BIO TEST 2 STUDY GUIDE
CHAP. 5
BIOLUMINESCENCE - Light produced from chemical reactions that change chemical energy to light energy, used by invertebrates and fishes to protect themselves from predators.

MEMBRANES – phospholipid bilayer, contains embedded and attached proteins, a fluid mosaic model (phospholipids are in constant lateral motion, but rarely flip to the other side of the layer)

PHOSPHOLIPIDS – many made from unsaturated fatty acids with kinks in the tail (kinks prevent liquid from packing tightly, keeps them in liquid form)

No unsaturated fatty acids = lower permeability i.e. safflower oil
With unsaturated fatty acids = higher permeability i.e. butter

CHOLESTEROL – found in animal cell membranes, stabilizes membranes at warm temps and keeps membranes fluid at lower temp

MEMBRANE PROTEINS – function 1) help maintain cell shape and coordinate changes inside and outside cell via attachments to cytoskeleton and extracellular matrix 2) receptors for chemical messengers from other cells 3) function as enzymes 4) Glycoproteins involved in cell-to-cell recognition 5) may participate in intercellular junctions that attach adjacent cells to each other

SELECTIVE PERMEABILITY – small nonpolar molecules move across quickly while charged or polar molecules cross slowly or not at all

DIFFUSION – tendency of particles to spread out evenly in a space, particles move from an area high particle concentration to low particle concentration (diffusing down the concentration gradient)

PASSIVE TRANSPORT – diffusion across a membrane without energy expenditure

OSMOSIS – diffusion of water or a solution across a selectively permeable membrane

TONICITY – the ability of a solution to cause a cell to gain or lose water, depends on the concentration of a solute on both sides of the membrane

ISOTONIC – solute concentration same on both sides
HYPOTONIC – solute concentration lower outside the cell, water molecules move into the cell and may burst
HYPERTONIC – solute concentration higher outside the cell, water molecules move out of the cell and may shrink

OSMOREGULATION – control of water balance, used by cells to survive hypotonic or hypertonic environments

FACILITATED DIFFUSION – movement of polar or charged substances across membranes with the help of transport proteins (DOES NOT REQUIRE ENERGY, RELIES ON CONCENTRATION GRADIENT)

AQUAPORIN – a protein channel that allows rapid diffusion into and out of cells, allows for passage of ions and other molecules

PASSIVE TRANSPORT – requires no energy i.e. diffusion, osmosis, facilitated diffusion
ACTIVE TRANSPORT – requires expenditure of energy usually occurs against concentration gradient

EXOCYTOSIS – export of large bulky molecules i.e. proteins or polysaccharides
ENDOCYTOSIS – import of large bulky molecules
*the material transported is packaged within a vesicle that fuses with the membrane

3 types of endocytosis:
PHAGOCYTOSIS – engulfment of particle by wrapping cell membrane around it
PINOCYTOSIS – engulfment of fluid into small vesicles
RECEPTOR MEDIATED ENDOCYTOSIS – use of receptor coated pit to interact with specific protein, initiating vesicle formation

*Cells use chemical rxn for cell maintenance, manufacturing cell parts, cell replication

ENERGY – capacity to cause change or to perform work KINETIC energy of motion POTENTIAL energy matter possesses as a result of location or structure.

HEAT/THERMAL ENERGY- type of kinetic energy associated with random movement of atoms or molecules

THERMODYNAMICS – study of energy transformations that occur in the collection of matter
SYSTEM – the matter under study SYSTEM - everything else in the universe (not the system)

FIRST LAW OF THERMODYNAMICS – energy is constant, only transferred
SECOND LAW OF THERMODYNAMICS – energy conversion increase the disorder of the universe
ENTROPY – measure of disorder or randomness

CELLULAR RESPIRATION – chemical energy stored in organic molecules converted to a form that the cell can use to perform work
EXORGONIC – release energy in the form of covalent bonds of the reactants, less energy formed
ENDORGONIC – require input of energy and yields products that contain more chemical energy

METABOLISM – sum of an organisms chemical reactions
METABOLIC PATHWAY – series of chemical pathways that build a complex molecule or break down a complex molecule into simpler compounds
ENERGY COUPLING – uses energy from exergonic reactions to drive endergonic reactions
ATP – adenosine triphosphate powers all forms of cellular work COMPOSED of: 1) nitrogenous base (adenine) 2) five carbon sugar (ribose) 3) three phosphate groups

PHOSPHORYLATION – hydrolysis of ATP by transferring its third phosphate to another molecule
3 TYPES OF CELL WORK: chemical, mechanical, transport

ENZYMES – speeds up a cells chemical barriers by lowering EA, increases rate of reaction without being consumed, usually proteins and some RNA molecule
ACTIVATION ENERGY (EA) – energy needed to be overcome for a chemical reaction can begin
SUBSTRATE – specific reactant that an enzyme acts on
ACTIVE SITE – site on an enzyme that a substrate fits on
OPTIMAL CONDITIONS – most effective for an enzyme i.e. temp (35-400 C), Ph neutral
COFACTORS – non protein helpers that bind to an enzyme site and function in catalysis can be organic (i.e. zinc, iron, copper)
COENZYME – when a cofactor is organic (i.e. vitamins)
COMPETITIVE INHIBITORS – blocks substrate from entering the active site and reduces enzyme productivity
NONCOMPETITVIE INHIBITORS – binds to an enzyme other than the active site, changes the shape of the active site and prevents the substrate from binding.
FEEDBACK INHIBITION – the product acts as an inhibitor of one of the enzymes in the pathway that produced it

CHAP 6
Life requires energy, most energy comes from the sun, 1% is converted to chemical energy by photosynthesis.
CELLULAR RESPIRATION – exergonic, transfers energy from bonds in glucose to form ATP, produces up to 30 ATP from each glucose molecule
KILOCALORIE kcal – quantity of heat to raise temp of 1kg of water by 10C, same as calorie

REDOX reaction – movement of electrons from 1 molecule to another LEO GER or OIL RIG
C6 H12 O6 + 6 O2  6 CO2 + 6 H2 O + ATP

STAGES OF CELLULAR RESPIRATION: 1) glycolysis 2) pyruvate proc 3) Krebs cycle 4) oxidative phosphorylation

GLYCOLYSIS – 2 PYRUVATE produced, 2 NAD+ are reduced to NADH, net 2 ATP molecules

SUBSTRATE-LEVEL PHOSPHORYLATION – an enzyme transfers a phosphate group from substrate to ADP form ATP
INTERMEDIATES – compounds formed between glucose (initial reactant) to pyruvate (final product)

PYRUVATE PROCESSING – Acetyl CoA is produced, 1 NAD+ to NADH, CO2 byproduct

KREB’S CYCLE – Acetyl CoA forms citrate and degraded back to 4 carbon compound CO2 released producing 1 ATP, 3 NADH, 1 FADH2 PROCESSES 2 Acetyl CoA so the products are doubled

OXIDATIVE PHOSPHORYLATION involves electron transport chain and chemiosmosis, requires oxygen produces 26 ATP NAD+ - impt. Enzyme in oxidizing glucose, accepts electrons and becomes reduced to NADH
ATP SYNTHASE – an enzyme complex that catalyzes the phosphorylation of ADP to ATP

WAYS CELLULAR POISONS INHIBIT OXIDATIVE PHOSPHORYLATION:
1) Block the electron transport chain
2) Inhibit ATP synthase
3) Make the membrane leaky to hydrogen ions

FERMENTATION – harvesting chemical energy without O2 use produces 2 ATP per glucose reduces NAD+ to NADH provides an anaerobic pathway for recycling NADH back to NAD+

LACTIC ACID FERMENTATION – a way for muscle cells and some bacteria to oxidize NADH to NAD+ and pyruvate is reduced to lactate (lactic acid is carried to liver and converted back to pyruvate)
ALCOHOL FERMENTATION – pyruvate reduced to CO2 and ethanol (makes beer, bread)

OBLIGATE ANAEROBES – requires anaerobic conditions, without O2
FACULTATIVE ANAEROBES – yeasts and bacteria can make ATP by fermentation or oxidative phosphorylation

CHAP 7
AUTOTROPHS – make own food by means of photosynthesis, self-sustaining
PHOTOAUTOTROPHS – use light energy to produce organic molecules
CHEMOAUTOTROPHS – prokaryotes that use inorganic chemicals as their energy source
HETEROTROPHS – consumers that feed on plants, animals or decomposed organic material

PHOTOSYNTHESIS – process of using sunlight to produce carbohydrates, occurs in CHLOROPLASTS
CO2 + 2 H2O + light energy  (CH2 O) n + H2O + O2 where (CH2 O) n stands for carbohydrate.

Usually, glucose (C6 H12 O6) is the carbohydrate made:
6 CO2 + 12 H2 O + light energy  C6H12O6 + 6 H2O + 6 O2

MESOPHYLL – green tissue in the interior of the leaf that contains most of the chloroplasts
STOMATA – tiny pores in the leaf that allow CO2 to enter and O2 to escape
LIGHT REACTIONS – occur in the grana CALVIN CYCLE – occur in the stroma

PHOTON – fixed quantity of light energy (shorter wavelength = greater energy)
CHLOROPHYLL A – absorbs blue-violet and red light, reflects green MAIN PHOTOSYNTHESIS PIGMENT
CHLOROPHYLL B – absorbs blue and orange light, reflects yellow green ACCESSORY PIGMENT
CAROTENOIDS – broaden the spectrum of colors that drive photosynthesis
*accessory pigments absorb light and pass the energy to chlorophyll A
PHOTOSYSTEM – composed of a reaction center surrounded by light-harvesting antenna complexes Two photosystems found in light reactions:
PHOTOSYSTEM II – functions first called P680 because pigment absorbs light with 680nm wavelength
PHOTOSYSTEM I – functions second called P700 because pigment absorbs light with 700nm

CALVIN CYCLE uses CO2, NADPH, and ATP to produce an energy rich 3 carbon sugar called Glyceraldehyde-3-phosphate G3P
STEPS OF CALVIN CYCLE: 1) carbon fixation 2) reduction 3) release of G3P 4) regeneration of starting molecule ribulose biphosphate RuBP RUBISCO – most abundant enzyme on earth, add CO2 to RuBP
C3 PLANTS – use CO2 directly from air, produces 3 carbon compound (3-PGA) from carbon fixation, lives in hot and dry
C4 PLANTS – saves water during photosynthesis, fixes CO2 into a four carbon compound (i.e. sugarcane)
CAM PLANTS – hot and dry environments, conserve water by opening stomata at night and admitting CO2 releases into Calvin cycle during the day (i.e. pineapple and cacti)
PHOTORESPIRATION – occurs in light, consumes O2 and release CO2 and uses ATP

CHAP 8
CELL DIVISION – reproduction at cellular level duplication of chromosomes
Used for: reproduction of single cell organisms, growth of multicellular organisms, repair/replacement of cells, sperm and egg production

ASEXUAL REPRODUCTION – offspring identical to original cell or organism, inheritance of genes from 1 parent
SEXUAL REPRODUCTION – offspring similar to parents, show variation in traits, inheritance of genes from two parents

PROKARYOTES (bacteria and archaea) reproduce by binary fission (dividing in half)
BINARY FISSION – 1) duplication of chromosome and separation of copies 2) elongation of cell and movement of copies 3) division into 2 cells

In the nucleus of a cell in interphase, DNA is wrapped around histones (proteins) to form long threads called chromatin. Prior to mitosis, DNA replicates (two sister chromatids attached by centromere). At the beginning of mitosis, chromatin condenses to chromosomes

MITOTIC SPINDLE – microtubules produced by centrosomes that divide chromosomes, centrosomes contain pairs of centrioles in animal cells.

INTERPHASE – cytoplasm contents double, 2 centromeres form, chromosomes duplicate in nucleus
PROPHASE – microtubules emerge from centrosomes form spindle, chromosomes compact, nucleoli disappear
PROMETAPHASE – spindle microtubules reach chromosomes, nuclear envelope disappears
METAPHASE – mitotic spindle formed, chromosomes align at equator
ANAPHASE – sister chromatids separate at centromeres, daughter chromosomes move to opposite poles
TELOPHASE – cell elongates, nuclear envelope forms around chromosomes, chromatin uncoils, spindle gone

CYTOKINESIS – cytoplasm divides into separate cells
CLEAVAGE FURROW – animal cells, forms from contracting ring of microfilaments interacting with myosin
CELL PLATE – plant cells, forms in middle from vesicles containing cell wall material that grows outward to edges

FACTORS THAT CONTROL CELL DIVISION: 1) presence of essential nutrients 2) GROWTH FACTORS – proteins that stimulate division 3) DENSITY DEPENDENT INHIBITION – when crowded cells stop dividing 4) ANCHORAGE DEPENDENCE – need for cells to be in contact with a solid surface to divide

CELL CYCLE CONTROL SYSTEM – cycling set of molecules in a cell that triggers and coordinates key events in a cell  3 major checkpoints: G1 G2 and M

TUMOR – forms when one or more cells in a multicellular organism divide in an uncontrolled fashion
BENIGN – non-invasive, non-cancerous MALIGNANT – invasive and spreads

SOMATIC CELLS – 23 pairs of homologous chromosomes, one member of each pair from each parent
*human sex chromosomes X and Y differ in size and genetic composition, the other 22 pairs are AUTOSOMES with the same size and genetic composition

HOMOLOGOUS CHROMOSOMES – matched in length, centromere position, and gene locations
LOCUS – position of a gene, different versions of a gene can be found on maternal and paternal chromosomes

FERTILIZATION – sexual reproduction when a sperm and egg unite to form a new individual
MEIOSIS – nuclear division that precedes formation of gametes converts diploid to haploid
DIPLOID – 2 homologous sets of chromosomes HAPLOID – one set of chromosomes
ZYGOTE – has a diploid chromosome number, one set from each parent

Meiosis and mitosis are preceded by the duplication of chromosomes. Meiosis is followed by two consecutive cell divisions and mitosis is followed by only one cell division

MEIOSIS I to PROPHASE I: 1) Chromosomes condense 2) Homologous pairs come together (synapsis to a tetrad) 3) Crossing over (exchange of DNA piece between homologous chromosomes)

Mitosis and meiosis both begin with diploid parent cells that have chromosomes duplicated during the previous interphase. The end products differ: Mitosis produces two genetically identical diploid somatic daughter cells.
Meiosis produces four genetically unique haploid gametes

INDEPENDENT ORIENTATION – each pair of chromosomes independently align at cell equator RANDOM FERTILIZATION – combination of each unique sperm and unique egg increases genetic variability
GENETIC RECOMBINATION - production of new combinations of genes due to crossing over
CROSSING OVER - exchange of corresponding segments between separate (non-sister) chromatids on homologous chromosomes

KARYOTYPE – ordered display of magnified images of an individual’s chromosomes arranged in pairs. Allows for observation of 1) homologous chromosome pairs 2) chromosome number 3) chromosome structure

TRISOMY 21 – inheritance of 3 copies of chromosome 21, aka Down Syndrome
Symptoms: mental retardation, char. Facial features, short stature, heart defects, shortened life span

NONDISJUNCTION – failure of chromosomes or chromatids to separate normally during meiosis. This can happen during: meiosis I, if both members of a homologous pair go to one pole or meiosis II if both sister chromatids go to one pole

Chromosome breakage can lead to rearrangements that can produce genetic disorders or changes in cells

DELETION – loss of chromosome segment; causes serious or lethal disorders i.e. Cri-du-chat
DUPLICATION – repeat of a chromosome segment
INVERSION – reversal of a chromosome segment
TRANSLOCATION – attachment of a segment to a non-homologous chromosome that can be reciprocal