BIOL 212 Section 1 SI

Exam 3 Review

Gene Control in Eukaryotes

The six levels of gene regulation in eukaryoteso Chromatin has to be remodeledo Specific genes can be transcripted o mRNA can be spliced in different wayso the life span of mRNA may be extended or shortenedo Translation rate may be controlledo The life span of proteins can be altered

Chromatin structure and remodelingo Eukaryotic DNA exists in the form of chromatin, or a complex of protein and

DNA. The main function of chromatin is to fit the entire DNA strand inside the nucleus.

o A nucleosome is an octamer of histone proteins with DNA wrapped around it twice.

o Nucleosomes can be compacted further into 30 nm chromatin fibers. This is

caused by interactions between the H1 proteins.

o Condensed chromatin is genetically inactive.

o Decondensed chromatin allows access to transcription machinery and is susceptible to DNase I

o DNA methylation is a signature of inactive or condensed chromatin. Methyl

groups are added to the cytosines by DNA methylase.

o Chromatin can be decondensed by histone acetylation. The enzyme histone

acetylase adds acetyl groups to the positive histones, neutralizing them. These acetyl groups can be removed by histone deacetylase.

o Changes in gene expression without altering the DNA sequence are called

epigenetic changes. These changes can have profound effects on the phenotype of an organism and can sometimes be passed down to the next organism.

Transcriptional controlo Eukaryotic promotors are much more complex!o Eukaryotes have a core promoter that the RNA polymerase binds and often also

have two or three regulatory sequences that serve as binding sites for other proteins needed for transcription.

o Transcriptional control of a eukaryotic gene depends on the cis-elements of the promotor and the trans-acting factors that interact with the cis-elements.

o Enhancer elements bind to the transcription factors called activatorso Silencer elements bind to the transcription factors called repressorso Coactivators mediate the interactions between the basal and specific

transcription factorso Summary of transcription in eukaryotes:

Post-transcriptional regulationo Can control gene expression post translation by

Splicing the RNA primary transcript in different ways Destroying particular mRNAs or altering the ability to translate them Inhibiting the translation of most mRNAs in the cell Altering activity of proteins after translation

o Exons are the coding regions of eukaryotic genes that will be part of the final mRNA, introns are the coded regions that will be spliced out.

o In alternative splicing, the primary RNA transcript is spliced in different ways to

include different exons

o After processing, a cap is added to the 5’ end, which can be recognized by

translation machinery. A poly(A) tail is added to the 3’ end to protect the mRNA from degradation.

o RNA interference occurs when a tiny, single-stranded RNA held by a protein binds to a complementary mRNA, silencing it by degrading it or blocking translation.

Cell Signaling

Hormoneso Hormones carry chemical information long distances through the blood stream

and are secreted from signaling cells.o Typically only present in small concentrations, but have large impacts on the

organism as a whole. Signal reception

o Hormones bind to specific receptor, which changes conformation to initiate a signaling response

o The binding of a hormone to a receptor is typically called a ligand/receptor interaction.

o Ligand/receptor reactions are controlled by two factors: Concentration of ligand Binding affinity

o The dissociation constant (Kd) describes the concentration of ligand needed to bind half the receptors are bound.

o In this case, ligand A has a higher Kd, but a lower affinity

Lipid soluble and insoluble hormones

o Lipid-soluble hormones, like steroids, are hydrophobic and can diffuse across the cell membrane.

o Lipid-insoluble hormones, like protein hormones, are large or hydrophilic, so they cannot cross the cell membrane.

o Lipid soluble hormones cross the cell membrane and bind to receptors inside the cell. The hormone-receptor complex can then be transported to the nucleus and alter gene expression.

o Lipid-insoluble hormones bind to receptors on the plasma membrane, which

trigger a signal transduction pathway, amplifying the signal

o The hormone receptors are linked to G-proteins that dissociate into two parts,

one of which catalyzes the production of a secondary messenger.

o Secondary messengers, like cyclic AMP, can diffuse around the cell, amplifying

the hormone signal by activating protein kinases. Enzyme-linked receptors

o Receptor tyrosine kinases are the best-known examples of this. They catalyze an enzymatic reaction inside the cell.

o Protein kinases are activated, which phosphorylate other proteins, creating a cascade, amplifying the initial signal.

Cell Specialization

How are cells differentiated?o All cells contain the same set of DNA, they are just different due to gene

expression.o Theoretically, we could take a nucleus from a differentiated cell and grow a

whole organism. Model organisms

o Most of what we know about development comes from studying model organisms

o Generally, they are adventitious because they are small, easy to study, and have short generation times.

o Examples include Arabidopsis, Drosophila, zebra fish, mice, etc. Pattern formation

o Involves the developmental events that determine the spatial organization of an embryo.

o Leads to the body axes: anterior-posterior, ventral-dorsal, left-righto Morphogens are distributed asymmetrically and act based on concentration,

promoting cellular changes. o Bicoid is a transcription factor that activates a suite of genes, which serially

activate other transcription factors, leading to anterior development. o Gap genes, in response to the gradient of bicoid, divide the embryo into broad

regions. o Pair-Rule genes divide the embryo into segments after being activated by the

interaction of the morphogen gradient and expression of gap genes.o Homeotic genes give identities to the various segments by coding transcription

factors.

Bithorax and antennapedia complexeso Bithorax and antennapedia complexes are gene complexes that confer identity

to the thorax and head segments. The genes are in order corresponding to their anterior-posterior position on the body

oo Homologs of this exist in mammals as the Hox genes

Biotechnology

Basic terminologyo Biotechnology is any technological application that uses biological systems, living

organisms, or derivatives thereof, to make or modify products or processes for specific use.

o Recombinant DNA is DNA from 2 or more sources combined together using laboratory techniques (new combinations of DNA)

o Genetically modified, or engineered, organisms are organisms who genetic material has been altered using recombinant DNA technology

o Transformation is insertion of foreign DNA into a recipient host cello Gene cloning is making identical copies of a piece of DNA through insertion into a

circular piece of DNA called a plasma or vector. Cloning requires the follow: An isolated gene fragment A vector or carrier Restriction enzymes Ligation of the gene to a vector Transformation of a recombinant DNA

Polymerase Chain Reaction (PCR)o Used to produce identical copies of the target gene.o A reaction mix is created with dNTPs, the target DNA, PCR primers, and a heat-

resistant DNA polymerase.

o There are three main steps in the PCR cycle

Using plasmids in cloningo Plasmids are small, circular DNA common in bacterial cells. They are separate

from the chromosomes and have their own origin of replication.o Plasmids used in cloning carry genes for antibiotic resistance or other traits that

allow a cell to grow under a selection pressure. Restriction endonucleases to cut DNA

o Enzymes cut the DNA molecule and plasmid at specific recognition sites. o The cut DNA and plasmid can then be put together and have complementary

base pairing. DNA ligation/joining

o DNA ligase is used to join the restricted gene and vector to form a recombinant plasmid.

o DNA transformation and screening

o The plasmids are injected into bacteria cells, which are then put on an antibiotic plate. Because our plasmid also contains a gene for antibiotic resistance, the bacteria with the recombinant DNA will survive and grow into colonies.

Application of PCRo Short tandem repeats (STRs) vary between individuals, so they are used in DNA

fingerprinting because they are short. o The STR GATA is commonly used by the FBI.

Human Genome Projecto The human genome was sequenced in 2001. Less than 2% consists of protein-

coding exons. Gene therapy

o Augmented defected copies of genes can be replaced with a normal gene. Very controversial and still experimental.

Cloning of mammalso Dolly the sheep was cloned by taking a nucleus from a mammary cell of one

sheep and injected into an egg cell from another. The resulting sheep was genetically identical to the mammary cell donor.

Biotechnology in agricultureo Golden rice was created by transferring recombinant DNA into plant cells via

Agrobacterium. o Genes that produced enzymes for the synthesis of beta-carotene were added to

the rice genome.

Animal Nervous Systems

The nervous system has two main subunitso The central nervous system (CNS) includes the brain and spinal cordo The peripheral nervous system (PNS) includes all other neurons o Sensory information enters the system and the PNS carries it to the CNS, which

processes the information, and then commands the PNS to respond.

There are three main types of neurons

o Sensory neurons detect information from the outside world or internal body conditions.

o Motor neurons send signals away from the CNS to elicit a responseo Interneurons form interconnections between other neurons in the CNS

Neuron structureo Neurons are signaling cellso Glial cells are multifunction and support.

Oligodendrocytes in the CNS and Schwann cells in the PNSo The dendrites collect the chemical signals from other neuronso The cell body integrates incoming signals and generate outgoing electrical

signals.o The axon passes chemical signals to dendrites of other cells or two an effector

cell Membrane Potential

o Electrical potential is the unequal distribution of ions on both sides of the cell membrane.

o The resting membrane potential is negative. Inside, there are high concentrations of K+ and organic anions Outside, there are high concentrations of Na+ and Cl- K+, Na+, Cl+ are the primary ions that generate resting potential

o The cell membrane is impermeable to charged ions, so they can only cross the membrane with aid:

Active transport: ions can be pumped against their electrochemical gradient by membrane proteins that use ATP, like the Na/K pump

They can diffuse down the electrochemical gradient through an ion channel.

Action potential

o A rapid, temporary changes in membrane potential. Very important and similar in all species and types of neurons.

o Action potential is a 3 phase signal: Depolarization (-+) Repolarization (+--) Hyperpolarization (---)

o Action potential is all-or-none, meaning that once it reaches threshold, it will

either happen or not. There is no partial action potential.o Action potential is driven by movement of ions across the membrane through

voltage-gated channels, which are open and closed based on charge. o Before action potential is triggered, a threshold potential must be reached.o Once the threshold potential is reached, depolarization occurs. Na+ channels

open and ions flow in, making the membrane potential positive.o During repolarization, Na+ channels deactivate and K+ channels open, causing K+

to flow out and making the membrane potential negative again.o So much leaves the cell though that it becomes hyperpolarized.o When Na+ enters the cell, positive ions are repulsed while negative ions are

attracted. This positive charge spreads and depolarizes adjacent portions of the membrane, causing the Na+ channels to open. This is an example of a positive feedback loop.

o During repolarization, the membrane cannot mount another action potential because the Na+ channels are inactivated. This keeps the action potential from moving backwards.

o Larger axons transmit action potential faster than smaller axons. Myelination

o Myelination from Schwann cells or oligodendrocytes insulate the axon, keeping ions from leaking out.

o Gaps in the myelin sheath called nodes of Ranvier have dense concentrations of voltage-gated ion channels to repropagate the signal. This “jumping” is called saltatorial motion.

o Multiple sclerosis develops as damage to the myelin sheath, impairing the electrical signal.

Synapse Structureo At the synapse, a neuron transmits information to another neuron or target cell.

Information is transferred between cells by chemical-signaling neurotransmitters.

o The space in between the presynaptic and postsynaptic cell is called the synaptic cleft.

o Neurotransmitters are held in synaptic vesicles inside the presynaptic neuron. Synaptic Transmission

o Step 1: Action potential reaches the end of the axono Step 2: The depolarization causes voltage-gated calcium channels to open,

allowing an inflow of Ca2+o Step 3: The higher concentration of Ca2+ causes the synaptic vesicles to release

the neurotransmitters into the synaptic cleft via exocytosis.o Step 4: Neurotransmitters bind to ligand-gated channels on the postsynaptic cell,

allowing either an inflow our outflow of ions. This depends on the channel activated.

o Step 5: When the signal is deactivated, the neurotransmitter is either broken down by enzymes or taken back into the presynaptic neuron.

o Postsynaptic potentials

o There are two general types of postsynaptic potential

o EPSPs and IPSPs are graded, meaning that they are not all-or-none. There can be

partial PSPs depending on the amount of neurotransmitter released.o Neurons typically have thousands of synapses. The additive nature of all of the

postsynaptic potentials is called summation. For example, if enough EPSPs happen in succession, threshold can be reached.

o Charges from the postsynaptic potentials eventually reach the axon hillock,

where action potential is triggered if threshold is reached. Learning and Memory

o Learning is the process of acquiring new information, enduring change in behavior.

o Memory is the retention of that information over time. Occurs in short-term memory or long-term memory.

The gill withdrawal reflex of Aplysiao This is a simple reflex that is modified by learning. Aplysia withdraws its gill when

water is forced on the siphon or the tail is shocked.o If a tail shock is paired with a light touch the siphon, the animal will eventually

learn to withdraw its gill and retain it after only a light touch.o The neurons associated with the neurons responsible for this behavior release

the neurotransmitter serotonin. o A sensory neuron was grown with two motor neurons. When serotonin was

applied to the synaptic clefts, the EPSPs dramatically increased over time. The motor neuron also established additional connections.