Biology Photo/Resp

Endosymbiotic Theory

ancestor of eukaryotic cells engulfed oxygen-using prokaryotic cell which became an endosymbiont (cell in other cell), most likely mitochondria and chloroplast as they both have 1. own DNA. own ribosomes to produce their own protein synthesis 3. double membrane 4. can reproduce by binary fission, eukaryotes may have come to have both archaeal/bacterial features through this process

Protists

unicellular groups of eukaryotes, structural complexity, change shape when feeding, most of Eukarya, life functions carried out by organs, many have chloroplasts (autotrophs), some are heterotrophs, most important aquatic photosynthesizer

Distinguishing Features of Eukaryotes

have a nucleus/membrane-enclosed organelles which provide specific locations for cellular function, well-developed cytoskeleton that extends through the cell which provides structural support

Homologous

similar in internal structures, indicate organs with similar positions, structures or origin, not necessarily same function, mitochondria/plastid enzymes/transport systems are homologous to bacteria

Cyanobacteria

transformed life by releasing oxygen during photosynthesis, aerobic bacteria were evolutionarily successful as they use oxygen in their processes

Chloroplast

site of photosynthesis, found in plants/algae, convert light energy into chemical energy of food

Compartmentalization of Chloroplast

intramembrane space, stroma and thylakoid which enable light energy conversion into chemical energy

Heterotroph

unable to make own food, feed off of others

Autotroph

“self-feeders,” sustain themselves without eating anything from other living beings

Chlorophyll

absorbs light energy to drive synthesis of organic molecules, in thylakoid membrane

Structure of Chloroplast (outside to inside)

outer membrane, inner membrane, intramembrane space, thylakoid space, thylakoid, grana, granum, stroma, ribosome, DNA

Photosynthesis

light dependent reaction and Calvin Cycle, INPUTS: light energy (photons), carbon dioxide, water, OUTPUTS: glucose, oxygen

Thylakoid

disk-like, membrane-bound structures inside chloroplasts, photosystems found within the membrane, site of light-dependent reactions, ETCs found on thylakoid membrane

Grana

stack of thylakoids

Lumen

space inside cellular structure, ETC used to pump hydrogen from stroma into thylakoid lumen

Stroma

fluid inside of chloroplast, contains important enzymes (rubisco)

Photosystems

protein complexes used to absorb light and transfer light energy to electrons, located in thylakoid membrane

Photosystem 1

2nd in the process, photons absorbed by chlorophyll excite electrons

Photosystem 2

1st in the process, enzyme in PS2 splits water into hydrogen ions, oxygen & gas (oxygen diffuses out of cell), electrons passed into chlorophyll absorb photons to become excited

Concentration Gradient

higher concentration of H+ inside thylakoid- can’t freely diffusion because of charge

Electron Transport Chain

electrons passed from PS2 to PS1, energy from redox reactions of electrons being passed from protein to protein is used by the cytochrome complex to push H+ into the lumen

Proton Motive Force

PMF builds in the lumen and travels toward ATP Synthase, through facilitated transportation H+ travels through ATP synthase

ATP Synthase

spins H+ to combine ADP and Pi to create ATP

NADP+ Reductase

ETC ends, NADP+ accepts an electron and a proton to become NADPH

Light Dependent Reaction (all together)

1. Photolysis- split of H2O, 2 electrons to PS2, H+ into lumen, O2 into stroma 2. PS2- photons excite chlorophyll and excite low energy electrons 3. ETC- redox reactions, utilize energy as electrons fall down chain in cytochrome complex (active transport) 4. Proton Motive Force- electrochemical gradient against conc gradient, build up of protons to push protons out of ATP synthase 5. ATP synthase- PMF builds and protons leave through facilitated transportation, lowers Ea to create ATP 6. PS1- same as PS2 7. Redox of NADP+- gains electron from ETC and electron and proton from stroma to become NADPH 8. End of linear electron flow- products go to Calvin Cycle

Calvin Cycle

requires NADPH and ATP from light-dependent reactions, 1. Fixation- rubisco uses water to attach a carbon dioxide molecule to RuBP to make a 6-carbon sugar, sugar is very unstable and splits into 2 3-carbon sugars (3-PG) 2. Reduction- Two enzymes convert 3-PG into G3P (which can be used to make sugar), first one uses ATP as cofactor to destabilize, second one uses NADPH as a cofactor (to reduce) 3. Regeneration- regenerate RuBP by taking a phosphate from ATP, 1 G3P is netted and the other 5 are rearranged to make RuBP

G3P

converted into glucose/sugar to provide energy for cell, glucose made used in glycolysis in cytosol

Sucrose

form of sugar that is transported in most cells

Mitochondria

site of cellular respiration, extracts energy from sugars to drive generation of ATP, uses oxygen

Compartmentalization of Mitochondira

mitochondrial matrix and intermembrane space

Cristae

infoldings on inner membrane, highly folded so it gives the inner membrane a large surface area and enhances productivity of cellular respiration

Glycolysis

cytosol, breakdown of glucose into ATP and pyruvate, INPUTS: glucose, 2 ATP and 2 NADP+, OUTPUTS: 2 pyruvate, 2 ATP, 2 NADH

Pyruvate Oxidation

in matrix, connection process, INPUTS: pyruvate OUTPUTS: Acetyl CoA, NADH, CO2

Cellular Respiration

catabolic, uses oxygen, INPUTS: organic molecules, oxygen OUTPUTS: CO2, water, ATP, 1. glycolysis 2. pyruvate oxidation 3. Kreb’s Cycle 4. oxidative phosphorylation- flow of OUTPUTS to INPUTS, requires G3P from Calvin Cycle

Citric Acid Cycle (Kreb’s)

matrix, 2 carbon acetyl coa added to 4 carbon structure (6 carbon citrate), citrate is oxidized to form electron carriers, breakdown of citrate is coupled to substrate-level phosphorylation of 2 ATP, INPUTS: Acetyl CoA, 3 NAD+, ADP, FAD, H2O, OUTPUTS: 6 NADH, 2 FADH2, 2ATP, CO2

Oxidative Phosphorylation

final step in aerobic respiration, occurs in mitochondria, produces 26-28 ATP, 1. NADH + FADH2-come from glycolysis, drop off electrons to ETC/proteins, protons go to matrix (hypotonic), intermembrane space is hypertonic 2. ETC- electrons go through redox reactions falling down ETC until O2 is reached (last acceptor, most electronegative and pulls electrons down the chain, no reaction without it) 3. Electron pass through protein complexes, fuels active transport of H+ from matric to space to build PMF 4. 4 H+ + 4 e- + O2 = 2 H2O 5. H+ in hypertonic intermembrane space travel through ATP synthase allowing formation of ATP from ADP and Pi

Chemiosmosis

movement of ions across electrochemical gradient to drive synthesis of ATP, steps 3-5 in photosynthesis & steps 2, 3 & 5 in cellular respiration

Central Dogma in Eukaryotic Cells

DNA→pre-mRNA→mRNA→protein

RNA Processing/Splicing

enzymes in eukaryotic nucleus modify pre-mRNA, both ends of primary transcript are altered and certain sections (introns) are cut out so remaining parts (exons) are spliced together, single gene can code for more than one polypeptide

5’ modification

receives 5’ cap, modified form of guanine added (GPPP)

3’ modification

receives poly-A tail, 50-250 adenine

5’ cap and poly-A tail

facilitate export of mature mRNA, help protect mRNA from degradation by hydrolytic enzymes, help ribosomes attach to 5’ end in cytoplasm

Introns

noncoding segments of nucleic acid that lie between coding segments

Exons

segments of mRNA that are eventually expressed

Spliceosome

made of small RNA and proteins, remove introns, bind to short nucleotide sequences along intron to degrade them and them join the 2 exons, small mRNA is a ribozyme that catalyzes the process

Structure of RNA

allows it to function as carrier of genetic code and catalyst, single-strand of nucleotides can hydrogen bond to itself to form 3D shape, hydrogen bond to other DNA/RNA, bases have functional groups that interact with substrate to catalyze reaction

Signal Peptide

sequence of about 20 amino acids near N-terminus, polypeptides destined for endomembrane system/secretion marked by signal protein, can make free ribosomes bound, recognized by protein-RNA complex (signal-recognition particle) that guides the ribosome to receptor in ER

Endomembrane System

many different membrane-bound organelles of eukaryotic cell, nucleus, nuclear envelope, ER, Golgi, lysosome, vesicles, vacuoles, plasma membrane

Smooth ER

detoxifies poison, synthesizes lipids, stores calcium ions, metabolizes carbohydrates

Rough ER

bound ribosomes, creates secretory proteins destined for Golgi, travel in transport vesicles

Golgi Apparatus

cis face (receive) and trans face (ships), modifies secretory proteins

Lysosome

hydrolytic enzymes digest macromolecules, autophagy-recycle cell’s own organize material

Vacuole

Food: storage, Contractile: pump excess water to maintain flow of ions/molecules, Central: growth of cells by intake of water, cell sap- repository of inorganic ions

Genotype

genes contain instructions for making proteins

Phenotype

3D shape of protein

Journey of Insulin

DNA→pre-mRNA→mRNA→preproinsulin→proinsulin→insulin→secreted insulin

Preproinsulin

after it docks into ER, protease cuts preproinsulin and degrades signal peptide, consists of A-chain and B-chain separated by C-chain

C-chain

released and degraded in Golgi Apparatus, lines up A-chain and B-chain to form their bonds

Exocytosis

active transport, cell transports molecules out of cell membrane

Gene Regulation

minimizes waste, cell differentiation, through coarse control or chromatin chemical modification (epigenetics), allows organisms to adapt to their environment, cells must express certain genes to perform their function

Epigenetics

changes in gene expression caused by mechanisms in anything other than changes in DNA sequence

Differential Gene Expression

expression of genes by cells within the same genome, function of cell depends on expressed genes

Euchromatin

loose, transcribed

Heterochromatin

highly condensed, not transcribed

Chromatin

structural organization of chromatin pack cell’s DNA into form that fits in nucleus and regulates gene expression

DNA Storage

packed in chromatin wrapped around histones, many histones- nucleosome, into chromosome

Histone

positive packing protein, positive charge allows binding to negative DNA

Nucleosome

DNA wound around histone, functional unit of chromatin packing

Histone Acetylation

addition of acetyl group to amino acid in histone tail, promotes transcription by loosening chromatin

DNA Methylation

addition of methyl groups on nucleotide bases, condenses chromatin and reduces transcription

microRNA

degrades target mRNA, blocks translation

siRNA

condense centromere chromatin into heterochromatin

Positive Feedback

stimulus→signal sent→response→stimulus increased, ex. birth

Negative Feedback

stimulus→signal sent→response→stimulus decreased, ex. sweating, most common

Set Point

homeostatic control systems maintain variable of particular value

Homeostasis

maintaining internal dynamic equilibrium

Thermoregulation

physiological evidence of homeostasis, process by which animals maintain body temperature within a normal range, VITAL because: 1. body temp outside range can reduce enzyme efficiency 2. alter fluidity of membranes

Endothermic

warmed by heat generated by metabolism, maintain stable body temp in face of large fluctuations, humans, mammals, birds

Ectothermic

gain most heat from external environment, can adjust body temp by behavioral means (shade/sun), amphibians, fish, reptiles, invertebraes

Radiation

emission of electromagnetic waves by all objects warmer than absolute zero, ex. lizard absorbs heat radiating from sun and radiates heat to surroundings

Evaporation

removal of heat from surface of a liquid that is losing some of its molecules as gas, ex. evaporation of water from lizard’s moist surface

Convection

transfer of heat by movement of air or liquid past a surface, ex. breeze contributes to heat loss from lizard’s dry skin

Conduction

transfer of heat between molecules of objects in contact with each other, ex. lizard on hot rock

Circulatory Adaptations

provide major route for heat flow from interior to exterior, adaptations that regulate extent of blood flow near body surface/trap heat in body core, vasodilation- widening of superficial blood vessels to increase blood flow, vasoconstriction- tightening of blood vessels to decrease blood flow

Acclimatization Adaptations

physiological adjustment to environmental changes, animals adjust fur in winter and shed in summer

Behavioral Adaptations

sensors responsible for thermoreg. in hypothalamus (thermostat), if body temps fall, thermostat inhibits heat loss (vasoconstriction), vice versa

Cell Communication

coordinate cell activity, use cell membrane

Epinephrine

activates fight or flight response, epinephrine stimulates breakdown of glycogen into glucose 1-phosphate which is converted into glucose 6-phosphate, glucose can be stripped of phosphate and released into blood to fuel cells, does not directly interact with glycogen

Signal Transduction Pathways

receptors in cell membrane require multistep pathway during transduction, provide opportunities for coordination, include activation of proteins by adding/removing phosphate groups, may amplify signal if each molecule transmits signals, ensures that activities occur in right cells, right time, proper coordination

Signaling Molecule/Ligand

fits perfectly into receptor protein, does not enter cell, binding of ligand and receptor protein triggers first step

Phosphorylation Cascade

regulate protein activity, on/off switch, pathway containing many protein kinases, signal transmitted by phosphorylation causes shape change (interaction of new P group), ability to turn off pathway when signal is not presentProtei

Protein Kinase

enzyme that transfers P groups from ATP to protein, relay molecules

Protein Phosphatases

enzymes that rapidly remove P groups

Secondary Messenger

molecule on pathway that is not protein, but continues message, ex. cAMP or calcium ions

Example of Signal Transduction

1. ligand binds to receptor and activates it 2. activated receptor binds to protein and activates it 3. activated protein binds to adenylyl cyclase 4. activated adenylyl cyclase converts ATP to cAMP 6. cAMP activates another protein and leads to cellular response

Signal Transduction Responses

activation of protein, turning on gene, transcription factor, change activity of metabolic enzyme

Amplification

signal is amplified in relay molecules

Autocrine

communication within a cell

Juxtacrine

direct contact between cells, ex. plasmodesmata, ligands move directly from one cell to another

Paracrine

communication between 2 nearby cells