AP Bio Semester 1 (Units 1-5)

open system

exchanges material with surroundings

closed system

encloses material/ energy in a system

First law of Thermodynamics

energy cannot be created or destroyed, only transferred or transformed

anabolic reaction

take small particles to build up bigger particles

catabolic reaction

take large particles and break down to smaller particles

exergonic reaction

spontaneous, releasing energy, -ΔG

endergonic reaction

nonspontaneous, requires energy, +ΔG

induced-fit

enzymes conform to substrate to break it down

enzymes

proteins (tertiary structure) that catalyze reactions by lowering activation energy, speeding up a reaction

Formula for Photosynthesis

6CO₂+6H₂O —light—> C₆H₁₂O₆+6O₂

Enzyme amino acid property interactions

side chains determine interactions between active site and substrate, usually weak interactions to bind temporarily. Ex. large/small, acidic/basic, hydrophobic/hydrophilic, negative/positive charge

activation energy

energy required to start a reaction

active site

where substrate binds with enzyme temporarily, has a specific shape that calls for specific substrate- lock and key

allosteric inhibitor

binds to enzymes allosteric site (not the same as active site), causing the enzyme to change shape and inhibit its ability to work, same as noncompetitive inhibition

catalyst

reactant that speeds up a reaction by providing alternate pathway that has a lower activation energy; not used up in reaction (can be reused). Ex. enzymes

competitive inhibition

when an inhibitor binds to active site of enzyme, blocking other substrates from entering therefore ceasing the work of that enzyme

denaturation

when an enzyme shape (breaks weak bonds) is altered due to extreme pH or temperature changes

enzyme-substrate complex

the temporary molecule that forms when an enzyme binds with substrate

feedback inhibition

cellular control mechanism where an enzyme is inhibited by the end product of a biochemical pathway; regulates how much product is made. Negative feedback is the stopping of a process, positive is the activation of a process

globular protein

protein that is spherical or ball-like, tertiary structure; enzymes are mainly globular

low temp to high temp vs enzyme activity

More collisions tend to happen as temperatures increase due to increase in kinetic energy, so enzymatic activity also would increase. However, too high of a temp causes denaturation. Optimal temperatures is when enzyme activity is highest without becoming denatured.

noncompetitive inhibition

when an inhibitor binds to allosteric site, conforming shape of enzyme and inhibits its ability to work

facultative anaerobes

organisms that can make enough ATP to survive using fermentation or respiration, ex. muscle cells

obligate anaerobes

organisms that carry out only fermentation of anaerobic respiration; cannot survive in presence of oxygen

fermentation vs. cellular respiration

fermentation: final electron acceptor is an organic molecule, 2 net ATP produced (from glycolysis), substrate-level phosphorylation

both: glycolysis, NAD+ accepts electrons

cellular respiration: final electron acceptor is oxygen, NAD+ is regenerated through electron-transport chain, ~32 net ATP produced, substrate-level and oxidative phosphorylation

substrate-level phosphorylation

when an organic molecule combines with ADP in an enzyme, and the ADP takes an inorganic phosphate group from molecule to combine and make ATP or GTP; used in glycolysis and Kreb cycle

oxidative phosphorylation

last step of cellular respiration, when ATP synthase synthesizes ATP from an inorganic phosphate and ADP; reaction is driven by protons cycling through electrochemical gradient that then combine with the negatively charged ½ O₂ to make H₂O

electron transport chain

collection of molecules (mostly proteins called cytochromes) in inner membrane of mitochondria; transport electrons to matrix through series of electron carriers that alternate form oxidized and reduced states to move down the “waterslide”; electrons at end of chain combine with ½ O₂ to produce negative charge on molecule

cytochromes

electron carrier protein that functions in ETC; last cytochrome is very electronegative and passes electrons to oxygen

chemiosmosis

process in which energy is stored on the form of H+ ion gradient across the membrane to do cellular work; protons are taken from NADH and FADH₂ and pumped across the mitochondrial membrane by transport proteins to the intermembrane space by using energy from ETC, developing a electrochemical gradient (more positive charge on intermembrane side); once across, the protons drive the production of ATP by traveling through ATPase

energy flow for cellular respiration

glucose → NADH → ETC → chemiosmosis → ATP

spontaneous reaction

reaction that requires no input of energy; downhill reaction

Stages of Cellular Respiration

1. Glycolysis

2. Pyruvate oxidation and Kreb Cycle

3. oxidative phosphorylation: ETC and chemiosmosis

summary of glycolysis

Happens in ALL cells; occurs in cytosol; requires 2 ATP and a 6-carbon glucose to commence; ATP undergoes ATP hydrolysis to make ADP, releasing energy to break down glucose by donating a phosphate group- this happens for both ATP, producing 2 3-carbon sugars; NAD+ is reduced to NADH by picking up 2 electrons and proton from sugar; by substrate level phosphorylation, the sugar combines with 2 ADP to create 2 ATP and a pyruvate; since there are 2 ATP, this happens for both and 4 total ATP and 2 pyruvate are made

acetyl CoA

produced when pyruvate molecule is transported to mitochondria through transport protein and releases a CO₂, NAD+ is reduced to NADH, and Coenzyme A forms a temporary bond to replace the CO₂

Summary of Kreb cycle

occurs in mitochondrial matrix; aerobic process- requires oxygen; 2 acetyl CoA are required to start reaction; CoA breaks off to form 2-carbon molecule that oxaloacetate combines with to make citrate (6-carbon molecule); a CO₂ breaks off as byproduct, NAD+ reduces to NADH by harnessing energy in reaction of breaking bond; another CO₂ leaves and powers ADP to make ATP through substrate-level phosphorylation and NAD+ reduces to NADH resulting in 4-carbon molecule; molecule is continuously broken down, and FAD is reduced to FADH₂; finally, NAD+ is reduced to NADH and resulting molecule is oxaloacetate which is recycled in the process; reaction happens twice to account for 2 acetyl CoA, producing total of 2 ATP, 6NADH, 2FADH₂ and 4CO₂

compartmentalization

separates materials for specialized functions

oxidative phosphorylation summary

occurs in mitochondrial matrix but requires a few steps before it can occur; first NADH/FADH₂ are broken down into 3 parts: 2 electrons, H+ ion, and NAD+/FAD (recycled); electrons are pumped across innermembrane through trasport protein and enter the ETC where they are pumped back across and attaches to oxygen. Since H+ are electronegative, they follow electrons across and create an electrochemical gradient that is necessary to do work (chemiosmosis); H+ ions are then used to power ATPase and get pumped back into the matrix, meanwhile, oxidative phosphorylation occurs and ATP is made from ADP and inorganic phosphate; H+ travels to negatively charged oxygen to make H₂O; products are 26-32 ATP, 1 H₂O, NAD+

paracrine signaling

cells communicate with other local cells in vicinity

growth factors

local regulation in animals that simulate target cells to grow and divide and simultaneously receive and report

synaptic signaling

in animal nervous system; electric signal along nerve cell triggers secretion of chemical signal carrying neurotransmitters eventually triggering response in target cell

hormones

both plants and animals use this for long-distance signaling (also called endocrine signaling)

types of local cell communication/signaling

cell-cell: gap junctions (animal cells) and plasmodesmata (plant cells)

paracrine, synaptic

Stages of cell signaling

reception, transduction and response

reception

target cells detection of signaling molecule from outside cell; signaling molecule (ligand) binds to receptor

transduction

step or series of steps that converts signal to bring cellular response

signal transduction pathway

sequence of changes in series of different molecules (relay molecules)

response

cellular activity that is triggered

ligand

molecule that specifically bonds to another molecule; usually changes shape of receptor, initiating interactions

G-protein coupled receptor (GPCR)

cell-surface transmembrane receptor that works with help of G-protein

G-protein

protein that binds to energy rich GTP

ligand-gated ion channel

membrane receptor with a region that can act as a “gate” for ions opening or closing due to induced fit

intracellular proteins

in cytoplasm on nucleosol target cells and must pass through plasma membrane. ex steroids

transcription factors

control what genes are transcribed into mRNA in particular cell and time

protein kinase

enzyme that transfers phosphate groups from ATP to a protein; compose most of relay molecules on signal transduction pathway

phosphorylation cascade

pathway of signal transduction pathway containing protein kinases where signals are transmitted by

protein phosphatases

enzymes that can rapidly remove phosphate groups from proteins- dephosphorylation; make protein kinases available for use

second messengers

small; nonprotein, water soluble molecules or ions that can spread throughout through diffusion

cyclic AMP (cAMP)

epinephrine binds to G-protein activating enzyme that converts ATP to cAMP; important in mitosis-

cell division

reproduction of cells; allows multicellular eukaryotes to develop from single cell and replace dead cells

cell cycle

life of a cell from the time it first formed during division of parent cell until own division into two daughter cells

genome

cells genetic information

chromosomes

structures of packaged DNA; structure maintained by proteins called histones; nuclei in humans contain 46 chromosomes

chromatin

entire complex of DNA and proteins of chromosomes

somatic cells

body cells except reproductive

gamete cells

reproductive cells; XX-female, XY-male

sister chromatids

2 in duplicated chromosomes; joined copies of original chromosome; cohesions connect chromatids along length by protein complexes- sister chromatid cohesion

centromere

region made up of repetitive sequences in the chromosomal DNA where chromatid is attached most closely to sister chromatid; mediated by proteins

mitosis

division of genetic material in nucleus into 2 genetically identical diploid cells; 5 phases

cytokinesis

follows mitosis; division of cytoplasm; cleavage starts process; outside, contractile ring of actin microfilaments interact wit myosin and contract, pinching cell into 2 cells

miotic phase (M phase)

part of cell cycle that includes mitosis and cytokinesis and usually shortest part of the cycle

Interphase

longer stage that alternates with M phase; divided into G₁ phase, s phase and G₂ phase

5 stages of mitosis

prophase, prometaphase, metaphase, anaphase, telophase

prophase

chromatin fibers tightly coil; nucleoli disappear; each duplicated chromosome appears as 2 sister chromatids joined at centromeres, mitotic spindle begins to form centrosomes and microtubules; centrosomes move away from one another by lengthening microtubules

nucleoli

large structures in nucleus that are involved in synthesis of rRNA and ribosomes; disappear in prophase and reappear in telophase

prometaphase

nuclear envelope fragments; microtubules invade nuclear area; chromosomes become more condensed; kinetochores forms at each centromere of chromatid; microtubules attach to kinetochores; non-kinetochore microtubules lengthen cell with interactions

metaphase

longest stage; centrosomes at opposite ends of poles; chromosomes arrive at metaphase plate; kinetochores are attached to kinetochore microtubules of opposite plates.

anaphase

shortest stage; cohesion proteins are cleaves\d and each chromatid becomes independent chromosome; 2 new daughter chromosomes begin moving toward opposite ends as kinetochore microtubules shorten; cell elongates as non-kinetochore microtubules cohesion; both ends have equivalent and complete chromosomes

telophase

2 daughter cells in nuclei form in cell; nuclear envelopes arise from fragments of parent cells; nucleoli reappear; chromosomes become less condensed; microtubules are depolymerized

cleavage furrow

shallow groove in cell surface near old metaphase plate; oustide

cell plate

in plant cells, vesicles from Golgi move along microtubules to center where they release cell wall material so that cell plate enlarges until it fuses with plasma membrane

binary fission

prokaryotic reproduction in which cell grows to double its size and divides into two cells; DNA replicates and splits to opposite sides then cell divides.

growth factor

protein released by certain cells that stimulate other cells to divide

meiosis I and meiosis II

2 consecutive cell divisions resulting in 4 daughter cells with one set of parent cell chromosomes

allele

different version of gene at corresponding loci; variations in gene nucleotide sequence

prophase 1

2 members of homologous chromosomes associate along length; synapsis and crossing over occurs, and duplicated homologs pair up and crossover

metaphase 1

pairs of homologous chromosomes align at metaphase plate

chiasma

location where crossing over and swapping of genes occur; holds together homologous chromosomes into a tetrad

recombinant chromosomes

individual chromosomes that carry genes from different parents; increases genetic variability; result of crossing over

independent assortment chromosomes

at metaphase 1, homologous pairs are situated at metaphase plate and each pair may randomly orient with either maternal or paternal homolog closer to given pole

character

heritable feature that varies among individuals

trait

each varient for a character

true breeding

breeding over many generations of self-pollination

hybridization

mating, or crossing of 2 true-breeding varieties

P generation

true-breeding parents, parental generation

F₁ generation

hybrid offspring- first filial generation

F₂ generation

allowing F₁ hybrids to self-pollinate produces this -second filial generation

law of segregation

2 alleles for heritable character segregate during gamete formation and end up in different gametes

phenotype

appearance or observable trait and physiological

genotype

genetic makeup