transcription factors)
* Binding of protein: protein substrate (enzyme), protein antigen (antibody), cyclin dependent kinase (cyclin)
By what can protein activity be regulated by?
Protein activity can be also regulated by proteolytic cleavage: insulin,
caspases
How can protein (enzyme) activity be regulated?
Negative regulation (feedback inhibition)
Positive regulation
How is protein degradation regulated?
Two means of protein degradation:
* degradation in lysosomes
* degradation in proteasomes
Degradation in proteasomes is based on enzymatic degradation: proteolysis, proteases
What is ubiquitin and what is a proteasome?
Ubiquitin: it labels proteins to be degraded
Proteasome: protein complex for protein degradation
Structural proteins
tubulin, keratin, actin, collagen
Protein enzymes
protein kinase C, DNA polymerase δ, pepsin
Motor proteins myosin, kinesin, dynein
myosin, kinesin, dynein
Transport proteins
hemoglobin, transferrin, albumin
Storage proteins
ferritin, casein, ovalbumin
Signaling proteins
insulin, EGF, erythropoietin
Receptor proteins
rhodopsin, insulin receptor, EGF receptor
Regulatory proteins
chaperones, transcription factors, cyclins
Protein antibodies
immunoglobulins
What are the functions of the cytoskeleton?
Internal support of the cell and its structures (“skeleton of the cell“) & internal organization of the cell
* Movements of the cell & intracellular transport
* Cell signalization
What is the structure of microtubules?
Protofilaments: polymer consisting of dimers of α tubulin a β tubulin
Microtubule: 13 protofilaments
+ end (β tubulin), - end (α tubulin) of microtubules
MTOC (microtubule-organizing center): ɣ tubulin
Dynamic instability (+end)
Polymerization (bound GTP), depolymerization (bound GDP)
What is the function of microtubules?
Mitotic spindle: centrosomes (MTOC)
* Flagella and cilia: structure (9 doublets +2)
movement (motor protein dynein)
* Tracks for the movement of organelles: motor proteins
(molecular motors) dynein and kinesin
What drugs affect the function of microtubules?
Colchicine (stabilization of free tubulin)
* Vinblastine, vincristine (stabilization of free tubulin): employment in tumor therapy
* Taxol (stabilization of microtubules): employment in tumor therapy
What are the monomers of intermediate filaments?
Monomers: lamins (nuclear lamina)
keratins (epithelial cells and their derivates)
vimentin (cells of mesenchymal origin)
desmin (muscle)
proteins of neurofilaments (neurons)
What is the structure of intermediate filaments?
Monomeric molecules: central α-helical domain and two peripheral
globular domains
Fibers: polymer of tetramers (2 antiparallel dimers)
Intermediate filaments: 8 twisted fibers (rope-like structure)
What is the function of nuclear lamina?
Nuclear lamina: structure (lamins) and localization function (mechanical support of nuclear envelope,disintegration and reintegration of nuclear envelope)
* Intermediate filaments in cytoplasm: tissue-specific types of proteins function (mechanical resistance of the cell)
What is the monomer of microfilaments?
Monomer: actin, known as G-actin (globular)
What is the structure of microfilaments?
Fibers: polymers of actin, known as F-actin (filamentous)
Microfilaments: double-helix
+ end, - end of microfilaments (determined by the orientation of actin molecule)
Treadmilling (+ end & - end)
What is the function of microfilaments?
Microvilli
* Cell cortex: structure and localization
function
* Lamellipodia, filopodia: amoeboid locomotion of the cell
* Contractile ring: cytokinesis
* Contractile bundles: “muscles“ of the cell
* Muscle cells: association with motor protein myosin → motility
What are the protein binding actin (microfilaments)?
Spectrin (shape of erythrocytes)
Dystrophin (binding of microtubules to basal lamina)
What drugs affect the function of microfilaments?
Latrunculin (prevents polymerization of free actin)
* Phalloidin (stabilization of microfilaments): poison from the Deathcup
What is the extracellular matrix?
It is an environment (net) between cells, non-cellular part of tissue
It influences many cell functions, behaviors
It is made up of Structural proteins (collagen, elastin), glycoproteins (fibronectin, laminin), proteoglycans (aggrecans)
What are the 4 types of tissues?
- Epithelia
- Muscle tissue
- Connective tissue
- Nerve tissue
What are epithelia?
Origin in ectoderm, entoderm and mesoderm
* Cells attach to each other
* Minimal extracellular matrix
Variable – structure, function
* Protective - epidermis
* Absorptive – epithelium
* Secretory – glandular epithelia
Where can we find stratified squamous epithelium?
Skin, esophagus. |t serves as a protection
What is the job of connective tissue?
Connects cells, tissues, organs, the most common tissue čin body
* Ensures support, nutrition, protection
* Origin mostly in mesoderm
What cells can we find in cartilage?
chondrocytes
* In ECM abundant proteoglycans + collagen fibers
What is the extracellular matrix in bones made up of?
Organic compound
* collagen
* proteoglycans
* glycoproteins
Anorganic compound
* hydroxyapatite
Ca10(PO4)6(OH)2
Central nervous system
Brain and spinal cord
Peripheral nervous system
ganglia and peripheral nerves
What are the characteristics of cells producing proteins?
Big active nucleus
* Abundant rough endoplasmic reticulum
* Polyribosomes
* Golgi apparatus
What is a regulated secretion?
involves a secretory vesicle
* High productivity of molecules
* Need of stimulus for exocytosis
What is a constitutive secretion?
No signal needed
* Secretion right after synthesis
* Collagen, fibronectin from fibroblasts
How is a cell adapted for regulated secretion (serous cell of pancreas)?
Pyramidal shape
* Epithelia
* Big active nucleus
* Abundant rough endoplasmic
reticulum
* Zymogenous granules
(digestive proenzymes)
How is a cell adapted for constitutive secretion (plasma cell)?
Connective tissue
* Round shape
* Big active nucleus
* Abundant rough
endoplasmic reticulum
(all over cell)
* Production of antibodies
What are typical characteristics of cells producing steroids?
Round active nucleus
* Smooth ER (SER)
* SER and Golgi – lipoproteins
* Tubular mitochondria
* Lipid droplets
What is typical for cells producing electrolytes?
Big active nucleus
* basal apparatus
invaginations of cell membrane
* ion channels Na+/K+
* Abundant mitochondria – ATP
source (Energy for ion channels)
What is typical for cell-forming mucus?
Goblet shape
* Flattened nucleus in basal part of cell
* Rough endoplasmic reticulum
* Well developed Golgi apparatus (glycosylation)
* Mucin vesicles – most of the cell
What is the function of basement membrane?
support, sepparates epithelium from connective tissue
Filter (selective barrier), keeps cell polarity
What is the basal lamina and reticular lamina products of?
basal lamina –
Product of epithelia cells found also in other cells (muscle, adipose, Schwann cell)
reticular lamina – Product of connective
tissue cells morse sparse
What is the composition of basement membrane?
Basal lamina:
On cell membrane integrin receptors
(provide contact with ECM)
* To these receptors connects laminin (net)
* Interconnection proteins (e.g. nidogen)
enable connection of collagen IV (forms net)
Reticular lamina:
Collagen III (reticular fibers)
What is the origin of epithelia?
Derived from all 3 germ layers
ectoderm
* Skin and its derivatives (sweat glands)
* Lining of ends of digestive tract
* Lining of vagina
entoderm
* Lining of respiratory tract
* Middle part of digestive tract and its glands
* Liver, pancreas
* Gallbladder lining
* Thyroid and parathyorid gland, thymus
mesoderm
* endotel lining veins
* mesotel lining body cavities
What are the functions of epithelia?
covering epithelium – cover outer surface or line
cavities
* glandular epithelium – production of liquid secretion
* respiratory epithelium – exchange of gasses
* sensory epithelium – reception function in taste bud or olfactory epithelium
* germinal epithelium - gonads
* myoepithelium – contractile cells in mammary, sweat and salivary glands
What are myoepithelial cells and where can we find them?
Characteristics of epithelium and smooth muscle cells
* Smooth muscle – contain actin, myosin (contractile fibers)
* Epithelium – contain keratin (intermediate
filaments)
- sit on basement membrane
We can find it in exocrine glands
(salivary, mammary, sweat)
On basement membrane
Contraction – helps secretion
What are some modifications of the apical surface?
Microvilli – cytoplasmatic projections
* Cilia – longer, motile cell projections
* Stereocilie – long, nonmotile, similar to microvilli
What are microvilli stiffened with?
Stiffened with actin filaments
What are cilia and kinocilia stiffened with?
stiffened with mcrotubules
What are the different cell junctions?
Tight junction- prevents molecules passage seals intercellular space
Adherent junction- mechanical cell attachement
actin filaments
Desmosomes- spot junction
intermediate filaments
Gap junction
rapid exchange of molecules
Hemidesmosomes
tight junctions – zonula occludens
1) Transmembrane protein – claudin, occludin
2) Adaptor proteins
3) Cytoskeleton - actin
Closest to the apical part of cell
* Closely attached plasma membranes
* Prevents passage of hydrophilic molecules,
ions between cells
Digestive system
* Blood-brain barrier
* Lungs
Adherent junction – zonula adherens
1) Transmembrane protein– cadherin
2) Adaptor proteins – vinculin
3) Cytoskeleton - actin
Strong connection of neighbouring cells
* Resistance to tension, press
* Single epithelia (e.g. endothelium)
Desmosome – macula adherens
1) Transmembrane protein – cadherins
2) Adaptor proteins – desmoplakin
3) Cytoskeleton – intermediate filaments
Spot junction
* Mechanical support of tissue exposed to pressure, tension
* Skin, intestine, cardiac muscle
Nexus – gap junction
Cell-cell communcation
* Various tisse types (nervous, muscle)
* Pore 1.5 nm
* Transmembrane proteins (connexins)
make channel (connexon)
* Permeable for small molecules, el. signals
Anchoring junctions- Hemidesmosomes
– anchors cell to cell lamina
1) Transmembrane protein – integrin
2) Adaptor proteins – e.g. plektin
3) Cytoskeleton – Intermediate filaments
(cytokeratins)
Focal adhesion
Dynamic structures, cell connection to extracellular matrix
* Protein complex
* Mediate signals transport between cell and outer environment
* Important for adhesion and cell migration
Integrins – in cell membrane – outside cell bind to ECM, inside cell bind
to cytoskeleton (actin filaments)
How do we organize epithelia?
Sheet epithelia: The most common, covering, respiratory epithelium
Trabecular epithelia: Cells organized into trabecules, Liver, endocrine glands
Reticular epithelium: Branched, mutually connected Special type, only in thymus
What are the layers in skin?
Stratum corneum, stratum granulosum, stratum spinosum, stratum basale
How can we tell if the epithelium is keratinized or not keratinized?
The nonkeratinized epithelium has cells with nuclei in the surface layer
