ESSENTIALS Flashcards
General characteristics of living system
1) Determined in space & time
2) Genetic & structural unity, hierarchical organization
3) Reproduction
4) Open thermodynamical systems (reduction of entropy); flow of matter, energy & information
5) Metabolism
6) Autoregulation: feedback system
7) Reactivity to external stimuli
8) Ontogeny
9) Phylogeny (evolution)
Why do viruses need a host?
No organelles:
- Can’t make ATP
- Can’t reproduce
Stages of viral replication
Attachment Penetration Synthesis of NA & proteins Maturation Release
People involved with modern cell theory (6)
Hooke Leeuwenhoek de Mirbel Lamarack Schwann, Schleiden Virchow Purkyne
Modern cell theory (6)
1) All know things are made up of cells
2) Cell = structural & functional unit of living things
3) Cells come from pre-existing cells
4) Cells are basically same in chemical composition
5) Cell contain hereditary information
6) All energy flow of life occurs within cells
Cell organelle
Compartments limited by membrane
“Cell” Hierarchy
Molecule Macromolecule Supramolecular complex Cell organelle Cell
Nucleus includes…
Nuclear pores
Nuclear lamina
Nuclear matrix
Nucleoplasm
Types of vesicles (GA)
Exocytotic v. (constitutive secretion)
Secretory v. (regulated secretion)
Lysosomal v.
Function of vacuoles
Maintain turgor pressure Maintain acidic internal pH Enable change shape of cell Remove unwanted substances Isolate harmful materials Push contents against cell membrane; chloroplasts closer to light Role in autophagy
Autophagy
Destruction of invading bacteria
Holism
System as a whole determines how the parts behave
Hypercycle
Organisation of self-replicating molecules connected in a cyclic manner
Capsomeres
Identical protein subunits that form capsid
Types of penetration (virus)
TRANSFER viral particle
TRANSFER viral genome
FUSION viral envelope
Proteases
Perform proteolysis
Gene Expression in Viruses:
ds(+/-)DNA
Bacteriophages
Animal viruses
Gene Expression in Viruses:
ss(+RNA)
Retroviruses
OR
Bacteriophages
Animal/plant viruses
Gene Expression in Viruses:
ss(-)RNA
Bacteriophages
Transformation
A bacterium takes up a piece of DNA floating in its environment
Transduction
DNA is accidentally moved from 1 bacterium to another by a virus
Conjugation
DNA is transferred between bacteria through a pilus
Fertility factors
Chunk of DNA that codes for proteins that make up pilus
Binary fission vs Mitosis PURPOSE
M: Cause organism to grow larger or replace old, worn-out cells with new ones
BF: How bacteria reproduce or add more bacteria to the population
Cytoplasm vs Cytosol
Cytosol: Fluid between organelles
Cytoplasm: Everything that’s inside the cell (cytosol + organelles)
Endomembrane system
All of the membranes that interact with each other inside of the cell
Phagocytosis (lysosome)
A section of macrophage’s plasma membrane invaginate, fold inward to engulf a pathogen
Invaginated section pinch off to form a phagosome
Phagosome then fuse with a lysosome, where digestive enzymes destroy the pathogen
Eukaryotic & Prokaryotic similarities
Vacuoles & vesicles
sER function
Synthesize steroid hormones & other lipids
Connects rER & GA
Detoxify cell
Carbohydrate metabolism
Plastids
Site of production & storage of important chemical compunds
Anthocyanines
Plant pigments present in vacuoles
Division of bacteria
Shape
Degree of flagellation
Cell Wall Composition
Domain Bacteria
Unicellular Most have CW; murein NO introns Often organized into operons May contain plasmids N-formylmethionin (starting AA) Asexual reproduction = BF/budding
Plasmid
Small, round extrachromosomal DNA that MAY contain genes for antibiotic resistance
Domain Archaea
Unicellular CW; pseudomurein Introns Methionine (starting AA) Asexual reproduction = BF/budding 20% of biomass Extremophiles
Groups of extremophiles
Halophiles (high salt conc.)
Thermophiles (high temp.)
Methanogens ( convert CO2+CO ->CH4)
Function of water
Essential to all known forms of life
Participation in chem. reactions (fill intra+intercellular spaces, provides H+)
Solvent for nutrients
Transport
Thermoregulation (maintain constant temp.)
Homeostasis (acidobasic eq., osmoregulation)
Function of proteins
Structure Enzyme catalysis Informative (signals, receptors) Regulation (hormones, messenger) Defense (antibodies, globular proteins) Transport (hemoglobin, transport O) Motion (actin) Source of energy
Function of lipids
Energy storage (lots of cal.)
Absorption of vitamins
Hormones
Structure (membrane, micelles)
Group of steroids of lipids
Cholesterol
Hormones
Vitamin D
Fluidity is influenced by
Temperature
Presence of cholesterol
Length & saturation of fatty acids
Function of membranes
Barrier Cell shape Form tissues & compartments (organelles) Regulation of transport of substances Contains receptors of chem. messages Enzyme activity Transformation of energy
Cell cortex function INNER FACE
Mechanical support
Cell-surface movements (animal cells)
Glycocalyx function OUTER FACE
Protects membrane from injury Cell adhesion (bind cells together) Fertilisation Embryonic development Immunity to infection Transplant compatibility Defense against cancer
Extracellular matrix function
Bound to cell membrane by integrins
Anchorage for cells
Regulation of intercellular communication
Cell wall function
Protection
Filtering mechanism
Prevents over expansion (hyptonic)
Ion channels importance
Electrical impulse (generation&conduction) Fluid balance (within & across cell mem.) Signal transduction (within & among cells)
Exocytosis, when?
Acrosome reaction (fertilisation) Antigen presentation (immune response) Cellular signalling (electrical to chem. signal)
Primary protein structure
Linear sequence of AA’s
Formed by covalent PB
Secondary protein structure
Linear sequence of AA’s folds upon itself
Determined by backbone interactions
H-bonds
Tertiary protein structure
Higher order of folding within a polypeptide chain (3D shape)
Depend on distant group interaction
H-bonds, v.d.Walls forces, disulphide bridge, hydrophobic interactions
Quaternary protein structure
Bonding between multiple polypeptide chain (subunit interactions)
Hydrolysis of ATP
Chemical energy is changed into mechanical energy AS energy stored in high energy bonds in ATPare released
SNARES
Protein that mediate vesicle fusion
Spectrin (cytoskeletal protein)
Line inner side of plasma membrane (EUK)
Maintain PM integrity & cytoskeletal structure
Integrin
Transmembrane receptors
Bind to extracellular matrix
Primary active transport
Energy is derived directly from breakdown of ATP
Secondary active transport
Use energy stored in gradients to move other substances against their own gradients
Cytoskeleton function
Allow change of shape of cell
Move organelles
Moving from place to place
Intermediate filaments function
Provide cell shape
Anchor organelles
Keep nucleus in place
Dynamic instability
Periods of rapid microtubule polymerization alternate with periods of shrinkage
Polymerization
Some small molecules can join together to make very long molecules called polymers.
Function of Actin Filaments
Structural (prject from cell, polymeration of actin in acrosome)
Movement
Mitosis ( contractile ring)
Function of microtubules
Maintain cell shape, anchor organelles
Movement
Mitosis (spindle)
Microtubules organizing centers
Mitotic spindle
Centrosome
Basal body
Types of motor movement
Cytoskeletal structure is fixed
Sliding
Motor is fixed
Intracellular transport
Transport of secretory vesicles by (K,D) along microtubules highway
Flagella & cilia structure
Basal body
Axoneme (9+2, radial spokes)
Dynein
Flagella & cilia function
Move things along surface
Used in locomotion
What makes up bacterial flagellum
Hollow filament of protein flagellin
Sharp hook
Basal body rings
Amoeboid movement principle
1) Protrusion of a pseudopodium
2) Pseudopodium is attached (integrin)
3) Rest of cell body is pulled
+ Actin polymerise, Myosin I bind to actin -> network contracts pulling cell in direction of pseudopodium (E from ATP)
Prophase (3)
Mitotic spindle is formed
Prometaphase (3)
Kinetochore MT bind at Kinetochore (dynein)
Metaphse (3)
Chromosomes line up
By polymeration/depolymeration of K MT
Anaphase (3)
Dynein pulls chromatids to opposite poles
Polar MT slide (kinesin) + polymerate at (+) end
Telophase
Kinetochore MT disappear
Polar MT still polymerate
Cytokinesis (Animal Cell)
Cleavage process
Formation of contractile ring
Actin filaments slide (by help of myosin II)
Cytokinesis (plant cell)
Vesicles from GA move along MT to middle of cell & fuse
Produce cell plate
Centrosome
Main MT organising center of animal cell
Regulator of cell cycle
Depolymerization
To break down (a polymer) into monomers.
Cell Cycle;
Replication of chromosomes (DNA) & cell growth
Separation of chromosomes
Cell division
G1 Checkpoint;
Cell size
Nutrients
Growth factors
DNA damage
G2 Checkpoint
DNA damage
DNA replication completeness (from S phase)
M checkpoint
Chromosome attachment to spindle at metaphase plate
Proteasome
Protein complexes that degrade unneeded damaged proteins by proteolysis
Proteolysis
Chemical reaction that breaks peptide bonds
Cyclins
Group of related proteins
Help drive events at certain “phase”
Increase levels at stage where it is needed
Cdks
Inactive enzyme
Activates by binding of cyclin
P group act like switch ->make target protein less/more active
Kinase
Enzymes that add phosphate group to other molecules
APC
Add Ub tag to securin
Securin is sent for recycling
Separase becomes active
Separase chops up cohesion that holds sister chromatids together -> allow them to separate
Synapsis
Fusion of chromosome pairs (zygotene)
Synaptonemal complex
Holds together homologous chromosomes
Crossing over
Exchange of genetic material (pachytene)
Proliferation
Increase in number of cells
Balance between cell divisions & cell loss (through death/differentiation)
Proliferation “steps”
Growth factors
Receptors
Signalling molecules
Transcription factors
Leptotene
Chromosomes begin to condense
Zygotene
Homologous chromosomes combineto form bivalent
Form synaptonemal complex (by synapsis)
Pachytene
Crossing over: random exchange -> recombination of genetic information
Diplotene
Synaptonemal complex degrades
Homologous chromosomes separate a little
Remain tightly bound at chiasmata (HC of bivalent)
Diakinesis
Nucleolus disappears
Nuclear membrane disintegrates
Mitotic spindle begins to form
Metaphase I
HC align
Anaphase I
K MT shorten & pull HC to opposite poles
Random segregation of chromosome - recombination
NonK MT lengthen -> cell elongates
Telophase I
Half number of chromosomes each consisting of a pair of chromatids MT disappear New nuclear membrane Chromosomes uncoil into chromatin Cytokinesis
Prophase II
Nucleoli + nuclear envelope disappear
Centromeres move to poles & arrange MT
Metaphase II
C align
Anaphase II
Centromeres are cleaved
MT pull sister chromatids apart
Sister chromatids = sister chromosomes
Telophase II
Uncoiling & lengthening of C
MT disappear
Formation of nuclear envelopes
Cytokinesis
Significance of meiosis
Facilitates stable sexual reproduction
Produce genetic variety in gametes
Apoptosis triggers: Internal signals (intrinsic pathway)
Oxidative damage (cause holes in mit. mem.)
Entry of CYTOCHROME C into cytoplasm
Caspase 9 -> 3 -> 7
Proteolytic cascade
Apoptosis triggers:
External signals (extrinsic pathway)
Tumor necrosis factor
TNF bind to cell mem. receptors
Caspase 8
Proteolytic cascade
Apoptosis triggers:
Apoptosis-inducing factor (AIF)
CASPASE INDEPENDENT PROCESS
Mitochondria release AIF
Migrate to nucleus
Bind to DNA -> trigger DNA degradation + cell death
Function of polysaccharides
Source to power chemical reactions Long-term energy storage Structure Part of mucus, slime, cartilage Part of glycoproteins, glycolipids
Thermodynamical law 1:
Law of conservation of energy
Energy cannot be created/destroyed in an isolated system
Only transformed from 1 form to another
Thermodynamical law 2:
Entropy of any isolated system increase over time
living organisms have very low entropy
How cells obtain energy from food:
Stage 1
Breakdown of large macromolecules to simple subunits
How cells obtain energy from food:
Stage 2
Breakdown of simple subunits to acetyl CoA accompanied by production of limited ATP & NADH
How cells obtain energy from food:
Stage 3
Complete oxidation of energy of acetyl CoA to H2O & CO2 involves production of much NADH, which yields much ATP via ETC
NADH
Crucial coenzyme in making ATP
Acts as a shuttle for electrons during cellular respiration. At various chemical reactions, the NAD+ picks up an electron from glucose, at which point it becomes NADH.
ETC proton pumps
NADH-dehydrogenase complex
Cytochrome b-c1 complex
Cytochrome oxidase complex
Glycolysis
Glucose undergoes chemical transformation & is converted into 2 molecules of pyruvate
Pyruvate oxidation
Each pyruvate goes into matrix
Bind to coenzyme A to form Acetyl CoA
Krebs Cycle
Acetyl CoA + 4C -> 6C intermediate which is broken down to reform 4C compund
ETC + Oxidative phosphorylation
Hydrogen carriers pass e to ETC
e lose E as they move through chain which is used to pump H ions from matrix to IMS against conc. graient
Protons return to matrix via ATP synthetase, releasing E which is used to produce ATP
Light dependent reactions
Light E is used to produce ATP & to split up water into hydrogen & oxygen
Light independent reactions
ATP & hydrogen are used to fix carbon molecules to make organic compounds
Calvin Cycle Steps
1) Carbon fixation
2) Reduction
3) Regeneration of RuBP
Carbon fixation
The Calvin cycle uses the energy from short-lived electronically excited carriers to convert carbon dioxide and water into organic compounds that can be used by the organism (and by animals that feed on it).
Cell signalling mediates
Reaction to signals from environment
Communication between cells
Teamwork of cells in multicellular organism
Stage of cell signalling
1) Reception
2) Transduction
3) Response
Cell signal pathway
Signal cells
Signal molecules
Receptors
Target cells
Chemical extracellular signals
Hormones
Neurotransmitters
Neurohormones
Cytokins
Cytokins
Proteins produced by cell as a signal for proliferation, differentiation or survival of cells
Paracrine signalling
Cells communicate over relatively short distances
“Talk to neighbor”
Autocrine signalling
Cell signals to itself
Development - reinforce identities
Endocrine signalling
When cell need to transmit signals over long distances
Travel through circulation, hormones
Contact-dependent
Gap junctions -> tiny channels that directly contact neighbouring cells
Small signalling molecules diffuse between cells
Neuronal signalling
Nerve cell transmits signal
Cell Signalling STEPS
1) Ligand bind to GPCR
2) GPCR - conformation change
3) a subunit exchange GDP for GTP
4) a subunit dissociates & regulate target proteins function
5) Target proteins relay signal via 2nd messenger
6) GTP is hydrolysed to GDP, ligand leave
Enzymatic function of Receptor Kinase Tyrosine
Transfer P molecules to intracellular proteins (tyrosine)
Imporance of RTK
Regulate cell growth, differentiation & survival
Can bind & respond to ligands (like growth factors)
Protein kinases
Act on proteins by phosphorylating them (can modify function of protein in many ways)
People involved with “gene”
Mendel (discreet elements) Johanssen (gene) Morgan (locus) Beagle, Tatum Watson, Crick
Structure of a gene
Coding strand, template strand
Promoter
Coding regions for protein/RNA
Enhancer = regulatory sequence (regulate promoter)
premRNA - mRNA Steps
1) Addition (synthesis) of 5’ cap to beginning of RNA
2) Removing introns & splicing exons
3) Addition (synthesis) of 3’ poly(A)tail
prerRNA - rRNA
1) Separation of pre-rRNA (by snRNA)
2) Formation of large subunit of ribosome
pretRNA - tRNA
1) Cleavage (remove extra segment at 5’)
2) Splicing (remove intron in anticodon loop)
3) Addition of CCCA (at 3’)
4) Base modification
Svedberg coefficient
Relative size of particle by rate of sedimentation
post(co)- translation modification;
Primary structure
Proteolytic cleavage
Phosphorylation
Functional groups
Disulphide bridge
Why RNAi?
Can shut down genes in cell to identify components necessary for particular cellular process
Transcription - initiation key words
RNA polymerase + sigma factor
Separate
Synthesis at initiation site
By rules of bp
Transcription - elongation key words
5-3 direction
Base U instead of T
Transcription - termination key words
Terminators Hairpin loop C & G, folds Polymerase stall Weak interaction Instability for enzyme to fall off
Transcription - termination key words (BACTERIA)
Rho
Climb up
Rho pulls apart
End transcription
tRNA Binding Sites functions
A: bind next-coming tRNA with an AA
P: bind tRNA with growing polypeptide
E: bind deacylated tRNA prior to its release
Genetic code
Full set of relationships between codons & AA’s
Universal
Used for protein synthesis
Translation - initiation
Ingredients + key words
Ingredients: a ribosome, mRNA, initiator tRNA
Initiator tRNA -> small subunit
Walk along mRNA -> Start codon
Large subunit -> P site
Translation - elongation key words
Peptide bond (by ribozyme) tRNAs through A, P, E
Translation - termination key words
Stop codon -> enters A site
Protein released
Eukaryotic gene expression
1) Chromatin accessibility
2) Transcription
3) RNA processing
4) RNA stability
5) Translation
6) Protein activity
lac Repressor
Protein that represses transcription of lac operon by binding to operator which partially overlaps with promoter
Homebox genes vs homeobox vs hox genes
Homeobox genes: direct development of particular body segments/structure, regulates transcription
Homeobox: DNA sequence within homeobox genes
Hox genes: subset of homeobox genes
Ubiquitination
Regulated degradation of proteins in the cell (ATP)
Ubiquitination steps
1) E1 activate ubiquitin
2) E2 add ubiquitin to substrate
3) E3 (ub. ligase) add 3 other ubiguitins to substrate
Ubiquitins & SUMO proteins
Ubiquitin: Small protein (76AA) used to target proteins for destruction
SUMP Proteins: Compete for binding sites w/ Ub, do not lead to their degradation
Central dogma
Transcription + translation
How genetic info flows from a DNA sequence to a protein product inside cells
Phosphodiester bond
Links 2 nucleotides between a phosphate group
Glycosidic bond
Bounds bases to sugar
DNA people
Franklin
Wilkins
Watson
Crick
DNA Structures
1) Sequence of bases in NA chain
2) dsDNA/RNA
3) DNA is organized into chromosome
Condensation of DNA into Chromosomes STEPS
1) Nucleosome
2) Chromatin fiber
3) Loops of fibers
4) Mitotic chromosomes
Topoisomerase
Enzyme that catalyses uncoiling of DNA
DNA Replication Steps + Key Enzymes
1) Initiation, Helicase (create rep. fork)
2) Priming, RNA Primase
3) Elongation, DNA Polymerase III
4) Termination, DNA Polymerase I + DNA ligase
DNA Mismatch Pair
1) Detection
2) DNA strand is cut out, mispaired nucleotide + neighbours are removed
3) DNA polymerase replace missing patch
4) DNA ligase seals gap in DNA backbone
Base Excision Pair
1) Deamination converts C -> U
2) U is detected & removed
3) Base-less nucleotide is removed
4) Hole is filled w/ right base by DNA polymerase, gap is sealed by DNA ligase
Pyrimidine Dimers
1) UV radiation produce thymine dimer
2) Detection, surrounding DNA opened & form bubble
3) Enzymes cut damaged region out of bubble
4) DNA polymerase replaces cut-out DNA & DNA ligase seals gap
DNA Replication - Initiation
DNA strands are unwound & cut out
DNA Replication - Priming
RNA primers are added to act as initiation points for DNA synthesis
DNA Replication - Elongation
New complementary DNA strands are synthesized in a 5’-3’ direction
DNA Replication - Termination
Primers replaced & fragments joined
Leading strand
Polymerase moving towards replication fork (can copy continuously)
Lagging strand
Polymerase moving away from replication fork (copes in short fragments; okazaki)
Transposons
“Copy & paste”
Cut out of its location & inserted into a new one
Requires enzyme - transposase
Retrotransposons
“Copy & paste”
BUT copy is made from RNA NOT DNA
RNA copies are then transcribed back to DNA (reverse transcriptase) -> inserted into new location in genome
Bacterial Transposons
Conservative Transposition
Replicative transposition
Eukaryotic Transposons
Class 1: DNA Transposons VSG genes, P elements, McClintok Elements Class 2: Retrotransposons LINEs SINEs
Repetitive sequence in eukaryotes DNA
Patterns of NA (DNA/RNA) that occur in multiple copies throughout the genome
Micro vs Minisatellites
Micros: 2-6bp -> 10-100x, nuclear+organellar DNA, polymorphic, used as molecular markers
Minis: 10-100bp, 1000locations
Molecular marker
Fragment of DNA associated with location in genome
Identify particular sequence of DNA in pool of unknown DNA
Gene interaction
When 2/more different genes influence the outcome of a single trait
Genotype
Genetic (allelic) constitution of organisms with respect to trait
Parental generation
Generation of parents that are different homozygous
F1 generation
1st generation of uniform offspring
From crossing of P generation
F2 generation
2nd generation of offspring
From crossing 2 individuals of F1 generations
B1 generation
1st generation of backcrossing
individuals of F1 & P generations
Hybrid
Heterozygous
Usually offspring of 2 different homozygous individuals in certain trait
Monohybrid cross
Cross involving parents differing in 1 studied trait
Dihybrid cross
Cross involving parents differing in 2 traits
Polyhybrid cross
Cross involving parents differing in more traits
Mendelian Principles
Principle of…
1) Uniformity of F1 hybrids
2) Identity of reciprocal crosses
3) Segregation
4) Idenpendent assortment
Mendelian principles hold true for…
Monogenic inheritance
Autosomal inheritance
Genes located on different chromosome pairs
Alleles (D&R)
D: Allele that is expressed over second allele, functional form
R: Allele that is expressed only if 2nd allele is the same, non-functional form
Relation between alleles
Complete dominance
Incomplete dominance
Codominance
Complete dominance
Heterozygotes has same phenotype as dominant homozygous
Incomplete dominance
Heterozygote has different phenotype than homozygote
Codominance
2 different alleles of 1 gene are responsible for different phenotypes Blood groups (1 gene, 3 alleles)
Reciprocal interaction
Interaction with change of cleavage ratio
Trait is present in more forms: each of them is encoded by 1 combination of parent alleles of genes
Ex: Color of peppers
9:3:3:1
Dominance Epistasis
Dominant allele of 1 gene suppresses the expression of a domiannt allele of a 2nd gene
Ex: Color of dahlia
12:3:1
Epistatic & Hypostatic
Epistatic: Gene suppressing
Hypostatic: Gene being suppressed
Recessive Epistasis
Recessive homozygous constitution of 1 gene suppresses the expression of a dominant allele of a 2nd gene
Ex: Color of salvia
9:4:3
Complementarity
Dominant allele of 2/more genes cooperate in realization of phenotype
Trait is expressed if at least 1 dominant alleles of both genes is present at the same time
Ex: Color of flower of vetch
9:7
Compensation
Function of dominant alleles of 2 different genes is contradictory, their phenotype effects exclude each other
Ex: Curvature of pea pod
10:3:3
Inhibition
Dominant allele of inhibitor gene suppresses the manifestation of dominant allele of other gene
Inhibitor gene itself has no effect on phenotype
Ex: Color of hen feather
13:3
Duplicity
In genes with the same phenotype
Intensity of effect depends on if genes cumulate or not, & if there is a relationship of dominance between alleles of a particular gene
Duplicity noncumulative with dominance
There is no cumulation of dominant alleles
Ex: Shape of a capsule in toothwort
15:1
Duplicity cumulative with dominance
COMPLETE DOMINANCE
Intensity is amplified by the number of dominant alleles
Ex: Color of barley grain
9:6:1
Duplicity cumulative without dominance
INCOMPLETE DOMINANCE
Intensity depends on total number of active alleles
1:4:6:4:1
(4-3-2-1-0)
Morgan principles
Genes located on 1 chromosome linearly running subsequently
Number of linkage groups equals to number of pairs of homologous chromosome
3 point cross
Interactions between 3 genes observed
Used for setting of k map = order of genes & their distance from centromeres
Test crossing
Similar to back crossing (cross hetero & homo)
Used to find frequency of genotypes according to phenotype ratio in offspring
Cell theory (3)
All living things are made of cells
Every cell comes from another cell that lived before it
Cell is the basic unit of structure & function in all organisms
Consequence of mutation
Spontaneous abortion Anomaly of growth Organ development disorder Reproduction disorder Immune development disorder Mental retardation
Examination of chromosome
1) Cell from amniotic fluid
2) Grow in vitro
3) Fytohemaglutinin stimulate mitosis
4) Stop mitosis after 2-3 days in metaphase by COLCHICINE
5) Lyse cells in hypotonic solution to release chromosomes
6) Stain chromosomes, group and photograph
Colchicine
Mitotic inhibitor
Prevents mitotic spindle from forming
Karyology
Study of whole sets of chromosomes: chromosomal aberrations and sex
Kayotype and karyology
Observed chromosome characteristics of individuals or species
k-Gram: format of chromosome arranged in pairs, ordered by size and position of centromere
Methods for chromosome identification
Chromosome banding
FISH
FISH Principle
1) Probe bind to specific region on target chromosome
2) Chromosome are stained & cells viewed using fluorescence microscope
Deletion
Part of chromosome is deleted
Interstitial/terminal
-Cry of the cat; K5
Duplication
Part of chromosome is duplicated
- Fragile Z
Insertion
Part of 1 chromosome is inserted into another chromosome
Translocation
Part of 1 chromosome is translocated in another chromosome
- Reciprocal (mutual)
Inversion
Changeover of segment in chromosome
Human X chromosome
>153m. bp 5% woman DNA cell 2.5% men DNA cell Gene-poor region (repeated segments) 2000 genes X-linked genetic disorders
Human Y chromosome
58m. bp
0.38% men DNA cell
Gene SRY
Holandric traits
Homologous chromosome
Chromosome with same genes at the same loci but possibly different alleles
Nonhomologous chromosome
Chromosome that contain alleles for different type of genes
G banding
Treat chromosome with trypsin (partially difest protein) in metaphase
Stain with giemsa (dark bands are A, T rich and gene poor)
R banding
Chromosomes are heated then stained with Giemsa
Produce a banding pattern -> reverse of that produced in G banding
Molecular genetics
Structure and replication of DNA and gene expression on molecular level
Classical genetics
Transfer of trait from 1 generation to another
Population genetics
Variation in genes (traits) in 1 population or between more populations
Sex-limited inheritance
Genes on autosomes of both sexes
Trait is expressed in 1 sex (anatomic predisposition)
Antlers, cryptochism
Sex-influenced inheritance
Genes on autosomes of both sexes
Phenotype of heterozygote is influenced by sex of carrier due to hormones (M/F)
Dominant in males, recessive in female
Baldness
Sex-controlled influence
Genes on autosomes of both sexes
Phenotype is controlled by sex hormones in heterozygote and homozygote
2 sex trait = beard in man
Complete sex-linked
Heterologous part of chromosome
X = trait exists in both sexes
Y = holandric inheritance
Incomplete sex-linked
Genes are located on homologous part of sex chromosome (crossing over usually blocked)
Hemizygote
Gene only have 1 version of allele on 1 of 2 chromosomes
Variation on X chromosome but not Y chromosome
Types of nonmendelian inheritance
1) Maternal inheritance
2) Maternal effect
3) Infectious heredity
4) Parental imprinting
5) Trinucleotide repeat disorder
6) Complex traits
Infectious heredity
An infectious particle within cell of host may bring changes in phenotype of host organism & then pass on the altered phenotype to its offspring
Parental imprinting cause
Gene deletion
Uniparental disomy
Methylation
PWS
Missing gene activity that normally comes from dad
When dad’s copy is missing/there are 2 maternal copies
AS
Missing gene activity that normally comes from mom
When mom’s copy is defective/missing or thare are 2 paternal copies
Trinucleotide repeat disorder
Having too many copies of a certain nucleotide triplet in DNA
Complex trait
Derived from multiple genes and their interaction with behavioral and environmental factors
Polygene heritability
Influenced by many genes (polygenes), each one which contributes a small amount to the variation of a character which give a continual variability of phenotype
Phenotype variability
Variability in phenotypes that exists in a population
Can be caused by genes, environmental factors or both
Heritability
Proportion of variation of traits due to genes among individuals
Broad-sense heritability
The degree to which a trait is genetically determined
Vg/Vp
Narrow-sense heritability
The degree to which a trait is passed from parent to offspring
Va/Vp
= 1 -> genes are only difference froom individuals
= 0 -> genes do not contribute to phenotypic individual differences
Usage of methods of molecular biology
Discovery of new genes and proteins Gene regulation and protein function Evolution study Diagnosis of pathogens Production of medicaments Food industry Gene engineering Forensic medicine Criminalistics Identification of animals Pedigree tests
DNA isolation principle
1) Mech./chem. disruption of cells using enzymes/detergents to remove membrane lipids
2) Removing contaminants using enzymes (proteinase) to remove proteins bound to DNA/RNA
3) DNA extraction by precipitating DNA w/ alcohol
PCR
Copies of DNA fragments
1) Denaturation, 95 - separates DNA strands -> ssDNA
2) Annealing, 55 - primer bind to DNA
3) Primer extension, 72 - polymerase extend primers, synthesize new strands of DNA
PCR Ingredients
Isolated DNA
Nucleotides
Primers
DNA (Taq) polymerase
Gel electrophoresis
Separate DNA fragments according to their size
1) Prepare agarose gel
2) Stain sample
3) Lay sample, set electrophoresis
4) Visualize DNA
RFLP
1) Restriction endonucleases cleave DNA molecule in specific restriction sites based on DNA sequence
2) Gel electrophoresis
3) Detected polymorphism in restriction fragment numbers/lengths give info about differences in DNA sequences
Hybridisation
Pairing of ss NA (based on complementarity) = opposite to denaturation of dsDNA
Use probe to detect complementary target sequence in DNA/RNA molecule
Southern blotting
1) Take DNA and cleave it
2) Gel electrophoresis (fragment separation)
3) Gel -> (fragments of ssDNA transfer onto filter)
4) Expose filter to radio-labeledD DNA (complement of gene of interest)
5) Expose to x-ray
DNA sequencing
Process of determining the sequence of nucleotide bases in pieces of DNA (set correct order)
1) PCR to amplify samples
2) Add ddNTP (No O2: termination of strand elongation when incorporated)
3) Gel electrophoresis
DNA Sequencing ingredients
DNA polymerase Primer 4 DNA nucleotides Template DNA to be sequenced 4 ddNTPs with different color dye
DNA Cloning bacteria
1) Restriction enzymes
2) Plasmid + ligase
3) Vial w/ bacteria -> copies
4) Petri dish
HW Equilibrium
Frequency of alleles and genotypes in population will remain constant from generation to generation if population is stable and in genetic equilibrium
Inbreeding + Autogamy
Allele frequencies are not changed
Genotype frequences are changed
Reduction of frequency of heterozygotes
Increasing of frequency of homozygotes
Outbreeding (selection)
Change in allelic and genotype frequencies
Important for evolution
Evolution
Change in allele frequencies over time
Genetic drift
(Mechanism of evolution, allele f of a pop. change over generations due to chance)
Change in allelic frequencies between generations (fixation of some, elimination of some)
Reduction of heterozygotes
Increasing of homozygotes
Decreasing of genetic variability
Gene flow
Change in allelic and genotype frequencies
Increasing genetic variability in population
Practical applicaiton of population genetics
Genetic diseases
Problems in small populations
Study of evolution
Genetic diseases, influence:
Mutation Selection Genetic drift Gene flow Inbreeding
Small populations
Fixation of unfavourable alleles
Increasing of homozygotes
Decreasing of genetic variability
Decreasing of fitness, leading to disease
Study of evolution
Phylogenetic tree - common ancestor
Biological evolution
Microevolution
Speciation
Macroevolution
Neodarwinism
Synthesis with Mendelian genetics and populations genetics
Basic mechanisms of evolution
Heritability variability (mutations and recombinations) Changing environment (adaptions) Natural (sexual) selection
Microevolution mechansim, ex, & long-term result
Inbreeding/genetic drift
Industrial melanism
Subpopulations -> subspecies -> new species
Anagenesis
Changes in species without cleavage into evolution lines
Cladogenesis
Cleavage of evolution lines
Cladogenesis -Allopatric
Speciation with geographic isolation
Squirrels
Cladogenesis - Sympatric
Speciation within population without geographic isolaton
Syngenesis
Fusion of originally separate ancestral lineages
Synklepton: species that requires input from another biological taxon to complete their reproductive cycle.
Macroevolution
Major evolutionary events on a geological timescale (evo. of higher taxa)
Theory of punctuated equilibrium: alternation of stasigenesis and evolutionary activity
Man as a source of evolutionary changes
Alters biosphere
Change criteria for advantages/disadvantageous phenotypes/genotypes
New genotoxins
Genome manipulation
Threat to biodiversity + existence for life (exponential growth)
Coevolution
When two or more species reciprocally affect each other’s evolution
- Mutualistic: benefit from each other
- Competitive: prey and predator
Adaptive radiation
Process in which organisms diversify rapidly from an ancestral species into a multitude of new forms.
Particularly when a change in the environment makes new resources available, creates new challenges, or opens new environmental niches.
- Development of mammals after extinction of dinosaurs
