NOTES - Week 1 - intro to course: Nucleic acids. DNA replication Flashcards
What is life? Properties of life?
No precise definition tho
Distinct physical form - the cell as a physical unit that can show all properties of the life
Genetic information - storage, realization
Metabolism
Homestaosis: able to regulate internal environment and also react or adapt to environment
Reproduction
Structural unit of living organisms - the cell
For example the humanbody
Only the features discussed in this course, examples on human body
The living cell has all the necessary properties
Storage and realization of genetic information - we have nucleic acids
Metabolism - ( We can synthesis different chemical substances which has ability to story energy in the chemical bounds e.g. synthesis of ATP)
Synthesis of proteins
Specific physical structure - based on cell functions (e.g erytrocytes a.k.a. red blood cells who are small, flexible and do not have nucleus because of its function. Ability to go through the smallest capillares in our body. In contrast to neurons who are bigger and have a different function & structure, are not flexible and not mobile. In conclusion- structure and function are linked.
Reproduction- cell division like mitosis and also sexual reproduction
General terms
Nucleus
Homeostas
Erythrocytes
Capillaries
Unicellular
Haploid
Diploid
Nucleus
Membrane
Chromosomes
Plasmids
Plasma membrane
Centrosomes
Uni and multicellular DNA
Not for ANSWERING
Erytrocytes - red blood cells
Prokaryotes vs Eukaryotes
Able to compare and name main difference in practical classes
8 things to compare
What do you see
Eukaryotic cell comparison
- Protists, plants, mold, yeast etc also have nucleus
- Compare size of bacteria and archea to the cells
- Eukaryotic cell has mitochondria, different membrane-bounded organells, cytoskeleton etc
The function of the different prokaryotic files
Nucleoid similar to nucleus but is not membranebounded. Is just DNA bounded with some protein and RNA molecules.
Some has capsule - protects from enviroment
Has pili: important for conjugation of bacteria and can transfer genetic matetrial like plasmids to other cells.
Fimbria: important for adhesion of prokaryotic cells on the surface
Sometimes has flagellum: important for movement of bacteria
Mesosome- artifacts that we get during physical fixing in lab, does not exist in natural enviroment
The different types of eukaryotic cells
Who has;
mitochondria? chloroplast? Centrosomes?
+Compare appearance and mobility?
Yani what does cellwalls contain?
Additional info on top of image
plantcells are immobile because it has celluloses, gives the cells strength.
LOOK AT THE PICTURE MF AND TELL ME OUT LOUD WHAT YOU SEE
Now compare with the plantcells, what is similar and what is missing? Why?
Explain how mtDNA and cpDNA came about and why they are special?
Endosymbiotic Theory
The endosymbiotic theory explains the origin of mitochondria and chloroplasts as a result of a symbiotic relationship that formed between ancient eukaryotic cells and free-living prokaryotic organisms (bacteria).
Viruses, viroids and prions
What are they?
Are they alive?
Characteristics?
Viruses, viroids and prions: Agents of chaos; causes diseases for us
- No specific cell structure
- Cant grow
- Cant selfproduce
- Metabolism not present
Functions are fullfilled if they infect hostcells → grow and reproduce
Basically these mfs on their own are useless
*Classical biology - nonliving forms. Yet new research being made. *
Consist of nucleid acid molecules (either DNA or RNA)
forms; either few linear or circular molecules
Nucleid acid surrounded by protein coat called capsid. Capsid + nucleic acid = nucleocapsid
INTERLUDE
Viroids are small, circular RNA molecules without capsid, their hosts are plant cells.
virions and provirus
Extracellular form av virus which has yet to infect hostcell = virion. Infects only plantcells.
If the virus is already inside hostcell and its genetic material has integrated into hostcell DNA = provirus
Virus vs viroid
Not an important picture
What can you see (outloud!)
OBS smallballs around influenza are proteincode
Spikes on influenza: different proteins –> recognize and binds/infect with hostcell
Virus that infects and replicates in bacterias = bacteriophage
Host cells of viruses
Viruses are …. species?
What is specifity determined by?
What can viruses infect?
Viruses are specific species, sometimes same virus can affect different species.
Specifity is determined by - proteins on the surface of the capsid → their ability to bind to hostcell receptors.
Can infect humans, animals, fungus and bacteria
NOT VERY IMPORTANT!!!!!!
Example of SARS Covid-2 viral entry
Know what it consists of and how it succeeded
EDITTTTTTT
Has specific spike proteins on the surface → binds to human ACE2 receptor
Protease are involved: type of enzyme that can degredate or cleave proteins
→ by cleaving specific site on virus spike protein → activates its bindning with the receptor → triggers next signal transduction process → triggers fusion of viral and host membrane
Prions
What are they, what it does, whats special about these weirdos?
Prions are infectious protein particles. NO nucleic acid yet they posses protein structure.
Infect cells in the nervous system
Special because: misfolded version of a normal protein that is in nerve cells.
When it infects a nerve cell → “promotes the misfolding of the normal proteins which becomes self-propgating.” Affects its function. Causes neurodegenrative disease in animals and humans.
Storage of information
How it stores in prokaryotic cells
In prokaryotic cells most genetic info is stored in the nucleoids and a small part in plasmids.
Plasmids can leave nucleoid and be transfered to other P-cells via conjugation of bacteria (when they transfer info between each other via direct contact).
- Also important in having genes specific to toxic substances for the bacteria eg antibacterial resistance caused by genes in the plasmids.
How it stores in eukaryotic cells
3 places
Main: nucleus (nDNA)
Also in
Mitochondria (mtDNA)
In Chloroplast DNA (cpDNA)
Comparison between nDNA and mtDNA?
Apperance, structure, contains what information?
Human as multicellular organism
From eurkaryotes to multicellular organisms
HINT: Start of new life in embroyonic development
What is the process called
Via celldifferentiation
(Ej viktigt) Number of cells we have
Distribution of cells?
Looking at purely the count of the cells not the mass!
To take away from the picture: 84% red blood cells
Big number relates to size of the cells too.
What types of cells do eukaryotes have (humans)
Somatic cells: vast majority building up our organism, not involved in sexual reproduction. They have 2 copies of genetic information → diploid
Germ cells: involved in sexual reproduction. Called germcells at any stage of its development. Contain 1 copy of information →, haploid. Logical because creating new organism can be made by fusing together 2 seperate haploid genomes.
Central dogma of molecular biology?
The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information.
It states that such information cannot be transferred
from protein to either protein or nucleic acid.
Information cannot flow back from the protein to the RNA and DNA.
What does nucleic acids consist of?
What is a nucleoside?
What is a nucleotide?
3 star players
- Nitrogen base
- Pentose sugar
- Phosphate
Base + pentose = nucleoside
1 with that contains these 3 are called nucleotide
→ Nucleic acids = polynucleotids in linear form
Name the 5 different nitrogenbases
That are divided into?
How can one see the difference?
Purines: Adenine (A) and Guanine (G)
Pyrimidines: Uracil (U), Thymine (T) and Cytosine (C)
Look at amount of rings! Purines have 2 and pyrimidines have 1.
The sugar in nucleic acids is called… because?
Different types of this sugar? What distinguishes them? Where are they used?
2 types of pentose that consists of 5 carbonatoms. Ribose and Deoxyribose.
Difference is marked on the 2nd carbon atom of the pentose. Deoxyribose lacks oxygen in 2nd carbonatom.
DNA contain Deoxyribose and RNA contain Ribose as you can tell in their names!
What is mentioned about this image?
Why is the result called “nucleotide (dAMP)” ?
Phosphoric acid residue attached to 5th carbonatom of pentose. 1 residue in the nucleic acid. C1 links between pentose and nitrogenbase.
dAMP: deoxyadenosine monophosphate
d= the sugar deoxyribose
A= nitrogenbase adenine
M= mono meaning 1
P= phosphate group
How does number of residues affect nomenclature
What sugargroup?
Adding 1 phosphate changes the name e.g. adenosine mono/di/tri-phosphate
Explain what you see
Nucleotids in a chain- polynucleotides.
Bounded between with Phosphodiester bond
Meaning of the 5’ (prime) end and the 3’ end
5 prime end” has a free hydroxyl (or phosphate) on a 5’ carbon and the “3 prime end” has a free hydroxyl (or phosphate) on a 3’ carbon. Video for understanding this linked below
For elongation (extend) polynucleotide - only attach to 3’ end!
https://www.google.com/search?q=5%27+end+vs+3%27+end+dna&rlz=1C5CHFA_enSE960SE960&oq=5%27+end+&gs_lcrp=EgZjaHJvbWUqBwgBEAAYgAQyBggAEEUYOTIHCAEQABiABDIICAIQABgWGB4yCAgDEAAYFhgeMggIBBAAGBYYHjIICAUQABgWGB4yCAgGEAAYFhgeMggIBxAAGBYYHjIICAgQABgWGB4yCAgJEAAYFhge0gEINTE0NWowajeoAgCwAgA&sourceid=chrome&ie=UTF-8#fpstate=ive&vld=cid:9ff776cd,vid:qWZYpHSXvJo,st:0
Difference between DNA and RNA
Explain the structure of DNA
also explain complementarity
Double helix, double stranded molecule.
DNA structure
- consists of two complementary strands wound around each other to form a double helix
- The double helix is stabilized by weak hydrogen bonds between A and T bases and stronger bonds between C and G bases. (Relate to number of bonds between them)
- The backbone is made by the sugar-phosphate alternating bond
What is incompatibility
Amount of nucleotide base relative to each other? Explain the numbers also.
Incompatibility in the chemical level of bases:
Adenine and Cytosine
Acceptor and donor which forms the bounds will not be compatible + molecular strucure puts it into distance = no hydrogen bonds.
Amount of A = T and C=G
Instead of T in RNA we will se U = difference between A and T in %
DNA is majority of nucleic acids in body, by a massive amount.
How is the double-helix formed?
Double-Helix
* Is stabilized by hydrogen bonds between bases and by stacking of the aromatic rings of the
bases in the center of the helix
* Aromatic rings on the one strand are building on top of each other and are slightly shifted by
forming approx. 36° angle twist from previous base pair
* Double-helix strands are antiparallel – one strand 5’ - 3’ direction, second strand 3’ - 5’ direction
The different parts of the double helix?
Is there any reason for having a double-helix form? Reason for grooves?
Its structure is serving its purpose and functionality
2 sort of DNA molecules? Where they are found, contains, arranged?
RNA structure
Primary: Single stranded RNA
Secondary: Base level, includes single stranded, double stranded and loop structure.
Tertiary: Similar to proteins
Structure depends on function, RNA is usually more varied than DNA
Biological function of
DNA,
RNA,
mRNA and
tRNA?
ADDITIONAL
DNA always locked and protected in the nucleus (except when cell divides and nuclear envelope is disintegrated → located free in the cytoplasm)
Biological function of rRNA
And regulatory RNA and its different types:
ribosomal complex consists of ribosomal RNA and many proteins.
DNA replication
What is it? Why do cells need this process?
Duplication of DNA based on the principle of complementarity.
To ensure cell division (sexual replication of cells) - we need duplicate genetic material to be distributed equally to the new daughter cells. Altho we have 2 copies of genteic material in somatic cells it still needs to be transferred to daughter cells as the 2 copies.
Explain what DNA replication essentially means
A-T and C-G are complimentary.
Where and why does DNA replication start?
(Initiated)
For prokaryots its simple in the same place.
Eukaryots have specific nucleotide sequence - recognised by specific initiation proteins. Repeated in many places. DNA replication can start in a few places in the long strand of DNA.
DNA replication
Initiation
To start initiaton of the DNA replication:
Initiator proteins need to recognise these specific sequences on the DNA.
Grooves of DNA molecules are able to bind with proteins → DNA can be bended and also unwinded
Initator protein task is to recognise where in DNA replication will start and bind with DNA to initate opening of the 2 strands of DNA.
Opening done by enzyme helicase: cuts hydrogen bonds between complementary nucleotids → opens strands of DNA → Y-shaped replication fork is formed.
To keep DNA molecules undamaged = we need enzyme topoisomerase. Prevents DNA from supercoiling. Can damage becuase creating an opening between 2 strands creates tension on the rest. Topoisomerase cleaves another strand further away to release tension - ensures DNA strand is not damaged.
Singlestrand binding proteins ensures holding the position of the replication fork. Binds to the opened single strand of DNA to prevent reforming of the doublestranded, essentially preventing complimentary bases to reform hydrogenbonds. Keeps it opened.
1 origin of replication
Explain the 2 types of of synthesis of new DNA strand
Look at video again
7.35
https://panopto.rsu.lv/Panopto/Pages/Viewer.aspx?id=1db06386-56c0-4b77-8684-b1db0064bf81
- The reason why it is a difference in leading and lagging strand is because the DNA
polymerase always synthesis the DNA
from 5´ to 3´. The strands are antiparallel,
meaning the leading strand will synthesis new DNA continuously while lagging strand will synthesis new DNA discontinosly creating okazaki fragments. This difference means that the leading starnd will only need one primer to synthesis the DNA while the lagging strand needs a primer for each okazaki fragment.
Initiation of DNA synthesis
To start we need small fragments called primers, built from RNA molecule.
Needed= new forming nucleotide can be added to the new synthesized strand only if hydroxygroup on C3 on pentose is available.
What does rNTP and dNTP do?
What is RPA
Synthesis of DNA
Elongation in DNA replication
Polymerases;
Leading strand is syntheized by… ?
Lagging strand is syntheized by…?
What do they have in common and what does it mean?
What does RNase H do?
What does DNA polymerase β (beta)
What does DNA ligase do?
They both have repair activity: DNA polymerase can detect if the wrong nucleotide is added into the newly syntheized strand and can remove it.
When you have lagging strand = have number of RNA primers joined together with newly syntheized okazaki fragments. BUT we dont RNA primers in the new DNA strand only DNA sequence. Here comes RNase H to recognise and degrades the primers
→ Now gap between okazaki fragments, needs to be filled in by DNA fragments, fills in by DNA polymerase β (beta)
Still unjoined ends of the DNA fragments, here comes DNA ligase to make sure it is uninterruted newly syntheized DNA strand.
Proteins involed in eukaryotic DNA replication and their function.
The ends of linear DNA is known as?
What do they consist of and how often are they repeated?
What problem are they associated with?
Solution to this problem?
Natural reasons for the telomeres shortening
End replication problem
The end-replication problem eukaryotes
The ends of linear DNA are known as telomeres, are made up of a 100-1000 timesrepeated TTAGGG sequence in humans.
At the 3’ end these are single stranded and form a cap.
After replication of the lagging strand, a problem arises since there are no free 3’ OH groups.
The enzyme telomerase consists of several sub-units and contain an integral RNA components that acts as a template for single stranded telomere cap synthesis.
Telomere length is lost through normal DNA replication, replication errors and oxidative DNA damage.
Replication in prokaryotes
Where does it start?
Explain this image
Similar idea to eukaryotes but a bit different.
Compare replication in prokaryotes vs eukaryotes
nt = nucleotides?
