Midterm Flashcards
what are the key steps of cell formation?
- generation of self-replicating RNA
- production of proteins
- formation of cell membrane
what are the different adaptations of cells to different environments?
natural selection- random genetic variation that’s passed on from one generation to the next and by selection of cells that can survive the environment in which they live
archaebacteria- harsh environments such as ocean depths, salt brines, and hot acid springs. Some are even capable of converting carbon dioxide to methane.
Cyanobacteria- obtain their nitrogen directly from atmospheric N2
anaerobic bacteria- thrived hen the earth’s atmosphere contained very little oxygen
structure of nucleic acids: prokaryotic DNA and RNA vs eukaryotic
pro DNA: Circular DNA In cytoplasm
eu DNA: Long stretches of DNA containing coding and non-coding regions, organized as chromatin and located in the nucleus
pro RNA: RNA and protein in the same compartment
eu RNA: RNA synthesized in the nucleus, proteins in the cytoplasm
what makes anaerobic generation of ATP via glycolysis efficient?
Adding an oxygen-requiring step makes it highly efficient for extracting energy from food molecules beginning with the Kreb Cycle and ending with oxidative phosphorylation
what happens during oxidative phosphorylation?
NADH and FADH2 transfer the electrons that they have accumulated to molecular Oxygen and release a large amount of ATP
where do reactions like oxidative phosphorylation, kreb cycle, and glycolysis happen?
mitochondria
where is the energy for biosynthesis of cellular proteins, lipids, and other macromolecules derived from?
hydrolysis of ATP
how are Large proteins and nucleic acids assembled from small activated precursor molecules?
by repetitive dehydration reactions.
explain how food is broken down to generate ATP
- digestion: protein broken down into amino acids, fats into fatty acids, and polysaccharides into sugars
- smaller molecules enter cells and further degraded in the cytosol
- carbon and hydrogen atoms of sugars converted into pyruvate via glycolysis which enters the mitochondria where its converted to the acetyl groups of acetyl CoA
- acetyl CoA gives rise to a large amount of energy
- Oxidation of fatty acids can also give rise to acetyl CoA
- ATP is generated when the acetyl group of acetyl CoA is completely degraded to carbon dioxide and water
define catabolism
breakdown of larger molecules occurs due to the action of specific enzymes or a process
why do cells continuously use ATP?
to drive internal processes of macromolecular synthesis and breakdown
prokaryotic vs eukaryotic cells vs plant cells
plant cells: surrounded by cell walls with an underlying plasma membrane and they also have large vacuoles and specialized structures called chloroplasts that are essential for photosynthesis.
eukaryotic cell: have Nucleus, mitochondria, endoplasmic reticulum, Golgi apparatus etc., animal cell: have a cell membrane and centrioles that play a vital role in cell division
aerobic metabolism
prokaryotic cell: doesn’t have Nucleus, mitochondria, endoplasmic reticulum, Golgi apparatus etc., ex. bacteria
anaerobic and aerobic metabolism
what is chromatin?
chromosomal DNA within the nucleus in a tightly wound form that uses histone proteins
what is the nucleolus?
dense body which is the site of RNA assembly
what are nuclear pores?
openings in the nuclear envelope that allow for exchange of contents between the cytosol and nucleus
what is the nucleus?
regulates gene expression, coordinates protein synthesis and determines how a cell responds to a stimulus.
what is the endoplasmic reticulum (ER)?
series of membranous tubes or sacs that lies adjacent to the nucleus.
membrane is continuous with the outer membrane of the nuclear envelope.
why is the rough ER called “rough” and what does it do?
has ribosomes attached to its surface which are involved in active protein synthesis
lumen serves as the receiving site for the secretion of assembled peptide chains.
what is the smooth ER?
tubular and does not have ribosomes on its surface
plays a role in lipid metabolism.
what is the golgi apparatus?
system of stacked flattened sacs that help to modify, sort and package proteins and macromolecules and also prepare them for shipment to various parts of the cell for further processing or secretion via small vesicles
what are lysosomes?
membrane bound vesicles that contain hydrolytic enzymes that are responsible for intracellular digestion
what are peroxisomes?
membrane-bound vesicles but they contain oxidative enzymes that generate hydrogen peroxide and scavenge oxidative radicals.
what is the mitochondria?
sites of power generation for all eukaryotic cells.
how does mitochondria generate ATP?
by using oxygen and nutrient molecules
They contain a large number of enzymes that participate in redox reactions involved in the electron transport chain. This generates protons that drive the formation of ATP that is used as an energy source by the cell.
what is cytosol
liquid that contains various chemicals and macromolecules where the organelles are suspended
also contains filaments that give the cell its shape and helps with movement and cell division.
what is the cell membrane composed of?
two layers of lipids with a variety of proteins and carbohydrates incorporated into it
list the three major types of lipids that make up cell membranes
phospholipids
cholesterol
glycolipids
list the two ways amphipathic molecules will burry and protect the hydrophobic tails and leave the hydrophilic heads exposed to water.
- forming micelles – spheres with hydrophobic tails inward
- forming bilayers – with hydrophobic tails sandwiched together between the hydrophilic head groups
why is the formation of the lipid part of the biological membranes spontaneous?
due to the amphipathic nature of these molecules
when does flip flop movement occur?
when molecules from one side of the monolayer migrate to the other side (i.e: a molecule from the top half moves to the bottom). This type of movement occurs less frequently.
when does lateral diffusion occur?
molecules within the same monolayer switch positions with their neighbors. This occurs at a very rapid rate
Movement of phospholipids within the cell membrane gives rise to membrane ______.
fluidity
In hotter environments, do cell membranes tend to be more fluid or less fluid?
more
how do hydrocarbon tails in phospholipids contribute to membrane fluidity?
They can have cis bonds which create a “kink”, affecting the fluidity of the cell membrane.
Along with these “kinks”, the varying lengths of the hydrocarbon tails can also influence the membrane fluidity.
The longer the hydrocarbon chain and the more cis bonds present, the more fluid the membrane.
how does cholesterol play an important role in membrane fluidity?
It can insert itself between phospholipids and enhance the mechanical stability of the membrane, making it less likely to fracture in colder temperatures, and keeping it from being too fluid in hotter temperatures.
what do uniports transfer?
a solute from one side of the membrane to the other
what are co-transporters and what is the example?
two solutes are transferred together
ex. Symports and antiports
what is the difference between symports and antiports?
Symports transport two solutes in the same direction
antiports transport two solutes in opposite directions
when does simple diffusion occur?
when the molecules flow passively across the membrane without the assistance of membrane proteins.
what structures are needed for facilitated diffusion to occur?
through the action of channel proteins or carrier proteins
what are channel proteins vs carrier proteins?
channel proteins: allow passive transport of the molecules that are appropriate in size
carrier proteins: can bind to a specific molecule and help it cross the membrane
what does active transport require?
use of another solute that is moving down its concentration gradient
favorable and therefore produces energy which is used in secondary active transport.
what macromolecules require the formation of membrane bound vesicles for transportation?
proteins, polynucleotides, polysaccharides
endocytosis
cells take in macromolecules and particles
Vesicle: clathrin- formed from coated pits and coated with proteins
pinocytosis and phagocytosis.
exocytosis
intracellularly fuse with the plasma membrane to release the contents that are held within the vesicles, when a cell needs to secrete a substance, whether that is a waste product or a protein product such as insulin
pinocytosis
cell drinking using small vesicles
phagocytosis
cell eating uses large vesicles for the uptake of other microorganisms or cell debris so that they can be digested by the cell.
what are histones?
proteins that help package the DNA into nucleosomes
what are the functions of histone proteins?
allows DNA to wrap around it and package it tightly
keeps the stray DNA that comes off the nucleosome attached so that it can stay condensed and tightly packed
how do histones play a role in gene regulation and expression?
- contain positively charged amino acids, such as arginine and lysine which can interact with the negative charge of DNA.
- These charges are in general what help to hold the DNA onto the nucleosome, and they play an important role in binding
what do histone acetylases do?
activate gene expression by acetylating histone proteins
removes the positive charge, and as a result, allows the DNA to be much more loosely associated with histone proteins, making it open to interacting with DNA replication proteins
what do histone deacetylases do?
remove acetyl groups from histone proteins, causing the amount of positive charges on the histones to increase, and thereby making the interaction between DNA and histone protein stronger, preventing the DNA from being expressed/regulated
DNA vs RNA
DNA
- double stranded
- thymine
- carries genetic information
RNA
- single stranded
- uracil
- messenger or coder for the different protein products that are produced by genes
introns vs exons
introns: non-coding region
exons: coding region
prokaryotic RNA synthesis
- RNA polymerase first recognizes promoter sequence
- RNA polymerase binds with promoter sequence
- starts synthesis of RNA in 5’-3’ direction, using DNA as template strand
- stops once prokaryotic RNA polymerase reaches terminal signal
- prokaryotic RNA polymerase dissociates from DNA and releases newly synthesized RNA
eukaryotic RNA synthesis
- RNA polymerase II transcribes all DNA to create immature mRNA which contains introns and exons
- RNA splicing complex removes introns to create mature mRNA which only contains exons
- 5’ cap and 3’ poly A tail is added to either ends of molecule to protect it from being digested by enzymes in cytoplasm
- once mRNA exits nucleus and goes into cytoplasm, it can be translated into proteins using ribosomes
what is RNA splicing and the importance of it?
removes introns to create mature mRNA which only contains exons
can allow the cell to make many different proteins using different combinations of exons, from the same RNA transcript
DNA methylation
one of the only gene regulation methods that account for cell memory
CpG (C=cytosine, p=phosphate, G=guanine) islands within the DNA are methylated and thereby inactivated
inherited through DNA replication
GC rich vs. AT rich strands and stability
1. how many hydrogen bonds between each
2. which base pair will have a higher melting point?
- GC: 3
AT: 2 - GC
what is transcription and how is it regulated?
takes genetic information from DNA and transcribes it into mRNA
- immature mRNA modified by RNA splicing (removes introns)
- RNA polymerase recognizes promoter sequence in DNA which binds to sequence and initiates transcription of downstream genes
- once RNA polymerase reaches termination sequence, it dissociates from template strand and releases synthesized immature mRNA to be modified by splicing
gene regulation protein, histone acetyl/deacetylation and methylation can affect whether or not certain genes transcribed
what is translation is and how is it regulated?
- when tRNA transferring amino acids, uses anticodon, telling tRNA which amino acid is next in polypeptide sequence
- ribosome catalyzes reaction of protein synthesis (peptide bond forms)
mRNA
messenger
rRNA
structure of ribosome
tRNA
carries specific amino acid based on genetic code to ribosome that creates peptides
process of DNA replication and the enzymes involved
DNA polymerase
- separates DNA strand and replicates each strand
- requires primase to start replication
- only synthesizes DNA on 5’-3’ direction
DNA helicase
- unzips DNA to make replication fork
leading strand
- DNA synthesis occurs continues in 5’-3’ direction starting at 3’ end of template strand
lagging strand
- discontinuous manner
- synthesis occurs in 5’-3’ direction but DNA polymerase will have to stop and continue behind previously synthesized fragments (okazaki fragments)
exonuclease proofreads and can move paired/unpaired bases for mistakes made by DNA polymerase suring replicatoin
what is the result of genetic recombination
increase in diversity of gene combinations in our chromosomes
describe general recombination
- process involves double strand breakage of a segment of DNA on a chromosome which is then switched with homologous region on the homologous chromosome
- only occurs between two homologous regions on chromosomes
- used in homologous recombination
what does site-specific recombination require?
recombination enzyme that recognizes specific sequences that are present on the recombining DNA molecules which are the ones that are involved in recombination
- commonly occurs in bacteria
in prokaryotic and eukaryotic chromosomes, what are the mobile genetic elements that function in the same way as site specific recombination and how does it work?
transposable elements
- move around in the host genome using recombination enzyme
- elements can insert themselves in the middle of important genes, causing a disruption which may lead to disease
How do viruses replicate?
they infect other cells and hijack their replicative machinery in order to replicate themselves
- genetic material can be either DNA or RNA, which can be linear, circular, double stranded, or single stranded
What is the difference between rough and smooth ER?
rER
- membrane bound ribosomes
~ direct their protein synthesis into the ER lumen when there is special signal sequence present in the mRNA
~ tells the ribosome that this protein needs to be transported to specific location via golgi apparatus
- cisternae: “stacks of flattened sacs” of the rough ER and is prominent in protein production and secretion
sER
- “meshwork of fine tubules”
- lipid metabolism and detoxification
glycosylation
What is the function of the Golgi apparatus
glycosylation
packaging of proteins
recycling of membrane components
What is the structure and function of a lysosome
- small vesicles filled with hydrolytic enzymes that are used to degrade macromolecules into waste products that are then exocytosed out of the cell
- transport proteins: uses ATP to pump H+ ions inside it to create an acidic environment
- docking markers: helps tag the lysosome so that specific transport vesicles in the cell can fuse with them
What is the structure and function of a peroxisome?
- formed by budding of sER
- major of site of oxygen utilization where the oxygen is used in catabolic reactions
- catalase and reaction: safety mechanism of sorts to prevent the accumulation of hydrogen peroxide in the cell, which is a toxic waste product
what is I-cell disease?
occurs when the patient lacks the lysosomal enzyme tag mannose-6-P. As a result, the lysosomal enzymes are not present in the lysosome and macromolecules cannot be broken down. There are a variety of mutations that cause lysosomal storage diseases, and some have a much more severe etiology than others
symptoms: coarse facial features, hepatomegaly (enlarged liver), splenomegaly (enlarged spleen), failure to thrive (child does not reach growth milestones), developmental delay (child does not reach developmental milestones), and restricted joint movement
