Bio 1500 Final Exam (Mizzou)

dragon fly size

-high O2 levels in carboniferous allowed them to grow big

-later in history predators constrained the max size

O2 levels in atomosphere

cyanobacteria and green algae chloroplasts contributed.... through photosynthesis

oldest fossils

3.5-4 bya

1st insects

480 mya

1st dinosaurs

240 mya

dinosaurs go extinct

66 mya

1st homosapiens

200k ya

diffusion

mvmt of molecules from high to low concentration

-driven by Brownian (thermal) mvmts

each molecule during diffusion

-moves randomly

-behavior unpredictable

-each individual molecule never stops moving

net movement of molecules in diffusion

-from high to low conc.

-predictable

-stops when it reaches equlibrium

Photosynthesis

-light energy is used to make carbs from CO2 and water

-takes place in chloroplasts

chloroplasts

-contain the pigment chlorophyll

-chlorophyll absorbs red, blue, & violet light

step 1 of photosynthesis

-light reactions

-ATP is synthesized, NADPH is generated

-water is split apart, releasing O2 as a by product

ATP

-used to transport E around cells

-chemical E stored in the bonds

-important bonds between 2nd and 3rd phosphate group

-going to lower energy state breaks bonds and releases the energy

step 2 of photosynthesis

-light independent reactions

-E from ATP & NADPH are used to build glucose from CO2 & water (Carbon Cycle)

Great Oxygenation Event

-3 -2.3 bya

-cyanobacteria evolved photosynthesis

-free O2 as a side effect... led to some O2 levels in atmosphere

O2 accumulation in atmosphere

-minerals formed (ex: banded iron ore)

-ozone layer formed (protection from UV light)

-free O2 toxic to cells

-O2 reacted with methane.... led to snowball ice age

-prokaryotes evolved ways to use O2... evolution of cellular respiration

Evolution

-a change in allele frequencies in a population

-natural selection is one of the mechanisms

gene

-a segment of DNA w/ instructions for building a protein molecule

-specifies the sequence of amino acids that makeup the protein

alleles

-different possible forms of the same gene

-differ in DNA sequence & in protein structure they code for

-may be many alleles for same gene

-any 1 person can have max of 2 different alleles

Natural Selection

-phenotypes are variable in population

-offspring have similar phenotype as parents

-mutations occur randomly, but doesn't create new alleles

-natural selection not goal directed

Postulates of natural selection

1. individuals vary in their traits

2. some of the variation is heritable (can be passed to offspring)

3. more offspring are produced than survive to reproduce

4. survival & reproduction are non random; those w/ favorable traits reproduce most & pass their genes on

-favorable traits become more common

population

group of organisms that breed w/ each other

phenotype

observable traits

fitness

ability to survive & reproduce in an environment

adaptations

-traits that increase fitness of individuals with this trait relative to others w/out it

-a trait produced by the process of natural selection

mechanisms of evolution

-selection (natural, sexual, artificial)

-genetic drift

-gene flow

-mutation

directional selection

-fitness increases/decreases with trait value

-shifts mean trait value

stabilizing selection

-intermediate trait values have highest fitness

-ex: human birth rate

-mean value doesn't change

-often the combo of 2 selective pressures (one for larger & one for smaller trait values

Selection on body size

-sexual selection: competition among males favors large size

-selection for female fecundity (egg/offspring number): large size

-selection for early reproduction: small size

-limited resource availability: small size

-predation: large size in predator, small in pray

-locomotion: flight favors small size

-temp: cold favors large size in mammals, small in insects

Respiration in insects

-no blood that transports O2

-trachea brings O2 directly to cells

-spiracles: opening to outside

-large & active insects: pump air in/out of air sacs & large trachea

-diffusion in small trachea

-respiratory system limits insect size

Why higher O2 results in evolution of larger insects

larger individuals:

-compete better for mates/food

-produce more/better eggs

-produce more/better sperm

-resist oxygen damage better

Cellular respiration overview

-produces ATP

-happens in mitochondria

-inputs: glucose, O2

-outputs: ATP, CO2, water

Step 1: Glycolysis

-glucose is broken into pyruvate, yielding 2 ATP & NADH

-bonds between 3rd & 4th carbons are broken

Step 2: pyruvate prep / Citric Acid Cycle

-pyruvate broken down

-generates NADH & FADH2 (carry potential E via electrons)

-produces CO2 as a by product

Step 3: Electron Transport Chain

-electrons supplied by NADH & FADH2

-series of redox rxns: 1 molecules loses electron (oxidation) & 1 molecule gains it (reduction)

-as electron is passed, it moves to lower E state, the E is used to pump H+ (protons) across the membrane, generating a proton gradient that stores E

-H+ re enters the mitchondrial matrix through ATP synthase

-O2 is the final electron acceptor, producting H2O as by product

- 34 ATP produced from ATP synthase

Flow of E in cellular respiration

bonds in glucose (ATP thru glycolysis)→ NADH/FADH2 → H+ conc. gradient → ATP

Important things about cellular respiration

-all steps happen at same time

-the electrons don't roll down a ramp

-the membrane is a surface not a line (mitochondrion is 3D)

-molecules other than glucose can enter CR at different stages

Connections between CR

-respiratory system: supplies O2, removes CO2

-digestive system:supplies glucose

-circulatory system: transports CO2 & glucose

When no O2 is available

-pyruvate undergoes fermentation (instead of citric acid cycle)

-coverts to alcohol & CO2 (yeast) or lactic acid

-no ATPs are produced through fermentation

-NAD+ is regenerated & the cell acquires 2 ATP thru glycolysis

Similarities between PS & CR

-electron transportation

-ATP synthase

-proton gradient

-electron carriers

-makes use of each other's by products

-cyclic component (Calvin/ Citric Acid)

Differences between PS & CR

-source of electrons in ETC (PS: water, CR: NADH/FADH2)

-final acceptor of electrons (PS: NAD+, CR: O2)

-function of process (PS: to make glucose, CR: to make ATP)

-rxns run in reverse

ATP Synthase

-enzyme brings 2 particles close together → form bond

-may require energy

-ATP synthase: ADP + P + energy → ATP

-energy is stored in gradient across mito-membrane: H+ outside, e- inside

-H+ pushing inward provides the energy

Rise in O2

-all org. molecules use C as a backbone

-all C in org. molecules is obtained from products of PS

-the C that makes up the body of a plant comes out of the air (from CO2)

-all plants are consumed by animals or decomposers → how C is put back into CO2 in atmosphere

atmospheric pressure

-the air that sits above us in the atmosphere

-high pressure at low altitude, low pressure at high altitude

At Sea Level

-101.3kPa (force of pressure per unit area)

-composition of atmosphere: 78%N2, 21% O2, 0.4% CO2

Mount Everest (8848m)

-33.7kPa (air pressure)

-partial pressure: 26kPa of N2, 7kPa of O2, .01kPa of CO2

Respiratory systems

-inhalation: brings air inside

-in lungs: O2 diffuses to red blood cells (RBCs)

-O2 bonds to blood pigments (hemoglobin) inside RBC

-in body: O2 released from hemoglobin → diffusion of O2 to cells

-O2 used in CR → CO2 diffuses to blood

-CO2 dissolved in blood plasma

-blood transports CO2 & RBCs (w/o O2) to lungs

-CO2 diffusion to air → exhalation back to air

Mammal Lung

-trachea, alveoli

-gas exchange happens in alveoli

-capillary network around alveoli

-humans: 300 million alveoli

-surface area of alveoli about 75m2

-Inhalation: diaphragm contracts

-exhalation: diaphragm & rib muscles relax

-heavy breathing: abdominal muscles contract

-12-20 breaths/min

Gas Exchange in Lung

-alveoli: close contact air and blood

-separated by thickness of 2 cells

-diffusion moves O2 & CO2 from high to low conc.

-O2 binds to hemoglobin in RBC → removes it from solution, keeps O2 conc. low & diffusion going fast

Breathing pattern

-total lung capacity 5-6 L

-at rest breathing: volume of lung 2.5-3 L

-air exchanged at rest 0.5 L

-max air exchange: 3-4.5L

-residual (never exchanged): 1-1.5L

Human/ Mammal Lung

-at rest breathing: volume of lung 2.5-3L

-air exchanged at rest: 0.5L

-atmosphere: PO2 = 21kPa PCO2 =0.04kPa

-inside of lung: PO2 =13-15 kPa PCO2=5-6 kPa

-lung atmosphere is different from outside atmosphere → depends on volume of gas exchanged

-"lung atmosphere is our "real" atmosphere"

-lung atmosphere could be under selection

Amino acids

- carboxyl group, N-CH-COOH backbone

-form peptide bonds w/ each other, generating chains called polypeptides

-chemical interactions between diff parts of the chain cause it to twist and fold

primary proteins structure

AA sequence

secondary protein structure

hydrogen bonds between the backbones of nearby AAs cause either an alpha helix or Beta sheet to form

tertiary protein structure

-interactions between R groups determine 3D structure

-chemical bonds form between distant parts of chain, causing it to fold into 3D shape

-determined by spatial distribution of hydrophilic & hydrophobic R groups

quarternary protein structure

-interactions between separate chains

-not every proteins has this structure

-the sequence of AAS determines how protein folds and therefore the shape of the proteins

hydrophobic AAs

tend to aggregate and end up in interior of protein

hydrophilic AAs

-polar:1 end of R group is slightly more negative than other end → form H bonds w/ each other & water

-basic/acidic: strongly polar

usually on outside of protein, most critical for forming bonds that hold protein in shape

special AAs

-glycine: small, allows flexible backbone

-proline: creates king in chain, restricts folding

-cystine: strong bonds form between S atoms of 2 cystine AAs

Hemoglobin (Hb, Hgb)

-O2 transport pigment in vertebrates: makes blood red

-in RBCs

-carries up to 20x more O2 than when O2 is dissolved

-metallo protein: contains iron

-4 globular protein subunits: 2 alpha, 2 beta

4 heme groups (w/iron): porphyrin ring, iron-iron covalent bond

-4O2 molecules can bond

iron

-forms covalent bond to globular protein

-reversible bond to O2

Affinity

-high affinity: grabs O2 easily & holds on to it tightly

-low affinity: grabs o2 less readily & lets it go easily

-O2 transporter needs: high affinity in lung, low affinity in body

-affinity described by O2 dissociation curve

Sigmoidal shape of O2 dissociation curve

-due to cooperative o2 binding

-if all 4 hemes w/O2: low O2 affinity

-when 1st O2binds O2 affin increases

-when 2nd binds affinity increases more

-3rd: affinity increases more

O2 curve changes w/ environment

-increase PCO2: right shift = lower affinity

-decrease in pH: right shift

- increase 2,3 BPG: right shift

-increase temp: right shift

→ right shift means easily release of O2

→ left shift means easy pick up of O2

2,3 BPG

-same level in lungs & body

-regulates long term O2 affinity of HB

Changes in O2 affinity of Hb

-CO2, H+, & 2,3 BPG are charged/polar

-they attach to charged amino acids on outside of Hb subunits

-changes tert. & quart structure of Hb → changes function

-changing a single amino acid could change function of protein

Bird Lungs

-para bronchi: site of gas exchange, fixed

-air sacs to store fresh & used air

-inhale: into posterior air sac, through PB into anterior sac

-exhale: from anterior air sac

-air flow in PB in one direction

Adaptions for high O2/energy demand of flight

-highly efficient lungs

-1 directional air flow

-little dead volume (just trachea)

-slow breathing (reduces effect of dead volume)

-thin diffusion distance in lung

-larger lung surface area than mammals

-heart volume bigger than mammals

-flight muscles: dense capillaries, small muscle fibers (short diffusion distances)

-substituting alanine for proline changes quat. shape, shifts curve to left (increasing O2 affinity)

Chromosomes

-each is a double stranded molecule of DNA wrapped around proteins (histones)

-DNA is a chain of nucleotides → 1 nucleotide (base, sugar, phosphate)

-4 types of nucleotides, differ in bases → A (adenine), T (thymine), C (cytosine), G (guanine)

-2 strands of DNA bind together across their bases according to rules: A binds w/ T. C binds w/ G, complimentary binding

What does DNA do

-instructs the cells to make proteins

-the structure & function of a protein is determined by the order of the AAs → which is determined by the order in which ATC & G occur in the DNA

Gene

-a segment of DNA specifying the sequence of AAs in a particular protein

-different regions of chromosome code for different proteins

Step 1: Transcription

-getting the info from DNA to the ribosome, where proteins are made

-the copy looks different & made of diff things, but the info is the same

-making a copy of info on genes

RNA

-similar to DNA

-U replaces T: bases CGAU

-binding rules are A-U & C-G

-during transcription MRNA serves as the messenger & delivers the instructions to the ribosome

What happens during transcription

-enzyme unzips the double stranded DNA pf the gene

-1 strand of DNA becomes template for mRNA

-the strand of mRNA leaves the nucleus thru a nuclear pore & goes to a ribosome

Step 2: Translation

-turning the sequence of bases into a sequence of AAs bound together

-ribosome binds to bases 3 at a time → each triplet mRNA bases is a codon (codes for AA)

-tRNA brings the correct AAs to the ribosome

-ANTICODON = group of 3 bases on the tRNA

-each tRNA carries 1 type of AA, depending on its anticodon

-tRNA whose anticodon binds complementary to the codon brings its AA to the ribosome

start codon

AUG → initiates translation by ribosome, ribosome ignores mRNA bases before AUG

stop codons

-UAG, UAA, UGA

-cause ribosome to release mRNA

point mutation

-1 base changes to another

-sickle cell anemia (change in 9th codon changes Valine & changes 3D structure)

insertion or deletion

-1 (or a few) bases is inserted or removed

-also called frame shift mutations

-all downstream codons /AA are affected

-proteins is likely dysfunctional → loss of function mutation

duplication mutation

-large chunk of DNA is duplicated within the strand

-sometimes makes new genes

chromosomal mutation

-large scale change in number or structure of chromosomes

what causes mutations

-mutations can happen spontaneously & randomly

-can be caused by:

-high energy radiation (X-rays, UV light)

-chemicals: mutagens & carcinogens (cancer causing)

-errors during replication

DNA repair

-can fix most mutations

-there are repair enzymes that flaot along the DNA

expressed gene

transcribed into mrNA & translated into protein, i.e. the protein is actually produced

gene expression regulated by:

1. turning genes "on" or "off"

-on → transcriptor

-off → no transcription

genes turned on/off depending on:

-developmental stage

-type of tissue

-stage of physiological cycle

-external environmental cues (food, sunlight, behavior)

How is expression regulated

-transcription begins when RNA polymerase (enzyme) binds to a sequence of DNA called a promoter

-transcription factors regulate attachment of RNA polymerase to promoter

types of TFs

-activator proteins: recruit RNA polymerase to promoters to initiate transcription

-repressor proteins: block RNA polymerase protein (stops transcription)

myoglobin

single protein chain of 154 amino aicds + heme

Possible solutions for geese wintering at ocean

-increase level of 2,3-BPG in RBC → lowers Hb O2 affinity

-express gene for Hb variant w/ lower Hb O2 affinity

-bar headed goose has genes for 2 alpha subinits

-alpha A subunit is high altitude version, alpha D not studied

-during migration mostly alpha A is expressed

-during winter no one knows

gene duplications

-extra copy of gene can then mutate & acquire new function

-causes of gene duplication

-unequal crossing over during meiosis

-mistakes during DNA rep.

-duplication of entire chromosome

sources of new genes

-mutations that make new start codons

-viral genes (horizontal gene transmission)

Fetal Hb

-2 alpha, 2 gamma globins

-2,3-BPG doesn't bind to HbF → higher affinity for O2

-birth: 70% HbF, 30% HbA

-HbF persists until ~6 months after birth

-expression of HbF genes can be induced w/ drugs; treatment for sickle cell

phylogenetic trees

-illustrate hypothesized evolutionary relationships

-best hypothesis based on available data; subject to change

-how closely 2 species are related is determined by how recently they shared a common ancestor, not by the number of nodes that separate them

Andean geese

- has high affinity Hb like bar headed geese

-mutation in the beta subunit

species

organisms with the potential to breed & produce live, fertile offspring

speciation

-process by which 1 species evolves into 2

-step 1: population splits into 2 isolated pops → geese will only mate w/ in own pop.

-step 2: genetic differences build up between pops due to different selection pressures

-if genetic differences are so great that birds from diff pops cannot produce viable offspring, then pops are now separate species

Hummingbirds

- many species in the Andes

-diversity evolved while Andes were rising

-much opportunity for geographic isolation → speciation

-small birds spend much energy for heating their bodies → need more O2 than geese

Greenhouse gases

CO2, CH4, N2O, H2O