Module 1 Flashcards
What are the three tenets of the cell theory?
- all living organisms are composed of one or more cells
- all cells come from preexisting cells
- the cell is the basic unit of structure and organization in an organism
what are prokaryote features? (nucleus, size, uni/multi, reproduction, example)
- no true nucleus or any membrane bound organelles (nucleoid region)
- smaller cells (1-5 µm)
- always unicellular
- reproduce through binary fission (asexual)
- e. coli
what are eukaryote features?
(nucleus, size, uni/multi, reproduction, example)
- has a nucleus and membrane bound organelles
- large cells (10-30 µm)
- usually multicellular
- undergo mitosis and meiosis (sexual or asexual)
- plants and animals
what are epithelial cells?
they are cells that form protective barriers in tissues and may be specialized to absorb or secrete specific compounds
what are muscle cells?
they are cells that are responsible for the movement of the skeleton, heart, and many internal organs, and they have specialized structures and proteins that allow them to generate motion
what are nerve cells?
they are cells that conduct electrical signals throughout the body, control the contraction of muscles and are responsible for our five senses
what are connective tissue cells?
they are cells that create extracellular material that holds cells together in tissue and they may be specialized to absorb or resist external forces (tendons or vertebral discs)
what are bone cells?
they are cells that form the bones of the skeletal system that give strength and support to the body
what are two types of bone cells?
- osteoclast cells which degrade bone
- osteoblast which creates new bone
what are secretory cells?
they are cells that form glands that secrete substances (mucous, hormones or enzymes)
what are adipose cells?
they are cells that are located throughout the body to store fats in the form of triglycerides which are released when the body is in a period of fasting
what are red blood cells?
they are cells formed primarily in the bone marrow and are released into circulation where they move and deliver oxygen throughout the body. they do not have nuclei or mitochondria so they have a limited lifespan and must be replaced continuously
what does the cytoskeleton do?
holds the cell together
1. actin, microtubules and intermediate filaments are structural filaments that stabilize membrane deformations
2. myosin, kinesin and dyein are motor proteins that generate force or motion
what are the four important properties of water?
- polarity
- specific heat capacity
- density
- surface tension
explain the polarity properties of water
- it is an excellent solvent (hydrophilic, can dissolve “like” (polar) substances)
- facilitates the delivery of nutrients and removal of waste
- allows the movement of chemical messengers within and between cells
explain the specific heat capacity properties of water
- allows for thermoregulation
- acts as a heat sink (absorbs excess heat) from chemical reactions occurring as the H bonds require high amounts of energy to break so water can absorb a lot of energy
- facilitates the exchange of heat between liquid and air
- allows animals to regulate their body temperature
explain the density properties of water
- water is liquid at room temperature and molecules expand during the freezing process
- allows ice to float, H bonds repel each other forming a crystal lattice structure
- allows life for aquatic organisms in the arctic
explain the surface tension properties of water
- cohesion, water molecules attract each other
- adhesion, polar molecules attract each other
- allows for capillary action
what are lipids?
they are the building blocks for oils and fats and are made of hydrocarbon chains (hydrophobic) but are commonly amphipathic
what are the three most common types of lipids and what do they do?
- cholesterol - regulates cell membrane fluidity
- phospholipids - amphipathic lipids that forms the membrane
- triglycerides - main component of body fat in animals and are used to store energy
what are the four types of carbohydrates?
- monosaccharides - single molecule
- disaccharides - two monosaccharides bonded together by a glycosidic bond
- oligosaccharides - 3-10 monosaccharides linked together
- polysaccharides - long complex chains
what are nucleotides?
they are the building blocks of nucleic acids (DNA and RNA) and they form ATP
what is the structure of an amino acid?
- carboxylic acid group
- amino group
- R group
what are the four types of amino acids?
- hydrophobic (non polar), aliphatic or aromatic, in core of protein
- charged hydrophilic, positive or negative charge, outside of protein interacting with water
- polar, form hydrogen bonds to stabilize protein, outside of protein
- aromatic, very large with ring structure with double bonds, gain or loss cause deformities in structure
what is a genome?
it is the complete set of genetic material in an organism (all the DNA)
what is a gene?
it is a sequence of nucleotides in DNA that determines a certain characteristic
what are the three things that make up a nucleotide?
- phosphate group
- five carbon sugar
- nitrogenous base
what is the nucleotide linkage structure?
- 5’ carbon, phosphate group
- 3’ carbon, phosphate group from another nucleotide linked via a phosphodiester bond
- 1’ carbon, nitrogenous base
what are the two nitrogenous group categories?
- purines (two ring structure), adenine and guanine
- pyrimidines (one ring structure), cytosine, thymine and uracil
what is the bonding of nitrogenous bases?
- C-G, triple bond
- A-T, double bond
why does DNA form a double helix?
this is due to nitrogenous bases being hydrophobic so the double helix formed prevents water contact
what are the structural differences of RNA?
- uracil replaces thymine
- ribose is used instead of deoxyribose, has an extra oxygen on carbon 2’
- single stranded, less stable
what are the types of RNA?
- mRNA, carries instructions for making proteins
- tRNA, brings amino acids for protein synthesis during translation
- rRNA, makes up ribosomes with ribosomal proteins
what is the structure of a gene (3 regions)?
- exons, coding DNA
- introns, non coding DNA
- regulatory sequences, controls when the gene is used
explain the process of semi conservative DNA replication
initiation:
1. DNA helicase binds to the origin of replication and unwinds the DNA into two single strands forming a replication fork, requires energy
2. RNA primer is added by primase which is a short number of RNA nucleotides
elongation:
3. DNA polymerase elongates complementary strand moving in the 5’ to 3’ direction
4. leading (only needs one RNA primer) and lagging strand (needs multiple RNA primers and forms okazaki fragments) created
5. to mitigate damage of the DNA while it is yet to be replicated single stranded binding proteins (SSBPs) bind
6. DNA polymerase replaces RNA primers with DNA (DNA replaced is not connected to other fragments)
7. DNA ligase catalyzes phosphodiester bonds sealing DNA gaps (joins okazaki fragments on lagging strand)
termination:
8. on lagging strand overhang is created as primase cannot add RNA primer
9. telomerase carries short piece of RNA that binds to the overhang extending past the RNA
10. an RNA template is formed and telomerase adds corresponding DNA to the extension
11. RNA primer added by primase and DNA polymerase adds DNA
12. once the overhang is recreated telomerase repeats the process creating a large section of non coding DNA
what is telomerase?
it is an RNA dependent DNA polymerase
what would happen if the overhang in DNA replication is left?
it would lead to the overhang being degraded as single stranded DNA is very unstable. this would lead to a gradual loss of DNA causing the chromosome to shrink damaging the cell
what are the three types of RNA polymerase
- RNA polymerase I, responsible for synthesizing rRNA
- RNA polymerase II, synthesizes mRNA
- RNA polymerase III, synthesizes tRNA as well as some other RNA molecules
what is are transcription factors?
they are a group of proteins that bind to regulatory regions of genes to signal transcription machinery. they can promote of block transcription by altering the ability of RNA polymerase to start transcription
explain the process of transcription
initiation:
1. binding of transcription factors occurs towards the 5’ end of the gene
2. RNA pol II binds to DNA at a specific location celled the promoter (start site with the sequence 5’ TATAAA 3’, called the TATA box)
3. DNA unwinded enough for RNA pol II to access the gene
4. RNA pol II activated by phosphorylation twice to allow transcription to begin
5. steps 2-4 are facilitated by transcription factors
elongation:
6. RNA pol II moves forward synthesizing mRNA in the 5’ to 3’ direction (adds nucleotides to the 3’ end)
7. region of unwound DNA is called the transcription bubble and it is covered by RNA pol II to protect the DNA
termination:
8. transcription ends when RNA is cleaved from RNA pol II by a separate enzyme
9. transcription bubble collapses and RNA dissociates and RNA pol II detaches from the DNA
what is the problem with RNA polymerase and is this problem compensated (transcription)?
RNA polymerase had a low fidelity (no proofreading function) so to compensate several short RNA molecules are made until one has the proper complementary hydrogen bonds that matches the template strand to ensure the correct mRNA molecule is made
explain post transcriptional RNA processing
methylated 5’ cap
1. guanosine triphosphate (GTP) is added to the 5’ end via a 5’ to 5’ triphosphate linkage
2. GTP has a methyl group added to the 7 position of the guanine base
3. protects the mRNA from premature degradation by nucleases
3’ polyadenylation (poly(A) tail)
4. poly (A) polymerase adds around 200 adenosines to the 3’ end of the mRNA
5. essential for binding proteins that are necessary to transport mRNA out of the nucleus
RNA splicing
6. introns are removed from the RNA
7. some genes use alternative splicing to create multiple mRNA molecules from a single gene
how does mRNA exit the nucleus (through where and what is used)?
after post transcriptional modifications are complete mRNA exits via a nuclear pore. complex of proteins bind to assist the transport and some of those proteins are recycled back to the nucleus and some help with translation
what is the exception to the central dogma?
some viruses use RNA as their genetic material such as hepatitis C. they have specialized enzymes such as RNA polymerase and RNA helicase
what is a codon and what are the start and stop codons?
- a codon is 3 nucleotides
- start codon, AUG (met)
- stop codon, UGA, UAG, UAA
how is it determined where the mRNA goes after transcription?
depending on the mRNA sequence the molecules either goes to the cytoplasm or ER
what are translation initiator factors?
factors that bind to the mRNA which include 5’ cap binding factor, poly(A) binding protein (PABP) and another factor that bind to the mRNA 3’ poly(A) tail. these factors allow for the small ribosomal subunit to identify the initiation site
what are translation elongation factors?
they are proteins that assist with elongation and some form complexes that help deliver tRNA and the GTP energy source to the ribosome
what does tRNA do?
tRNA delivers amino acids by recognizing the codon and containing the anticodon. the bond holding the amino acid to the tRNA provides energy to make a new peptide bond
explain the process of translation
initiation:
1. initiation factors bind to the mRNA
2. small ribosome subunit attaches to the mRNA at the 5’ end, guided by initiation factors
3. ribosome small subunit attaches to initiator tRNA (met) and moves along the mRNA until the start codon is found so tRNA can bind to the codon
4. large subunit attaches with the tRNA on the P site
5. PABP (poly (A) binding protein) falls off once translation begins
elongation (requires energy):
6. tRNA with anticodon to A site binds
7. GTP converts to GDP and peptidyl transferase moves growing peptide in P site onto tRNA amino acid on A site
8. ribosome moves down a codon on mRNA, tRNA from A to P and P to E site (E site tRNA ejects)
termination:
9. stop codon is reached which attracts a complimentary release factor which fits in the A site (substitutes water for the amino acid)
10. production of carboxylic acid and release of peptide
11. peptide releases and ribosome release factor occupies A site leading to the release of the small and large ribosome subunit
what are the factors that lead to DNA being damaged?
- error during replication
- ultraviolet light
- oxidation
- DNA strand breaks
what are the two type of DNA repair?
- DNA polymerase proofreading function
- DNA repair proteins that continuously scan DNA for errors and make repairs
what are the four types of mutations?
- point, single nucleotide changes (silent - same amino acid, missense - difference amino acid, nonsense - replaced with stop codon)
- insertion, extra base added (3 base added is a frameshift mutation)
- deletion, base pair removed (3 deleted is a frameshift mutation)
- large scale deletion, insertion or recombination (change is lethal, cancer caused by production of fusion genes creating new combinations of proteins with new functions)
how would you know if a missense mutation has major consequences?
the consequences is dependent on whether the properties of the amino acids are similar or different
