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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