Exam 2 Bio Review Dr. Sata

recognize and rationalize the major time lines in the origin and evolution of life on earth

-4.5 billion years ago= Earth

-500 years after Earth's formation= life started

-4 billion years ago= simple bacteria that lived off chemicals

-2.5 bya= photosynthetic cyanobacteria

-1.8 bya= oldest unicellular eukaryotic organisms

-1.7 bya= multicellular organisms appeared

-last 500 million years= various life forms

-6 million years ago= lineage that led to modern humans broke off

-last 200,000 years ago= our species homo sapiens

understand Miller and Urey's experiment and basic results and make logical connections to the possible origin of life on earth

Miller and Urey's experiment= to show that life could have formed from simple chemicals available 4 billion years ago

-used hydrogen, water, methane, ammonia in a setup with high power electrodes in order to simulate lightning to provide energy for further reactions

-after cooling the reaction products, they noticed that simple organic molecules including urea, organic acids, simple sugars, amino acid had been formed

-showed that monomers of complex molecules could have formed under reducing atmosphere present in early periods of earth's history

predict logical processes by which simple monomers were formed and led to polymers, protobionts and early forms of cells

reactions probably took place in shallow water beds exposed to reducing atmosphere or deep ocean vents that are rich in methane and sulfur

once simple monomers and macromolecules are formed, they can aggregate to form simple structures= protobionts

-were essential for cells to evolve and to keep internal conditions separate from the surrounding environment

protobionts can incorporate other macromolecules such as nucleic acids and proteins

explain how the first possible macromolecule could be RNA to store genetic info and be able to catalyze reactions

RNA can form a variety of secondary structures similar to proteins which may have allowed for the formation of a self-replicating cell

RNA can form spontaneously in prebiotic conditions similar to those in Miller-Urey experiment

apply different methods of microscopy, centrifugation and gel electrophoresis commonly to study structure and function of cells depending on the purpose of the experiment

microscopy

-magnification= how big

-resolution= how clear

-observe live specimens in their natural colors or with stains

-study internal structures and cross-sections of cells or structures

centrifugation

-used to disrupt cells and isolate cellular components based on density, size and shape

-separate solutes in solution by using centripetal acceleration

gel electrophoresis

-used to fractionalize DNA, RNA or protein molecules based on size

-negative charges on DNA/RNA make them migrate towards the anode (+) through tiny pores in cell

-molecules migrate depending on size and electric voltage

-large molecules move slow and small molecules move fast

-agarose gels= fractionalize DNA/RNA

-polyacrylamine gels= fractionate protein and DNA sequencing

recognize obvious images derived from various microscopes and reorder the sequence of events in a cell fractionation experiment

1) select suitable tissue to isolate proteins expressed from other molecules

2) break cells by grinding them in liquid nitrogen

3) centrifuge broken cells to purify proteins

4) lead protein in polyacrylamine gel electrophoresis and separate them

compare and contrast prokaryotic and eukaryotic cells; and plant and animal cells

prokaryotic

-no nuclei; ex= bacteria

-DNA in nucleoid region

-no proteins attached to DNA

-no endomembrane system

-no organelles

-cell size small, limited by metabolic requirements

eukaryotic

-true nuclei; ex= plants, fungi, animals

-DNA within nucleus

-proteins (histones) are attached to DNA

-vast endomembrane

-membrane-bound organelles such as mitochondria and cholorplasts

-cell size much larger

plant cells

-cell wall

-chloroplast

-large central vacuole

-no lysosomes

-glyoxysomes

animal cells

-no cell wall

-no chloroplast

-lysosomes

analyze given information in Table or Figure formats and use them to answer given questions on the properties of various cell types

prokaryotic= bacteria

eukaryotic= plants, animals, fungi

classify all the different components of a eukaryotic cell with a concept map

1) nucleus

2) cytoplasm

-energy organelles= mitochondria, chloroplasts

-endomembrane system= smooth ER, rough ER, golgi apparatus, lysosomes, microbodies, vacuoles, plasma membrane

-ribosomes

3) cytoskeleton

-microtubules

-microfilaments

-intermediate filaments

4) cell surface

-cell wall/ECM

-cell junction

identify the eukaryotic cell components from a given diagram and assign their functions

apply cell structure and function knowledge to selected examples of diseases, mentioned in class or discussions with reference to some organelles or cell components

lysosomes

-Tay-Sachs= genetic disease due to lipid digesting enzyme missing from lysosomes

-undigested lipids affect brain

draw structure of plant or animal cell and label contents and write functions

plant cell

-cell wall

-plasma membrane

-cytosol

-central vacuole= stores organic compounds

-smooth ER= synthesizes lipids; detoxes drugs

-rough ER= synthesizes membrane bound proteins

-nucleus= DNA replication, transcription, RNA processing

-nucleolus= organizing center; makes ribosomes from ribosomal RNA

-mitochondrion= energy organelle; utilization of carbs

-chloroplast= energy organelle; generation of carbs

-peroxisome= lipid degradation

-golgi apparatus= package and ship proteins

animal cell

-plasma membrane

-mitochondrion= energy organelle; utilization of carbs

-rough ER= synthesizes membrane bound proteins

-smooth ER= synthesizes lipids; detoxes drugs

-lysosome= membrane bags with hydrolytic enzymes

-nucleus= DNA replication, transcription, RNA processing

-nucleolus= organizing center; makes ribosomes from ribosomal RNA

-centrioles

-golgi apparatus= package and ship proteins

-peroxisomes= lipid degradation

connect the various cell parts in terms of their functions or flow of information or membranes

relate the functions of cytoskeleton elements in terms of the cell movements and transport

1) microtubules

-hollow tubes with tubulin proteins

-functions= cell motility, cell shape, chromosomes, serve as tracks for movement of organelles

2) micorfilaments

-solid rods of two intertwined strands of actin

-functions= cell motility, cell shape and change, muscle contraction, cytoplasmic streaming in plant cells, cleavage furrow

3) intermediate filaments

-hollow made up of heterogeneous proteins; keratin

-functions= structural, tensile strength, cell shape, anchoring nucleus and other cell organelles, formation of nuclear lamina

develop practical application of the knowledge about cell wall components in various organisms

plant cell wall

-contains cellulose, hemicellulose, cutin, pectin

-middle lamella, primary cell wall, secondary cell wall and plasma membrane

-cellulose can be degraded by enzyme cellulase

fungal cell wall

-contain chitin (NAG)

-can be degraded by chitinase

bacterial cell wall

-contains NAM-NAG

-can be degraded by lysozyme

design a cell with specific properties to perform specific functions to survive and reproduce

trace the pathway of proteins as they are synthesized, modified, sorted out and shipped to carious organelles

proteins synthesized in ribosomes

modified in rough ER

sorted out in golgi apparatus and shipped out

interpret given Tables, paragraphs or figures from research papers on cell structure and function

given the components of biological membrane, draw a picture of fluid mosaic model of a membrane, name its components and list their functions

phospholipid= main fabric of membrane

cholesterol= attached between phospholipids and between the two phospholipid layers

integral proteins= embedded within phospholipid layers; may or may not penetrate through layers

peripheral proteins= on inner or outer surface of phospholipid bilayer; not embedded within phospholipid

carbohydrates (components of glyocoproteins and glycolipids)= generally attached to proteins on outside membrane layer

predict how is the fluidity of the membranes is affected by its composition of saturated or unsaturated lipids, cholesterol and temperature

unsaturation increases membrane fluidity and lowers melting temperature

saturation reduces membrane fluidity and increases melting temperature

identify a molecule as small, medium or large and their polarity to deduce the different ways such molecules can be transported through a lipid bilayer or proteins

know some specific examples

small= 1-100 Da

medium= 100-1000 Da

large= greater than 1000 Da

through lipid portion of bilayer

-hydrophobic molecules such as steroids, non-polar small molecules and small polar molecules can easily pass

through transport proteins

-medium uncharged polar molecules such as glucose; charged ions (such as Na+ and Cl-) and molecules ( nucleotides and amino acids)

define diffusion (simple and facilitated), osmosis, osmoticum, active transport and passive transport

diffusion/passive transport (simple)= tendency of molecules and ions to spread out in the available space until they reach equilibrium fie to their thermal motion; passive; from high to low concentration

1) osmosis= diffusion of water from high concentration to low concentration through selectively permeable membrane

-hypertonic=greater solute concentration

-hypotonic= lower solute concentration

-isotonic= sae concentration

2) facilitated transport= passive transport of molecules through an integral membrane protein specific for each type of solute

-diffusion of charged solutes/ion (Na+, Cl-, amino acids) through transport proteins (ion channels)

active transport= energy is used to transport solutes against the concentration gradient; major force used to maintain internal concentrations of solutes and produce many biochemical reactions

-ex= Na+/K+ pump; uses ATP to transport 3 Na+ ions out and bring in 2 K+

-transport due to electric voltage difference

-coupled transport ot cotransport

predict how the solute concentration of the surroundings affect the water movement and structure of an animal or plant cell

isotonic external solution= same solute

-animal cells= stable

-plant cells= flaccid

hypertonic external solution= high solute

-animal cells= shrivel

-plants cells= plasmolyzed

hypotonic external solution= low solute

-animal cells= lysis

-plant cells= turgid

compare and contrast passive and active transport with some examples and situations in which they work

passive transport

-osmosis

-facilitated transport= diffusion of charged ions (Na+, Cl-) or solutes (amino acids)

active transport

-electrogenic pumps= H+ pump and Na+/K+ pump

-coupled transport= primary active transport (H+ pump); secondary active transport (H+/glucose or H+/amino acid)

know examples of uniport, symport, antiport, electrogenic pump and apply the knowledge to given situations and problems

uniport= single solute, one direction; ex= H+ pump

symport= two solutes, moving in one direction; ex= sucrose/H+ pump

antiport= two solutes, moving in two opposite; ex= Na+/K+ pump

electrogenic pump= ion channels that drive the generation of membrane potential by transporting ions

-ex= H+ pump, Na+/K+ pump

-making outside more positive, inside more negative

understand exocytosis and endocytosis; phagocytosis, pinocytosis and receptor-mediated endocytosis

exocytosis= vesicles from ER or golgi bodies carrying macromolecules and other materials to be secreted fuse with plasma membrane and open outside to secrete material

endocytosis= cells must also take up molecules or cells that are outside of cell; used for metabolism or need to be destroyed

1) phagocytosis= macrophage engulf bacteria identified for destruction; amoeba

2) pinocytosis= refers to cells gulping droplets of extracellular fluid

3) receptor mediated endocytosis= specific receptor proteins recognize large molecules such as cholesterol changing conformation and engulf low density lipoproteins containing several cholesterol molecules and related proteins into cell for processing

predict which of the above mechanisms would be used in a given situation of cell transport based on size of molecule, concentration gradient and polarity of the molecule

endocytosis and exocytosis used for transport of large molecules

-active transport processes

going against concentration gradient

-from low to high concentrations

Exocytosis (secretion)= neurotransmitters, secretion of mucus, sweat glands, and viruses

Endocytosis= (engulfing)

compare how biological membranes behave differently compared to a dialysis (synthetic) membrane in permiability

selective permeiability

design and experiment to study cell transport with given materials by developing a hypothesis, treatments, observations and results analysis

understand why cells need to communicate with each other and inside them

1) recognition= cells need to recognize neighboring cells and surfaces

2) reproduction= cells and organisms send and receive reproductive cues

3) response to stimuli= respond to environmental stimuli such as light, touch, gravity

4) growth and development= requires coordinated effort by billions of cells

5) survival and defense mechanisms= sensors on cell surface can recognize potential dangers; trigger cell to make defense proteins

6) metabolic functions= most metabolic functions are internal to cells and highly coordinated; efficient and effective

7) movement= at organismal level, movement is response due to a stimulus or signal received from CNS

8) adaptation to environment= cumulative result of several signaling pathways over period of time can maintain the temperature of internal ion concentrations

differentiate the signal mechanism that communicate directly, or to nearby cells or far away cells

intracellular communication= occurs within cell

-ex= in cytoplasm, nucleus, between cytoplasm and other cells

intercellular communication= occurs between cells located close to or far away from each other

-signal secreted through gap junctions or communicated by cell surface proteins on plasma membrane to receptors on another cell -close by= paracrine signaling

-from the endocrine cells to cells located far away= endocrine signaling

-signaling between nerve cells= synaptic signaling

see the big picture of cell communication starting with signal reception followed by signal transduction and finally cell response

1) signal response= first messenger to be recognized by specific receptors; signal activates signaling pathway inside the cell

2) signal transduction= inside cell, signal is converted by activating another protein which may activate another protein and start cascade of signaling pathways

-secondary messengers= cAMP, inositol phosphate

3) cellular response= once signaling pathway is activated, cell or organism responds through increased gene expression and metabolic activity, growth, defense and movement

compare various signals, signal transduction mechanisms and cell or organismal responses

signal receptors

1) g-linked protein= membrane

2) tyrosine kinase= membrane

3) ion channel= membrane

4) intracellular= soluble

signal transduction

1) phosphorylation cascade= phosphorylation is catalyzed by kinase's removal of phosphates; ex: blood clotting response

2) second messenger system= cAMP or Ca++ are sometimes used to relay signals inside

-increased Ca++ concentration causes various cellular responses

cellular response

predict the cascade of cell communication under given situation and diagnose a cellular or tissue defect with given info

understand how bacteria utilizes restriction; methylation system and toxins to protect itself

restriction and modification system against bacteriophages (virus)

-ex= methylates own DNA; cuts phage DNA by EcoRI

-bacteria have enzymes to add methyl groups to their DNA to create a pattern to recognize own DNA

-restriction enzymes can recognize viral DNA and degrade it to death

toxic proteins= anthrax, cholera

-kills host cell to take over

antibiotic resistance

1) capsule= prevents uptake of antibiotic

2) degrade antibiotics by enzymes caused by genes of their genome or picked up from outside

3) mutate DNA to change the protein target that antibiotic binds with

how do fungi defends itself against bacteria and infect plants?

1) physical barriers= cell wall

-made of chitin (NAG)

2) makes toxic chemicals (antibiotics) to kill bacteria and others

-toxins to infect host cells= mycotoxins

-ex: penicillin

3) make enzymes (cellulase); degrade plant cell wall

**hard to control fungi

-multicellular and prolific in growth; yeast/fungi

list various ways plants defend against bacteria, fungi and animals utilizing various barriers, toxins and chemical signals

1) physical barriers

-bark

-epidermis

-trichomes= hairs

-spines= protect against animals

-waxy coating= prevents bacterial/fungal infections

2) make toxic chemicals (protective) and proteins= ex: ricinin

3) make volatile organic compounds

chemical/secondary metabolites (protective)

-isoflavanoids

-citronella oils

-heem oil

-tumeric

-capcicin

4) enzymes

-chitinase= protect against fungal infections

5) systemic acquired resistance= exposure to signaling molecules

what are some examples of innate immunity and acquired immunity in animals and humans?

innate immunity

-physical barriers= skin, fur, hair; mucus

-generic immune cells= macrophages

-chemicals= histamines

acquired immunity

-antibodies against specific pathogens

-B cells= memory cells; make antibodies

-vaccines strengthen acquired immunity

**don't make toxic proteins because can't be toxic to us

how does bacteria protect itself from viral infection?

-bacterial enzymes degrade virus once enter bacteria

-cell capsule

most antibiotics are derived from

fungi

-they kill bacteria

plants can defend against grazers by producing

secondary metabolites

-chemicals

what of the following produce antibodies in animal cells?

B cells

how does bacteria develop resistance against antibiotics?

detox system

-using beta-lactamase and enzymes

vaccines protect animals by

preparing antibodies that will mark virus for degradation