department of molecular biology and human genetics...6 chemical bonds covalent bonds, (strong bond)...
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Department of Molecular biology and
Human geneticswww.biologiemoleculara.usmf.md
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Molecular biology1st semester Lectures – 34 hours
Practical lessons (seminars) – 51 hours 3 concluding tests (written + computer tests)
Scientific project
Average mark – 50% of final mark
Exam Admission to examination
All concluding tests passed
Absences recovered
E-learning activities
Current consultations
Extra-curricular activities
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Systems of
organs
Organs
Tissues
Cells
Macromolecules
Micromolecules
Molecular
biology
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Units used in molecular biology Length
1 mm = 10-3 m
1 μm = 10-6 m
1 nm = 10-9m
1 Å = 10-10 m
Weight 1 Da = 1,66.. X10-24g (1u)
kDa = 1000 Da
Length of DNA 1 pb = 1bp
1 Kb = 1000 bp
1 Mb = 1 000 000 bp
Sedimentation coefficient S
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Chemical organization
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Cell structure
Plasma membrane
Cytoplasm and organelles
Nucleus
Metabolism
apparatus
Synthesis of
organic
substances
Lysis of OS
Detoxification
Energetic
Signaling
Genetic
apparatus DNA
Components for
replication
Components for
DNA repair
Components for
transcription
Surface
components
Barrier
Transport
Reception
contacts
Protection
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Prokaryotic cell
Eukaryotic cell
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Cell structure functions properties
Based on molecules
DNA – contains information
RNA – involved in protein synthesis
Proteins – all cellular functions
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Interactions of macromolecules
DNA RNA Proteins
Carbohydrates Lipids
Transcription Translation
Synthesis
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Main functions of macromolecules
• Genetic information, identical in all cells of bodyDNA
• Responsible for protein synthesis RNA
• Responsible for almost of cellular functions, enzymatic Proteins
• EnergeticCarbohydrates
• Structural, in membranesLipidswww.biologiemoleculara.usmf.md
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Supramolecular complexes
DNA + proteins = DNP (deoxyribonucleoprotein)
• e.g.: chromosomes
RNA + proteins = RNP (ribonucleoprotein)
• e.g.: ribosome
Lipids + protein = lipoprotein
• e.g.: plasma membrane
Carbohydrate + protein = glycoprotein
• e.g.: receptors on surface of cells
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DNP
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RNP
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Membrane
Ribosomes
Membrane
LysosomeGolgi body
Centromere
Nucleus
CytoskeletonMicrovili
Smooth ER
Rough ER
Mitochondrion
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Chemical bonds
Covalent bonds, (strong bond)
• Peptide bond – in proteins
• Phosphodiester bond – in nucleic acids
• Glycosidic bond – in carbohydrates
• Disulphidic bridge – in proteins
Non-covalent interactions, (weak bonds)
• Hydrogen bond
• Hydrophobic bond
• Ionic bond
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Structure of macromolecules
Primary structure
A chain of several
monomers (building blocks)
Monomers connected via
covalent bonds
Secondary structure
Coiling of polymer
Hydrogenbonds
Tertiary structure
3-D conformation by
folding
Hydrogen, ionic,
electrostaticbonds
Quaternarystructure,
supramolecular
A combination of several
polymeres
Hydrogen, ionic,
electrostaticbonds
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a.a. a.a. a.a.a.a. a.a. a.a.
a.a.
N N NN
NN N
dN dN dNdN
dN dNdN
Deoxyribonucleotide
Ribonucleotide
Amino acid
Monomer Polymer
DNA strand
RNA strand
Polypeptide chain =
protein
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Structure of macromolecules
Monomers of DNA (deoxyribonucleic acid):
• 4 types of deoxyribonucleotides– dNTP
• dATP
• dGTP
• dCTP
• dTTP
Monomers of RNA (ribonucleic acid):
• 4 types of ribonucleotides –NTP
• ATP
• GTP
• CTP
• UTP
Monomers of proteins:
• 20 types of amino acids
• Ala
• Val
• Ser
• His
• Pro
• ....
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Structure of macromolecules
Primary structure of DNA Polynucleotide chain
Nucleotides connected by phosphodiester bonds;
The sequence of nucleotides is inherited = genetic code;
5' AGTGCATACGTACGGACATT ... 3‘
Primary structure of RNA Polynucleotide chain
Nucleotides connected by phosphodiester bonds;
The sequence of nucleotides is determined by DNA;
5' AGUGCAUACGUACGGACAUU ... 3‘
Primary structure of proteins Polypeptide chain
Amino acids connected by peptide bonds
The sequence of amino acids is determined by mRNA
NH2.Ser-Ala-Tyr-Val-Arg-Thr...www.biologiemoleculara.usmf.md
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Structure of macromolecules Secondary structure of DNA
Two strands connected by hydrogen bonds: Complementarity – AT and G C;
Antiparallel;
Double helix;
Secondary structure of RNA Folding of polynucleotide chain:
Complementary bases connected by hydrogen bonds
AU and G C
Each loop – functional site:
Each type of RNA has specific loops.
Secondary structure of proteins Folding of polynucleotide chain
Hydrogen bonds
-helix
-sheet
5' A T G C A T A C G T A C G A T 3‘
3‘ T A C G T A T G C A T G C T A 5'
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Secondary structure
α-helix
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Structure of macromolecules
Tertiary structure of DNA
DNA + histones + non-histones
Chromatin
Chromosome
Tertiary structure of RNA
RNA + proteins
rRNA + ribosomal proteins ribosome
tRNA + proteins
mRNA + proteins
Tertiary structure of proteins
Folding of -helixes and -sheets
Globular shapewww.biologiemoleculara.usmf.md
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Structure of macromolecules Quaternary structure of proteins
Combination of several polypeptides
Ex:
2 -globin + 2 -globin = Hb
2 -peptide + 2 -peptide = insulin receptor
2 L chains (light) + 2 H chains (heavy) = Ig
(-tubulin + -tubulin)n = microtubules
…..
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Nucleic acids
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Nucleic acids
DNA:
Double stranded molecules;
Contains genetic information
RNA – single stranded molecules:
mRNA – contains genetic information, template for protein
synthesis
tRNA – transfers amino acids, translates genetic code
rRNA – part of ribosomes, participates in translation
microRNA – control of gene expression
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Monomers of DNA
N
PPP
3’
C
CC
C
C
O
2’
4’
5’
1’
αβγ
dNTP – nucleotide – nucleoside triphosphate
nucleoside
N – Base
-Pu – Adenine
Guanine
-Py – Thymine
Cytosine
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Monomers – nucleotides
Primary structure:
polynucleotide chain
Secondary structure:
double helix
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Primary structure of DNA
5' GCGT ... 3‘www.biologiemoleculara.usmf.md
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James Watson and Francis Crick
Rosalind Franklin Maurice Wilkins
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Base complementarity ensures:
Stability of DNA;
Replication – duplication of DNA;
Transcription – copying of DNA;
Recombination;
DNA repair
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Types of DNA double helixesType Length of tour Bases/tour
A 24,6 Å ~11
B 33,2 Å ~10
Z 45,6 Å ~ 12
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Tertiary structure
DNA + proteins = DNP
DNA + site specific proteins = functional comples
Nuclear DNA + histones = chromatin ↔ chromosomes
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Properties of DNA
Replication
Repair
Denaturation
Renaturation
Heterogeneity
Flexibility
Fragility
Migration in electric field (DNA is “—”)
Hybridisation
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Replication
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Functions of DNA
Contains genetic information:
About proteins
About other macromolecules
Transmits genetic information:
1DNA — replication → 2DNA
Realization of genetic information
DNA — transcription → RNA — translation → protein
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Types of DNA sequences:
Coding sequences = genes: Protein coding mRNA ~ 30 000
pro-rRNA coding ~ 250
5S rRNA coding ~ 2000
tRNA coding ~ 1300
microRNA coding
Noncoding sequences Regulatory
Spacers
Satellite DNA
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Location of DNA
In nucleus 95 - 98%
Long linear molecules
Associated with histones
In interphase – chromatin ↔ in division -
chromosomes
In mitochondria 2-5%
Small circular molecules
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Peculiarities of human DNA
Nuclear DNA (in somatic cells, diploid number of
chromosomes)
Length ~ 6,4x109bp; 7 picograms
46 molecules;
Associated with histones;
heterogeneous:
Contains ~ 30000 pairs of genes;
Replication takes place in S phase of cell cycle;
50% has maternal origin and 50% has paternal
origin.
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Peculiarities of human DNA
Mitochondrial DNA
Length – 16,6 kb
Ring molecules
A number of identical molecules (2-10)
Contains 37 genes
There are no free spaces between genes
Replication on cell demands
Always has maternal originwww.biologiemoleculara.usmf.md
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RNA –ribonucleic acid
Monomers – NTP (ATP, GTP, CTP, UTP);
Primary structure – a polynucleotide chain;
Secondary structure – loops;
Tertiary structure – RNP (RNA+proteins)
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Monomers of RNA - NTP
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mRNA – messenger RNA
Single-stranded molecule
There is a lot of types in the cell
Represents a template for protein synthesis
Each mRNA contains information about
synthesis of one or some polypeptide
molecules
In eukaryotes is produced as result of
processing of a primary transcript (pro-mRNA)
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tRNA – transfer RNA
•Single-stranded molecules
•Contain unusual basis (thymine, pseudouridine,
dihydrouridine)
•secondary structure – based on complementary pairing
of basis and formation of functional loops
•Ensure transfer of amino acids to the ribosome
•Represents the translator of genetic code
•In the cell may be present up to 61 types
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rRNA – ribosomal RNA
Single-stranded molecules
Part of the ribosome
In eukaryotes most types are prodused in nucleolus
Ensures interaction between ribosomal subunits, tRNA and mRNA during protein synthesis
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Secondary structure of
rRNA
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rRNAs
Types of the cells Coefficient of sedimentation
Prokaryotes
5S
16S
23S
Eukaryotes, nucleus
5S
5,8S
18S
28S
Eukaryotes, mitochondrion12S
16S
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microRNAs
snRNA
scRNA
iRNA
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Structure of the proteins
Monomers – 20 types of amino acids
Primary – a polypeptide – chain of amino
acids linked by peptide bond (the sequence
of amino acids is determined by DNA)
Secondary – α-helixes and β-sheets
Tertiary – globular
Quaternary – some polypeptides and / or
other molecules (nucleic acids, sugars, lipids)
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Formation of peptide bonds
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Structure of proteins
Primary structureAmino acids
Secondary structure
α-helix
Quaternary structureTertiary structure
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Arhitectura proteinelor
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Environment factors –to, pH, P, hν (light), etc.
Chemical structure –primary
3-D configuration –conformation (shape)
Properties
Functions
Relationship:
structure – environment – function
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