Molecular Biology Flashcards
DNA of prokaryote
Single circular double stranded DNA concentrated in the nucleoid
Can the plasmid of prokaryote (bacteria/archae) replicate independently?
Yes
What is the difference between eukaryotic plasma membrane and prokaryotic plasma membrane?
Do all prokaryotes have cell membrane?
Eukaryotic plasma membrane has cholesterol to provide membrane integrity whereas prokaryotes have similar steroid-like molecule that function the same.
Prokaryotes have invaginations called mesosomes in their plasma membrane whereas eukaryotes do not.
Yes all prokaryotes have phospholipid bilayer membrane.
Structural difference between gram positive and gram negative bacteria
Gram positive bacteria have a thick PTG wall outside the plasma membrane whereas gram negative bacteria has a very thing layer of PTG outside plasma membrane and there is another layer of plasma membrane outside of this thin PTG.
What is a teichoic acid?
Teichoic acids are a protein molecule that extend to the surface of the gram positive bacterial cell. Only found in gram positive bacteria. “Wall”, it protects the bacteria. It protrudes to the surface of gram positive bacteria, stemming from either the plasma membrane or the thick layer of PTG.
What is lipopolysaccharides?
Lipopolysaccharides are polysaccharides that are present in the outer membrane of the gram negative bacteria, the outer membrane just outside the thin PTG cell wall. It stabilizes the membrane, and acts as an endotoxin to provide defense for the gram negative bacteria (protect from drugs, surface adhesion, structural integrity)
It has an O-antigen and elicits a strong immune response in animals
In peptidoglycan cell wall of gram positive and gram negative bacteria, what kind of linkage links the N-acetylglucosamine (G) and N-acetylmuramic acid (M)?
Beta (1,4) linkage
Propeller direction of bacterial flagella and the major protein component of bacterial flagella
Counter-clockwise
flagellin
In bacterial conjugation, what is the sex factor?
During conjugation, how is the F factor replicated?
Sex factor is a plasmid in a bacteria that allows the bacteria to form a sex pili (sex bridge) that transfer the genetic information to another bacterium.
The F factor replicates via the rolling circle mechanism of replication. The single stranded DNA is passed down first and as it is transferred to another bacterium, it begins and continues its replication process.
What happens when sex factor is integrated into the host chromosome through transformation?
The F factor is integrated into the bacterial chromosome and this host chromosome is transferred.
In eukaryotes, how is the DNA condensed? Explain “Beads on a string”, the structure of nucleosome and linker. Do prokaryotes have histones?
Nucleosome, 4 histones with DNA wrapped around it, are linked with a “linker” consisting of Histone 1 protein. H1 protein condenses the series of nucleosomes further, creating a 30nm chromatin fiber. This type of condensation of DNA is unique to eukaryotes only.
Explain the structure of different lipid structures: micelles, and liposomes.
Micelles: spherical structure where the polar heads are outside and the hydrophobic tails are congregated on the inside.
Liposomes: lipid bilayer folding onto itself forming a circle.
How does the speed of lateral diffusion differ from transverse diffusion in the phospholipid bilayer?
The speed of lateral diffusion is very fast whereas the speed of transverse diffusion is very slow. Transverse diffusion occurs rarely.
What is the difference between integral membrane proteins and trans-membrane proteins? What forces hold the integral membrane proteins embedded? What kind of conditions are required to remove them? And when these conditions do occur, what usually happens to the cell?
Trans-membrane protein is a sub-class of integral proteins that span the whole lipid bilayer. Integral membrane proteins are tightly bound to the membrane by hydrophobic forces and harsh conditions are needed to remove them. Once removed, the membrane is usually disrupted.
What forces keep the peripheral membrane proteins attached to the lipid bilayer?
Hydrogen bonding or electrostatic interactions. Removal of the peripheral membrane proteins occur in mild conditions and removal usually keeps the membrane intact.
Do symports and antiports require ATP?
No, they are examples of facilitated diffusion where it does not require ATP. Key in distinguishing facilitated diffusion is that molecules move DOWN their concentration gradient.
What is a secondary active transport.
Transport mechanism by which molecules are moved against its concentration gradient by using an already established concentration gradient of another solute.
Importance of bulk transport
Compartmentalization - endoctosis and exocytosis
Are histones acidic or basic? What charges do they have and what amino acids are found in high percentages?
Histones are basic bearing a positive charge at physiological pH. They have lots of lysine and arginine.
Is nucleolus a membrane-bound organelle? What special function does a nucleolus have?
Nucleolus (only found in eukaryotes) are not membrane-bound. Nucleolus synthesize rRNA which makes up a part of a ribosome.
Ribosome size of eukaryote vs. prokaryote vs. mitochondria
Eukaryote: 40 + 60 = 80S
Prokayote: 30 + 50 = 70 S
MItochondria: 55 S - similar to prokaryotic ribosome (note, mitochondria is a double-membrane organelle found only in eukaryotes)
Function of sRER especially in liver cells
lipid synthesis
detoxification via hydroxylation
Ca2+ sequestering
Function of rER
Synthesis of proteins destined for the membrane or to be secreted outside the cell
Post-translational modification begins in the lumen of the rER. Post-translational modification continues in the golgi.
Function of lysosomes
Enzyme activation via proteolytic cleavage
Autolysis - cell suicide, selectively choosing when to release these enzymes.
What is the function of peroxisome?
Energy metabolism
They are involved in the catabolism of very long chain fatty acids, branched chain fatty acids, D-amino acids, and polyamines, reduction of reactive oxygen species - specifically hydrogen peroxide through Catalase
Can also produce hydrogen peroxide as a byproduct of both amino acid oxidation and fatty acid oxidation
Compare the permeability of inner vs. outer membrane of mitochondria
Outer membrane: has porins, transmembrane proteins (carriers or channels) that allows small molecules to freely pass.
Inner membrane: essentially impermeable to all molecules
Examples of intermediate filaments
Keratin and desmin
Collection of fibers that maintain the overall integrity of cytoskeleton
Function of microtubules
chromosomal segregation during mitosis and meiosis. Structural integrity, movement (flagella), centrioles and etc.
How do naked viruses get inside the host cell?
Receptor-mediated endocytosis
Attach to the receptors of clathrin coated pit (scaffold that fold into a vesicle). Once a vesicle is formed, the vesicle becomes acidic, disassembling the clathrins. As the pH of the vesicle continued to fall, the nucleocapsid disrupted the membrane of the endosome and is released into the cytoplasm.
How do enveloped viruses get inside the host cell?
Receptor-meidated endocytosis or direct fusion
In case of direct fusion, need fusion proteins. When the virions get out, they can leave with the envelop fused with the host membrane.
In case of receptor-mediated endocytosis, the process is the same except that acidity of accumulation of hydrogen disrupts the viral envelope and releases the capsid.
True or False: Only animal cells (excludes fungi) have centrioles
True
What are the ways bacteria create genetic recombination?
explain each
conjugation - chromosomal genetic material exchanged while the plasmids are getting exchanged especially when the plasmid is an episome. F factor and R factors are the plasmids getting exchanged.
Transformation: taking up external DNA fragments from the environment
Transduction: genetic material exchange through virus
Explain how the nuclear region is different in bacteria than eukaryotes
single circular double stranded molecule of DNA supercoiled into nucleoid region (tightly coiled) without histones (proteins similar to histones but not histones). This region where circular DNA is supercoiled and visible under the microscope is called the nucleoid region
G1 of interphase
Growth in size, active transcription, translation and replication
Interphase, G2
Cell prepares to divide; organelles double in number
