AP Bio Review

MPF

"M-phase-promoting factor" - triggers cell's passage past the G2 checkpoint into fragmentation of nuclear envelope during prometapahse of mitosis - cyclin-Cdk complex that was discovered first (in frog eggs) - peaks of MPF activity correspond to peaks of cyclin concentration

"The ability of phospholipids to form membranes is inherent in their molecular structure," says your book. Whatever does that mean?

"The ability of phospholipids to form membranes is inherent in their molecular structure," says your book. Whatever does that mean? Please 'splain. Phospholipids are amphipathic molecules, meaning that they have both a hydrophobic region (fatty acid end) and a hydrophilic region (phosphate group). The fact that one end of the molecule is nonpolar and the other is polar allows it to form a membrane, with the hydrophilic region facing water and the hydrophobic regions facing each other (making a phospholipid bilayer).

Golgi complex: What does it look like and what does it do?

"Warehouse" for receiving, sorting, shipping, and even some manufacturing Products of ER (like proteins) sent to be modified and stored and then sent to other places Made up of flattened membranous sacs (cisternae) like pita bread (yum) Cell can have up to hundreds of these stacks Membrane of each cisterna in a stack separates its internal space from cytosol A Golgi stack has distinct structural directionality (membranes of cisternae on opposite sides of stack differing in thickness and molecular composition- cis face and trans face that act as receiving and shipping departments) Cis (receiving) usually near ER, trans opposite end (shipping)

binary fission

"division in half" - prokaryote (bacteria and archaea) undergo asexual reproduction where the cell grows to roughly double its size and then divides to form two cells - no mitosis - most genes are on a single bacterial chromosome (circular DNA molecule and associated proteins) - starts replicating at origin of replication, cell elongates - when replication is done and cell is twice in size, plasma membrane pinches inward and cell becomes 2 identical daughter cells - movement of bacterial chromosomes is like poleward movements of centromere regions of eukaryotic chromosomes during anaphase but bacteria don't have mitotic spindles or microtubules

refractory period

"downtime" when a second action potential cannot be initiated - occurs because sodium channels remain inactivated during the falling phase and early part of the undershoot, so if a second depolarizing stimulus occurs during this period, it will be unable to trigger an action potential - sets a limit on the maximum frequency at which action potentials can be generated and also ensures that all signals in an axon will travel in one direction

bicoid

"two-tailed" - embryo whose mother has two mutant alleles of bicoid gene lacks the front half its body and has posterior structures at both ends - found that bicoid mRNA is highly concentrated at anterior end, as hypothesized - research identified a specific protein required for some of earliest steps in pattern formation - increased understand of mother's critical role in embryonic development

chlorophyll a

(different chlorophyll pigments have diff absorption spectrums so have diff effectiveness w certain wavelengths) - this pigment participates directly in light reactions - absorbs violet-blue and red light (so these are best for photosynthesis)--- green is least effective bc it reflects green, which is why plants are green

replicative cycle of enveloped RNA virus

(template)

receptor tyrosine kinases

*** Cell growth and reproduction (cancer often associated with mutations in receptor tyrosine kinases*** - kinase: add phosphates to protein - belong to major class of plasma membrane receptors characterized by having enzymatic activity - tyrosine kinase: enzyme that catalyzes transfer of a phosphate group from ATP to the amino acid tyrosine on a substrate protein - receptor tyrosine kinases: membrane receptors that attach phosphates to tyrosines (themselves) - one receptor tyrosine kinase complex may activate ten or more different transduction pathways (DIFFERENT FROM G-PROTEIN COUPLED RECEPTORS) 1. Receptors exist as individual units (monomers), each has extracellular ligand-binding site, an alpha helix spanning membrane, and intracellular tail with tyrosines 2. Binding of signal molecule (like a growth factor) causes two receptor monomers to associate closely with each other, forming a dimer (process called dimerization) 3. Dimerization activates the tyrosine kinase region of each monomer; each tyrosine kinase adds a phosphate from an ATP molecule to a tyrosine on the tail of the other monomer (so it is autophosphorylation) 4. Receptor is fully activated and it is recognized by specific relay proteins inside the cell. each protein binds to a specific phosphorylated tyrosine and it changes shape that activates bound protein. Each activated protein triggers a transduction pathway that leads to a specific cellular response.

ligand-gated ion channel

*** nervous center*** - neurotransmitter molecules released at a synapse between two nerve cells bind as ligands to ion channels on receiving cell to open or close gate, and the ions that flow in or out trigger an electric signal that propagates down length of receiving cell - type of membrane receptor containing a region that can act as a "gate" when receptor changes shape - signaling molecule binds as ligand and the gate opens or closes to allow or block the flow of specific ions through a channel in the receptor 1. Gate here remains closed until ligand binds to the receptor 2. When ligand binds to receptor and the gate opens, specific ions can flow through the channel and rapidly change the concentration of that particular ion inside the cell. This change can directly affect activity of cell in some way. 3. When ligand dissociates from this receptor, the gate closes and ions no longer enter the cell.

Three Stages of Cell Signaling

*1. Reception* - Target cell's detection of a signaling molecule coming from outside cell - chemical signal detected when the signaling molecule binds to receptor protein located at the cell's surface or inside cell *2. Transduction* - Binding of signaling molecule changes the receptor protein in some way to initiate transduction - Converts signal to a form that can bring about specific cellular response - Can happen in single step but more often than not series of steps (signal transduction pathway) *3. Responses* - Transduced signal triggers a specific cellular response (catalysis by enzyme, rearrangement of cytoskeleton, activation of specific genes in nucleus, aggregation of two or more receptor molecules--- anything)

diff bw anaerobic respiration and fermentation

*Anaerobic* - No O2 BUT ETC used (just not oxygen at the end- it's sulfur in sulfate or other electronegative compounds--- stinks like in swamps bc H2S produced) - prokaryotic organisms that live in environments without oxygen *Fermentation* - No O2 AND No ETC used (so no cellular respiration) - How can oxidation occur wo cellular respiration?Well, you get a little ATP from glycolysis--- fermentation is an extension of glycolysis that allows continuous generation of ATP by substrate-level phosphorylation of glycolysis - Wo a way to recycle NAD+ from NADH, glycolysis would deplete supply of NAD+ and it would stop (aerobic- NAD+ regenerated through dropping off electrons to ETC but fermentation also does this)

G Protein-Coupled Receptors

*G protein-coupled receptor* is a cell-surface transmembrane receptor that works with the help of a *G-protein* (binds GTP when active and GDP when inactive) - all G protein receptor proteins with a secondary structure where the single polypeptide has 7 alpha helices - involved with cholera, whooping cough, and botulism because they interfere with G protein function 1. G protein either on (GTP) or off (GDP). Receptor and G protein work together with another protein (usually an enzyme) 2. When appropriate signaling molecule binds to extracellular side of receptor, receptor is activated and changes shape. Cytoplasmic side binds inactive G protein, GDP replaced with GTP to activate G protein. 3. Activated G protein dissociates from receptor, diffuses along membrane, binds to enzyme (almost like allosteric regulation bc it changes shape of enzyme so that its active site works and the enzyme is activated) 4. Changes in G protein and enzyme are only temporary because G protein functions as GTPase enzyme (hydrolyzes GTP to GDP), inactive G protein then leaves enzyme which is now inactive again. GTPase function allows pathway to shut down quickly when signaling molecule is no longer present.

cell cycle

*Mitotic (M) Phase* - Includes mitosis and cytokinesis - Usually shortest part of cell cycle *Interphase* - Much longer stage, often accounts for 90% of cell cycle - Cell that is about to divide grows and copies chromosomes - Split up into G1, S phase, and G2 phase (in all three, proteins and cytoplasmic organelles produced, but only chromosomes during S phase) *G1 Phase* - "First Gap" *S Phase* - "Synthesis" *G2 Phase* - "Second Gap" *G0 Phase* - Cell that is not dividing

Stages of mitosis

*Prophase* - Chromatin fibers become more tightly coiled, condensing into chromosomes - Nucleoli disappear - Sister chromatids formed - Mitotic spindle begins to fomr - Centrosomes move away from each other *Prometaphase* - Nuclear envelope fragments - Microtubules from centrosome go into nuclear area - Chromosomes even more condensed - Each of chromatids has kinetochore - Some microtubules connect to kinetochores to become "kinetochore microtubules" to jerk chromosomes back and forth - Polar/nonkinetochore microtubules interact with those from opposite pole of spindle *Metaphase* - Centrosomes at opposite poles of cell - Chromosomes line up at metaphase plate which is equidistant from two poles - Kinetochores attached to microtubules coming from opposite poles *Anaphase* - Shortest stage of mitosis - Begins when cohesin proteins cleaved by separase - Each chromatid becomes chromosome - Two daughter chromosomes begin moving toward opposite ends of cell as kinetochore molecules shorten - Cell elongates as polar/nonkinetochore microtubules lengthen - Two ends of cell now have equivalent collections of chromosomes *Telophase* - Two daughter nuclei form in cell - Nuclear envelopes arise from fragments of parent cell's nuclear envelope and portions of endomembrane system - Nucleoli reappear - Chromosomes become less condensed - Any remaining spindle microtubules are depolymerized - Mitosis (division of one nuclei into two identical nuclei) is done! *Cytokinsesis* - Cleavage furrow or cell plate

ribosomes

*Protein Factories!* - complexes made of ribosomal RNA and protein - FUNCTION: carry out protein synthesis - Cells w high rates of protein synthesis have large numbers of ribosomes (structure and function) - *Free ribosomes*: suspended in cytosol, make proteins that function within cytosol - *Bound ribosomes*: attached to outside of endoplasmic reticulum or nuclear envelope, make proteins that are destine for insertion into membranes, for packaging within organelles like lysosomes, or export from cell (secretion) - These two types are structurally identical, ribosomes can switch bw the 2 roles - *What are they made of*: ribosomal RNA (made from instructions in DNA) - *Where can you find them*: cytosol, rough ER, nuclear envelope - *What gets made*: Proteins ! They are universal among all cell types because they have the same function among these cells: to make proteins. Therefore, different structures to dictate different functions for these ribosomes are not needed.

95% CI and Error Bars

*SEM* +- SEM 95% Confidence intervals (sample size larger than 10) +- 2 SEM 95% confident that true pop is within these bars As sample size increases, 95% CI get smaller bc more confident we are that our mean is correct If 95% confidence bars DO NOT overlap bw two diff samples, diff bw sample means is statistically significant (DIFF BW GROUP A AND GROUP B of red mulch and no mulch)

Endoplasmic Reticulum

*Smooth ER* - No ribosomes - Functions in diverse metabolic processes (vary w/cell type) including: synthesis of lipids/steroid hormones, metabolism of carbohydrates, detoxification of drugs and poisons, and storage of calcium ions - Enzymes allow for the production of aforementioned stuff - Think metabolism, functions vary based on cell type - Synthesis of lipids - Metabolism of carbohydrates - Detoxification drugs/poisons (Detoxification: usually adds -OH groups to poisons...why does this work?--- make more soluble to dissolve in water!) - Storage Ca2+ for muscle contraction *Rough ER* - *Secretory protein* production - Studded with ribosomes on outer surface of membrane - Protein production (secretory proteins), folding ER membrane keeps secretory proteins separate from proteins formed in cytosol - Secretory proteins leave in transport vesicles - Membrane factory: Grows in place by adding membrane proteins and phospholipids to its own membrane and portions of it transferred in form of transport vesicles to other parts of endomembrane system

T cells

*Structure of Antigen Receptor* - consists of two diff polypeptide chains, an alpha chain and a beta chain, linked by a disulfide bridge - transmembrane region near base of receptor that anchors molecule in cell's plasma membrane - at outer tip of molecule, V regions of alpha and beta chains form the antigen-binding site, remainder of molecule is made up of constant C regions *Antigen Recognition by T Cells* - Antigen receptors of B cells bind to epitopes circulating, while T cells only bind to fragments of antigens that are displayed on the surface of host cells (why it's cell-mediated) 1. *Antigen recognition by a T cell* - Inside host cell, antigen fragment from a pathogen binds to an MHC I molecule and is shown by MHC I molecule (this is what I look like!) - Combo of MHC I molecule and antigen fragment recognized by specific T cell T CELL IS ACTIVATED *Clonal selection* - for each activated cell, result of proliferation is a clone (pop of cells identical to original) - some of cells from clone become *effector cells* (short-lived cells that take effect immediately against antigen and any pathogens producing that antigen): effectors for T cells are helper T cells and cytotoxic T cells

B cells

*Structure of Antigen Receptor* - two identical heavy chains and two identical light chains, w disulfide bridges linking two chains together, heavy chain extends into cytoplasm - each of chains have a constant C region and a variable V region *Antigen recognition by B Cells and Antibodies* 1. B cell antigen receptors and antibodies - Antigen receptor of a B cell binds to an epitope (particular part of antigen) circulating in body fluids (interacts directly w pathogen) - Following binding (activated!), B cell gives rise to cells that secrete a soluble form of antigen receptor (aka secrete antibodies!) - antibody specific for epitope just like original B cell - antibodies, NOT B cells, fight and are the defense! 2. *Antigen receptor specificity* - different antibodies can recognize distinct epitopes on the same antigen - antibodies can recognize free antigens as well as antigens on a pathogen's surface 3. Clonal selection - for each activated cell, result of proliferation is a clone (pop of cells identical to original) - some of cells from clone become *effector cells* (short-lived cells that take effect immediately against antigen and any pathogens producing that antigen): effectors for B cells are plasma cells (produce antibodies)

biosynthesis

*anabolic pathways* - not all organic molecules of food are used for energy- we need substance too! - we either get monomers from food or get specific molecules that we don't eat as intermediates of glycolysis and the citric acid cycle - these are endergonic processes (they use ATP)

____________ ____________ drives the cellular economy by extracting the energy stored in sugars and other fuels

*cellular respiration* drives the cellular economy by extracting the energy stored in sugars and other fuels

long distance signaling

*endocrine signaling* Ex: hormones - specialized cells release hormone molecules which travel via the circulatory system to other parts of body nervous system signal - electrical signal travels nerve cell, converted to chemical when signaling molecule released, cross synapse to another nerve cell to be electrical signal again (both paracrine and endocrine)

norm of reaction

*nature vs nurture* - genotype not associate w rigid phenotype but a range of phenotypic possibilities due to environmental influences

local signaling

*paracrine signaling* - local regulators that are secreted by signaling cell to travel short distances to influence cells in vicinity *synaptic signaling* - occurs in animal nervous system - electrical signal along nerve cell triggers secretion of neurotransmitter molecules carrying chemical signal

apoptosis

- "programmed cell death" - cellular agents chop up the DNA and fragment the organelles and other cytoplasmic components - cell shrinks and becomes lobed ("blebbing") - cell's parts packaged in vesicles that are engulfed and digested by specialized scavenger cells - protects neighboring cells from damage triggered by signals that activate a cascade of "suicide' proteins in the cells destined to die - regulation occurs at the level of protein activity rather than gene activity (proteins always made and present, but are usually inactive) - 15 different pathways for apoptosis (one used depends on type of cell and the signal) - Besides extracellular signaling molecule, two other alarm signals inside cell signaling apoptosis 1. Nucleus- signal generated when DNA has suffered irreparable damage 2. ER when excessive protein misfolding occurs - development of the nervous system - normal operation of the immune system - normal morphogenesis of hands and feet in humans and paws of other animals - evidence of involvement in degenerative diseases like Parkinson's and Alzheimer's disease, as well as cancer

What all cells have in common

- *Plasma membrane*: cells' outer boundary. Barrier between inside and outside. - *Cytoplasm*: Jello-like stuff inside. Cytosol = cytoplasm minus organelles - *Genetic material*: nucleus in eukaryotic cells (all packed up), nucleoid in prokaryotic (all loosey-gossey)

complement system

- 30 proteins in blood plasma - circulate in inactive state, activated by substances on surface of many microbes - activation: leads to bursting of invading cells

An organism maintains homeostasis by feedback mechanisms. Differentiate between a positive and negative feedback loop in general terms. Does positive mean good and negative mean bad? Example of each

- A negative feedback loop is the most common form of regulation in living systems, in which accumulation of an end product of a process slows that process (such as excess ATP inhibiting an enzyme). There are also many biological processes regulated by positive feedback loops, in which an end product speeds up its own production (such as blood clotting). Positive doesn't mean good and negative doesn't mean bad; these terms are just to differentiate between whether the end product is slowing down a process(negative) or speeding it up(positive). - Another example of a negative feedback loop is that of blood glucose levels. When an animal eats, the blood glucose levels rise, and specialized cells in the pancreas sense the increase and release insulin. Another example of a positive feedback loop would be the release of a hormone known as oxytocin that speeds up contractions during childbirth.

stomata

- CO2 enters, oxygen exits through these! (nail polish) (water goes in through roots of soil and up through capillary action)

Why do we need statistics?

- Can't "prove" everything in science (will never have ALL of the data) - Need to make sense of recorded data

chemiosmosis

- Cell uses energy of existing ion gradient to power ATP synthesis - Power source for ATP synthesis is difference in concentration of H+ on opposite sides of inner mitochondrial membrane (diff in pH) - Chemiosmosis: energy stored in form of H+ gradient across a membrane is used to drive cellular work like the synthesis of ATP - Cell uses exergonic flow of electrons from NADH and FADH2 down (described above) to pump H+ across the membrane, from mitochondrial matrix into intermembrane space (opposite of light reactions--- high concentration outside, low concentration inside)--- H+ has tendency to diffuse back across which powers ATP synthase *** List factors that affect ATP yield

polymerase chain reaction

- DNA cloning in cells is best method to prepare large quantities of particular gene or other DNA sequence - If DNA is impure, then PCR: any specific target segment within one or many DNA molecules can be quickly amplified in a test tube

eukaryotic viruses vs phages

- DNA or RNA genomes, single-stranded or double-stranded - Many have a lipid envelope that surrounds the protein coat

What are descriptive statistics?

- Describe data, allow you to see patterns, ie. mean, median or mode (NOT inferential stats, like sd, chisquare etc)

Delta G to stability, work capacity, and spontaneous change

- Diver (see slides)

What is a lipid?

- Diverse group of molecules. *ALL ARE HYDROPHOBIC* - Insoluble in H2O - Long-term energy storage b/c of energy in C-H bonds - Makes sense for animals to carry fat vs. carbs b/c it's a more compact form of fuel. Plants use carbs—they don't walk around! - Not really polymers! (So no true monomer)

Protein synthesis

- ENDERGONIC! - Decrease in entropy ! - Product has more free energy than reactants (amino acids)

synthesis of membranes

- ER and Golgi apparatus 1. Membrane proteins and lipids are synthesized in the ER, carbohydrates are added to transmembrane proteins making them glycoproteins 2. Inside Golgi, lipids get carbohydrates= glycolipids, carbohydrates in glycoproteins further modified 3. Glycoproteins, glycolipids, and secretory proteins transported in vesicles 4. As vesicles fuse w plasma membrane, exocytosis

gametes

- Half as many chromosomes as somatic cells - Humans: 23 chromosomes - Haploids

Some spontaneous reactions occur very slowly. How come they don't all occur instantly?

- High activation energy - Ex: paper doesn't burst into flames (have to apply heat to it--- activation energy is just too high, but once you overcome it, release of energy is greater than activation energy which is why it's exergonic)

explain free energy equation and why spontaneous reactions are important in a cell

- If delta G is negative, it is spontaneous and is an exergonic reaction (net release of free energy/ products have lower free energy than reactants) - This means that there was a decrease in enthalpy (negative delta H) and/or an increase in entropy (T delta S) - Spontaneous reactions provide energy to do work in cell

Cells need to do what to stay alive?

- Process matter - Process energy (energy comes from sun or from food) - Process information (info from outside and within cell) Many cells will reproduce and communicate too !

mitosis

- Process of cell division of the genetic material in the nucleus - The nucleus divides - We get two new nuclei - Both nuclei have the same number of chromosomes and the same DNA sequence (that's a lot of ATP there!)

lactic acid fermentation

- Pyruvate reduced directly by NADH to form lactate as an end product (no release of CO2--- lactate is 3-carbon) - where: fungi and bacteria in yogurt, in our muscle cells when we exercise (excess lactate taken by blood to liver, where it is converted back to pyruvate by liver cells which can then under presence of oxygen go into mitochondria for Krebs cycle)

So why do we need to eat?

- Regeneration of ATP! - Requires energy to go back from ADP to ATP (endergonic) - Energy release from ATP to ADP goes to endergonic processes

What's wrong w sandwich model to describe plasma membrane?

- Sandwich model isn't fluid - If the fatty acid tails (hydrocarbon chains) are unsaturated (have double bonds/less H), the membrane remains fluid at lower temperatures b/c the phospholipids can't pack together. Animal cell plasma membranes have cholesterol wedged between the phospholipid molecules. Cholesterol can be thought of as a "temperature buffer." At body temperature, cholesterol makes the membrane less fluid b/c it restrains phospholipid molecules. At lower temperatures, it prevents the membrane from freezing b/c the phospholipids can't pack together as easily. (ALL examples of structure and function !) - Better model: fluid mosaic model ! - Notice that the plasma membrane aka the cell membrane, is a whole lot more than phospholipid molecules. Phospholipid molecules are the foundation but there are more than 50 kinds of proteins associated with the membrane. There are also glycolipids (lipids+carbs) and glycoproteins (proteins+carbs) for cell-cell recognition. Think ABO blood groups! - integral proteins: some amino acid groups are hydrophillic and some are hydrophobic

What are the two factors aIncreasing pressure affecting water potential? How?

- Solute concentration - Pressure Increasing solute → decreasing water potential Increasing pressure → increasing water potential

Negative Delta G

- Spontaneous - Products have less free energy than the reactants - Focused on positive entropy and negative enthalpy (spontaneous at all temperatures) and negative entropy and positive enthalpy (non-spontaneous at all temperatures)

ATP

- Structure: Bonds of negatively charged phosphate groups make ATP unstable and easily hydrolyzed ! - Contains ribose, nitrogenous base adenine and chain of three phosphate groups bonded to it - Loss of free energy when ATP hydrolyzed (potential energy decreases) - Spontaneous and exergonic reaction w/ negative delta G - Energy released from reaction: Can do work ! - ADP has higher entropy/is more stable than ATP

Pressure potential

- Sum of all pressure on water - In units of pressure: MPa or Bars *Turgor pressure* - forced caused by cell membrane pushing against cell wall. *Wall pressure* - an equal and opposite force exerted by the cell wall. Counteracts the movement of water due to osmosis. Other pressures - tension, cohesion, atmospheric, root, etc. - increasing pressure potential = increasing water potential

endocytosis

- TAKES ENERGY - Large molecules (like proteins and polysaccharides) cross the membrane in bulk by mechanisms that involve packing in vesicles - Cell takes in biological molecules and particulate matter by forming new vesicles from the plasma membrane - Looks like reverse of exocytosis (but diff proteins used) - Three types: phagocytosis ("cellular eating"), pinocytosis ("cellular drinking"), receptor-mediated endocytosis (allows cell to acquire bulk quantities of specific substances, even though those substances may not be very concentrated in the extracellular fluid)

exocytosis

- TAKES ENERGY - Large molecules (like proteins and polysaccharides) cross the membrane in bulk by mechanisms that involve packing in vesicles - fusion of vesicles with the plasma membrane - transport vesicle from Golgi moves along microtubules of cytoskeleton to plasma membrane and specific proteins help the vesicle to fuse with the plasma membrane - secretory cells use exocytosis a lot - in plant cells, exocytosis delivers proteins and carbohydrates from Golgi to outside of cell for development of cell wall

Endomembrane system

- Tasks: synthesis/transport proteins into membranes or out of the cell, metabolism/movement of lipids, detoxification of poisons - Members of this exclusive club: Nuclear envelope ER Golgi Lysosomes and vacuoles Plasma membrane (not really an endo membrane but close enough) - Made of: Plasma membrane (mostly phospholipids and some proteins!)

Effect of location conditions on enzyme activity

- Temperature and pH! (optimal temp depends on enzyme- efficient substrate breakdown) - Optimal pH for enzymes too - Also affected by chemicals that specifically influence that enzyme

List/briefly explain some functions of membrane proteins.

- Transport- Hydrophilic channel across membrane that is selective for a solute or by providing channel that changes shape - Enzymatic activity- Enzyme with active site exposed to substances in adjacent solution - Signal transduction- Binding site w/ specific shape of chemical messenger (like a hormone) - Cell-cell recognition- Glycoproteins can serve as ID tags to be recognized by membrane proteins of other cells (cell-cell binding) - Intercellular joining- Membrane proteins of adjacent cells can hook together in gap junctions or tight junctions (much more long lasting than bonding in cell-cell recognition) - Attaching to cytoskeleton and extracellular matrix- Microfilaments/cytoskeleton can be bound to membrane proteins (cell shape, stabilize location of certain membrane proteins)

mitochondria

- Two membranes - Its own DNA, - Serious energy transformation

how did they discover that our O2 didn't come from CO2?

- Van Niel Stanford: bacteria do photosynthesis w/o releasing O2 - some do it w H2S, not H2O, and CO2 (and released yellow globs of sulfur rather than oxygen) - all photosynthetic organisms require a hydrogen source (proton gradient for energy!) but that source varies

Vacuoles

- Various functions depending on cell type

When is a cell uncondensed vs condensed?

- When not dividing/replicating DNA, it is uncondensed bc it needs to be able to access the genes to make proteins/DNA is being checked or used (G0, G1, S, G2) - Condensed when transporting: M phase

Duchenne muscular dystrophy

- X-linked disorder that progressively weakens the muscles and causes loss of coordination

hemophilia

- X-linked recessive disorder defined by the absence for one or more of the proteins required for blood clotting

operator

- a switch for a gene - segment of DNA that is turned on or off - located between the promoter and the enzyme-coding genes - controls access of RNA polymerase to the genes

benign tumor

- abnormal cells remain at original site, have too few genetic and cellular changes to survive at another site - most benign tumors do not cause serious problems and can be completely removed by surgery

entropy

- about stats: more likely to be disorganized than organized (think about pile of bricks) - to increase order, (decrease in entropy), energy has to be added - to decrease order, (increase in entropy), energy is released

fluorescence

- absorption of photon makes electron go on higher energy level: but can't stay there long - goes back down and light energy is released as heat and light energy (light is fluorescence) - chlorophyll outside of chloroplast: fluorescence, but IN chloroplast energy is used to pump protons in so none is emitted as light - energy transferred from pigment molecule to pigment molecule in a "wave" until energy passed to reaction-center complex

crossing over

- accounts for recombination of linked genes (in addition to independent assortment of non-linked genes)

how do activation energy and enzymes regulate metabolism

- activation energy keeps complex molecules in our cells from spontaneously breaking down into lower energy products all the time (so that you need enzymes instead and can then regulate this breakdown in response to cell's environment) - enzymes lower activation energy

Down syndrome

- affects approximately one out of every 700 children - usually result of extra chromosome 21 - risk of Down Syndrome increases with maternal age

innate immunity

- all animals (invertebrates and vertebrates) - rapid - non-specific *Invertebrates* - Barrier: exoskeleton - Lysozyme (enzyme that breaks down bacterial cell walls) protects insect digestive system - If pathogen gets past barrier: internal immune defenses - Hemocytes: phagocytosis or trigger production of chemicals that kill pathogens - Insect immune cells secrete specialized recognition proteins to bind to fungi or bacteria *Vertebrates* BARRIERS - Skin or shell (can't seal off entire body bc we need gas exchange, nutrition, and reproduction) - Mucous membranes: mucus enhances defenses by trapping microbes and other particles - Secretions: Trap or kill microbes bc it's acidic, they also physically inhibit microbial entry CELLULAR INNATE DEFENSES *Phagocytosis* Detect fungal or bacteria using receptors (Toll-like receptors) that bind to fragments of molecules characteristic of a set of pathogens (general) (types of phagocytic cells listed below: neutrophils, macrophages, and dendritic cells) - Neutrophils: type of phagocytic cell that circulates in the blood, are attracted by signals from infected tissues and then engulf and destroy the infecting pathogens - Macrophages: "big eaters", larger phagocytic cells that migrate throughout the body or reside permanently in organs/tissues that are likely to encounter pathogens - Dendritic cells: type of phagocytic cell that mainly populates tissues (like skin) that contact the environment, stimulate adaptive immunity against pathogens *Natural Killer Cells* - cells circulate through body and detect abnormal array of surface proteins characteristic of some virus-infected and cancerous cells - do not engulf, but release chemicals that lead to cell deal, inhibiting spread of virus or cancer ANTIMICROBIAL PEPTIDES AND PROTEINS - Pathogen recognition triggers production and release of variety of peptides and proteins that attack pathogens or impede reproduction - Interferons: Proteins interfering with viral infections Virus-infected cells secrete interferons to induce nearby uninfected cells to produce substances that inhibit viral reproduction - Complement system: 30 proteins in blood plasma that circulate in an inactive state and are activated by substances on the surface of many microbes, activation results in a cascade of biochemical reactions that can lead to lysis of invading cells (also in inflammatory response) INFLAMMATORY RESPONSE - Pain and swelling of a splinter, for example, are brought about by signaling molecules released upon injury or infection - Signaling molecules include *histamine* stored in mast cells - Histamine stored in vesicles or granules of mast cells - Histamine released at sites of damage triggers nearby blood vessels to dilate and become more permeable - Activated macrophages and neutrophils discharge *cytokines*, signaling molecules that enhance an immune response to promote blood flow to the site of injury - Activated complement proteins promote further release of histamine, attracting more phagocytic cells that enter injured tissues and carry out additional phagocytosis 1. mast cells release histamines and macrophages secrete cytokines, both of which cause nearby capillaries to dilate 2. capillaries widen and become more permeable, allowing fluid containing antimicrobial peptides(complement proteins) to enter tissue, signals released by immune cells attract neutrophils 3. neutrophils digest pathogens and cell debris at the site, and the tissue heals

somatic cells

- all body cells except the reproductive cells - Humans: 46 chromosomes - Diploids

allosteric regulation

- allosteric; "other site" - conformational change and regulation of enzyme activity which is essential for a cell - activation: stabilizes active state of enzyme - inhibition: stablizes inactive state of enzyme - (no regulation: just switches back and forth between two states)

diff bw transcription and translation in archaic and eukaryotic cells

- bacteria DNA doesn't separate ribosomes etc from DNA, so translation can begin while transcription is still in process

mRNA degradation

- bacterial mRNA molecules typically degraded by enzymes within a few minutes of their synthesis, so they can change their patterns of protein synthesis very quickly in response to environmental changes - eukaryotic mRNA lasts hours, days, or weeks (nucleotide sequence that affect how long an mRNA remains intact are often found in untranslated region UTR at 3' end)

stroma

- basically cytosol of chloroplasts - surrounded by 2 membranes, then another membrane system inside stroma w/thylakoid membranes

electron transport chain (ETC)

- breaks fall of electrons to oxygen into several energy-releasing steps - consists of mostly proteins built into inner membrane of mitchondria (eukaryotic) and plasma membrane (prokaryotic) - electrons removed from glucose shuttled by NADH to "top", high energy end of chain - low-energy end of chain has O2 which captures electrons and protons to make water (exergonic) - each downhill carrier is more electronegative than and thus capable of oxidizing its uphill neighbor in the series of redox reaction steps - After glycolysis and Krebs cycle, only 4 ATP for glucose molecule produced - Electrons in NADH and FADH2 link glycolysis and Krebs cycle to oxidative phosphorylation which uses energy released by ETC to power ATP synthesis - Form of mitochondria: lots of folds to increase surface area (so there's space for lots of ETC chain) 1. Electrons in NADH transferred to FMN 2. FMN is oxidized as it passes electrons to FeS in complex I 3. Then to ubiquinone (small hydrophobic molecule, only one that's not a protein)- it's uniquely mobile, doesn't sit in a certain complex 4. Rest of electron carriers are cytochromes (has iron atom that accepts and donates electrons)--- cytochromes each have a diff protein w slightly diff electron-carrying heme group (each one is a little more electronegative than the last) 5. FADH2 adds electrons from complex II (lower energy level than NADH) 6. Last cytochrome of chain passes electrons to oxygen (very electronegative), each oxygen atom also picks up pair of hydrogen ions from solution to make water ETC makes no ATP directly- it eases fall of electrons from food to oxygen and breaks the large free-energy drop into a series of smaller steps to release energy in manageable amounts; electron transport and energy release coupled with ATP synthesis

beta oxidation

- breaks fatty acids down to two-carbon fragments, which enter Krebs cycle as acetyl CoA - also produces NADH and FADH2 which can be used in ETC - fat break down produces twice as much ATP as carbohydrates due to chemical structure and high energy level of electrons (why you have to work so hard to burn fat--- bc there are so many calories in each gram compared to carbs)

obligate anaerobes

- can only carry out fermentation or anaerobic respiration - can't survive in the presence of oxygen

chi-square test

- categorical data - comparing observed results to expected results (and seeing if it's different enough to not be by chance mathematically) 1. Calculate the Chi-Square value 2. Determine the degrees of freedom (n-1) 3. Use the critical values table (provided to you) to determine the p value according to the Chi-Square value and the degrees of freedom.

meiosis

- cell division of the gamete cells - yields *nonidentical* daughter cells that only have one set of chromosomes

aquaporins

- channel proteins - allows entry of up to 3 billion water molecules per second single file

regulation of transcription initiation

- chromatin-modifying enzymes provide initial control of gene expression by making a region of DNA either more or less able to bind the transcription machinery - transcription factors: eukaryotic RNA polymerase requires the assistance of transcription factors (general transcription factors--- a few independently bind DNA sequence, usually bind proteins including each other and RNA polymerase II) - Only when complete initiation complex has assembled can RNA polymerase II begin to transcribe - Interaction of general transcription factors and RNA polymerase II w promoter leads to low rate of initiation--- high rates of initiation have to do with *specific transcription factors* (activators--- DNA binding domain and activation domain, or repressors are examples) - Eukaryotes: Precise control of transcription depends on binding of activators to DNA control elements (*COMBINATION* of control elements in an enhancer associated w gene that is important in regulating transcription of gene, even w only 12 control elements, there are many combos possible)

complete dominance

- classic crosses: phenotypes of homozygous dominant and heterozygous are the same

chromatin

- complex of DNA and proteins making up chromosomes - when cells aren't dividing: stained chromatin appears as diffuse mass vs distinguishable chromosomes

resting membrane potential

- concentration of K+ highest outside cell, concentration of Na+ highest inside cell (maintained by *sodium-potassium pumps*, which do active transport and use ATP: 3 Na+ moved outside cell, 2K+ moved in so that there is a negative charge) - voltage difference is so large bc of movement through ion channels (pump AND ion channels) - *ion channels*: pores formed by clusters of proteins across membrane (specialized to the type of ion where ions go down their concentration gradient) - K+ channels are usually open and others aren't: K+ outflow down concentration gradient leads to a net negative charge inside the cell - reason that buildup of negative charge stops is bc excess negative charges inside the cell exert an attractive force that opposes the flow of additional positively charged K+ ions out, so separation of charge (voltage) thus results in an electrical gradient that counterbalances chemical concentration K+ gradient

what explains differences in how we have so many different antigen receptors

- constant C region vs variable V region (changes!!) - we have a bunch, bunch, bunch of receptors encoded by V region of our genes just in CASE we encounter that type of pathogen *genetic rearrangement* 1. Recombination deletes DNA between randomly selected V segment and J segment 2. Transcription of permanently rearranged, functional gene 3. RNA processing (removal of intron; addition of cap and poly-A tail) 4. Translation diff bc does removal before transcription instead of after

chromosomes

- discrete units of DNA - structures that carry the genetic information - each chromosome contains one long DNA molecule associated with many proteins

lipid

- diverse group of molecules - long term energy storing b/c of energy in C-H bonds - nonpolar--- insoluble in H2O - lipids grouped together b/c of nonpolar/hydrophobic qualities - not really polymers! so no true monomer

histone acetylation

- do not entail change in DNA sequence, yet they can be passed along to future generations of cells for specialization acetyl groups are attached to lysines in histone tails, so positive charges in acetylated lysines are neutralized and histone tails don't bind to neighboring nucleosomes (chromatin looser, so transcription proteins have easier access to genes in acetylated region) - other chemical groups like methyl and phosphate groups can attach to aa in histone to condense chromatin for opposite effect - histone code hypothesis: specific combinations of modifications (and the order of these) help determine the chromatin configuration, which in turn influences transcription

cancer cells

- do not stop dividing when growth factors depleted - cancer cells do not need growth factors in culture medium to grow and divide - may make required growth factor themselves, or may have abnormality in signaling pathway that conveys growth factor's signal without it being there, or abnormal cell cycle control system even in absence of factor usually all caused by a change in one or more gene - if and when they stop dividing, it's at random points in cycle vs checkpoints - "immortal" (all normal cells divide only about 20 to 50 times before aging and dying) - avoid normal controls that trigger a cell to undergo apoptosis when something is wrong (like when irreparable mistake occurred during DNA replication before mitosis)

protein processing and degradation

- eukaryotic polypeptides often need to be processed to become functional proteins (regulation in steps for modifying/transporting proteins) - length of time each protein functions in the cell is strictly regulated by means of selective degradation (CYCLINS): to mark for destruction, cell attaches ubiquitin to the protein, then proteasomes take it apart

Second law of thermodynamics

- every energy transfer results in an increase in disorder (entropy) of the universe - bear releases heat and C02/H2O (much more stable than macromolecules in fish) from cellular respiration - the reason we can't just recycle our energy over and over again

X Inactivation

- female mammals - we don't get twice as many proteins as males - most of one X chromosome in each cell in female mammals becomes inactivated during early embryonic development - females are a mosaic of two types of cells (about half with active X from father and half with active Y from mother) - region of each X chromosome contains sevreal genes involved in inactivatoin process

glycolipids, glycoproteins

- glycolipids: membrane carbohydrates that are covalently bonded to lipids - glycoproteins: membrane carbohydrates that are covalently bonded to proteins - FUNCTION: cell-cell recognition ! (very important in sorting of cells into tissues and recognizing foreign cells)

peas

- good choice bc available in many varieties - only focused monogenic traits, not a continuum - short generation time, large number of offspring - self-fertilize: Mendel mutilated them so that he could control fertilization and cross fertilize

animal cell vs plant cell: which solution is best?

- hypotonic: animal will burst, plant will be turgid (firm) and healthy-- plants that aren't wood bound need this structure - isotonic: animal cell healthy, plant cell flaccid - hypertonic: animal cell shrivel, plant cell plasmolyzed

How do enzymes lower activation energy?

- induced fit between an enzyme and its substrate - not a lock and key - when the substrate enters the active site, it causes the enzyme to change shape (like the enzyme is hugging the substrate) - often weakening bonds of substrate: stressing bonds of substrate and leading to transition state - enzyme goes back to original shape

spectrophotometer

- instrument that measures ability of a pigment to absorb various wavelengths - directs beams of light of different wavelengths through a solution of pigment

intracellular receptors

- intracellular receptor proteins found in either the cytoplasm or nucleus of target cells - chemical messenger (signaling molecule) passes through plasma membrane bc they are nonpolar or small enough (or both) to cross it: steroids and thyroid hormones, NO - Testosterone hormone released by cells in testes, enters cells all through body but only cells that contain receptor molecules for testosterone respond bc hormone binds to receptor protein in these cells to activate them - Activated hormone-receptor complex turns on genes through transcription factors (testosterone receptor is an example) 1. Testosterone passes through plasma membrane 2. Testosterone binds to receptor protein in cytoplasm, activating it 3. Hormone-receptor complex enters nucleus and binds to specific genes 4. Bound protein acts as transcription factor, stimulating the transcription of the gene into mRNA 5. mRNA translated into a specific protein

sister chromatids

- joined copies of original chromosome (identical sisters) with two arms - once they separate, the chromatids become individual chromosomes

fatty acid

- kind of a monomer - long C-H chains in a carboxyl group

chromosome modification

- location of a gene's promoter relative to nucleosomes and to the sites where the DNA attaches to the chromosome scaffold or nuclear lamina can affect whether gene is transcribed - genes within heterochromatin (highly condensed) not usually prescribed - certain chemical modifications to the histone proteins and to the DNA of chromatin can influence both chromatin structure and gene expression

codons

- mRNA nucleotide triplets - usually written in 5' to 3' direction (read by machinery in 5' to 3' direction) - AUG dual function (codes for aa and also functions as a "start" signal) - redundancy but not ambiguity (each codon only codes for a single aa but each aa has 3 codons) - almost universality of genetic code: evolution!

carbohydrate

- made of carbon + water (1:2:1 ratio) - compounds with C, H, and O - simple sugars

chromosomes

- makes replication and distribution of so much DNA in mitosis manageable - consists of one very long, linear DNA molecule associated with many proteins

nucleolus

- mass of densely stained granules and fibers adjoining part of the chromatin - ribosomal RNA (rRNA) is synthesized here from instructions in the DNA - Proteins imported from cytoplasm are assembled along w rRNA into large and small subunits of ribosomes to exit the nucleus through nuclear pores - can be more than one (depends on species and stage in cell's reproductive cycle)

intersexual selection

- mate choice - individuals of one sex (usually females) are choosy in selecting their mates from the other sex - male showiness may not seem adaptive in any other way and may in fact pose some risk, but if this benefit outweighs the risk from predation, then the it will have higher reproductive success

inhibitory postsynaptic potential (IPSP)

- membrane potential is brought further from threshold (hyperpolarization) - K+ -Cl-

chemiosmosis

- method by which chloroplasts and mitochondria generate ATP - electron transport chain assembled in membrane pumps protons across membrane as electrons passed through series of carriers that are progressively more electronegative - transform redox energy to proton-motive force (potential energy stored in form of an H+ gradient) - this membrane has ATP synthase enzyme - HIGH CONCENTRATION INSIDE, LOW OUTSIDE mitochondria vs chloroplasts: - mitochondria: high energy electrons dropped down transport chain extracted from organic molecules that are oxidized (exergonic), uses chemiosmosis to transfer chemical energy from food molecules to ATP - chloroplasts: high energy electrons come from water, don't need food to make ATP, use chemiosmosis to transform light energy into chemical energy in ATP

extranuclear genes

- mitochondria contain small circular DNA molecules that carry a number of genes - these organelles reproduce themselves and transmit their genes to daughter organelles - these genes are not distributed to offspring through same meiosis rules, so they don't follow Mendelian inheritance patterns - mitochondrial and chloroplast have their own DNA so that they can make proteins and enzymes necessary for their functions - we inherit mitochondria from mom (chloroplasts for plants from maternal plant, too)

primary electron acceptor

- molecule capable of accepting electrons and becoming reduced - in reaction-center complex

aerobic fermentation

- most prevalent and efficient catabolic pathway - oxygen is consumed as a reactant along w organic fuel aer- air bios- life

incomplete dominance

- neither allele is completely dominant - F1 hybrids have phenotype somewhere between those of te two parental varieties - BUT not blending bc if you look at F2, you'll get red, pink, and white (red and white will reappear)

nuclear lamina

- netlike array of protein filaments that maintains the shape of the nucleus by mechanically supporting the nuclear envelope - also nuclear matrix: framework of protein fibers extending throughout the nuclear interior

peripheral proteins

- not embedded in lipid bilayer - appendages loosely bound to surface of membrane, usually exposed parts of integral proteins - on cytoplasm side some membranes attached to cytoskeleton and on extracellular side some proteins held in place by attachment to extracellular matrix

heterotrophs

- obtain organic material by second major mode of nutrition: live on compounds produced by other organisms - heterotrophs: consumers of biosphere - can be eating plants or animals, or dead organisms like carcasses, feces, and fallen leaves (dead eaters- decomposers)

human genome

- only 1.5% of DNA is protein-coding DNA - Very small fraction of non-protein-coding DNA consists of gene for RNAs like rRNA and tRNA, and the theory was that most of DNA was junk DNA - recent research shows that a significant amount of this junk DNA is actually transcribed into non-protein-coding RNAs (noncoding RNAs)

completing and targeting functional protein

- polypeptide chain coils and folds as a result of aa sequence (primary structure), forming a protein w specific shape, 3d molecule with secondary and tertiary structure - post-transitional modifications may be required before protein can do job (polypeptides combining etc)

excitatory postsynaptic potential (EPSP)

- potential in which the membrane potential is brought towards threshold (depolarization) - Na+ alone, or Na+ and K+

active transport

- pump solute across membrane *against* its concentration gradient: cell needs/expends energy ! - Requires: ATP, carrier protein - transport proteins that move solutes against concentration gradients/participate in active transport are ALL carrier proteins (channel proteins allow solutes to diffuse down concentration gradients rather than picking them up and transporting them against their gradients) - enables a cell to maintain internal concentrations of small solutes that differ from concentrations in its environment (for example, in animal cell, it has super high concentration of potassium ions and low concentration of sodium ions, and plasma membrane w carrier protein pumps out Na + and K+ in)

catabolism

- release energy by breaking down complex molecules to simpler compounds - AKA breakdown pathways EX: MAJOR one is *cellular respiration* (sugar glucose and other organic fuels broken down min presence of oxygen to carbon dioxide and water-- energy stored in organic fuels is used to do cell's work) DOWNHILL - some bond are broken and others formed, releasing energy and resulting in lower-energy breakdown products

anaerobic fermentation

- some prokaryotes use substances other than oxygen as reactants in a similar process that harvests chemical energy without oxygen an- without (cellular respiration has both aerobic and anaerobic processes)

kinetochore

- structure of proteins associated with specific sections of a chromosomal DNA at each centromere - two kinetochores of a chromosome face in opposite directions - *Prometaphase*: some of spindle microtubules attach to kinetochores (kinetochore microtubules) - When chromosome kinetochore is captured by microtubule, it moves toward pole that microtubule is attached to - Movement checked as soon as microtubules from opposite pole attach to the other kinetochore, in a tug-of-war, back and forth until in middle: *metaphase* - Microtubules that aren't attached to kinetochores have been elongating (*polar microtubules*), by metaphase they overlap and interact w other nonkinetochore microtubules from opposite pole - Microtubules of asters have also grown and are in contact w plasma membrane by metaphase- spindle is complete! - Form of spindle follows function for *anaphase*: cohesins holding sister chromatids together broken by enzyme (separase), polar microtubules responsible for elongating cell, they don't overlap as much during anaphase (motor proteins walk them away from each other w ATP)

Griffith experiment

- studying bacterium that causes pneumonia in mammals - two strains of bacterium (one pathogenic and one non-pathogenic) - when he killed pathogenic bacteria with heat and then mixed the cell remains with living bacteria of the nonpathogenic strain, some of the living cells became pathogenic - some chemical component of heat killed cells caused heritable change (passed on over and over in fourth example of mouse) - this was called *transformation*: change in genotype and phenotype due to assimilation of external DNA by a cell - Avery treated heat-killed bacterium with an agent that inactivated one type of molecule (DNA, RNA, or proteins), and only when DNA was active did the fourth type of mouse die

logistic growth

- there is a limit to the number of organisms that can live in a habitat (carrying capacity)! - we use K to symbolize the maximum population size than a habitat can sustain - Carrying capacity is determined by the limiting resources, e.g. energy, shelter, refuge, nutrients, water, nesting sites. dN/dt = rmaxN(K-N/K) growth rate is the highest when the population size is half the carrying capacity - logistic growth equation similar to the exponential growth equation but has an expression that reduces the per capita rate of increase as N approaches K. - K - N is the number of additional individuals the environment can support and K - N/K is the fraction of K still available for growth. - Think about it, as the number of organisms in the population approaches the carrying capacity, growth will slow dramatically. If N is small/close to zero, the population will grow exponentially. - Populations don't always perfectly fit the model! Nature doesn't really care about our models (population size oscillates around carrying capacity)

gel electrophoresis

- uses a gel made of a polymer - gel acts as a molecular sieve to separate nucleic acids or proteins on the basis of size, electrical charge (longer molecules take longer to move) - each band consists of many thousands of DNA molecules of the same length (sickle cell mutation destroys one of restriction sites to make diff fragments)

transmission of info at synapse

- usually APs are not transmitted from neurons to other cells, but info is transmitted - *electrical synapses*: (Bw neurons), allow electrical current to flow directly from one neuron to another - most are *chemical synapses*: involve the release of a chemical neurotransmitter by the presynaptic neuron - at each terminal, presynaptic neuron makes neurotransmitter and packages in synaptic vesicle (lab) - arrival of an action potential at synaptic terminal depolarizes the plasma membrane, opening voltage-gated calcium channels - the rise in Ca2+ in terminal causes some of synaptic vesicles to fuse w terminal plasma membrane, releasing neurotransmitter - once released, neurotransmitter diffuses across synaptic cleft (gap bw presynaptic neuron from postsynaptic cell)

generation of postsynaptic potentials

- usually neurotransmitter goes to ligand-gated ion channels, usually opening ion channels and resulting in a postsynaptic graded potential - at some synapses, ligand-gated ion channel permeable to both Na+ and K+: inside will depolarize at a value in bw Ek and ENa (more positive than RMP, so it's excitatory!) - only Na+: excitatory - at others, ligand-gated ion channel is selectively permeable for only K+ or Cl-: inside will hyperpolarize and moves membrane potential further from threshold (inhibitory) - how do postsynaptic potentials end: some neurotransmitters are actively transported back into the presynaptic neuron (repackaged into synaptic vesicles, transported into glia, metabolized as fuel) - other neurotransmitters are removed from synaptic cleft by simple diffusion or by enzyme that catalyzes hydrolysis of neurotransmitter (lab) - magnitude of postsynaptic potential varies w amount of neurotransmitter released, distance (more distance, smaller the magnitude) - by the time a single EPSP reaches axon hillock, it is usually too small to trigger an action potential in a postsynaptic neuron - on some occasions, 2 EPSPs occur at a single synapse in such rapid succession that the postsynaptic neuron's membrane potential has not returned to resting before arrival of second EPSP (temporal summation) - EPSPs produced nearly simultaneously by different synapses on the same postsynaptic neuron can add together (spatial summation) - Through spatial and temporal summation, several EPSPS can can combine to depolarize the membrane at the axon hillock to threshold, causing postsynaptic neuron to produce an action potential (same thing applies to IPSPs)

polypeptide

-long chains formed from amino acids -the polymer of proteins -connects with other polypeptides to make proteins (that twist, coil, etc.)

humoral immune response

1) After an APC engulfs pathogen, it displays antigen fragments of MHC II Specific helper T cell binds to complex through antigen receptor and accessory protein (CD4) APC/Helper T complex causes APC to secrete cytokines 2) When B cell w receptors for the same epitope internalizes antigen, displays antigen fragment w MHC II Activated helper T cell bears receptors specific for displayed fragment binds to B cell: ACTIVATES B CELL 3) Activated B cell proliferates and differentiates into memory B cells and plasma cells (see below)

two different ways to inhibit enzyme activity

1. *Competitive Inhibition* - competes w/ substrate - if the competitive inhibitor binds at the active site, the substrate can't bind there 2. *Noncompetitive Inhibition* - doesn't bind at the active site but its binding changes the shape of the active site and the substrate can't bind - can tell if inhibitor is competitive or noncompetitive if you keep adding substrate. If reaction rate increases, then it is a competitive inhibitor but if the reaction rate doesn't change, then it is a noncompetitive inhibitor Ex: Poisons often enzyme inhibitors but also enzyme inhibitors large part of cell regulation mechanisms

transcription

1. *Initiation* - Eukaryotes: collection of proteins, *transcription factors*, mediate binding of RNA polymerase and the initiation of transcription - The whole complex of transcription factors and RNA polymerase II bound to the promoter makes up the *transcription initiation complex* 2. *Elongation* - RNA polymerase moves along DNA and untwists DNA, enzyme adds nucleotides to 3' end of RNA molecule 3. *Termination* - Differs bw bacteria and eukaryotes - Terminator in bacteria - RNA polymerase II transcribes a DNA sequence to code for signal AAUAAA in pre-mRNA, 10-35 nucleotides downstream to release from polymerase

translation

1. *Ribosome Association and Initiation of Translation* - ribosomal subunit binds to mRNA - bacteria: mRNA binding site recognizes specific sequence, initiator base-pairs w start codon - arrival of large ribosomal subunit completes initiation complex, initiation factors (proteins) and hydrolysis of GTP 2. *Elongation of Polypeptide* - Codon recognition - Peptide bond formation - Translocation 3. *Termination of Translation* - Elongation continues until a stop codon in the mRNA reaches A site of ribosome (UAG, UAA, UGA) - Release factor binds to stop codon

Four Levels of a Protein's Structure

1. All proteins begin with *amino acids*, the monomers of polypeptides. Despite the complexity and diversity of proteins, they are all combinations of 20 different amino acids (some essential- meaning we need to consume them and can't form them within our body). Therefore, the primary structure of proteins consists of a linear chain of amino acids. They are connected through peptide bonds (formed through a dehydration reaction) to create a polypeptide backbone. One end of the polypeptide chain has a free amino group, while the opposite end has a free carboxyl group, but function is determined by the side groups (they outnumber the terminal ends). The sequence of amino acids eventually result in the specific function of a protein. 2. The secondary structure of proteins are the *coils and folds* that contribute to a protein's overall shape; these coils and folds are because of hydrogen bonds between atoms of the polypeptide backbone, as the oxygen atoms have a partial negative charge (second-most electronegative element). Though hydrogen bonds are relatively weak compared to intramolecular bonds, they are repeated enough through folds that they can support a particular shape. An example of secondary structure is the helix or the pleated sheet. 3. The tertiary structure of proteins is the overall shape of a polypeptide resulting from interactions between the *side chains (R groups)* of the amino acids (this is why their exact sequence is so important!). A hydrophobic interaction helps to form the three-dimensional shape, as the amino acids with hydrophobic side chains cluster together and held by London Dispersion forces and leave the hydrophilic side chains to be held together by hydrogen bonds/ionic bonds. Disulfide bridges made up of covalent bonds also reinforce the shape of a protein. 4. The quaternary structure of proteins is the *association of multiple polypeptides to form a functional protein*. Some examples of functional proteins include collagen and hemoglobin. Primary = unique sequence of aa Secondary = 3D shape due to H bonding between parts of the aa backbone (NOT the R groups). Think alpha helices and β-pleated sheets. Tertiary = globular shape due to the R groups Quaternary = association of 2 or more polypeptide chains

5 things that upset HWE !

1. Mutation 2. Gene flow 3. Non-random mating (increases homozygotes if assortative or heterozygotes if disassortative) 4. Genetic drift(random/statistical chance, doesn't create adaptations) 5. Selection (only factor that creates adaptive changes in allele frequencies!)

Oparin-Haldale hypothesis

1. abiotic synthesis of small organic molecules, such as aa and nitrogenous bases 2. joining of these small molecules into macromolecules, such as proteins and nucleic acids 3. the packaging of these molecules into *protocells* (droplets with membranes that maintained an internal chemistry different from their surroundings) 4. origin of self-replicating molecules that eventually made inheritance possible - early earth had a reducing atmosphere, in which organic molecules could've formed from simpler molecules - energy for synthesis from lightning and UV radiation

Hydrogen bonds play a big role in biology. Define what a H bond is and discuss why they form.

A hydrogen bond is the strongest type of intramolecular force (compared to dipole-dipole attraction and then London dispersion forces). H bonds can be found when there is a covalent bond between H and O, N, or F (such as in water). They occur because there is a strong electronegativity difference between H and O, N, or F, and not only is the bond polar but the molecule is extremely polar. Because of this, one end of the molecule is positive and the other is negative, so an intramolecular bond forms between the positive H atom and the negative O, N, or F atom.

Describe a process which occurs in your body that involves hydrolysis.

An example of hydrolysis in our bodies would be digestion because the organic material in our food is in polymers are too large to enter our cells, so they need to be broken up. Enzymes speed up this endothermic reaction. Our cells use the monomers and assemble them into new, different necessary polymers through dehydration reactions.

Fats are excellent for energy storage--why do animals use fats for energy storage while plants mostly use starch?

Animals use fats for energy storage because it's a compact form of fuel (solid), but plants don't walk so this is not necessary for them! The fats of plants (and fishes) are usually unsaturated, made up of one or more types of unsaturated fatty acids and are liquid at room temperature (because they are unsaturated they have cis double bonds, and have kinks that prevent the molecules from packing close together like saturated fatty acids making up saturated fats).

aquatic biomes

Aquatic biomes make up the largest part of the biosphere and are categorized as fresh water or marine. Aquatic biomes typically show vertical stratification and this is all about light! Photosynthesis occurs in the photic zones b/c light can penetrate. Lots of O2 in the atmosphere made by phytoplankton. Marine biomes include coral reefs, which are extremely productive. But ocean acidification is affecting thing greatly.

This is a huge structure/function example and one of my favorites: Discuss how structure and bonding of starch and cellulose determine the properties of the polysaccharides. (Think pasta versus Raisin Bran!)

Both plants and animals store sugars for later use in the form of the aforementioned storage polysaccharides. Plants store starch, a polymer of glucose monomers (starch represents stored energy). Most animals have enzymes like plants that can hydrolyze plant starch to make glucose available. Animals store glycogen, a polymer of glucose. Cellulose is a structural polysaccharide and is a major component of plant cell walls. Cellulose is also a polymer of glucose, but the glycosidic linkages differ (there are two slightly different ring structures for glucose), with the two hydroxyl groups in different positions. These differing glycosidic linkages in starch and cellulose make the two macromolecules unique shapes: starch molecules are helical, and cellulose molecules are straight. Parallel cellulose walls are held together by hydrogen bonds bw the molecules. Enzymes that digest starch by hydrolyzing its linkages can't hydrolyze the linkages of cellulose because of the marcomolecules' two different shapes. So, to speak of Raisin Bran and pasta, Raisin Bran is not digested by human bodies (unlike pasta, of which we have enzymes to hydrolyze). It stimulates the lining of the digestive tract and helps food to pass more smoothly (INSOLUBLE FIBER = cellulose!).

Carbohydrates

CHO 1:2:1 ratio Monomer: Monosaccharides (then disaccharides) Polymer: Polysaccharides

proliferation of B cells and T cells

CLONAL SELECTION - binding of antigen to specific lymphocyte (or to host cell which binds to T cell) activates B and T cells - for each activated cell, result of proliferation is a clone (pop of cells identical to original) - some of cells from clone become *effector cells* (short-lived cells that take effect immediately against antigen and any pathogens producing that antigen): effectors for B cells are plasma cells (produce antibodies), effectors for T cells are helper T cells and cytotoxic T cells

many factors that regulate population growth are density-dependent

Clockwise starting with the plants: competition for resources, accumulation of toxic wastes, disease, territoriality, predation. (a birth/death rate that does not change w/ density is density-independent.)

law of independent assortment

Each pair of alleles segregates independently of each other pair of alleles during gamete formation - two characters at the same time - shown with dihybrid cross: YyRr - Dependent assortment: when F1 plants self-pollinate, are alleles transmitted in same combinations from which they were inherited from P generation? If so, it'd just be YR yr, making phenotypic ratio 3:1 in F2 just like monohybrid BUT - Independent assortment: two pairs of alleles segregate independently of each other (they are each on different chromosomes), so F1 plant will have four types of gametes of equal numbers: YR, Yr, yR, yr- causes phenotypic ratio of 9:3:3:1 - ONLY applies to genes on separate chromosomes or very far apart on same chromosome

alterations of chromosome structure

Errors in meiosis (crossing over- unequal crossing over) or damaging agents such as radiation can cause breakage of a chromosome, which can lead to four types of changes in chromosome structure 1. *Deletion* - occurs when a chromosomal fragment is lost - affected chromosome is then missing certain genes 2. *Duplication* - the "deleted" fragment may become attached as an extra segment to a sister chromatid - detached fragment could attach to a non-sister chromatid of a homologous chromosome, so duplicated segments might not be identical bc homologs could carry diff alleles (deleted from mom could add on to dad) 3. *Inversion* - chromosomal fragment may also reattach to the original chromosome but in reverse orientation 4. *Translocation* - Fragment to join non-homologous chromosome

What is a buffer?

Essential to living tissues to maintain pH homeostasis. Minimizes the changes in pH by accepting H+ when they're in excess and donating H+ when they are not. ie. carbonic acid.

Eukaryotic cells have ____________ _________________ that compartmentalize their structure. Why is this an advantage?

Eukaryotic cells have *internal membranes* that compartmentalize their structure. - can keep certain parts making things that could be toxic to rest of cell

second law of thermodynamics

Every energy transfer or transformation increases the entropy of the universe - order can increase locally, but there is an unstoppable trend of randomization of universe

Every transformation results in some unusable energy: __________ !

Every transformation results in some unusable energy: *heat* !

What is the natural world?

Everything physical that can be measured.

Amino

Found in: Proteins Amino acts as a base and can pick up/take a proton from the surrounding solution (particularly water in living organisms). It is found in cells in the ionized form with a charge of 1+ (because it accepts hydrogen ions).

The hydrophilic molecules on the outside can get in with some extra help--tell me how they move across the membrane and tell me specifically how water gets in.

Hydrophilic molecules can get into the cell with the help of proteins (through channel proteins w hydrophilic channels or carrier proteins that hold onto passengers and change their shape that can shuttle them across the membrane). Water specifically gets in through a type of channel protein, aquaporins. Thus, the selective permeability of a membrane depends on the lipid bilayer and the type of transport proteins built in the membrane.

Why is carbon important?

It has the ability to form large, complex and diverse molecules because it has 4 valence electrons that can form covalent bonds. - can form chains, rings, or branches

dendritic cells

INNATE - type of phagocytic cell that mainly populates tissues (like skin) that contact the environment - reside outside lymphatic system but migrate to lymph nodes after interaction w pathogens, go to lymph nodes to stimulate adaptive immunity - stimulate adaptive immunity against pathogens: show the flag of the pathogen using MHC molecules

Which molecules are left on the outside of the membrane and why?

Large nonpolar and polar molecules, ions, and charged molecules are left on the outside of the membrane because they cannot pass through the hydrophobic middle of the lipid bilayer (or if they can, it's with a very slow speed).

What are the benefits to compartmentalization in eukaryotic cells?

In eukaryotic cells, the compartmentalization provides different local environments that facilitate specific metabolic functions so that incompatible processes can go on simultaneously inside a single cell. Also, many enzymes are built into the membranes of the cell and its organelles which are necessary for a cell's metabolism.

Water as a Solvent

Lastly, water's role as a versatile solvent is because of its polarity: many substances dissolve in water (whether ionic or molecular) because they are more attracted to water's hydrogen bonds rather than other molecules of its own substance. Many different polar and ionic compounds are dissolved in water within biological fluids such as blood, the sap of plants, and the liquid within all cells.

binomial

Latin scientific names

Lysosomes: Where do they come from and what do they do?

Membranous sac of hydrolytic enzymes that animal cell uses to digest macromolecules (HYDROLYSIS) Hydrolytic enzymes and lysosomal membrane are made by rough ER and then transferred to the Golgi apparatus for further processing (some prob come from budding on trans face of Golgi) Phagocytosis: eat by engulfing smaller organisms (food vacuole formed fuses w lysosome, whose enzymes digest food)- some human cells do this Autophagy: Lysosomes use hydrolytic enzymes to recycle the cell's own organic material so that cell can continually renew itself

Differentiate between monosaccharides, disaccharides and polysaccharides.

Monosaccharides generally have molecular formulas that are some multiple of CH2O; thet are monomers ("building blocks" ) of carbohydrates. Glucose is the most common monosaccharide, and glucose along w other monosaccharides are major nutrients for cells. Disaccharides is made up of two monosaccharides joined by a glycosidic linkage (covalent bond bw two monosaccharides by a dehydration reaction). Polysaccharides are macromolecules (few hundred to a few thousand monomers) of carbohydrates. They serve as storage material, and can be hydrolyzed to provide sugar for cells. Polysaccharides can also serve as building material for structures that protect the cell or the entire organism (function determined by sugar monomers and position of glycosidic linkages).

More free energy with higher free energy have a tendency to _______________ achieve a __________ state. That's a loss of free energy and the release of free energy can be used to do ______.

More free energy with higher free energy have a tendency to *spontaneously* achieve a *stable* state. That's a loss of free energy and the release of free energy can be used to do *work*.

example of enzyme regulation through negative feedback loop

NEGATIVE FEEDBACK LOOP ! - pathway shows how isoleucine, an amino acid, is synthesized from threonine, another amino acid. If the cell has enough isoleucine, why waste the energy making more...so feedback inhibition is the perfect way to prevent excess isoleucine synthesis! - Isoleucine, the end product, will allosterically bind to enzyme 1, inactivating it. And this shuts down the isoleucine synthesis pathway. If isoleucine gets used up, the active site of enzyme 1 is available again.

does transcription alone constitute gene expression in eukaryotes?

NO! Expression of a protein-coding gene is ultimately measure by amount of functional protein that is made (a lot happens bw synthesis of transcript and the protein activity- post-transcriptional regulation) - RNA processing - mRNA degradation - initiation of translation - protein processing and degradation

Does standard deviation get smaller as sample size increases?

NO! Just more accurate- sometimes a population will be very far from the mean (ex: household income bc of Bill Gates)

Natural selection is only mechanism that consistently causes ________________ evolution

Natural selection is only mechanism that consistently causes *adaptive* evolution 1. *relative fitness* - contribution an individual makes to the gene pool of the next generation relative to the contributions of other individuals 2. *directional selection* - occurs when conditions favor individuals exhibiting one extreme of a phenotypic range, thereby shifting a population's frequency curve for the phenotypic character in one direction or the other - common when a population's environment changes or when members of a population migrate to a new (and different) habitat - ex: beak size bc of seeds, only long beaks bc hard seeds 3. *disruptive selection* - occurs when conditions favor individuals at both extremes of a phenotypic range over individuals with intermediate phenotypes - ex: both short beaks for soft seeds and long beaks for hard seeds 4. *stabilizing selection* - acts against both extreme phenotypes and favors intermediate variants - ex: birth weights of babies

DNA and RNA molecules have structural similarities and differences that define function. List the similarities and differences between the two molecules.

Nucleic acids determine the primary structure of proteins (i.e sequence of amino acids) so that we have proteins to do everythinggg! Nucleic acids are polymers made of monomers called nucleotides. Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) are the two types of nucleic acids. DNA is inherited from an organisms' parents, and contains genes that have information that program all of the cell's activities. The DNA isn't directly invovled in running the operations of the cell; proteins are needed to implement the instructions of the DNA. Each gene along a DNA molecule directs the synthesis of a type of RNA, mRNA (messenger RNA). This mRNA interacts with the cell to produce a polypeptide (so info in gene expression goes from DNA to RNA to protein). Protein synthesis occurs on organelles called ribosomes (little dots!). mRNA transfesr genetic instructions from DNA in the nucleus to ribosomes in the cytoplasm (in eukaryotic cells).

F1 generation

Offspring of the P generation (filial) - heterozygous - if he stopped here, he wouldn't have seen patterns of inheritance: wouldn't have seen the white flowers spur up again - if blending was correct, these would've been pale purple

metabotropic receptor

Opening/closing these ion channels depends on one or more metabolic steps - binding of neurotransmitter activates signal transduction pathway in postsynaptic cell w a second messenger - slower onset compared to ligand-gated but longer effect

light reactions

PHOTO: solar energy is captured and transformed into chemical energy 1. Photon hits a pigment molecule in light-harvesting complex of PSII, boosts electron to higher energy level, wave effect until energy is relayed to the pair of chlorophyll a molecules. 2. Electrons transferred from chlorophyll a to primary electron acceptor. 3. Enzyme catalyzes the splitting of a water molecule into two electrons and two protons and an oxygen atom, with the electrons being transferred to the primary electron acceptor and the H+ released into the thylakoid lumen to create high concentration of protons on the outside of the thylakoid membrane. 4. Each excited electron passes from primary electron acceptor of PS II to PS I through the electron transport chain. The electrons fall to a lower energy level (which is exergonic) which provides energy for the synthesis of ATP (ATP synthase- electrons pass through the cytochrome complex as H+ are pumped into thylakoid to contribute to proton gradient). 6. Light energy also transferred through pigment molecules in PS I to that reaction-center complex- wave effect here too. 7. Chlorophyll pair excited and transfer electrons to primary electron acceptor (which leaves chlorophyll molecule P700+ with a hole for electron- accept electron from bottom of electron transport chain from PS II). 8. Series of redox reactions to pass electrons from primary electron acceptor down a second electron transport chain (no proton gradient and thus does not produce ATP). 9. Enzyme NADP + reductase catalyzes the transfer of electrons to NADP+ (2 electrons to make NADPH). NADPH is at a higher energy level than water, and electrons are more readily available for reactions of Calvin cycle than those of water (bc of solar energy). NADP+ to NADPH also takes away a H+ from stroma.

What establishes direction of traffic across a membrane (will a particular substance enter the cell or leave the cell)/ what mechanisms drive molecules across membranes>?

Passive transport, active transport !

Phospholipids are essential to cells. What is special about this molecule and how is a phospholipid molecule's structure a beautiful example of how form fits function?

Phospholipids are another type of lipid that are essential for cells because they make up cell membranes. Phospholipids are composed of fatty acids at one end and glyceryol, phosphate and choline at the other end (this is the polar end that is attracted to water molecules). Thus, it forms a cell membrane and self arranges with the hydrophilic head facing the water (due to the polarity of water molecules) and the hydrophobic heads facing each other, forming a bilayer. This bilayer forms a boundary between the cell and its external environment (semipermeable membrane- ions/other polar molecules can't pass through this membrane so protein channels are needed instead).

Why is water the unversal solvent?

Polar and ionic substances can dissolve in water because of polarity. Water-soluble substances are hydrophilic.

What is water?

Polar molecule, overall neutral. (equal numbers of protons and electrons, just distributed differently throughout the molecule) DIHYDROGEN MONOXIDE (SCARYYY)

What are the levels of protein structure?

Primary= unique sequence of aa Secondary= 3D shape due to H bonding Tertiary= globular shape due to R groups Quarternary= association of 2 or more polypeptide chains

glycolysis

SUGAR SPLITTING ! - Where: Cytosol - What kind of phosphorylation: substrate - What: Breaks glucose into two molecules of pyruvate - Energy investment (2 ATP) and energy payoff (net 2 ATP, 2 NADH + 2 H+) and 2 pyruvate/ 2 H2O (most of potential energy still within pyruvate) - allosteric regulation in step 3 by ATP for the enzyme - NO carbon released as CO2! (CoA is like a shuttle to bring the 2 carbon from glycolysis to the Krebs cycle) - Anaerobic !!! (can occur without oxygen)

Calvin cycle

SYNTHESIS: chemical energy is used to make organic molecules of food *Phase 1: Carbon fixation* Incorporates each CO2 molecule one at a time by attaching it to a five carbon sugar (RuBP)- rubisco (RuBP carboxylase is the enzyme that catalyzes this reaction) Product: 6-carbon intermediate that is so unstable that it immediately splits in half, forming two molecules of 3-phosphoglycerate for every one CO2 *Phase 2: Reduction* Each molecule of 3-phsophoglycerate receives a phosphate group from ATP to become 1,3-bisphosphoglycerate (ADP + Pi) Pair of electrons from NADPH to reduce 1,3-bisphosphoglycerate (NADP +) to make G3P, which has more potential energy Every 3 molecules of CO2, 6 molecules of G3P BUT only one net product molecule of G3P cycle can leave bc 5 have to go back to form the 3 molecules of 5-carbon RuBP (15 carbon atoms in total circulating in this cycle, with the 3 CO2 molecules providing the three extra carbons for the one molecule product of G3P). *Phase 3: Regeneration of the CO2 acceptor (RuBP)* Carbon skeletons of the five molecules of G3P are rearranged by last steps of Calvin cycle into three molecules of RuBP Cycle spends three more molecules of ATP to do this

What is difference between saturated and unsaturated? Structure and function?

Saturated fats can pack close and form solids. Unsaturated fats have double bonds, less H atoms and have kinks. Here's another structure-function example. Lard and olive oil are both fats but one is a solid and one is a liquid. Why? Because one is saturated with H (saturated) and one is not (unsaturated). See the next slide for a visual. They have different health benefits/harm b/c of simple H atoms!

alternation of generations

Second type of life cycle: diploid and haploid stages that are multicellular (Alternation of meiosis and fertilization is common to all organisms that reproduce, sexually, the timing of these two events in life cycle varies, depending on species) - * Sporophyte*: Multicellular diploid stage, meiosis inn the sporphyte produces haploid cells called *spores*, haploid spore doesn't fuse with another cell but divides mitotically to generate multicellular haploid stage called *gametophyte* - Cells of gametophyte give rise to gametes by mitosis - Fusion of two haploid gametes at fertilization results in a diploid zygote (sporphyte) - In this type of life cycle, sporphyte generation produces gametophyte as offspring, and gametophyte generation produces next sporophyte generation

We know by now that the cell membrane is selectively permeable. So, which molecules can get past the velvet rope into the club, aka the inside of the cell?

Small molecules and ions can move across the plasma membrane in both directions. Nonpolar molecules of relatively small size can pass through the membrane easily. Polar molecules like glucose and even a very small polar molecule like water take a long time to pass through the membrane; ions or charged molecules have even more of a difficult passing through the membrane.

Endoplasmic reticulum: What roles does the ER, both smooth and rough, play in the cell?

Smooth ER: No ribosomes Functions in diverse metabolic processes (vary w/cell type) including: synthesis of lipids/steroid hormones, metabolism of carbohydrates, detoxification of drugs and poisons, and storage of calcium ions Enzymes allow for the production of aforementioned stuff Rough ER: Studded with ribosomes on outer surface of membrane Protein production (secretory proteins), folding ER membrane keeps secretory proteins separate from proteins formed in cytosol Secretory proteins leave in transport vesicles Membrane factory: Grows in place by adding membrane proteins and phospholipids to its own membrane and portions of it transferred in form of transport vesicles to other parts of endomembrane system

Solute (osmotic) potential

Solute potential (ΨS ) = -iCRT i = The ionization constant (number of particles formed) for NaCl this would be 2 for sucrose or glucose, this number is 1 C = Molar concentration (moles/liter) R = Pressure constant = 0.0831 liter bar/mole K T = Temperature in degrees Kelvin K = 273 + °C - increasing solute potential = decreasing water potential (fewer free water molecules to move)

What is cohesion/adhesion?

The ability of water to be attracted to it self and to other molecules causing surface tension and capillary action. The four emergent properties of water are cohesion, moderation of temperature, expansion upon freezing, and versatility as a solvent. Cohesion occurs because the attraction between water molecules (in the form of hydrogen bonds) is stronger than the attraction between water molecules and other molecules. Cohesion is important for life because it allows water to not evaporate quickly through surface tension (so that plants and organisms can use it in a liquid form). In addition to contributing to surface tension, cohesion (and adhesion) contribute to capillary action. Capillary action allows the transport of water through stems to leaves and therefore plays an essential biological role.

Details of the cytoskeleton are beyond the scope of this course and the AP exam. However, you should know what the cytoskeleton is/does. (If you are taking the SAT bio subject test this year, read/learn this section.) So, what is the cytoskeleton made of (tell me which macromolecule) and what is its role? (A very brief answer is fine here.)

The cytoskeleton is made of proteins- 3 types of protein filaments (microtubules, microfilaments, and intermediate filaments). Its role is to support the cell and give it motility (both within the cell w/ organelle motility as well as the cell's overall motility).

The diversity in cell _________ reflects the different functions of cells.

The diversity in cell *shape* reflects the different functions of cells. (Structure and function!!)

Discuss how the electronegativity of atoms determines whether a molecule will be polar or nonpolar.

The electronegativity of atoms determines whether a molecule will have polar or nonpolar bonds because the more electronegative an atom is, the more strongly it pulls shared electrons toward itself. (Electronegativity is the attraction of a particular atom for the electrons of a covalent bond.) If two atoms have the same electronegativity (like Cl and Cl in Cl2), then the bond is a nonpolar covalent bond. When one atom is with a more electronegative atom, the bond is a polar covalent bond. And when the electronegativity is vastly different, the bond approaches ionic behavior (though nothing is truly ionic).

What are the organelles of the endomembrane system and how do they function together? An image with a brief description is fine here.

The endomembrane system includes the nuclear envelope, the endoplasmic reticulum, the Golgi apparatus, lysosomes, various kinds of vesicles and vacuoles, and the plasma membrane. This system carries out protein synthesis, protein transport into membranes and organelles or export, metabolism and movement of lipids, and detoxification of poisons.

"Mitochondria (singular = mitochondrion) and chloroplasts create energy." No! Not true! What is wrong with that statement? Make sure you tell me (briefly) what mitochondria and chloroplasts actually do when answering that question.

The law of conservation of energy is a thing! You can't create energy- energy can neither be created nor destroyed, it can only be transformed from one form to another. Mitochondria are the sites of cellular respiration (metabolic process that uses oxygen to generate ATP by extracting energy from sugars, fats, and other fuels)-- energy comes from somewhere/doesn't appear out of nowhere! Chloroplasts are the sites of photosynthesis as they convert solar energy to chemical energy (transformation vs creation of energy!) by absorbing sunlight and using it to drive the synthesis of organic compounds such as sugars from CO2 and H2O.

Water always moves from a _________ water potential to a __________ water potential.

Water always moves from a *higher *water potential to a *lower* water potential. (higher free energy to lower free energy)

Why is the density of ice important?

Water expands when it freezes. In ice the bonds are stable and hold molecules farther apart. The floating ice on bodies of water acts as an insulator.

Moderation of temperature

Water moderates air temperature by absorbing heat from air that is warmer and releasing the stored heat to air that is cooler. This occurs because water has a high specific heat due to its hydrogen bonds; when it absorbs heat, hydrogen bonds are broken rather than increasing the kinetic energy of water molecules; because of this, water can absorb or release large amounts of heat with a small change in temperature. Water's high specific heat allows a large body of water to absorb and store a huge amount of heat from the sun and not change temperature by more than a few degrees (which is why August is the best beach month in Jersey!). Stable ocean temperatures allow for a favorable environment for marine life. Also, most organisms are primarily made of water so water's high specific heat helps organisms to maintain homeostasis. Water's moderation of temperature also involves evaporative cooling (because when the hottest water molecules become gaseous, it makes the average kinetic energy of the liquid water decrease and cool down); evaporative cooling occurs in human bodies with sweat and keeps organisms cool (such as plant's leaves on a hot day).

Calculating water potential

Water potential is calculated using the formula: Ψ = ΨP + ΨS Pressure potential (ΨP ): In a plant cell, pressure exerted by the rigid cell wall limits further water uptake. Solute potential (ΨS ): The effect of solute concentration.

Water potential is determined by _________ potential and __________ potential. Equation?

Water potential is determined by *solute* potential and *pressure* potential. Equation? Ψ = Ψp + Ψs

Ribosomes: what are they made of, where can you find them in the cell, what gets made there and why are they universal among all cell types?

What are they made of: ribosomal RNA (made from instructions in DNA) Where can you find them: cytosol, rough ER, nuclear envelope What gets made: Proteins ! They are universal among all cell types because they have the same function among these cells: to make proteins. Therefore, different structures to dictate different functions for these ribosomes are not needed.

cycle control system

a cyclically operating set of molecules in the cell that both triggers and coordinates key events - one event doesn't just lead to the other (like in a metabolic pathway) - cell cycle driven by specific signaling molecules present in the cytoplasm - cycle control system has been compared to the control device of an automatic washing machine (internal control, like the sensor that detects tub is full, and external, like clicking start button: regulated at certain internal and external checkpoints)

maternal effect gene

a gene that, when mutant in the mother, results in a mutant phenotype in offpsring, regardless of offspring's own genotype (codes for actual molecules that make up cytoplasmic determinants and induction process) - control orientation (polarity) of egg

locus

a gene's specific location along the length of a chromosome

clone

a group of genetically identical individuals - genetic differences occasionally arise in asexually reproducing organisms bc of mutations (which is why there are bacteria that are resistant to antibiotics)

population

a group of organisms of the same species that live in same area and interbreed (fertile offspring)

photons

a particle of light that has a fixed quantity of energy which is inversely related to the wavelength of the light: the shorter the wavelength, the greater the energy of each photon of that light

cyclin

a protein activates kinases that drive the cell cycle, gets name from cyclically fluctuating concentration in the cell

activator

a protein that binds to DNA and stimulates transcription of a gene (positive gene regulation)

inducer

a specific small molecule that inactivates the repressor

tonicity

ability of a surrounding solution to cause a cell to gain or lose water - depends in part on concentration of solutes that cannot cross membrane

aminoacyl-tRNA syntheatases

accurate translation requires two instances of molecular recognition 1. tRNA binds to mRNA codon must carry amino acid and no other to the ribosome (matching up of tRNA and aa is carried out by a family of related enzymes called aminoacyl-tRNA syntheatases, each type fits only a specific combo of aa and tRNA, 20 for each aa) 2. Pairing of tRNA anticodon w mRNA codon

threshold

action potentials occur whenever a depolarization increases the membrane voltage to a particular value (usually about -55 mV in mammalian neurons) - once initiated, the action potential has a magnitude that is independent of the strength of the triggering stimulus - all or none response to stimuli (positive feedback loop either goes or it doesn't)

why doesn't paper burst into flames/glucose combine instantly w O2?

activation energy ! - we could burn glucose except we don't want fire inside our bodies - enzymes do the job instead !

somatic cells

all cells of the body except the gametes and their precursors - diploid set of chromosomes

positional information

all of pattern formation - cues tell a cell its location relative to the body axes and to neighboring cells

gene pool

all of the alleles of all of the loci in the individuals in a population

lysogenic cycle

allows replication of the phage genome without destroying the host

selective permeability

allows some substances to cross it more easily than others - ability of cell to discriminate in its chemical exchanges with its environment is fundamental to life (plasma membrane and component molecules make this selectivity possible) - not only outer boundary but enable cell to carry out functions (i.e proteins!)

origin of self-tolerance

antigen receptor genes are randomly rearranged, so some immature lymphocytes produce receptors specific for epitopes on organism's own molecules (BAD) but we eliminate/inactivate these lymphoctyes - as lymphocytes mature in bone marrow (B cells) or thymus (T cells), the antigen receptors are tested for self-reactivity and are either destroyed by apoptosis or inactivated

DNA ligase

associations are only temporary but can be made permanent by DNA ligase

poly-A tail

at the 3' end, an enzyme adds 50-250 A nucleotides

Free energy

available, useful energy Examples: - Sun - Corn/beef - Protons on one side of mitochondrial membrane

metabolic pathway

begins with a specific molecule, which is then altered in a series of defined steps, resulting in a certain product - mechanisms that regulate enzymes balance metabolic supply and demand (ex: enzyme inhibitors)

polytomy

branch point from which more than two descendant groups emerge

testcross

breeding organism of unknown genotype with recessive homozygote because it reveals genotype (if it is always dominant phenotype then unknown genotype is PP, if half of it is recessive then unknown genotype is heterozygous)

macroevolution

broad pattern of evolution above the species level (speciation)

microevolution

change in allele frequencies in a population over a number of generations - natural selection is not the only cause of microevolution: 1. natural selection (only one that consistently improves match bw organisms and their environment) 2. genetic drift (chance events that alter allele frequencies) 3. gene flow (transfer of alleles bw populations)

point mutations

changes in single nucleotide pair of a gene - if in gamete, can be transmitted to offspring - somatic cell: not usually transmitted to offspring, depends how early on in life how bad it is

gated ion channels

changes in the resting membrane potential occur because neurons contain these types of channels that open or close in response to stimuli

paraphyletic

consists of an ancestral species and some, but not all, of its descendants

polyphyletic

consists of taxa with different ancestors

checkpoint

control point where stop and go-ahead signals can regulate the cycle (signals transmitted within cell by signal transduction pathways) - animal cells have stop signals that halt cell cycle until overridden by go-ahead signals - signals come from cellular surveillance mechanisms (has everything up to this point occurred and occurred correctly?), signals can also come from outside cell - 3 major checkpoints: G1, G2, M phases - G1 checkpoint is most important (it will usually divide if it passes this one, if not then cell will enter G0 phase) - regulatory molecules: protein kinases and cyclins

TATA box

crucial promoter DNA sequence in eukaryotic promoters

RNA splicing

cut-and-paste - removal of large portions of RNA molecule that is initially synthesized (get rid of introns, keep exons)

deletion

deletion of nucleotide

Punnett square

diagram used in study of inheritance to show predicted genotypic results in genetic crosses

sexual dimorphism

difference bw two sexes in secondary sexual characteristics

differential gene expression

differences between cell types are not due to different genes but to differential gene expression -expression of different genes by cells with the same genome

neutral variation

differences in DNA sequence that do not confer a selective advantage or disadvantage

genetic engineering

direct manipulation of genes for practical purposes

molecular systematics

discipline that uses data from DNA and other molecules to determine evolutionary relationships

domains

discrete structural and functional regions called domains

synapse

each branched end of an axon transmits info to another cell at this junction - synaptic terminal: part of each axon branch that forms this specialized synapse function - number of synapses: neuron can be simple or complex

clades

each includes an ancestral species and all of its descendants

trait

each variant for a character

electrons in cellular respiration path

electrons go downhill ! glucose --- NADH --- ETC --- oxygen (to make water)

adenylyl cyclase

enzyme that converts ATP to cAMP in response to extracellular signal - ex: epinephrine - Epinephrine binds to specific receptor protein, and this activated receptor activates adenylyl cyclase which can catalyze the synthesis of many molecules of cAMP - cAMP broadcasts signal to cytoplasm - signal doesn't last for long in cytoplasm in absence of epinephrine bc another enzyme, phosphodiesterase, converts cAMP to AMP (so that you need more epinephrine for more response)

protein phosphatases

enzymes that can rapidly *remove* phosphate groups (opposite of protein kinase) - dephosphorylation: deactivate protein kinase, provide mechanism for turning off signal transduction pathway when signal no longer present - makes protein kinases available for reuse

restriction enzymes

enzymes that cut DNA molecules at a limited number of specific locations, protect bacterial cell by cutting up foreign DAN from other organisms or phages

pedigree

family tree describing the traits of parents and children across the generations

reduction

gain of electrons (or partial gain)- bc we're not really dealing w ions here

allopatric speciation

gene flow is interrupted when a population is divided into geographically isolated subpopulations - how formidable? depends on animal/organism and situation (birds can fly over a canyon that a mouse can't climb over) - once geographic separation occurs: different mutations, natural selection/genetic drift/sexual selection may alter allele frequencies in different ways in the separated populations - reproductive isolation may then arise as by-product of selection or drift - evidence: regions that are isolated typically have ore species than do otherwise similar regions, reproductive isolation bw two populations generally increases as the distance bw them increases

life cycle

generation-to-generation sequence of stages in the reproductive history of an organism, from conception to production of its own offspring

linked genes

genes located near each other one the same chromosome and tend to be inherited together in genetic crosses

X-linked genes

genes located on the X chromosome (very few Y-linked disorders bc so few genes on the Y chromosome compared to X chromosome - Most genes on Y chromosome linked to sex - Many genes on X chromosome are for characters unrelated to sex - Fathers pass X-linked alleles to all of their daughters, but none to sons; moms can pass X-linked alleles to both sons and daughters

proteasomes

giant protein complexes that recognize ubiquitin-tagged proteins

morphogens

gradients of these substances establish an embryo's axes

absorption spectrum

graph plotting pigment's light absorption versus wavelength

action spectrum

graphs effectiveness of different wavelengths of radiation against rate of photosynthesis - illuminate chloroplasts w light of diff colors and then plot wavelength against measure of photosynthetic rate (like CO2 consumption or O2 reaction)

monohybrid

heterozygous for one particular character

P site

holds tRNA carrying the growing polypeptide chain

spliceosome

how is pre-mRNA splicing carried out? - signal for RNA splicing is short nucleotide sequence at end of each intron - snRNPs recognize splice sites, they are in nucleus - several different snRNPs join w additional proetins to form an even larger assembly called spliceosome (snRNP; catalyze) - splicing has to be accurate: or else reading frame is off

human population growth

human population still growing but not exponentially - we don't rly know carrying capacity for humans

hypertonic

hyper = "more" - cell will lose water (and can die) - solution that has a higher solute concentration compared to other solution (fewer free water molecules)

virus

infectious particle consisting of little more than genes packaged in a protein coat (level of organization: eukaryotic cell to bacteria/prokaryote to virus) - viruses cannot reproduce or carry out metabolic activities outside of a host cell (not alive but exist in a shady are between life-forms and chemicals) - experiments with viruses gave important evidence that genes are made of nucleic acids

epigenetic inheritance

inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence

gamma-aminobutyric acid (GABA)

inhibitory

provirus

integrated viral DNA that never leaves host's genome, remaining permanent resident of cell (prophage leaves host cell's genome at beginning of lytic cycle)

heat/thermal energy

kinetic energy associated with the random movement of atoms or molecules (ex: temperature is average kinetic energy)

mass extinction

large numbers of species become extinct throughout Earth

demographics

life tables- show age-specific survival patterns of a population. Ecologists follow the fate of a cohort: a group of individuals born at the same time.

local/graded potential

ligand-gated ion channels! on dendrites! shift in membrane potential in response to hyperpolarization or depolarization - has a magnitude that varies with the strength of the stimulus(neurotransmitter!), w a larger stimulus causing a greater change in the membrane potential - local potentials induce a small electrical current that leaks out of the neuron as it flows along the membrane (they decay w distance from their source) - they aren't the nerve signals that travel along axons but have a major effect on the generation of nerve signals

acetyl CoA

link between glycolysis and Krebs cycle ! - once enters mitochondrion, pyruvate converted to acetyl CoA (3 reactions that are carried out by multienzyme complex) 1. Pyruvate carboxyl group (fully oxidized and little potential energy) is removed and given off as molecule of *CO2* 2. Now the 2-carbon molecule oxidized to make acetate--- electrons go to NAD+ to make NADH 3. CoA attached via sulfur atom to acetate to make acetyl CoA (high potential energy)

protein

made of these elements: CHON(S) - most complex chemical compound - made up of many polypeptide chains - MANY diverse structures and functions

egg polarity genes

maternal effect genes

cytoplasmic determinants

maternal substances in the egg that influence the course of early development

saltatory conduction

mechanism for action potentials - APs are not generated in regions bw nodes - inward current produced during risign phase of AP at a node travels all the way to the next node, where it depolarizes the membrane and regenerates the AP - time-consuming process of opening and closing ion channels occurs only at limited number of positions along the axon

proteins

monomer: amino acid many diff functions: - build molecules - digest molecules - carry out chemical reactions (enzymes) - copy DNA and RNA - receive and send messages to environment/other cells

multiple alleles

most genes exist in more than two allelic forms (BUT each human still has only two of those alleles) - Ex: bunnies

embryonic lethals

mutations with phenotypes causing death at the embryonic or larval stage (can't be bred to study)

neurons

nerve cells that transfer info within the body - long-distance electrical signals and short-distance chemical signals

postsynaptic cell

neuron, muscle, or gland cell that receives the signal

nerves

neurons in CNS and PNS

interneurons

neurons in the brain - integrate (analyze and interpret) the sensory input, taking into account the immediate context and experience

peripheral nervous system (PNS)

neurons that carry info into and out of the CNS (motor function)

NADP+

nicotinamide adenine dinucleotide phosphate - accepts two electron and proton from one split water molecules to become: NADPH !

branch points

nodes, represents divergence of two evolutionary lineages from a common ancestor (speciation)

recombinant (types)

nonparental phenotypes (new combinations) - 50% recombination frequency means that two genes are located on different chromosomes and aren't linked

prosthetic groups

nonprotein components essential for the catalytic functions of certain enzymes

cofactors

nonprotein enzymes that are sometimes required for an enzyme to be active - can be inorganic—think zinc, iron, copper—or it can be organic. When the cofactor is organic, it's called a coenzyme. Vitamins are often coenzymes!

proto-oncogenes

normal versions of oncogenes (mutated); code for proteins that stimulate normal cell growth and division genetic changes from proto-oncognenes to oncogenes: - movement of DNA within the genome - amplification of a proto-oncogene - point mutations in a control element or in the proto-oncogene itself

anticodon

nucleotide triplet that base-pairs with a complementary codon on mRNA

mutagens

number of physical and chemical agents that interact w DNA in ways that cause mutations

dendrites

numerous highly branched extensions of a neuron that *receive* signals from other neurons

homologous chromosomes

one from mom, one from dad - same length, centromere position, and staining pattern (BUT different alleles)

sticky end

one single stranded strand, can form hydrogen-bonded base pairs w complementary sticky ends on any other DNA molecules cut w same enzyme

template strand

only one of DNA stands is transcribed: template strand - for any given gene, the same strand is used as the template every time the gene is transcribed (BUT for other genes on the same DNA molecule, the opposite strand may be the one that always functions as the template) - mRNA is complementary to template strand and almost identical to coding strand

operon

operator, promoter, and the genes they control (entire stretch of DNA required for enzyme production for the pathway) - By itself, the operon is either turned on or off (depending on if it's a repressor or an inducer)

genetic map

ordered list of genetic loci along a particular chromosome - recombination frequency depends on distance between genes on a chromosome - farther apart the two genes arek the higher the probably that a crossover will occur between then and therefore the higher the recombination frequency the farther apart you go

ectotherm

organism that gains most of their heat from external sources - doesn't need to eat as often - usually tolerate larger fluctuations in their own body temperature

phenotype

organism's appearance/observed traits

polyploidy

organisms that have more than two complete chromosome sets in all somatic cells - fairly common with plants

true-breeding

organisms that produce offspring of the same variety over many generations of self-pollination

wild type

phenotype for a character most commonly observed in natural populations (vs *mutant phenotypes*)

epistasis

phenotypic expression of a gene at one locus alters that of a gene at a second locus ex: chocolate labs

oxidative phosphorylation

powered by redox reactions of ETC (adds inorganic phosphate to ADP)

p-value

probability of getting your results or more extreme if the null hypothesis is true (so if extremely low- below .05 value, then you reject null hypothesis) - if p-value larger than .05 value, then you fail to reject null hypothesis cuz not unique enough

DNA replication

process by which a DNA molecule is copied

thermoregulation

process by which animals maintain an internal temperature within a tolerable range (imp. cuz reactions/enzymes need heat but not too much)

horizontal gene transfer

process in which genes are transferred from one genome to another through mechanisms such as exchange of transposable elements and plasmids, viral infection, and perhaps fusions of organisms

spontaneous process

process that can occur without any input of energy (loss of free energy in products AND increase in entropy)

genetic recombination

production of offspring with combinations of traits that differ from those found in either parent

start point

promoter of a gene includes the start point (nucleotide where RNA synthesis starts)

interferons

proteins that provide innate defense by interfering with viral infections

transcription factors

proteins that regulate transcription (both activators and repressors)

alcohol fermentation

pyruvate is converted to ethanol in two steps - first step releases CO2 from pyruvate--- turns into 2- carbon acetaldehyde - then Acetaldehyde reduced by NADH to ethanol - Regenerates supply of NAD+ needed for continuation of glycolysis - Where: Many bacteria do this, yeast does this

substrate

reactant an enzyme acts on

How do catabolic pathways that decompose glucose and other organic fuels yield energy?

redox reactions ! (transfer of electrons- relocation releases energy to produce ATP)

depolarization

reduction in magnitude of resting membrane potential (making inside of membrane less negative) - usually involves gated sodium channels (if stimulus causes them to open, Na+ goes down concentration gradient into cell)

concentration gradient

region along which the density of a chemical substance increases or decreases - each substance has its own concentration gradient (unaffected by concentration gradients of other substances)

nucleotide-pair substitution

replacement of one nucleotide and its partner with another pair of nucleotides - *silent mutation*: if code for same codon, doesn't have an effect- silent - *missense mutation*: substitutions that change one aa to another one (can have little effect depending on it crucial are of protein or not) - *nonsense mutation*: point mutation can change codon for aa into stop codon (causes tranlsation to be terminated prematurely: BAD, nonfunctional protein)

chiasmata

result of crossing over, hold pairs together due to sister chromatid cohesion

HIV (human immunodeficiency virus)

retrovirus that causes AIDS - enveloped virus that contains two identical molecules of single-stranded RNA and two molecules of reverse transcriptase 1. Envelope glycoproteins enable virus to bind to specific receptors on certain white blood cells 2. The virus fuses with cell's plasma membrane, and capsid proteins removed, releasing viral proteins and RNA 3. Reverse transcriptase catalyzes the synthesis of a DNA strand complementary to viral RNA 4. Reverse transcriptase catalyzes synthesis of second DNA strand complementary to first 5. Now double stranded DNA as provirus into host cell's DNA 6. Proviral genes transcribed into RNA molecules, which serve as genomes for next viral generation and as mRNAs for translation into viral protein 7. Viral proteins include capsid proteins and reverse transcriptase (made in cytosol) and envelope glycoproteins (made in ER) 8. Vesicles transport glycoproteins to cell's plasma membrane 9. Capsids assembled around viral genomes and reverse transcriptase molecules 10. New viruses bud off from host cell

All chemical reactions are ____.

reversible

ribosomal RNAs (rRNA)

ribosome consists of large subunit and small subunit, w proteins and one or more rRNAs, functional ribosome only when attached to mRNA -eukaryote ribosome a little bitter than prokaryote

How to measure SEM?

s/(square root n)

phylogenetic tree

same as a cladogram - intended to show pattern of descent, not phenotypic similarity - sequence of branching in a tree does not necessarily indicate actual/absolute ages of the particular species - we should not assume that a taxon on a phylogenetic tree evolved from the taxon next to it - in some phylogenetic trees, branch lengths are proportional to amount of evolutionary change or to times at which particular events occurred

genetics

scientific study of heredity and hereditary variation

inositol trisphosphate (IP3), diacylglycerol (DAG)

second messengers involved in calcium release pathways - produced by cleavage of certain kind of phospholipid in plasma membrane

control elements

segments of noncoding DNA that serve as binding sites for the proteins called transcription factors, which in turn regulate transcription - proximal: close to promoter - distal: upstream or downstream or even within intron - combination: only a dozen control element sequences available, but many unique combinations to created unique enhancers for each gene!

intrasexual selection

selection within the same sex (individuals of one sex compete directly for mates of the opposite sex) Ex: patrolling male

RNA polymerase

separates two strands of DNA and joins together RNA nucleotides complementary to the DNA template strand (can only add to 3' end, but they don't need a primer like DNA polymerase) - bacteria only have one RNA polymerase - eukaryotes have three types, RNA polymerase II makes mRNA

cleavage furrow

shallow groove in the cell surface near the old metaphase plate

a factor

signaling molecule that can bind to receptor proteins on alpha cells

signaling pathways can ___________ with one another- they are not __________ pathways

signaling pathways can *interact* with one another- they are not *linear* pathways

induction

signals that impinge on an embryonic cell and cause changes in target cells

alternative RNA splicing

single gene can encode more than one kind of polypeptide - sex diffs in fruit flies are largely due to alternative splicing in male vs female

asexual reproduction

single individual is the sole parent and passes copies of all its genes to its offspring *without* the fusion of gametes - Ex: single-celled eukaryotic organisms - genomes of offspring are virtually exact copies of parent's genome

functional difference between receptor tyrosine kinases and G protein-coupled receptors

single ligand-binding event in receptor tyrosine kinases can trigger up to ten pathways compared to the single one that G protein-coupled receptors trigger

microRNAs (miRNAs)

small single-stranded RNA molecules that are capable of binding to complementary sequences in mRNA - made from longer RNA precursors that fold back on themselves to form hairpins held together by H bonds, one of two strands degraded and the other strand is miRNA - miRNA allows the complex to bind to any mRNA molecule w 7-8 complementary nucleotides

second messengers

small, non-protein, water soluble molecules that are involved in signal transduction Ex: AMP, Ca2+ - participate in both G-protein and receptor tyrosine kinase pathways

smaller molecules are assembled into ___________, which may be _________ later as the needs of the cell change

smaller molecules are assembled into *polymers*, which may be *hydrolyzed* later as the needs of the cell change

cells

smallest unit that can carry on purposes of life

viral envelopes

some viruses have accessory structures that help them infect their hosts (envelope can surround the capsids of viruses) - outer membrane that is used to enter the host cell - viral glycoproteins on envelope that bind to specific receptor molecules on surface of a host cell - viral envelope is derived from the host cell's plasma membrane (this replicative cycle doesn't kill host cell like lytic cycles of phages) - herpesviruses are temporarily cloaked in membrane derived from nuclear envelope of the host, and then shed this membrane in cytoplasm and acquire new envelope made from membrane of Golgi, have a double-stranded DNA genome and replicate within host cell nucleus, using viral and cellular enzymes to replicate and transcribe their DNA

transcription factors

special proteins that control which genes are turned on (transcribed into mRNA) in a particular cell at a particular time

meiosis

special type of cell division that reduces the number of sets of chromosomes to one for sexual reproduction (to counterbalance doubling at fertilization) to maintain constant number of chromosomes in each species from one generation to the next MEIOSIS I *Prophase I* - Chromosomes begin to condense, and homologs loosely pair along their lengths, aligned gene by gene - Paired homologs become physically connected to each other along their lengths by a zipper-like protein structure (*synapsis*) - *Crossing over*, forms recombinant chromosomes, chiasmata - Centrosome movement - Spindle formation - Nuclear envelope breakdown - Microtubules from one pole or the other attach to two kinetochores, protein structures at centromeres of homologs *Metaphase I* - Pairs of homologous chromosomes now arranged at metaphase plane - Both chromatids attached to kinetochore microtubules from one pole; those of other homolog are attached to microtubules from opposite pole *Anaphase I* - Breakdown of proteins responsible for sister chromatid cohesion to let homologs separate - Homologs move toward opposite poles guided by spindle - Sister chromatid cohesion persists at centromere causing chromatids to move as unit *Telophase I and Cytokinesis I* - Each half of cell has complete haploid set with two sister chromatids - no chromosome duplication/S phase - cleavage furrow like mitosis bc sister chromatids separating: MEIOSIS II Prophase II Metaphase II Anaphase II Telophase II and Cytokinesis II

germ cells

specialized diploid cells in the gonads (ovaries and testes)

signal transduction pathway

specific cellular response in a series of steps when information from a signal molecule to a receptor and relay molecules (usually through a series of shape changes brought about by phosphorylation)

origin of replication

specific place on chromosome where cell division is initiated and chromosome begins to replicate, producing two origins

specificity of an enzyme results from its _________ (which is consequence of *amino acid* sequence)

specificity of an enzyme results from its *shape* (which is consequence of *amino acid* sequence)

metastasis

spread of cancer cells to locations distant from their original site - tumor cells that have separated from the original tumor to travel to other parts of the body

nucleic acids

stores information to make proteins (protein synthesis)

reinforcement

strengthening of reproductive barriers (hybrids cease eventually to be formed)

transcription unit

stretch of DNA that is transcribed into an RNA molecule

population ecology

study of populations in relation to their environment, specifically how biotic and abiotic factors influence density, distribution, size and age of the population Evolution too!

saturated enzyme

substrate concentration in which as soon as product exists an active site, another substrate molecule enters (only way to make it faster now is to increase enzyme concentration not substrate concentration or increase temperature slightly)

serial endosymbiosis

supposes that mitochondria evolved before plastids through a sequencwe of endosymbiotic events (why not all eukaryotes have plastids)

transcription

synthesis of RNA using information in the DNA - info rewritten as RNA from DNA

translation

synthesis of a polypeptide using the information in the mRNA - change in language: cell must translate the nucleotide sequence of mRNA to amino acid sequence of polypeptide

why aren't all unfavorable alleles cut out?

tendency for directional and stabilizing selection to reduce variation is countered by mechanisms that preserve or restore it - diploid: considerable amount of genetic variation is hidden from selection in the form of recessive alleles (harmful recessive can stay in form of heterozygous individuals) - balancing selection: occurs when natural selection maintains two or more forms in a population

proton-motive force

the H+ gradient that results from the pumping of H+ outside of the mitochondrion due to the ETC; this force emphasizes the capacity of the gradient to perform work (in this case, to make ATP!)

determination

the events that lead to the observable differentiation of a cell (irreversible) - outcome of determination marked by expression of genes for *tissue-specific proteins* - first evidence: appearance of mRNA for these proteins - eventually you can see w microscope (diff sets of genes are expressed in regulated manner as new cells arise) - different steps in gene expression regulated during differentiation, transcription most important

diffusion

the movement of molecules of any substance so that they spread out evenly into the available space - each individual molecule moves randomly BUT diffusion of a *population* of molecules may be directional - in the absence of other forces (SUCH AS PRESSURE IN WATER POTENTIAL), a substance will diffuse from where it is more concentrated to where it is less concentrated (substance moves down its *concentration gradient*) - NO WORK MUST BE DONE: spontaneous process that doesn't need an input of energy

metabolism

totality of an organism's chemical reactions - manages the material and energy resources of the cell

electrogenic pump

transport protein that generates voltage across a membrane Ex: NaCl carrier protein (major electrogenic pump of animal cells), proton pump- store energy for ATP synthesis (plant cells)

sexual reproduction

two parents give rise to offspring that have unique combinations of genes inherited from the two parents - offspring vary genetically from their siblings and both parents but there is family resemblance (genetic similarity but also variation)

genomic imprinting

variation in phenotype depending on whether an allele is inherited from the male or female parent - compared to sex-linked genes, most imprinted genes are on autosomes - occurs during gamete formation and results in the silencing of a particular allele of certain genes - zygote only expresses one allele of imprinted gene, depending on inherited fro either female or male - in each generation, the old imprints are "erased" in gamete-producing cells and the chromosomes of the developing gametes are newly imprinted according to sex of individual who is producing gametes - to live, need exactly one copy of these imprinted genes

ecological species concept

views a species in terms of ecological niche (how do members of the species interact w nonliving and living parts of their environment)

action potential

voltage-gated ion channels! on axons! - if depolarization/local potential passes threshold sufficiently, the result is a massive change in membrane voltage (action potential) - have a constant magnitude, all or none/do not decay - can regenerate in adjacent regions of the membrane(can spread along axons) - they arise bc some of ion channels in neurons are voltage-gated ion channels, opening or closing when the membrane potential passes a particular level (threshold) - depolarization opens voltage-gated Na+, there is further depolarization, which opens more voltage-gated channels (positive feedback loop) - usually initiated at an axon hillock 1. *Resting State* When membrane of axon is at resting membrane potential, most voltage-gated sodium channels are closed. Some potassium channels are open, but most of them are closed as well. 2. *Depolarization* - A stimulus(neurotransmitters) depolarizes the membrane by opening ligand-gated sodium channels which causes some voltage-gated sodium channels to open, which causes further depolarization, which opens even more voltage-gated channels 3. *Rising Phase of Action Potential* - Once threshold is crossed, the positive-feedback cycle rapidly brings the membrane potential close to ENa (bc all voltage-gated ion channels open) 4. *Falling phase of the action potential* Two events prevent the membrane potential from actually reaching ENa: - Voltage-gated sodium channels inactivate soon after opening, halting Na+ inflow - Most voltage-gated K+ channels open, causing rapid outflow of K+ to make inside of cell negative again 5. *Undershoot* - Membrane's permeability to K+ is higher than at rest, so membrane potentail is closer to EK than it is at resting potential, but the gated potassium channels eventually close and membrane potential returns to RMP

nodes of Ranvier

voltage-gated sodium channels are restricted to gaps in myelin sheath (nodes of Ranvier) - APs are not generated in regions bw nodes - inward current produced during risign phase of AP at a node travels all the way to the next node, where it depolarizes the membrane and regenerates the AP - time-consuming process of opening and closing ion channels occurs only at limited number of positions along the axon

genetic drift

when chance events can cause allele frequencies to fluctuate unpredictably from one generation to the next - can have effect until population becomes large enough that it doesn't have much of an effect - A random change in allele frequency - Happens in small populations, things happen just by chance -Small group of individuals colonizes a new habitat: founder's effect, bottleneck effect - Individuals carry alleles in different relative frequencies compared to original large population

heterozygote advantage

when individuals who are heterozygous at a particular locus have greater fitness than do both kinds of homozygotes - if so, natural selection tends to maintain two or more alleles at that locus - can be stabilizing or directional selection (depending if heterozygote has a diff phenotype or not) Ex: sickle cell anemia (recessive gives you sickle cell anemia), homozygous dominant doesn't protect you from severe effects of malaria

cell body

where most of a neuron's organelles and nucleus are located

how can populations be described

density (# individuals per unit area or volume)- not static bc births, deaths, immigration cause it to change a lot dispersion (clumped, uniform, or random) demographics

alternative RNA splicing

different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns (type of gene regulation in EUKARYOTES, bc prokaryotes don't do RNA processing- no protection needed from nucleus to cytoplasm bc no nucleus so ribosomes are right there) - helps explain relatively low number of human genes (75-100% of human genes that have multiple exons prob undergo alternative RNA splicing)

E site

discharged tRNAs leave ribosome

AIDs (acquired immunodeficiency syndrome)

disease that results from HIV

host range

each particular virus can infect cell so f only a limited number of host species - host specificity results from the evolution of recognition systems by the virus - "lock and key" fit between viral surface proteins and specific receptor molecules on the outside of cells

restriction site

each restriction enzyme is specific, recognizing a particular short sequence (restriction site) - most are symmetrical

early versions of today's cell-signaling mechanisms __________ well before the first multicellular creatures appeared on Earth

early versions of today's cell-signaling mechanisms *evolved* well before the first multicellular creatures appeared on Earth (yeast and mammal signal transduction pathway similar yet it's been a very long time since common ancestor)

cytotoxic T cells

effector cells for T cells (cell-mediated response!) to become activated: - require signaling molecules from helper T cells - interaction w a cell that presents antigen when activated: - cytotoxic T cells can eliminate cells that are infected by viruses or other intracellular pathogens 1. Activated cytotoxic T cell binds to class I MHC-antigen fragment complex on infected host cell through receptor and accessory protein (CD8) 2. Cytotoxic T cell releases perforin molecules which make pores in infected cell membrane, granzymes (enzymes that break down proteins) - granzymes enter infected cell by endocytosis 3. Granzymes initiate apoptosis within the infected cell leading to fragmentation of nucleus and cytoplasm and eventual cell death - released cytotoxic T cell can attack other infected cells

photosystem

- *reaction-center complex* with several light-harvesting complexes

Golgi Apparatus

- Secretory proteins from ER modified (carbohydrate monomers removed/added) - Tagged for delivery to certain destinations

What is a positive feedback loop?

- There is an excess of product that causes an excess of production. More rare.

first law of thermodynamics

energy of universe is constant Conservation of energy: energy can be transferred and transformed, but it cannot be created or destroyed Ex: plant converts solar energy to chemical energy

potential energy

energy that matter possesses because of its location or structure (NOT kinetic energy- about its position)

facultative anaerobes

- can make enough ATP to survive using either fermentation OR respiration - Ex: yeast, bacteria, our muscle cells

anabolism

- consume energy to build complicated molecules from simpler ones - AKA biosynthetic pathways Ex: synthesis of an amino acid from simpler molecules AND synthesis of a protein from amino acids UPHILL

sodium-potassium pump

- creates membrane potential (inside of cell is more negative than outside)- potential energy

coordinately controlled genes

- genes of related function need to be turned on at same time (bacteria: operon; eukaryotes: scattered over diff chromosomes, so it depends on association of a specific combination of control elements with every gene of dispersed group so that the same activators turn all of the genes on) ex: estrogen stimulating pregnancy

survivorship curves

- made using life table data - Most oysters don't survive when they're young while most humans do

purpose of allosteric regulation and feedback inhibition

- not make too much stuff! - be efficient - Ex: ATP (if excess, then there's enough to bind to enzymes in allosteric regulation)

electromagnetic spectrum

entire range of radiation

reverse transcriptase

enzyme in retroviruses that transcribes an RNA template into DNA, providing an RNA to DNA information flow, the opposite of the usual directions - opposite of the usual direction - HIV

reaction-center complex

- organized association of proteins holding a special pair of chlorophyll a molecules - pair is special because their molecules enable them to use energy from light not only to boost one of electrons to higher level but to transfer electron to the primary electron acceptor

kinase

enzyme that catalyzes the transfer of phosphate groups

protein kinase

enzyme that catalyzes the transfer of phosphate groups from ATP to a protein (often another protein kinase)

List 4 types of lipids.

1. Triglycerides (aka fats made of 3 fatty acids and one glycerol) 2. Phospholipids (cell membrane) 3. Waxes 4. Steroids

glutamate

excitatory

serotonin

excitatory

biogenic amines

excitatory (norephinrine- excitatory)

reproductive isolation

existence of biological factors that impede members of two species from interbreeding and producing viable, fertile offspring

exons

expressed! except for UTRs of exons at ends of RNA that help w ribosome binding but aren't expressed, all exons are expressed

axon

extension that *transmits* signals to other cells - often much longer than dendrites - some are over a meter long (spinal cord of giraffe to its feet) - axon hillock: where signals that travel down the axon are generated - bottom of axon divided into many branches

density-dependent inhibition

external physical factor on cell division - phenomenon in which crowded cells stop dividing - cultured cells normally divide until they form single layer of cells on inner surface of culture container, and then they stop dividing - cancer cells do not exhibit density-dependent inhibition or anchorage dependence

zygote

fertilized egg - diploid bc it contains 2 haploid sets of chromosomes (both mom and dad)

genus

first part of binomial and general to genus to which species belongs (epithet is second part, specific to species)

sex-linked gene

gene located on either chromosome

crossing over

genetic rearrangement between non-sister chromatids involving the exchange of corresponding segments of DNA molecules

cline

graded change in a character along a geographic axis

sister taxa

groups of organisms that share an immediate common ancestor and are each other's closest relatives

fertilization

haploid sperm from father fuses with a haploid egg from the mother

RNA processing

happens ONLY in eukaryotes !

brain/ganglia

higher-order processing neurons organized together

A site

holds tRNA carrying the next aa to be added to chain

RNA processing

ONLY eukaryotes - both ends of primary transcript are altered(5' cap, poly-A tail) PROTECT mRNA during transport, from degradation from hydrolytic enzymes, and help ribosomes attach to 5' end of mRNA - in most cases, certain interior sections of RNA molecule are cut out and the remaining parts spliced together (RNA splicing)

What is RNA?

Ribose, single stranded, not stable, codes for amino acids and acts as messenger between DNA and ribosomes.

hypotonic

hypo = "less" - solution that has a lower solute concentration compared to other solution (more free water molecules) - water will enter cell faster than it leaves (it can burst)

aneuploidy

if abnormal gamete resulting from nondisjunction unites with a normal one at fertilization to create a zygote with an abnormal number of a particular chromosome

malignant tumor

includes cells whose genetic and cellular changes enable them to spread to new tissues and impair the functions of one or more organs - excessive proliferation - unusual numbers of chromosomes

hyperpolarization

increase in magnitude of membrane potential (becomes more negative) - Ex: Gated potassium channels open, letting even more potassium out - results from any stimulus that increases outflow of positive ions (like K+) or inflow of anions (like Cl-)

autopolyploid

individual that has more than two chromosome sets that are all derived from a single species

Is sample size important?

Yes, it is more difficult to detect a difference between experimental and observed in a small sample. - Stats numbers get more accurate w larger sample size

primary transcript

initial RNA transcript from any gene, including those specifying RNA that is not translated into protein (i.e. still has introns and other junk)

rooted

a branch point within the tree (often drawn farthest to left) represents the most recent common ancestor of all taxa in the tree

frameshift mutation

insertions and deletions: alter reading frame!

hybrid zone

a region in which members of diff species meet and mate, producing at least some offspring of mixed ancestry (allopatric populations can come into contact again) 1. Three populatos of species connected by gene flow 2. Barrier to gene flow established 3. Population begins to diverge from other two populations 4. Gene flow re-established in a hybrid zone 5. Possible outcomes: reinforcement or fusion or stability

insertion

addition of nucleotide

antibody

aka immunoglobulin (Ig) -

alleles

alternative versions of a gene that may produce distinguishable phenotypic effects

geographic variation

differences in the genetic composition of separate populations

high rates of transcription

high rates of transcription are controlled by specific transcription factors (activators or repressors). Activators facilitate a series of protein-protein interactions that result in transcription of a given gene.

virulent phage

phage that only replicates by a lytic cycle

scaffolding proteins

large relay proteins to which several other relay proteins are simultaneously attached - increase efficiency of signal transduction - facilitate phosphorylation cascades - keeps rate of protein-protein interaction not dependent on diffusion of such large molecules within cytoplasm

major site of photosynthesis in most plants

leaves (with stomata!)

autotrophs

"self-feeders" - sustain themselves without eating anything derived from other living beings (ie: plants) - produce organic molecules (sugars) from CO2! (where their mass comes from) - plants are *photoautotrophs* - autotrophs: producers of biosphere

MHC molecule

*Major Histocompatability Complex Molecule*

phospholipid

- 2 fatty acids and a phosphate group connected w/glycerol - makes up cell membranes in all cells as well as organelle membranes - hydrophilic head and hydrophobic tail - form and function related!

Hardy-Weinberg principle

- Allele frequencies remain constant unless one or more factors cause it to change. - Math! Not too difficult math! - Constant allele freq = genetic equilibrium

Surface area to volume ratio

- As cells increase in volume, the relative surface area decreases and demand for material resources increases - More cellular structures needed for exchanging materials/energy with the environment. Sooooo, cell size is limited!

Water potential

- Free energy per mole of water - Predicts which way water diffuses through plant cells

three types of genes involved in pattern formation

- Maternal effect genes: code for cytoplasmic determinants/induction signal molecules (beginning development) - Segmentation genes - Homeotic genes: code for transcription factors (more final touches)

exergonic

- Negative Gibb's free energy: spontaneous - Reactants have more free energy than products - Energy released (net release of free energy) WHY SPONTANEOUS: Bc universe prefers stability/order and low energy EXOTHERMIC AND EXERGONIC ARE NOT the same CELLULAR RESPIRATION !

semiconservative experiment

- Nucleotides labeled with heavy isotope of nitrogen, 15N - They then transferred bacteria to a medium with only 14N, a lighter isotope - Sample taken after DNA replicated once and after it replicated again - First replication had a band of hybrid (15N and 14N) DNA, eliminating conservative model - Second replication produced both light and hybrid DNA, supporting semiconservative model

endergonic

- Positive Gibb's free energy: not spontaneous - Products have more free energy than reactants - Energy required WHY NOT SPONTANEOUS: Bc universe likes stability/order and low energy PHOTOSYNTHESIS !

Measures of variability

- Range (NOT resistant) - Standard deviation (NOT resistant) - Variance - IQR (Resistant)

Measures of confidence?

- Standard error of the mean - 95% confidence interval (used with larger data sets)

population dynamics

- all populations have hanging environmental factors that disrupt them. - boom and bust cycles and complex interactions that affect population size and make it super dynamic

fermentation vs anaerobic respiration vs aerobic respiration

- all three use glycolysis /use NAD+ as oxidizing agent to accept electrons from food ! - each have different mechanisms for turning NADH back into NAD+ (fermentation- electrons end up in pyruvate/acetaldehyde, anaerobic- electrons end up in electronegative compound like sulfate, aerobic - electrons end up in oxygen) - anaerobic and aerobic respiration: much more ATP bc of ETC (can extract energy from pyruvate molecules !)

antigen

- any substance that elicits a response from a B cell or T cell - part of a pathogen (sometimes a protein)

connection between yeast cells

- cell conversation: sex

quorum sensing

- concentration of small signaling molecules that can be detected by other bacterial cells that allows them to monitor the local density of cells - allows bacterial populations to coordinate their behaviors so they can carry out activities that are only productive when performed by a given number of cells in synchrony - example: biofilm (aggregation of bacterial cells adhered to a surface that derive nutrition from the surface they are on)

antibody function

- do not kill pathgens - bind to antigens and mark pathogens in various ways to inactivate it or mark it for destruction

relationship of metabolic rate to body size in relation to cellular respiration

- each gram of a mouse requires about 2- times as many calories as a gram of an elephant, even though the whole elephant uses far more calories than the whole mouse - higher metabolic rate per gram for smaller animals, demands a higher rate pf oxygen delivery

amplification effect

- elaborate enzyme cascades amplify the cell's response to a signal - number of activated products in the next step is much greater than in the preceding step. - proteins persist in the active form long enough to process numerous molecules of substrate before they become inactive again (this is why each step sees an increase in the number of molecules than the prior)

NAD+

- electron carrier like NADP+ ! (can cycle bw NAD+ and NADH easily) - coenzyme - carries electrons when pair of H atoms from substrate - oxidizing agent - electrons lose very little of potential energy when transferred from glucose to NAD+, each NADH molecule formed during respiration represents stored energy that can be used to make ATP when electrons complete fall down energy gradient from NADH to oxygen

First law of thermodynamics

- energy is *not* created/destroyed BUT is transferred/transformed - chemical energy in fish that bear is eating is converted to heat when it moves - total energy of isolated system constant

Anton van Leeuwenhoek

- first person to observe living cells (1673), called them animalcules - ... my work, which I've done for a long time, was not pursued in order to gain the praise I now enjoy, but chiefly from a craving after knowledge, which I notice resides in me more than in most other men. And therewithal, whenever I found out anything remarkable, I have thought it my duty to put down my discovery on paper, so that all ingenious people might be informed thereof.

fossil fuels

- formed from remains of organisms that died hundreds of millions of years ago - represent stores of the sun's energy from the distant past

particulate hypothesis

- gene idea - parents pass on discrete heritable units (genes) - more like deck of cards vs pail of paint (can be shuffled and passed along)

diploid cells and alleles

- genetic locus represented twice in each diploid (could be identical, as in P generation, or different as in F1)

carotenoids

- group of accessory pigments - various shades of yellow and orange because they absorb violet and blue-green light - may broaden spectrum of colors that can drive photosynthesis BUT photoprotection is more important: absorb and dissipate excessive light energy that would otherwise damage chlorophyll or interact with oxygen to make dangerous molecules (they are in our eyes to protect us too)

amphipathic

- having both a hydrophilic region and a hydrophobic region (like a phospholipid molecule and most proteins within membranes)

antigen receptor

- how recognition of pathogen occurs in T and B cells - specific enough to bind to just one part of one molecule from a particular pathogen - cells of immune system produce millions of diff antigen receptors but all of the antigen receptors made by a single B or T cell are identical

RNA interference (RNAi)

- injecting double-stranded RNA molecules into a cell somehow turned off expression of a gene with the same sequence as the RNA (due to siRNAs)

cyclin-dependent kinases (Cdks)

- kinases that drive cell cycle (bc they require cyclins to be active) - activity of Cdk rises and falls with changes in the concentration of its cyclin partner (bc kinases in cell in pretty constant concentration) - cyclin rises during S and G2 phases and falls abruptly during M phase

photosynthesis

- life on earth is solar powered! - chloroplasts of plants capture light energy taht has traveled 150 million km from sun and converts it to chemical energy that is stored in sugar and other organic molecules SIMPLIFIED EQUATION: 6CO2 + 6H2O (presence of light energy)--- C6H12O6 + 6O2 Really (still simplified but this too): 6CO2 + 12H2O (presence of light energy)--- C6H12O6 +6H2O

mitotic spindle

- many of events of mitosis depend on *mitotic spindle* - begins to form in the cytoplasm during prophase - consists of fibers made of microtubules (made of tubulin, a protein)

fluid mosaic model

- membrane is fluid structure with "mosaic" of various proteins embedded in or attached to a double layer (bilayer) of phospholipids

genetic variation

- occurs among individuals of all species - differences among individuals in the composition of their DNA (in the form of genes) - some phenotypic variation is not inheritable: (environmental factors, too-- acquired traits), only genetic part of phenotypic variation can have evolutionary consequences How common is genetic variation? - Individual organism is heterozygous for many genes - Varies per species...insects heterozygous for up to 15% of genes, less in mammals - In humans, heterozygosity high for enzymes. - A gene is said to be fixed if only one allele exists at a particular loci in a population. All individuals are homozygous

plasmolysis

- occurs when plant cell is in hypertonic solution - plasma membrane pulls away from the wall: causes plant to wilt and can lead to plant death

temporal summation

- on some occasions, 2 EPSPs occur at a single synapse in such rapid succession that the postsynaptic neuron's membrane potential has not returned to resting before arrival of second EPSP - added together, you get temportal summation

integral proteins

- penetrate the hydrophobic interior of the lipid bilayer - majority are transmembrane proteins (span the entire membrane) - some only go partly into hydrophobic interior - some have hydrophilic channel through center to allow passage of hydrophilic substances

molecular recognition

- receptor molecules bind specifically to molecules from foreign cells or viruses (distinguish nonself from self)

speed of axons

- the larger the diameter, the faster the speed at which APs are conducted - vertebrate axons are narrow but insulated (myelin sheath), so depolarizing current associated w an AP can spread farther along the axon interior

cyclic electron flow

- uses PS I but not PS II - no production of NADPH or release of oxygen (no splitting of water) but it does generate ATP - these organisms are better in low light but can't do photosynthesis in intense light

Dehydration reaction

-Monomers add to form polymers (short+short=long) -Each time a monomer is added, a molecule of H2O is released/taken away DEHYDRATED=DOESN'T HAVE WATER

What is a feedback loop?

-Regulation of a chemical process - The output or product regulates the process

Nucleotide

-monomer of nucleic acids - 5C sugar phosphate group (PO4) and a nitrogenous base (A, T, G, C)

amino acid

-monomer of protein (only one amino acid has nitrogen, so some essential amino acids can't be made in the body-- they have to be eaten) - since amino acids are the only monomer that has nitrogen, protein consumption is necessary for survival

Cell Theory

1. All organisms composed of 1 or more cells. 2. Cells are the smallest living things/basic units of organization for organisms. 3. Cells arise only by division of previously existing cells

membrane potential

voltage(electric potential energy) across a membrane - affects traffic of all charged substances across the membrane - cations attracted to it

What two forces drive the diffusion of ions across a membrane?

1. Chemical force (ion's concentration gradient) 2. Electrical force (the effect of membrane potential)

What are the four emergent properties of water?

1. Cohesive behavior 2. Expansion upon freezing 3. Moderation of temperature 4. Solubility.

eukaryotic gene expression

1. DNA Access: chromatin modification 2. Pre-Transcription: most common! Think transcription factors! 3. Post-transcription: RNA processing 4. Pre-translation: microRNAs. Cool stuff! 5. Post-translation: messing with the proteins

energy coupling

linking an exergonic reaction with an endergonic reaction - If an endergonic reaction requires less free energy than an exergonic reaction produces, coupling those two reactions allows for maximum efficiency, and an overall negative delta G. - this is how we complete endergonic processes in our cells that our bodies need to have happen occur - Example: (net delta G is negative) - phosphorylated intermediate is unstable (drives reaction forward !)

lymphatic system

1. Interstitial fluid bathing the tissues, along w the white blood cells in it, continually enters lymphatic vessels 2. Fluid inside the lymphatic system (lymph) flows through lymphatic vessels throughout the body 3. Within lymph nodes, pathogens and foreign particles in the circulating lymph encounter and activate macrophages and and other cells that carry out defensive actions

lymphatic system

1. Interstitial fluid bathing the tissues, along w white blood cells in it, continually enters lymphatic vessels 2. Fluid inside lymphatic system (lymph) flows through lymphatic vessels throughout the body 3. Within lymph nodes, pathogens and foreign particles in circulating lymph encounter and activate macrophages and other cells that carry out defensive actions

sources of genetic variation

1. Mutations: Animal and plant mutation rates tend to be low (1 per 100,000 genes per generation). Bacteria and viruses have higher mutation rates. 2. Sexual reproduction: Gene shuffling! Happens during production of gametes. - Crossing over - Independent assortment - Random fertilization

Conditions for Hardy-Weinberg principle

1. Random mating - Not random mixing of gametes 2. Large population - Too small a population: allele frequencies will fluctuate from one generation to the next 3. No movement in/out - Gene flow can alter allele frequencies 4. No mutation - Gene pool is modified if mutations alter alleles or if entire genes are duplicated or deleted 5. No natural selection - Differences in survival and reproductive success

Why natural selection doesn't make perfect organisms

1. Selection can act only on existing variations 2. Evolution is limited by historical constraints 3. Adaptations are often compromises 4. Chance, natural selection, and the environment interact

What is a polysaccharide?

2 or more simple sugars linked together. Notice that the monomers for all three of these polysaccharides are the same but they are arranged differently via bonding. Here's another structure-function example. We (and all animals) store our excess glucose as glycogen in liver and muscle cells. We can break it down, obviously. But we can't break down cellulose!

How are the carbon atoms in the sugar molecule are numbered and what 5' and 3' mean.

3' and 5' refer to the number of the carbon in the ring making up the sugar (deoxyribose). The phosphate in a nucleotide attaches to a 5' carbon while the 3' carbon at the other end has a hydroxyl group. While RNA molecules exist as single polynucleotide chains, DNA molecules have two polynucleotides that spiral around to form a double helix. The two sugar-phosphate backbones run in opposite 5' to 3' directions (antiparallel), with the nitrogenous bases on the inside of the helix. The strands are held together by hydrogen bonds between the nitrogenous bases (nitrogen is an extremely electronegative element). You can tell the sequence of bases of the other strand if you know one strand (bc adenine always pairs with thymine and guanine always pairs with cytosine).

how efficient is cellular respiration?

34% of chemical energy in glucose converted to chemical energy in form of ATP (the rest lost as heat in exergonic fall of electrons-- we use some of it to keep our body temp, rest is expelled through sweat and other mechanisms)

Trace all atoms of chemical equation

6 CO2 --- Carbon end up in glucose (really G3P), O2 also end up in glucose 12 H2O- Split into Oyxgen, H+, electrons C6H12O6- C from carbon dioxide, hydrogen from water, oxygen from carbon dioxide 6 H2O- Oxygen comes from carbon dioxide

Why does a ball bouncing down a flight of stairs represent a good analogy for energy levels of electrons?

A ball bouncing down a flight of stairs represents a good analogy for energy levels of electrons because there is no "in between" energy levels. Though it is almost impossible to imagine, electrons jump from one energy level to the next (just like a ball bouncing). It spends virtually no time in between energy levels.

How does structure affect function?

A change in structure causes a change in function. ie. glucose and cellulose.

What is a functional group?

A cluster of atoms that influence the characteristics of the molecules they compose.

What is the difference between a condensation/dehydration reaction and hydrolysis?

A dehydration reaction occurs when monomers are connected (to form polymers); a dehydration reaction is when two molecules are covalently bonded to each other with the loss of a water molecule. One monomer provides a hydroxyl group while the other provides a hydrogen (contributing part of the water molecule that is released during the reaction). Hydrolysis occurs when polymers are disassembled to monomers (the opposite process). The bond between the monomers is broken through the addition of a water molecule, as the hydrogen from the water attaches to one monomer and the hydroxyl group attaches to the monomer next to it.

What is SEM?

A measure of how far your calculated mean is from the true mean of the population.

Adding more solute causes the water potential to _____________.

Adding more solute causes the water potential to *decrease*.

equilibrium potential (Eion)

magnitude of membrane voltage at equilibrium for that particular ion - K+: -90 mV(RMP is slightly less negative bc of the few sodium ions coming in through the sodium channel) - Na+: +62mV (RMP much closer to Ek bc so many open potassium channels and so few open sodium channels)

plasma cells

make antibodies! form follows function

How does cholesterol affect the fluidity of the plasma membrane?

At high temperatures (body temp), cholesterol makes the membrane less fluid by restraining phospholipid movement. Cholesterol, however, keeps the phospholipid molecules from packing so tightly, so it lowers the temperature at which membranes solidify. Cholesterol can therefore be thought of as a "fluidity buffer" for the membrane, resisting changes in membrane fluidity that are caused by changes in temperature-- important bc if membrane solidifies or is too fluid it can't function properly.

Cambrian explosion

many present-day animal phyla appear suddenly in fossils formed early in Cambrian period - prior to this, all large animals soft-bodied, little predation - after, predators w claws and other features for capturing prey along w new defense adaptations

theory

Broad natural explanation for a wide range of phenomena, answers WHY,tons of evidence (centuries worth), can be modified if real evidence arise (can include law, above law)

local regulators

messenger molecules that travel short distances, influences cells in vicinity with those receptors

What are chemical reactions due to?

Collisions. The more collisions result in a higher rate of reaction.

chromosome theory of inheritance

Combination of chromosomes and genetics - Chromosomes and genes both present in pairs in diploid cells - homologous chromosomes separate and alleles separate in metaphase I - fertilization restores paired condition of both chromosomes and genes

recombinant DNA

DNA molecules formed when segments of DNA from 2 different sources are combined in vitro

95% confidence

Defines a range of values that you can confident contains the true population mean.

mitosis vs meiosis

Differences: *Synapsis and Crossing Over* *Homologous pairs at the metaphase plate* *Separation of homologs* *Two different divisions* - creates 4 unique haploid cells vs 2 identical diploid

What is hydrolysis?

Each time a monomer is removed from a polymer, a molecule of water is added. Breakdown of polymers.

Vacuoles: They're diverse. What three types are described in your chapter? Briefly describe the role of each.

Food vacuoles: Formed by phagocytosis (mentioned above), that serves a digestive function (fuses w lysosome i.e described above) Contractile vacuoles: (Freshwater protists) Pump excess water out of cell to maintain suitable concentration of ions and molecules inside the cell; in plants and fungi, certain smaller vacuoles carry out enzymatic hydrolysis for digestion like lysosomes; smaller vacuoles can also hold reserves of important organic compounds, help to protect plant against herbivores by storing compounds poisonous to them Central vacuole: Mature plant cells (smaller vacuoles described above all together), cell sap on inside (plant cell's main repository of inorganic ions), growth of plant cells-- they enlarge as vacuole fills w water so cell can become larger wo having more cytoplasm

For any character, the observed dominant/recessive relationship of alleles depends on the level at which we examine ________________

For any character, the observed dominant/recessive relationship of alleles depends on the level at which we examine *phenotype*

Hydroxyl

Found in: Carbohydrates Hydroxyl is polar because oxygen is more electronegative and thus is slightly negative. Because it is polar (vast difference between electronegativity values of O and H), it can form hydrogen bonds with water molecules, which can help to dissolve organic compounds such as sugars (perhaps why our KoolAid dissolved in water).

Phosphate

Found in: DNA, RNA (nucleic acids) Phosphate contributes a negative charge to the molecule of which it is a part (2- at the end of a molecule, and 1- when inside a chain of phosphates). Molecules that have phosphate groups have the potential to react with water and release energy (in an exothermic reaction).

Carboxyl

Found in: Proteins (Hydrogen bonds- polypeptide) Carboxyl acts as an acid as it can donate a proton because the covalent bond between oxygen and hydrogen is so polar. Carboxyl is found in cells in the ionized form (gave away proton) with a charge of 1-, a carboxylate ion.

ras gene

G protein that relays a signal from a growth factor receptor on plasma membrane to cascade of protein kinases (proto-oncogene)

What is a base?

Has a pH higher than 7. Decreased H+. Removes hydrogen ions from a solution.

What is an acid?

Has a pH less than 7. Increased H+. Releases a hydrogen ion when dissolved in water.

citric acid cycle/Krebs cycle

Input: - 1 Acetyl CoA Output: - 2 CO2 - 3 NADH + 3H+ - 1 ATP - 1 FADH2 - 1 ATP through substrate level phosphorylation BUT - most of chemical energy transferred to NAD+ and FAD (both oxidizing agents) during redox reactions to make NADH and FADH2 that bring electrons to ETC - extracts energy in acetyl coA through substrate-level phosphorylation to make ATP and transferring electrons to electron carriers (the remaining carbon is given off as CO2) Step 1: Acetyl group of acetyl coA joins Krebs by joining oxaloacetate Step 2:

Why is the specific heat of water important?

It is very high, causing it to be able to absorb and release a lot of heat without changing its own temperature. Important because to the temperature of the air, the biosphere and your body.

most enzyme names end in ______

most enzyme names end in *-ase*

adaptive immunity

ONLY VERTEBRATES - relies on T and B cells (types of white blood cells called lymphocytes) - recognition occurs when a B or T cell binds to an antigen, such as a bacterial or viral protein, through an *antigen receptor) HUMORAL RESPONSE - occurs in blood and lymph - antibodies!!! 1. After an APC engulfs pathogen, it displays antigen fragments of MHC II - Specific helper T cell binds to complex through antigen receptor and accessory protein (CD4) - APC/Helper T complex causes APC to secrete cytokines 2. When B cell w receptors for the same epitope internalizes antigen, displays antigen fragment w MHC II - Activated helper T cell bears receptors specific for displayed fragment binds to B cell: ACTIVATES B CELL 3. Activated B cell proliferates and differentiates into memory B cells and plasma cells (see below) CELL-MEDIATED RESPONSE - attack the infected host cells!!!

pleiotropy

most genes have multiple phenotypic effects (explains how diseases have multiple symptoms)

glucose vs cellulose

STRUCTURE vs FUNCTION! Note the minor structural differences between glucose and cellulose. Both are polymers of glucose molecules. But these minor structural differences have a large effect on how the molecules are used. Starch is stored by plants and is an energy molecule. We can break it down. Cellulose is a structural component of plant cells. We eat it but can't break it down. Think FIBER!

restriction fragment length polymorphismn (RFLP)

mutation that will prevent a restriction enzyme from cutting there(sickle cell)

Some more structure/function! Discuss how the R group of amino acids plays a role in protein structure and thus function. Your book provides some "striking examples of the marriage of form and function" in proteins. Read that paragraph and throw some examples out to me here please.

Some examples of structure and function (relating specifically to proteins) include the match of shape between an antibody (a type of protein) and the alien substance on a flu virus that the antibody can bind to and mark for destruction (exact structure is so so important). Also, endorphins (signaling molecules), bind to specific receptor proteins to produce euphoria and relieve pain. (Morphine, heroin, and other drugs mimic endorphins).

What are the differences between free and bound ribosomes? Think about where the proteins made end up.

Structurally, free and bound ribosomes are identical (and a ribosome can switch between the two roles). Whether a ribosome is free or bound depends on its location within the cell- whether it is in cytosol or it's attached to the outside of the ER or nuclear envelope. If it is a free ribosome, it most likely is producing proteins that function within the cytosol, while bound ribosomes produce proteins for insertion into membranes, headed towards specific organelles for packaging, or for secretion.

Where does oxygen from CO2 end up?

Sugar molecules and water

taxon

named taxonomic unit at any level of the hierarchy

recessive allele

no noticeable effect on phenotype of heterozygote; only expressed in absence of dominant allele

independent assortment

no right or wrong way for homologous pairs to line up at the metaphase plate 2^n possibilities

What does nature tend toward and why?

The lowest possible energy level because it is more stable.

G0 phase

nondividing state for cell

coenzymes

nonprotein enzyme that is sometimes required for enzyme to be active and is ORGANIC ex: many vitamins !

relative frequency

number of times allele occurs in a gene pool, compared with the number of times other alleles for the same gene occur (not related to whether it is dominant or recessive, dominant does not mean better!)

sympatric speciation

occurs in populations that live in the same geographic area (less common, but can occur if gene flow is reduced by polyploidy, habitat differentiation, and sexual selection) 1. *Polyploidy* - when a species originates from an accident during cell division that results in extra sets of chromosomes 2. *Habitat differentiation* - when genetic factors enable a subpopulation to exploit a habitation or resource not used by parent population 3. *Sexual selection* - Typically females select males for their appearance

parental types

offspring that inherit a phenotype that matches either of parents/P generation - occurrence of parental types greater than 50% indicates that genes were linked

hybrids

offspring that result from interspecific mating

endosperm

organism that is warmed mostly by heat generated by metabolism (regulates its own heat independent of environment) - greater food needs, higher metabolic rate - can survive w large fluctuations in temp of environment - Ex: humans, walrus

fermentation

partial degradation of sugars or other organic fuel that occurs without the use of oxygen - alcoholic and lactic acid fermentation

lytic cycle

phage replicative cycle that culminates in death of the host cell

temperate phages

phages capable of using both modes of replicating within a bacterium (lytic cycle and lysogenic cycle)

cotransport

When a single ATP- powered pump that transports a specific solute can indirectly - a substance that has been pumped across a membrane can do work as it moves back across the membrane by diffusion-- like water being pumped uphill and then doing work flowing back downhill (there can even be a separate transport protein that is a cotransporter separate from the pump that aids in this downhill movement)

What is a hydrogen bond?

When the electrons are not shared equally in a molecule, making it polar, the partially positive charge of H in water is attracted to the partially negative charge of the other molecule. ie. proteins, nucleic acids, etc.

Transmembrane proteins contain both hydrophobic and hydrophilic regions. Explain where these regions are when the protein is spanning the membrane. (Make sure you connect this to the hydrophilic and hydrophobic amino acids you recently learned about in a general sense.)

When the protein is spanning the membrane, the hydrophobic region (with an amino acid sequence of amino acids with hydrophobic R groups) is on the inside of the phospholipid bilayer, while the hydrophilic region (with amino acids w/hydrophilic/polar R groups) faces the water and the cytosol.

Which types of chemical reactions occur faster at equilibrium, the formation of products from reactants or reactants from products?

Which types of chemical reactions occur faster at equilibrium, the formation of products from reactants or reactants from products? When a chemical reaction is occurring at equilibrium, it depends whether the reactant or product has a greater concentration. If the reactant concentration is large, then the reactant molecules collide more frequently. The same is true for products. And when a reactant forms a product, the reactant rate of disappearance is equal to the product rate of formation. They occur at the same rate, because the definition of a reaction that's at chemical equilibrium is that the concentrations of the reactants and products have stabilized at a certain ratio.

sex chromosomes

X and Y chromosomes that determine an individual's sex XX- female XY- male

Are the arrangements of atoms and the ratio important?

Yes! They cause the macromolecules to carry out very different functions.

Do prokaryotes carry out cellular respiration and protein synthesis without organelles?

Yes, cellular respiration occurs in cytoplasm (they have ribosomes)

cohesins

protein complexes that attach sister chromatids in *sister chromatin cohesion*

nucleus

*Information House* - contains most of genes in eukaryotic cell (some in mitochondria and chloroplasts) - enclosed w a *nuclear envelope*, separating contents from cytoplasm (double membrane, pore complex)

How we discovered that DNA is genetic material

*Is it DNA or proteins?* - Nucleic acids seemed far too uniform to account for multitude of possible traits

sexual selection

a form of selection in which individuals with certain inherited characteristics are more likely than other individuals to obtain mates

What is a negative feedback loop?

- There is an excess of product which causes production to slow.

chloroplasts

- Three membranes - Its own DNA - solar energy → chemical energy...wow (clearly the best organelle)

heterozygous

- different alleles - Pp

thylakoids

- plural of thylakoids are grana (granum singular)

motor neurons

- responsible for motor output - extend out of the processing centers and trigger muscle or gland activity - Somatic motor function: consciously controlled - Autonomic motor function: involuntary

recombinant chromosomes

- result of crossing over

initiation of translation

- some mRNAs: initiation of translation can be blocked by regulatory proteins that bind to specific sequences or structures within the untranslated region at 5' or 3' end to prevent attachment of ribosomes - mRNAs in eggs: stored mRNAS lack poly-A tails to allow translation, but a cytoplasmic enzyme will add more A during embryonic development to prompt translation to begin - translation of *all* mRNAs in cell may be regulated simultaneously (inactivation or activation of one or more protein factors required to initiate translation): starts translation of mRNAs stored in eggs or plants under light

where does all of our O2 come from ?

- splitting of water (not CO2) from photosynthesis!

ligands

any molecule that binds specifically to a receptor site on another molecule (ex: LDLS- cholesterol)

average heterozygotity

average percentage of loci that are heterozygous (measure of genetic variation)

What can "high energy" electrons do?

From glucose, enter the ETC in mitochondria to make ATP. (ATP synthase)

active site

restricted region of enzyme that binds to substrate

self-pollination

sexual reproduction of plants

thermodynamics

study of energy transformations that occur in a collection of matter

linear electron flow

flow of electrons through the photosystems and other molecular components built into the thylakoid membrane

small interfering RNAs (siRNAs)

found to cause RNAi

chemical energy

term used by biologists to refer to the potential energy available for release in a chemical reaction

central nervous system (CNS)

organization of neurons that carry out integration of information - brain, longitudinal nerve cord

signal-recognition particle (SRP)

protein-RNA complex that functions as an escort that brings the ribosome to receptor protein built into the ER membrane - other signal peptides can target protein for other places other than ER but translation is completed in cytosol before polypeptide imported into organelle like mito or chloroplast

what are most receptors made out of

proteins

prezygotic barriers

barriers that block fertilization from occurring 1. Habitat isolation 2. Temporal isolation - Breed during diff times, seasons, or years 3. Behavioral isolation - Diff courtship rituals 4. Mechanical isolation - Doesn't fit (snails) 5. Gametic isolation - Sperm of one species may not be able to fertilize eggs of another (sperm may not survive in reproductive tract)

postzygotic barriers

barriers that may contribute to reproductive isolation after the hybrid 1. Reduced hybrid viability - Genes of different parent species may interact in ways that impair hybrid's developmental or survival in its environment (they don't survive) 2. Reduced hybrid fertility - Hybrids are healthy but sterile (donkey, mule) 3. Hybrid breakdown - Some first-generation hybrids are healthy and fertile, but over generations become unhealthy or sterile

restriction fragments

because short DNA sequence (restriction site) will occur many times in long DNA molecule, a restriction enzyme will make many cuts to yield a set of *restriction fragments*

repressor

binds to the operator and blocks attachment of RNA polymerase to the promoter, preventing transcription of the genes - protein product of a regulatory gene

macroevolution

broad pattern of evolution above the species level

gene expression

the process by which DNA directs the synthesis of proteins (or in some cases, just RNAs) Two stages: transcription and translation

speciation

the process by which one species splits into two or more species

oncogenes

cancer-causing genes

energy

capacity to cause change - some forms of energy can be used to do work (like gravity and friction) - also ability to rearrange a collection of matter (ex: expend energy to turn pages of book but also to transport certain substances across membranes)

cell regulates __________ activity

cell regulates *enzyme* activity

haploid cells

cell with one chromosome set (gametes) - n chromosomes

genome

cell's endowment of DNA/genetic information

communication between cells essential for ________________ organisms and ________________ organisms

cell-to-cell communication between cells essential for *multicellular* organisms and *unicellular* organisms

myoblasts

cells in which determination has occurred, start to churn out large amounts of muscle-specific proteins and fuse to form mature, elongated, multinucleate specified cells - there are master regulatory genes that have protein products that commit cells to being a specific type (transcription factors)

why does phosphorylation often change protein shape

changes interactions between polar/charged R groups and phosphate molecules

microevolution

changes over time in allele frequencies in a population (variation within species)

mutations

changes to genetic info in a cell (RNA polymerase doesn't proofread)

ion channels

channel proteins that transport ions - many ion channels function as *gated channels* which open or close in response to a stimulus (electrical, or when specific substances other than one transported binds to channel)

voltage-gated ion channels

channels that open or close when membrane potential passes a particular level

shared derived character

character shared by all descendants but not found in their ancestors (hair of mammals- distinguishes mammals from other vertebrates)

morphological species concept

characterizes a species by body shape and other structural features - can be applied to asexual and sexual organisms and don't need gene flow information

membrane potential

charge difference or voltage as a result of the attraction of opposite charges across the plasma membrane

neurotransmitters

chemical messengers that pass info from transmitting neuron to receiving cell in synapses (ex: dopamine, serotonin)

three types of cellular work

chemical, transport, mechanical

trisomic

chromosome is present in triplicate in the zygote

Barr body

compact object- inactive X in each cell of a female condensed, lies along inside of nuclear envelope - most of genes in Barr body are not expressed - barr bodies reactivated in ovaries so each gamete has an active X - selection of which X chromosome forms barr body is random and independent in each embryonic cell

ribosomes

complex particles that facilitate the orderly linking of amino acids into polypeptide chains

change in population size

consideration births (B) and deaths (D) as well as immigration (i) and emigration (e) (but we ignore immigration and emigration) dN/dT = B - D (we ignore the + i - e part) births/deaths expressed per individual average capita ecologists care about difference between per capita birth and death rates, which is called r r = b - d

DNA methylation

when enzymes methylate certain bases in the DNA itself (usually cytosine) - occurs in most plants, animals, and fungi - long stretches of inactive DNA are generally more methylated - individual genes are usually more heavily methylated in cells in which they are not expressed (removal of extra methyl groups can turn on some of these genes) - long-term inactivation of genes that occurs during normal cell differentiation in embryo (methylation pattern in body which also accounts for genomic imprinting in mammals, where methylation permanently regulates expression of either the maternal or paternal allele of particular genes at start of development

facilitated diffusion

when polar molecules and ions that can't pass lipid bilayer travel through transport proteins (channel proteins and carrier proteins) - certain cells have higher concentrations of protein channels - NO energy input needed (bc moving down concentration gradient): type of passive transport - both channel proteins and carrier proteins

previous explanation of heredity before Mendel

"blending" hypothesis - over many generations, we'll end up looking the same

What is the Chi-Squared equation?

(o-e)^2 / e GOAL: When do I think my results are so unusual that the differences in data are NOT due to chance?

direct contact

*juxtacrine signaling*

law

- Generalizes body of observations -Doesn't describe WHY, often mathematical

Cytokinesis

- Generally begins during anaphase or telophase *Animal Cells* - *Cleavage* - *Cleavage furrow*: shallow groove int he cell surface near the old metaphase plate - Pulling of a drawstring *Plant Cells* - Plant cells have cell walls so there is no cleavage furrow - During telophase, vesicles from Golgi move along microtubules to middle of cell to make a *cell plate* - Materials in vesicles collect in cell plate as it grows - Cell plate enlarges until surrounding membrane fuses w plasma membrane

Structure and function

- Glucose and cellulose - Saturated vs unsaturated - Phospholipids (cell membrane) - Functional groups - Amino acids in proteins - Nucleic acids (DNA and RNA)

Hydroelectric system

- Isolated, open, or multistep - We are multistep !

where do light reactions and Calvin cycle occur?

- Light reactions: Thylakoid - Calvin cycle: stroma of chloroplast (with a good pH for Calvin cycle)

Measures of central tendency

- Mean (NOT resistant) - Median (resistant) - Mode (USE WHEN NOT UNIMODAL-- not accurate to use mean and median when it's bimodal or more)

Which type of cells have a cell wall and what the cell wall is made of

- Plant cells have a cell wall - Made of cellulose

How are "organisms islands of low entropy in an increasingly random universe"?

- Sun! - Supplies free energy (keeps it going and ordered)

chlorophyll b

- accessory pigment - olive green

chlorophyll

- green pigment that gives leaves their color - in the thylakoid membranes of the chloroplast

channel proteins

- hydrophilic channel that certain molecules or ions use as tunnel - aquaporin is example (water)

Tay-Sachs disease

- inherited disorder in humans - brain cells cannot metabolize certain lipids bc a crucial enzyme doesn't work properly - only homozygotes have the disease: at the *organismal* level, the Tay-Sachs allele is recessive - But level of enzyme activity in heterozygotes is in between that of homozygous recessive and homozygous dominant: phenotype at *biochemical level* shows incomplete dominance - Phenotype at *molecular* level: normal allele and Tay-Sachs allele are codominant bc equal numbers of normal and enzyme molecules

carbon fixation

- initial incorporation of carbon into organic compounds (CO2 into organic molecules already present in chloroplast) - Calvin cycle reduces fixed carbon to carbohydrate by addition of electrons (potential energy increase !)

internal and external signals (stop and go signs)

- internal: M phase checkpoint (anaphase doesn't happen unless all chromosomes lined up on spindle correctly) - external: essential nutrient, growth factors

enzymes

- lower activation energy - delta G stays the same

messenger RNA (mRNA)

- made during transcription - carries genetic message from the DNA to protein-synthesizing machinery of cell

equilibrium

- maximum stability

why does each pigment have a unique absorption spectrum?

- molecules of pigment only absorb photons with exact amount of energy to excite electrons to a higher orbital, so wavelength of that photon is unique to that pigment

oligodendrocytes

- produce myelin sheath - in CNS

Schwann cells

- produce myelin sheath - in PNS

ATP synthase

- protein complex that produces ATP - inner membrane of mitochondrion - protons kind of move it like a waterwheel

growth factor

- protein released by certain cells that stimulates other cells to divide - more than 50 types - different cell types respond specifically to different growth factors or combinations of growth factors

what is necessary to keep cellular respiration going?

- proton gradient (for oxidative phosphorylation/aerobic respiration, at least) - supply of NAD+ and FAD+ to be reduced - oxygen (in aerobic respiration) - glucose ! (or other carbs, fats, proteins to be broken down and enter metabolic pathway)

aster

- radial array of short microtubules extends from each centrosome - spindle includes the centrosomes, the spindle microtubules, and the asters

homozygous

- same alleles - PP, pp - true breeders

cyclic AMP or cAMP

- second messenger - epinephrine and many other hormones and other signaling molecules that trigger formation of cAMP - immediate effect of cAMP is activation of protein kinase A which phosphorylates various other proteins depending on the cell type

chloroplast

- site of photosynthesis - three membranes (2 surrounding stroma and one around thylakoids)

how does nerve reset after AP

- sodium potassium pump! (resets the concentrations

geometric record

- study of fossils has helped geologists establish this - Earth's history divided into three eons: Archaean, Proterozoic, and Phanerozoic (most of time w animals on earth)

glial cells/glia

- supporting cells for neurons - nourish neurons, insulate the axons of neurons, and regulate extracellular fluid surrounding neurons

energy transformations

- think about diver - NO energy is ever lost

mesophyll

- tissue in interior of the leaf - chloroplasts found in these cells - typical cell has 30-40 chloroplasts

cooperativity

- type of allosteric activation - substrate molecule binding to one active site in a multisubunit enzyme triggers shape change in al subunits to increase catalytic activity at all other active sites

ligand

- usually polar/can't pass through plasma - signaling molecule (molecule that can specifically bind to another molecule)

light-harvesting complex

- various pigment molecules (chlorophyll a, chlorophyll b, and carotenoids) bound to proteins - number and variety of pigments allow photosystem to absorb light over larger surface area and larger spectrum than single pigment molecule

how do enzymes actually lower activation energy

1. 2 substrates- bringing them together in correct position 2. Enzyme can stretch substrate molecules toward transition-state form 3. Provide microenvironment that is more conducive to a particular type of reaction than environment wo enzyme 4. Direct participation of active site in chemical reaction

Chargaff's rules

1. The base composition varies between species 2. Within a species, the number of A and T bases are equal and the number of G and C bases are equal

antiparallel

5' to 3' and 3' to 5' (opposite of each other)

What is a carbohydrate?

A fuel and building material. ie. glucose, galactose, fructose.

What is the monomer of a carbohydrate?

A monosaccharide. Can exist in a liner form.

A set of chromosomes is ___________.

A set of chromosomes is *haploid*.

What is a monomer?

A simple sugar.

How does ATP typically transfer energy from exergonic reactions to endergonic reactions?

ATP transfers energy by phosphorylating (adding phosphate groups) to other molecules to drive the reaction forward.

All energy traced back to the _______ !

All energy traced back to the *sun* !

APCS

Antigen-presenting cells - Macrophages, B cells, and especially dendritic cells

What is the supernatural world?

Anything that cannot be seen or measured.

effector cells

B cells: antibodies T cells: Cytotoxic T cells and helper T cells

Difference between animal and plant cells

Beyond size, the main structural differences between plant and animal cells lie in a few additional structures found in plant cells. These structures include: chloroplasts, the cell wall, and vacuoles.

If you move one number on the pH scale, how much does the concentration of H+ change by?

By a factor of 10.

Trace all atoms in chemical equation

C6H12O6- carbon atoms end up in 6CO2, hydrogen atoms end up in water, oxygen atoms end up in CO2 and water O2- becomes water

List all monomers and polymers of the 4 classes of organic compounds. Then give the function and an example of each.

CARBOHYDRATES CHO 1:2:1 Monomer: Monosaccharide Polymer: Polysaccharide Function: -provide energy and structural materials - short term energy storage Example: Glucose LIPIDS CHO (1:2: less than 1) Monomer: Fatty acids/glycerol but a monomer doesn't truly exist since lipids aren't technically polymers! Polymer: Triglyceride, Steroid, Phospholipid, Wax Function: Nutrients, Long term energy storage, cell membrane structure Example: Peanut Butter PROTEINS CHONS Monomer: Amino Acid Polymer: Polypeptide Function: Provides structure, can deliver messages b/w cells, marks bad things in the body for destruction, transportation, and MANY MORE Example: Keratin (hair, nails), collagen (structural protein in skin and bones), oxytocin (hormone), antibodies, toxins, hemoglobin (transports oxygen in the blood) NUCLEIC ACIDS CHONP Monomer: Nucleotide Polymer: DNA or RNA Function: carries genetic information to make proteins Example: DNA (in nucleus) and RNA (in cell)

What are the ingredients of organic molecules?

Carbohydrates (CHO), Lipids (CHO), Proteins (CHON S), Nucleic Acids (CHONP).

What are organic compounds primarily made of?

Carbon atoms. Exception: CO2 is inorganic!

Catabolic pathways do not ___________ move flagella, pump solutes etc. Catabolism is linked to work by a chemical drive shaft- _______.

Catabolic pathways do not *directly* move flagella, pump solutes etc. Catabolism is linked to work by a chemical drive shaft- *ATP*.

Lysosomes

Cell/self renewal - Membranous sacs of hydrolytic enzymes - Macromolecule digestion (break stuff down into components/monomers for renewal)! - Come from RER and Golgi

Why are cells microscopic? Why don't large organisms just have really big cells compared to smaller organisms?

Cells are microscopic because there is a need for a surface area to accommodate a large volume. The surface area to volume ratio needs to stay the same for a smaller organism compared to a larger organism so that bodies can maintain homeostasis and respond to their environment. Cells have to allow just a certain number of molecules pass through, and if we were just one giant cell, there would not be enough surface area so that enough of the molecules we need would get through the plasma membrane at a fast enough rate. *small cells allow for large surface area to volume ratio !*

evolution

Change over time in the genetic composition of a population sources of evolution: - genetic drift - natural selection

exponential growth

Conditions for reproduction are ideal in exponential growth and the rate of increase is at its maximum (rmax). - rmax is constant and population adds more individuals when it's large compared to when it's small, thus the J-shaped curve - higher rmax means a steeper curve! dN/dt = rmaxN

Cell equilbrium

DEATH ! - There are always new things coming in and new things coming out - A to B to C to D-- the products of reactants are in next step (drive reactions forward)

DNA

DNA (a type of nucleic acid): - found in the nucleus (as chromosomes or chromatin) - stores and transmits information on protein synthesis - usually double-stranded

What are the 2 main nucleic acids?

DNA and RNA

nuclease

DNA-cutting enzyme that cuts segment of strand contain damaged

nucleotide

DNA: nucleotide has one 5 carbon sugar (deoxyribose), a nitrogenous base (A, T, G, C), and a phosphate group

spatial summation

EPSPs produced nearly simultaneously by different synapses on the same postsynaptic neuron can add together

What is a consequence of the loss of usable energy during energy transfer or transformation?

Each event makes the universe more disordered (increasing entropy)

What is a dehydration reaction?

Each time a monomer is added to a polymer, a molecule of water is removed. Facilitated by enzymes. Synthesis of polymers.

Energy is _____________; chemical elements essential to life are _____________.

Energy is *transferred*; chemical elements essential to life are *recycled*.

Enzymes can catalyze a _______ or _______ reaction.

Enzymes can catalyze a *forward* or *reverse* reaction.

During equilibrium, the forward and reverse rates are ____.

Equal. But that doesn't mean the concentrations of reactants and products are the same.

Robert Hooke

First to observe cells in 1665. Looked at cork and called the shapes cellulae (small rooms)

Humans store with ________ (similar to chemical structure of amylose.)

Glycogen (short term energy storage)

Alternate hypothesis

H1= alternative hypothesis There is a difference between the two groups

What is the formula of a basic amino acid?

H2NCH(R)COOH

Hydrolysis

HYDRO(water)LYSIS(break) -Polymers break down to form monomers (long= short +short) - H2O is added/ needed -OH added to one monomer, H to the other

Hydrophilic

HYDRO(water)PHILIC(love) attracted to water/ water loving

Hydrophobic

HYDRO(water)PHOBIC(afraid) not attracted to water/ hates water

What is a phospholipid?

Has a hydrophilic head, a hydrophobic tail and composes cell membranes. Form a stable configuration in water.

Why is the electronegativity of oxygen important?

It is very electronegative, causing it to be good at attracting electrons and able to play it's role in the electron transport chain.

What drives the structure of proteins?

Low energy states. (evolutionarily) Also DNA!

reductional division

Meiosis I - halves the number of chromosome sets per cell - DIPLOID TO HAPLOID

equational devision

Meiosis II

Most cells are in _____ in your body.

Most cells are in *G0* in your body.

Null hypothesis

No difference between the control and experimental group (any observed difference will be due to chance)

F2 generation

Offspring of F1 generation

What is the difference between a saturated and unsaturated triglyceride or fat?

One saturated with H is solid and one not saturated is in liquid form.

Organisms are amazing energy _______________ !

Organisms are amazing energy *transformers* !

important substance needed for cellular respiration that moves into the cell by simple diffusion

Oxygen ! (O2- nonpolar and tiny !)

What major elements make up organic compounds?

PS CHON (Phosphorus, Sulfur, Carbon, Hydrogen, Oxygen, Nitrogen)

How does carbon enter the biosphere?

Photosynthesis.

transformation of energy

Potential energy: diver at top Kinetic: transferred to water, ripple effect etc, lower potential Climbing up: Muscle (kinetic) to potential - always some lost to heat (can only put this heat to work when the heat flows from a warmer location to a cooler one- temperature is uniform in a cell only use for het energy is to warm the organism-- why crowded rooms are hot)

Pure water has a solute potential (Ψs) of ________. That's high! Most of the time, the water potential is a __________ number

Pure water has a solute potential (Ψs) of *zero*. That's high! Most of the time, the water potential is a *negative* number.

Buffers

Pure water is neutral and has a pH of 7. Buffers are essential to living tissues to maintain pH homeostasis. Buffers minimizes changes in pH by accepting H+ when they're in excess and donating H+ when they are not. Carbonic acid (H2CO3) is an important/common buffer that we'll talk about this year. - High concentrations of weak acid and its conjugate base - High concentrations of weak base and its conjugate acid

Hershey and Chase experiment

Question: Want to know if DNA or protein is genetic material - Mixed labeled phages with bacteria (either radioactive sulfur for proteins or radioactive phosphorus for DNA) - Centrifuge separates bacterial cells and contents, above liquid parts have phage parts - Radioactivity only showed up inside bacteria that had phages with radioactive DNA - Chargaff provided further evidence: showed that each species has different base composition of DNA , and he showed that adenines equal to thymines and guanines equal to cytosines: showed molecular diversity

What make amino acids unique?

R groups, or side chains.

RNA

RNA (another type of nucleic acid): - in the cell, helps for protein synthesis - a copy of DNA? - found in ribosomes - usually single-stranded

retroviruses

RNA animal viruses with the most complicated replicative cycles - have reverse transcriptases (makes DNA copy of genome, then spliced into host chromosome)

ribozymes

RNA molecules that function as enzymes - in some molecules, intron RNA functions as a ribozyme and catalyzes its own excision

SEM or SD smaller?

SEM is smaller (just looking at the math)

ATP cycle

Shuttling of inorganic phosphate and energy - ATP synthesis from ADP + Pi requires energy (energy from catabolism) - ATP hydrolysis to ADP + Pi yields energy (energy for cellular work)

Spontaneous reactions occur with no energy input from the cell, but they can occur _____ _________ !

Spontaneous reactions occur with no energy input from the cell, but they can occur *very slowly* !

Plants store glucose in the form of ______.

Starch!

lymphocytes

T and B cells - T cells originate from bone marrow to thymus (organ in the thoracic cavity above the heart) - B cells are lymphocytes that remain and mature in bone marrow

What did Stanley Miller's experiment show?

That synthesis of basic and essential compounds could have been accomplished on primitive earth. - The abiotic synthesis of organic compounds in the context of evolution.

What does the pH scale measure?

The acidity/basicness. The concentration of H+ ions.

Relation between energy level and potential energy?

The higher the level, the more potential energy the electrons has.

Currently, we use the "fluid mosaic model" to represent the plasma membrane. Break those words down: why is it considered fluid and why do we use the word mosaic to describe it?

The plasma membrane is considered "fluid" because the membrane is held together primarily through hydrophobic interactions, leaving most of the lipids and proteins to shift about laterally (remains fluid until temp decreases and, as average kinetic energy of molecules decreases, the membrane solidifies). The fluidity also depends on whether the phospholipid molecules have saturated (not fluid, packed) or unsaturated (fluid, not as packed) hydrocarbon tails. The word "mosaic" is used to describe it because the membrane is not just composed of phospholipid molecules- it also contains more than 50 kinds of proteins (usually determine function of membrane), cholesterol molecules and an array of other molecules (like carbohydrates and glycolipids).

What determines the potential energy of electrons?

The potential energy of electrons is determined by how they are arranged in relation to the nucleus (potential energy is the energy that matter possesses because of its location or structure).

The remarkable ability of an organism to harness light energy and use it to drive the synthesis of organic compounds emerges from __________ of the cell

The remarkable ability of an organism to harness light energy and use it to drive the synthesis of organic compounds emerges from *structure* of the cell (form follows function !)

P generation

The true-breeding parents (homozygous)

What is evolution through natural selection?

There is *variation* in a population and some variations result in *adaptation*. This is determined by an organism's environment. There is then *differential reproduction*, those with adaptations survive. Over time the population changes.

What is the key element of hypotheses?

They are testable and falsifiable. EXPLAIN

Expansion upon freezing

Water's expansion upon freezing occurs again because of water's hydrogen bonds! Water is less dense as a solid than as a liquid because as a solid, water is in a crystalline structure with stable hydrogen bonds. When water becomes a liquid, some of these hydrogen bonds break and the molecules can move closer together. Ice is able to float because of this property, and keeps entire large bodies of water from freezing whole.

shared ancestral character

a character that originated in an ancestor of the taxon (backbone of mammals- doesn't distinguish mammals from other vertebrates)

systematics

a discipline focused on classifying organisms and determining their evolutionary relationships

corepressor

a small molecule that cooperates with a repressor protein to switch an operon off (tryptophan is example of how gene expression can respond to changes in the cell's internal and external environment)

centrosome

a subcellular region containing material that functions throughout the cell cycle to organize the cell's microtubules - centrioles not that important (mitosis still occurs if laser beam hits them, plants don't have centrioles)

monophyletic

a taxon is equivalent to a clade only w this type of clade - consists of an ancestral species and all of its descendants

glyceraldehyde 3-phosphate (G3P)

actual product of Calvin cycle

heterochrony

an evolutionary change in the rate or timing of developmental events

homoplasies

analogous structures that arose independently of one another (ex: bat's wing and bird's wing)

passive immunity

antibodies passed from blood of pregnant female to fetus, bc antibodies provided by mother guard against pathogens that have never infected the newborn

diploid cell

any cell with two chromosome sets (one from mom, one from dad) - 2n chromosomes (46 for humans)

natural killer cells

circulate through the body and detect the abnormal array of surface proteins characteristic of some virus-infected and cancerous cells - release chemicals that lead to cell death (they don't engulf infected)

transcription initiation complex

cluster of proteins that assembles on promoter sequence at the "upstream" end of gene

meiosis II

cohesins- sister chromatids last until metaphase of mitosis, homologous pairs until anaphase I, sister chromatids anaphase II of meiosis

transcription factors

collection of proteins that mediate binding of RNA polymerase and the initiation of transcription

electrochemical gradient

combination of forces acting on an ion

cladistics

common ancestry is primary criterion used to classify organisms

plate tectonics

continents are part of great plates of Earth's curst that essentially float on the hot, underlying portion of the mantle

osmoregulation

control of solute concentrations and water balance - cells wo cell wall have to figure this out esp in hypotonic and hypertonic situations: evolutionary adaptations

analogy

convergent evolution

dihybrid cross

cross between F1 dihybrids

monohybrid cross

cross between heterozygotes

active immunity

defenses that arise when a pathogen infects the body and prompts a primary or secondary immune response

phylogenetic species concept

defines a species as the smallest group of individuals that share a common ancestor

dominant allele

determines organism's appearance; fully expressed in phenotype of heterozygote

passive transport

diffusion of a substance across a membrane with no energy investment - molecules have thermal energy (heat) which results in things such as diffusion (so energy still involved, just not required for this transport)

osmosis

diffusion of free water across a selectively permeable membrane (where solute can't pass but water can) - in most biological situations, solutes do not affect water concentration significantly: clustering of water molecules around the hydrophilic solute molecules makes water unavailable to cross membrane (not as many free water molecules)- FREE water concentration is important ! - effect is same: water diffuses across membrane from region of lower solute concentration (higher free water concentration) to higher solute concentration (lower free water concentration)

enhancers

distal control elements - a given gene may have multiple enhancers, but usually those enhancers are generally associated with only that gene and no other

wavelength

distance between crests of electromagnetic waves

dominant does not necessarily mean it is more _________ in a population

dominant does not necessarily mean it is more *frequent* in a population

each chromosome has _________ DNA molecule(s)

each chromosome has *one* DNA molecule(s)

immune system

enables an animal to avoid or limit many infections

open system

energy and matter can be transferred between the system and its surroundings Ex: organisms (we absorb energy, release heat and metabolic waste like CO2 to environment)

kinetic energy

energy associated with the relative motion of objects

activation energy

energy needed to start reaction - can be lowered through heat (burning paper) or enzymes !b

rubisco

enzyme that catalyzes reaction bw RuBP and CO2 in carbon fixation, forming extremely unstable 6-carbon sugar

surroundings

everything outside system (rest of universe)

adaptive evolution

evolution that results in better match bw organisms and environment

phylogeny

evolutionary history of a species or group of species

allergens

exaggerated responses to certain antigens

acetylcholine

excitatory

dopamine

excitatory

wobble

flexible base pairing (U can go w either A or G, explains why there are 61 codons but only 45 tRNAs)

enzyme-substrate complex

formed when enzyme binds to its substrate (or substrates if there is more than one reactant) enzyme + substrate(s) --- enzyme-substrate complex --- enzyme + products

homeotic genes

genes that control pattern formation in the late embryo, larva, and adult (code for TRANSCRIPTION FACTORS!) - experiments with flies: find all segmentation genes - identified 1,200 genes essential for pattern formation , 120 of them essential for normal segmentation

tumor-suppressor genes

genes whose normal products inhibit cell division (proteins they code help prevent uncontrolled cell growth)

genotype

genetic makeup

linkage map

genetic map based on recombination frequencies

genes

hereditary units from parents with coded information - genetic link to parents - account for family resemblance - program the specific traits that emerge as we develop from fertilized eggs into adults

character

heritable feature that varies among individuals

taxonomy

how organisms are named and classified

metaphase plate

imaginary plane (rather than actual structure) that the centromeres of all the duplicated chromosomes are on

terminator

in bacteria, sequence of DNA that signals the end of transcription

isotonic

iso = "same" - if cell without a wall, such as an animal cell, is immersed in an environment that is *isotonic* to cell, no *net* movement of water across the plasma membrane

introns

junk! segments that are not transcribed and cut out during RNA processing in eukaryotes

basal taxon

lineage that diverges early in the history of a group, lies on a branch that originates near common ancestor of group

virus

little more than DNA enclosed by a protective protein coat

oxidation

loss of electrons (or partial loss)- bc we're not really dealing w ions here

biotechnology

manipulation of organisms or their components to make useful products

nondisjuction

members of a pair of homologous chromosomes do not move apart properly during meiosis I or sister chromatids fail to separate during meiosis II

resting potential

membrane potential of a resting neuron (one that is not sending a signal) - usually bw -60 and -80 mV

local regulators

messenger molecules that are secreted by signaling cell and only travel short distances to influence cells in the vicinity ex: growth factors (compounds that stimulate nearby target cells to grow and divide on tyrosine kinase receptors)

monosomic

missing chromosome/no copy of a particular chromosome

5' cap

modified form of a guanine nucleotide added onto the 5' end of mRNA after transcription of first 20-40 nucleotides

signal peptide

molecule that targets the protein to the ER

monosaccharide

monomer of carbohydrates - instant source of energy! - main fuel molecules for cellular work

continental drift

movements in the mantle that cause the plates to move over time

neutral theory

much evolutionary change in genes and proteins has no effect on fitness and therefore is not influenced by natural selection

mitochondria and chloroplasts

multiple membranes for more compartmentalization

What is the monomer of a nucleic acid?

nucleotide (A T G C)

substrate-level phosphorylation

occurs when an enzyme transfers a phosphate group from a substrate molecule to ADP

karyotype

ordered display of chromosomes in an organism

synapsis

pairing of two homologous chromosomes that occurs during meiosis

morphogenesis

physical processes that give an organism its shape (diff cells are not randomly distributed but organized into tissues and organs into a particular 3D arrangement)

polysaccharide

polymer of carbohydrates (ex: cellulose, amylose) - storehouses of energy

free energy

portion of a system's energy that can perform work when temperature and pressure are uniform throughout the system, as in a living cell

transformation

process that converts a normal cell to a cancer cell

regulatory gene

produces the repressor protein

gene cloning

production of multiple copies of a single gene

centromere

region containing specific DNA sequences where the chromatid is attached most closely to its sister chromatid

alpha factor

released in alpha cells when a factor binds to receptor

cell division

reproduction of cells

gametes

reproductive cells (sperm or egg cells) that have a haploid set of chromosomes - vehicles that transmit genes from one generation to the next

sdfsdf

sdfdsf

sdfsdf

sdfsdfsdf

aldfjkdsf

sdlfksdlfj

sdsdf

sdsdaf '

cyclic AMP (cAMP)

second messenger- positive gene regulation

variation

sisters/brothers not identical unless they are twins; there is inherited similarity and *variation*

plasmids

small circular DNA molecules that replicate separately from bacterial chromosome/can be passed from bacterium to bacterium

epitope

small, accessible portion of an antigen that binds of an antigen receptor

outgroup

species or group of species from an evolutionary lineage that is known to have diverged before the lineage that includes the species we are studying (ingroup) - can compare members of ingroup w each other and w the outgroup to determine which characters were derived at the various branch points of vertebrate evolution

promoter

the DNA sequence where RNA polymerase attaches and initiates transcription - direction of transcription: downstream - promoter is said to be usptream - bacteria: RNA polymerase recognizes and binds to promoter - eukaryotes: collection of proteins, *transcription factors*, mediate binding of RNA poymerase and the initation of transcription

autosomes

the chromosomes excluding the sex chromosomes

hybridization

the crossing of two true-breeding varieties

map units

the distance between genes (1% recombination frequency)

frequency-dependent selection

the fitness of a phenotype depends on how common it is in the population

reading frame

the frame of symbols in which we read the intended message

triplet code

the genetic instructions (amino acids) for a polypeptide chain are written in the DNA as a series of nonoverlapping, three-nucleotide words (64 possibilities- enough for 20 amino acids; but if it were a double code, there would only be 16 possibilities)

system

the matter under study

endosymbiont theory

the original chloroplast was a photosynthetic prokaryote that lived inside an ancestor of eukaryotic cells

differentiation

the process by which cells become specialized in structure and function - almost all cells in an organism have same genome (only sex cells diff), so differntial gene expression results from the genes being regulated differently in each cell type - how do the activators, that regulate each diff type of cell, become diff? what regulates the regulators?

bioenergetics

the study of how energy flows through living organisms

reducing agent

the substance that is oxidized

oxidizing agent

the substance that is reduced

anchorage dependence

to divide, most animal cells must be attached to a substratum (like inside of culture jar of extracellular matrix of tissue) - like density, anchorage signaled to cell cycle control system via pathways (another external factor)

polygenic traits

traits that are controlled by more than one gene ex: eye color

transfer RNA (tRNA)

transfer RNA: transfers amino acids from the cytoplasmic pool of aa to a growing polypeptide in a ribosome - synthesized like other RNAs from DNA

redox reactions

transfer of electrons (or "partial" transfer)

heredity

transmission of traits from one generation to the next; inheritance

sensory neurons

transmit information from eyes and other sensors that detect external stimuli (info sent to processing centers in the brain or ganglia)

presynaptic cell

transmitting neuron

helper T cell

triggers both the humoral and cell-mediated responses - they do not carry out responses themselves ACTIVATION: - foreign molecule (epitope of antigen) must be present that can bind to antigen receptor of T cell - epitope of antigen must be displayed on an APC (dendritic, macrophage, or B cell) APC vs host cell (APC have both MHC I and II, host cells only have MHC I) HOW IT WORKS - Helper T cell and APC displaying epitope have complex interaction, signals (cytokines!) exchanged in both directions (cytokines from dendritic cell act w antigen to stimulate helper T cell, making it produce its own cytokines) - APC activates helper T cell, which proliferates, clone, B cells present antigens to already activated helper T cells, which activates B cells then you get antibodies

triglyceride

triglycerides= FATS - 3 fatty acids and glycerol - can be saturated or unsaturated depending on hydrogen atoms - butter, oils, peanut butter, etc.

p53 gene

tumor-suppressor gene (encodes protein that is a specific transcription factor that promotes synthesis of cell cycle inhibiting proteins)

codominance

two alleles each affect the phenotype in separate, distinguishable ways

law of segregation

two alleles for heritable character separate/*segregate* during gamete formation and end up in different gametes - only gets one of two alleles - in terms of chromosomes, refers to separation of homologous chromosomes in meiosis I

disaccharide

two monosaccharides (ex: sucrose) - also instant source of energy

double helix

two strands of DNA twisted

isolated system

unable to exchanged either or matter with its surroundings Ex: an insulated water bottle (that doesn't actually exist)

population growth

use an exponential or logistic growth model!

evolution

variation in life history (how much you reproduce- balance!)

bacteriophages

viruses that infect bacteria

visible light

wavelength of 380nm to 750 nm in wavelength- what we can seer (can be detected as various colors by human eye)

photophosphorylation

when ADP + Pi become ATP (endergonic process that occurs with ATP synthase and a proton gradient)

semiconservative model

when a double helix replicates, each of the two daughter molecules will have one old strand, from the parental molecule, and one newly made strand

polyploidy

when a species originates from an accident during cell division that results in extra sets of chromosomes - more common in plants - two ways: autopolyploid (in one generation) or allopolyploid (when two different species interbreed and produce hybrid offspring)

pattern formation

when cytoplasmic determinants and inductive signals both contribute to development of spatial organization in which tissues and organs of an organism are all in their characteristic places

allopolyploid

when various mechanisms can change a sterile hybrid into a fertile polyploid

work of life depends on ability of cells to _________ energy

work of life depends on ability of cells to *transform* energy