Eco phys test 1

what is ecological Physiology

How do animals function and respond to their natural habitats at all stages of their life cycle?

what are some things we can find out about eco phys in a lab setting

Developmental Biology

Genetics

Physiology

Neuroscience/Animal Behavior

Immunology

Animal Nutrition

Gerontology (Aging)

Etc.

what are some things about eco phys can we find outside lab setting

Natural History

Ecology

◦ Population Ecology (competitors)

◦ Community Ecology (predators)

◦ Disease Ecology (vectors)

◦ Evolutionary Ecology (past conditions)

Climatology (abiotic factors)

Hydrology (water dynamics)

Plant Biology (food (direct or indirect)

Etc

Genotype examples

Genome

Sex Chromosomes

Epigenome

Random processes example

mutation

weather

enviorment examples

Predators,

Competitors, Disease, Food

Availability, Shelter Availability

phenotype examples

Immune state,

Nutrient reserves

development examples

Resource Availability,

Maternal Behavior,

Paternal Behavior

morphology examples

Size, color,

anatomy

Biochemestry examples

Steroid levels,

Glucose levels

behavior examples

Reproductive

decisions,

habitat choice,

antipredator

what is adaptation

he means by which natural selection adjusts the frequency of

genes that code for traits affecting fitness [across a population of animals,

or even across species

fitness definition

number of offspring surviving in the succeeding generations

plasticity definetion

traits are expressed in a variable manner depending on the

environment

what is acclimation

phenotypic change within an animal (an

example of plasticity)

what is a reaction norm

• graphical/mathematical representation of how the phenotype of a single genotype changes across different

environmental conditions.

• maps the range of phenotypes that a single genotype can produce in response to varying environmental factors.

what is canalization

strong stabilizing selection. a single phenotype is strongly prefered over a broad enviormental range

what is polymorphism

two main morphs occur: very rapid transitionbetween these two morphs occur at particular points on the enviormental axis

what is physiology

Physiology is about what proteins are present

what are the protiens working as parts of physiology

Enzymes

Transporters

Receptors

Structural components

Motor proteins

Hormones

what is included in adaptation

parent to offspring

Ecological and Environmental

variables:

• act as agents of natural

selection

• influence the frequency of

genes in the next generation

what comes in acclimation

• offspring to gene expression to physiology

• Transcription and Translation

• Ecological and Environmental variables influence both

homologus chromosomes

One came from mom. One came from dad. THEY ARE NOT IDENTICAL

sister chromatids

Sister chromatids (when you see chromosomes in this

configuration, this means DNA replication is complete and cell

division is occurring). Sister chromatids are identical.

chromosome definition

a string of DNA wrapped around associated proteins that give the connected nucleic acid bases a structure (contains thousands of genes)

autosome definition

any chromosome other than the sex chromosome

sex chromosome

chromosome associated with sex determination

gene definition

the unit of heredity; a sequence of DNA that affects one or more traits in an organism, usually through an encoded protein produced based on the sequence of nucleotides

Allele definition

The different forms of a gene, corresponding to different DNA sequences in each different form. They arise as a result of mutation.

genome definition

The genetic material transmitted from a parental cell or organism to its offspring.

what kind of dna molecules do eukaryotic chromosomes have

linear DNA molecules associated with a large amount of protein (Histones)

Chromatin def inition

DNA is precisely combined with proteins in a complex

called chromatin

types of chromosome packing

Chromosomes fit into the nucleus through an elaborate, multilevel system ofpacking

◦ Heterochromatin-remains condensed through interphase

◦ Euchromatin-dispersed/unraveled chromatin (accessible by proteins)

what are the nitrogeonous bases

thymine, adenine, cytosine, guanine

Gene regulatory protiens job

• several % of all proteins manufactured

• determine cell fate etc (e.g., neurons vs glia)

• often affect polymerase affinity

• Many levels of control

• ‘enhancers’, master control genes

what do introns do

they are cut out and the exons are spliced together

why are there so few proteins

• typical protein has 300 amino acids.

• -> with 20 amino acids: 20300 = 10390 combinations possible

• Selected for reliable and stable folding

• Small conformational changes do not change in large changes in

activity and can therefore be ‘controlled’

how does DNA repair work

• each day, thousands of bases are randomly altered (radiation

etc)

• DNA nucleases recognize altered sequence, and cut it out

• DNA polymerase -> uses undamaged DNA strand to fill correct

base in

• DNA ligase seals the gap

• Overall: point mutations only lead to 1 heritable nucleotide

change in 200,000 every 1,000 years. -> more fine tuning of

processes. [but: frame shifts!]

• Instead: Recombination! Transposable elements!

what are the general Physiological processes

-Respiration

-Digestion

-Circulation

-Excretion

what are protien channels

where most substances enter and exit the cell

what does protein channel movement depend on

Substance gradient

• Electrochemical gradient

• Channel structure

what are transporters

another way substances exit and enter a cell

what does transporters movement depend on

Energy investment

what does Protein Facilitated Movement of Ions and Molecules look like

Key words:

• Inheritance

• Expression Levels

• Location

What is primary active transport

Driven by ATP hydrolysis and affinity changes

what are the three major types of channeles in cells

• Leak channels

not gated, but modifiable

• Voltage gated channel

Shape/function changes with charge

• Ligand gated channel

Shape/function changes upon binding another

substance (ligand)

Action Potential Propagation

other types of transport in a cell

Endocytosis

• example: receptor mediated

• requires GTPase

Exocytosis

Transcytosis

Intracellular receptors

• Bind lipophilic compounds (steroids, vitamin A, retinoids,

thyroid hormones)

• Hormone Response Elements-SEQUENCE OF DNA to which

receptors bind

Extracellular receptors

• Bind hydrophilic compounds outside of the cell (peptide

hormones, neurotransmitters)

• Relay message to the interior of the cell

• Enzyme linked receptor (kinases and integrin)

• Ion Channel-Linked receptor

• G-protein coupled receptor

Lipophilic Ligands

• Estrogen Receptor

• Androgen Receptor

• Glucocorticoid Receptor

• Thyroid hormone Receptor

• Retinoid X Receptor

Hormone Response Elements without Thyroid hormone 3

1. Thyroid hormone receptor (TR): bound to DNA as heterodimer with the retinoid X receptor (RXR) at the thyroid hormone response elements (TREs).

2. The TR-RXR complex recruits a TR corepressor complex

3. The corepressor recruits histone deacetylases (HDACs)

4. HDACs remove acetyl groups from the histone proteins -> positive charge -> DNA coils around histones

Hormone Response Elements with Thyroid hormone 3

1. T3 binds TR->conformational change.

2. -> Corepressor dissociates from the TR-DNA complex.

3. Coactivators are recruited, containing histone acetyltransferase (HAT).

4. Histones are acetylated -> removal of positive charge.

5. -> Chromatin is decondensed and transcription is enabled

Intracellular-Steroid hormone (estrogen) effects on egg related

gene expression

• Estrogen activates promotor regions of Ovalbumin

• Estrogen increases Thyroid- Binding Globulin -> more T3 transport to the proteins

Intracellular mediators(second messangers)

• Serve to activate/deactivate proteins within the cell

• Cyclic AMP

G-Protein-coupled Receptors

Serve to activate/deactivate proteins within the cell

• Calcium

• Inositol triphosphate (IP3)

• Diacylglycerol (DAG)

Effector Pathways of G-protein Coupled Receptors

Effector protein → second messenger → later effector protein

Gs: adenylyl cyclase → cAMP → protein kinase A (stimulatory)

Gq: phospholipase C → diacylglycerol and IP3 (second messengers) → protein kinase C and Ca2+ (second messenger)

Gi: ↓ adenylyl cyclase → ↓ cAMP → ↓ protein kinase A (inhibitory

Epigenetics

For this course, think of epigenetics as “On/OFF” Switches of

gene transcription

• Many epigenetic processes involve making DNA accessible to proteins-> Proteins can either access it or they can’t

• Caused by environmental factors

• Influence gene expression without altering the underlying DNA sequence.

• Can be passed down through generations (transgenerational epigenetic inheritance) via modifications to germ cells DNA

• Some epigenetic marks persisting beyond a few generations

Epigenetics Major processes

• Histone Acetylation

• Histone Methylation

• DNA Methylation

Histone Acetylation

• Occurs on histone tail, often the N-terminal which are rich in Lysine and Arginine. Acetylation happens at Lysine residues (-> lowers positive charge)

• -> lower positive charge -> decreased affinity to DNA.

• -> DNA uncoils

• Two enzymes:

• Histone Acetyl Transferase (HAT)

-adds acetyl group to histone

-facilitates gene expression (“on”)

• Histone Deacetylase (HDAC)

-Removes acetyl group

-Hinders gene expression (“off”)

Histone Methylation

• Also occurs on histone tail (Lysine)

• Prevents acetylation

• Enzymes:

• Polycomb Repressive Complex II

(PRC2): adds methyl mark (“off”)

• “Jumonji” enzymes (JMJD3)

demethylate: (“on”)

Promiscuous repression

• by regulatory protein that inhibits the expression of multiple different genes

• by binding to various short and ubiquitous DNA or RNA sequences (but with specificity)

• Dysregulation of PRC2 (the ‘off’ switch’): linked to developmental disorders andcancer.

Temperature-dependent sex determination (TSD) and its underlying mechanisms

involves

• Alternative Splicing

• Histone Demethylation

• Transcription Factors

How does the Y chromosome induce the formation of testes?

• SRY gene on Y chromosome

• master gene -> triggers male development (testis formation)

• member of the SOX (Sry-type HMG box) gene family

• contains the high-mobility group (HMG) box domain -> binds & bends DNA

• HMG is highly conserved between species.

• activates transcription of downstream factors, including SOX9 transcription factor -> male

Histone demethylase KDM6B

activity is temperature dependent (removes repressive marks -> more expression)

KDM6B expression increases at cooler (male producing) temperature and

decreases at warmer (female producing) temperatures

How does temperature regulate gene expression?

• CDClike kinases (CLKs): highly responsive to temperature changes

• Lower body temperature activates CLKs -> increased phosphorylation of SR proteins

• -> temperature-dependent alternative splicing (exon inclusion at lower

temperature, exon skipping at higher temperature)

• -> KDM6B (demethylase, leads to males) remains functional at cold temperatures

How is temperature sensed to regulate alternative splicing?

Two hypotheses:

1. Temperature-sensitive TRP channels -> Calcium influx

2. Temperature-sensitive GPCR-> opening of CNG channel -> Calcium influx