BIO AP TEST REVIEW 😔

what are the four macromolecules (monomer, bond, function, example), and what are macromolecules made up in general?

macromolecules are made up of polymers and monomers

• carbohydrates: monosaccharides, glycosidic bonds, gives energy and structural support, glucose/starch/cellulose

• proteins: amino acids, peptide bonds, speeds up reactions + transport, enzymes

• lipids: fatty acids and glycerol, ester bonds, stores energy, fats/oils/phospholipids

• nucleic acids: nucleotides, phosphodiester bonds, stores genetic information, DNA/RNA

saturated fats vs unsaturated fats, and what are the 3 major groups of lipids

• saturated: no double bonds between carbon atoms, saturated with hydrogen atoms, solid

• unsaturated: one or more double bonds between carbon atoms, liquid

• fats: for insulation, energy, and protection

• phospholipids: cell membrane

• steroids: hormonal and structural components of cell membrane

four levels of protein structure

1. Primary structure: sequence of amino acids in polypeptide chain to determine genetic code

2. secondary structure: folding polypeptide chains into structures like alpha helices and beta sheets

3. tertiary structure: overall structure of a single polypeptide chain; protein changes through interactions with R-groups (side chains) to determine active sites

4. quaternary structure: multiple polypeptide chains come together into a single function protein

what is polymerization reaction? Hydrolysis?

The interaction with a smaller molecule (like water) that alters the shape of macromolecules

polymerization (dehydration) reaction: where monomers combine to form polymers with a loss of water

Hydrolysis: where a compound is broken down with the use of water

describe denaturation (reversible vs irreversible, what structures it affects, and the causes of denaturation)

a process that alters a protein’s natural structure and biological activity

• reversible denaturation: where a denatured protein can refold back to its original structure if the denaturing agent is removed

• irreversible denaturation: proteins cannot regain their original structure

• it affects the secondary, tertiary, and sometimes quaternary structures

• pH and temperature cause denaturation by changing its shape and function

adhesion, cohesion, surface tension, capillary action, evaporative cooling, heat of vaporization, floating of ice, hydrophilic vs hydrophobic

• adhesion: hydrogen bonds sticking to other surfaces

• cohesion: hydrogen bonds sticking together

• surface tension: the measure of how difficult it is to break the surface of a liquid

• capillary action: moving liquid up a tube

• evaporative cooling: as liquid evaporates, surface of liquid that is left behind cools down (ex: perspiration)

• heat of vaporization: amount of heat needed to turn liquid to gas

• floating of ice: ice is less dense due to oxygen held apart at cooler temps

• hydrophilic (likes water) vs hydrophobic (repels water)

catabolic vs anabolic pathways

catabolic: releases energy by breaking down pathways (cell respiration)

anabolic: consumes energy by building complicated molecules (photosynthesis)

exergonic vs endergonic reactions

exergonic: spontaneous with energy being released

endergonic: non-spontaneous with energy being absorbed

explain enzyme, active site, activation energy, induced fit, and substrate and the relationship they have with each other

• enzyme: speeds up metabolic reactions

• activation energy: energy barrier required for reactions to occur

• active sites hold substrate, and they work together to make products

• induced fit is where an enzyme changes its shape to better fit and bind the substrate to it

• in relation, enzymes have active sites that are used to produce products. enzymes lower activation energy so substrates can make products more easily.

cofactors and coenzymes

cofactors: nonprotein helpers that enzymes need for catalytic activity (inorganic or organic)

coenzymes: a specific cofactor that carries electrons or other functional groups (always organic- from vitamins)

competitive vs noncompetitve inhibitors

competitive: competes with substrate to prevent them from accessing active site (inhibits reaction)

noncompetitive: binds to allosteric site and alters enzyme’s function, reduces enzyme activity and cannot catalyze reaction (cannot be overcome with increasing substrate)

3 parts of nucleotide

• left: phosphate group- provides energy and links nucleotides together

• middle: 5-carbon sugar- links base to phosphate group

• right: nitrogenous base- carries genetic information in pairs with bases

covalent vs ionic bonds in electronegativity

electronegativity: the likelihood of atoms to share electrons

• covalent: when two atoms share electrons, when electronegativity is less than 1.7

• ionic: when one atom transfers electrons to another (creates charged particles), when electronegativity is more than 1.7

nucleus and its parts

controls cell

• nuclear envelope: double membrane surrounding nucleus

• nuclear pores: large protein complexes that help with exchange of materials

• nucleoplasm: semi-fluid substance inside nucleus

• chromatin: has DNA and proteins, makes chromosomes

  • euchromatin: less condensed, active

  • heterochromatin: more condensed, inactive

• nucleolus: makes rRNA and ribosomes

ribosomes

synthesizes proteins

vesicles

small enclosed sacs that are pinched off membrane to move materials from one site to another

rough ER vs smooth ER

• rough: synthesizes proteins

• smooth: synthesizes lipids, detoxifies drugs and proteins

golgi apparatus and its faces

modifies and process proteins, packages and transports products

• cis face: receives products (near ER)

• trans face: transports/packages products (near cell membrane)

lysosome

digests and cleans

cell wall vs cell membrane

• cell wall: made of cellulose and provides protection

  • primary cell wall: outermost later of cell wall (newer)

  • middle lamella: acts like glue to hold together plant cell layers

  • secondary cell wall: inner thicker layer (fully developed)

• cell/plasma membrane: made up of double layer phospholipids; used for communication, selectivity, and as a barrier

vacuoles

• central vacuole: stores organic compounds, food, and water, gives shape to plant

• tonoplast: membrane surrounding the central vacuole in plant cells

• contractile vacuole: pumps out excess water in protists

peroxisome

contains specialized enzymes for specific metabolic pathways, detoxifies alcohol

mitochondria and its parts

performs cellular respiration to produce ATP

• double membrane: encloses mitochondria

• intermembrane space: transfers molecules and ions, space between inner and outer membrane

  • ETC is here becuz electrons from NADH and FADH2 pass here to use energy for ATP

• mitochondrial matrix: innermost compartment surrounded by inner membrane

  • has Krebs cycle: has the electron carrying molecules to break down products of glucose

• cristae: folds of the inner membrane, helps increase surface area to produce ATP

chloroplasts and its parts

performs photosynthesis

• double membrane with an intermembrane space

• stroma: viscous-like fluid space, where Calvin cycle is

  • calvin cycle occurs

• thylakoids: structures containing chlorophyll, stacked in grana/granum

  • light dependent reactions occur here

chromoplasts vs amyloplasts

chromoplasts: stores pigments other than chlorophyll, gives color

amyloplasts: stores starch, colorless

cytoskeleton (type, size and nmd, what its made out of, flexibility, function, cell division?)

parts of cytoskeleton: they all maintain the shape of the cell and supports it structure (nmd= nm in diameter)

• microfilaments: smallest, made from actin (2 intertwined strands), thin and flexible, for muscle and cell contraction, forms cleavage furrow

• intermediate filaments: medium, made from various proteins (like keratin), stable and less flexible, anchors organelle positions and helps cells stick together

• microtubules: biggest, made from tubulin (hollow tubes), thick and rigid, helps move organelles and materials to different parts of cell and forms cilia and flagella, forms mitotic spindle

centriole

creating and anchoring microtubules

cell junctions

plant cells

• plasmodesmata: connects cytoplasm of plant cells through their cell walls (makes channels) so it can move substances between cells

• middle lamella: acts as glue to hold cells together

animal cells

• tight junctions: forms seals between two cells, makes a barrier that prevents leakage and maintains polarity

• desmosomes: forms rivets between two cells, attaches muscle cells to each other and provides mechanical support

• gap junctions: forms channels, allows cell communication and transfer of molecules

what is the phospholipid bilayer and selective permeability

• two layers of phospholipids (with a hydrophilic head and two hydrophobic tails) that separate the inside of cell from the outside environment

• selective permeability: ability of cell membrane to allow certain substances to pass through while blocking others

  • factors like size, polarity, and transport proteins allow things to go through

  • small molecules, nonpolar molecules, and molecules that use transport proteins are allowed through

integral proteins vs peripheral proteins

integral: embedded in the membrane, transmembrane (goes through membrane)

peripheral: loosely attached to surface of membrane, either in the inner or outer surface only

what is cell to cell recognition

the ability of ell to determine if other cells it encounters are alike or different from itself; helps with rejecting foreign cells by immune system or sorting cells into tissuespa

passive vs active transport and their types

passive: moves along concentration gradient (high to low), no energy need

• simple diffusion: movement of small, nonpolar molecules directly across the membrane

• facilitated diffusion: large or polar molecules through a membrane protein

• osmosis: diffusion of water through a semipermeable membrane

active: moves against concentration gradient (low to high), needs energy

• active transport: goes against gradient with carrier protein

• exocytosis: large molecules exiting cell

• endocytosis: large molecules entering cell

  • phagocytosis: cell eating

  • pinocytosis: cell drinking

  • receptor mediated endocytosis: attached to membrane to bring in solutes to acquire bulk quantities of specific substances

explain why osmosis is important, types of solutions,

importance: maintaining cellular homeostasis (regulates internal environment), helps keep structure for plants in the cell wall (turgor pressure), and helps with transportation

• isotonic solution: solution with same solute concentration as cell's interior, no net movement of water

  • cell stays the same: flaccid

• hypertonic solution: solution with higher solute concentration than cell’s interior, water will move out of cell

  • cell will shrink: crenation (animal cells) or plasmolysis (plant cells)

• hypotonic solution: solution with lower solute concentration than cell’s interior, water will move into cell

  • cell will swell: lysis (animal cells) or turgid (plant cells)

electrochemical gradient

IT DRIVES ION MOVEMENT ACROSS CELL MEMBRANE

• concentration gradient: ions will move from HIGH TO LOW CONCENTRATIONS (driving force for movement)

• electrical gradient: ions will be attracted to areas with opposite charges and repelled by areas with similar charges, so one side of the membrane will be positively charged while the other side will be negatively charged; BASED ON WHAT SIDE THE IONS WANT TO BE FROM POLARITY

photosynthesis (what it does, and only light dependent reactions)

- uses CO2, water, and light energy to make glucose and oxygen

- light dependent reactions: in thylakoid membranes

• photosystem II

  • absorbs light photons by chlorophyll and the energy excites electrons.

  • excited electrons are move to primary electron acceptor while also splitting water into O2 molecules, H+, and electrons.

  • moves up in ETC, which lose energy as they go but that energy pumps protons to create proton gradient

• photosystem I

  • absorbs light photons again

  • excited electrons go to primary acceptor and transfer throughout ETC

  • NADP+ is reduced to NADPH

• chemiosmosis: proton gradient created by the ETC is used to produced ATP. Protons flow back from lumen into the stroma with ATP synthase

photosynthesis (light independent reactions)

Calvin cycles three main stages of grief

• carbon fixation:

  • RuBisCO combines CO2 and RuBP together to make 6-carbon sequence

  • splits into two molecules of 3-PGA

• Reduction:

  • ATP uses energy as lubricant for H+ molecule to stick to 3-PGA, NADP puts H+ molecule on 3-PGA, making G3P

  • for every 3 CO2 molecules that enter, 6 G3P are produced. however, one is used for glucose and other carbs, while the rest regenerate RuBP

• Regeneration of RuBP

  • 5 G3P rearrange to regenerate RuBP, which requires ATP

cellular respiration (what is it, and only glycolysis and pyruvate oxidation)

uses glucose and oxygen to make CO2, light, and water

• glycolysis: in the cytoplasm, anaerobic (no oxygen required)

  • energy investment phase: glucose enters and gets phosphate group (G6P) to it, G6P is rearranged into fructose-6P (F6P), then another phosphate is added F6BP, split into G3P and DHAP, DHAP is converted to G3P so total is 2 G3P

  • energy payoff phase: break down G3P and get 2 ATP, 2 NADH, and 2 pyruvate

• pyruvate oxidation: in mitochondrial matrix, needs oxygen

  • 2 pyruvate enters and removes CO2, converts NAD+ to NADH, and uses coenzyme A (CoA) to make acetyl-CoA

  • 2 pyruvate + O2 → 2 NADH + 2 CO2 + 2 acetyl-CoA

cellular respiration (krebs cycle- what it does and inputs vs outputs, and oxidative phosphorlyation)

aka citric acid cycle

• circular pathway that will turn food into energy

• inputs: acetyl-CoA, NAD+, FAD, ADP, H2O

• outputs: NADH, FADH2, ATP, CO2

oxidative phosphorylation: occurs in the inner mitochondrial membrane

• ETC: NADH and FADH2 carry electrons (produced from krebs cycle) throughout integral proteins (complexes I-IV). As they move through the complexes, they release energy to pump protons into the intermembrane space (making a proton gradient)

  • at the end, electrons combine with oxygen to form water

• chemiosmosis: the proton gradient (in intermembrane space) creates potential energy. They then flow into ATP synthase, making ADP Pi into ATP

fermentation

converts sugars into acids, gases, or alcohol without the use of oxygen

• lactic acid fermentation: glucose is converted to pyruvate through glycolysis. pyruvate is reduced to lactic acid and also produces ATP

• alcohol fermentation: glucose is converted to pyruvate through glycolysis. pyruvate is then decarboxylated to produce ethanol, ATP, and CO2

explain the cell communication of direct contact, paracrine signaling, and synaptic signaling

• direct contact: where the cells communicate by touching each other, usually with the help of receptors or proteins

• paracrine signaling: releases the signaling molecules (ligands) from a cell into the space surrounding it, it will then diffuse to nearby target cells

• synaptic signaling: signaling in the nervous system, communicate through synapses using neurotransmitters

explain the factors of signaling transduction (the pathwyas, cascade effect, ligand, cell surface receptors, and gene expression)

• signal transduction pathway

  • reception: a ligand binds to a specific receptor on the surface of cell, triggers change in receptor

  • transduction: amplifies signal and transmits it through the cell

  • response: cell will carry out function based on initial signal

• cascade effect: amplification of a signal within the cell, leads to a downstream of small initial signals spreading

• ligand: signaling molecule that binds to specific receptor on target cell

• cell surface receptors: proteins on cell membrane that bind to ligand to trigger change in receptor

• gene expression: end of pathways led to changes in gene expression so it can adapt to environment and respond to signals

explain the changes from signaling transduction pathways (types of mutations)

• point mutations: a change in a single nucleotide base pair

  • substitution: one base is replaced by another

    • silent: no change in sequence

    • missense: results in a different amino acid

    • nonsense: creases a premature stop codon

• insertions and deletions: adding or removing one or more nucleotide pair

  • causes a frameshift mutation

• large scale mutations

  • duplication: a segment of DNA is duplicated

  • inversion: DNA is reversed in order

  • translocation: a section of DNA moves from one location to another

  • deletion: a large segment of DNA is removed

• chromosomal mutations: changes structure or number of chromosomes

explain these feedback methods: homeostasis, negative and positive feedback

• homeostasis: a process in living organisms that maintain a stable internal environment despite external conditions, this responds to feedback based on the outside

• negative feedback loop: the output of the process reduces the change from the stimulus, and tries to set system back to its normal state

• positive feedback: the output of the process enhances the change from the stimulus, leading to a greater response

explain interphase

• considered the longest phase

• G1 phase: cell grows and carries out functions

• S phase (synthesis): cell’s DNA replicates and makes two identical copies of chromosomes

• G2 Phase: cell continues to grow for cell division

IPMATC, what do the kinetochores do

• interphase: longest of the phases

  • G1 phase: cell grows and carries out functions

  • S phase (synthesis): cell’s DNA replicates and makes two identical copies of chromosomes

  • G2 Phase: cell continues to grow for cell division

• Prophase: chromosomes condense and become visible, nuclear envelope begins to break down

• Prometaphase: chromosomes are completely visible, envelope is completely broken, kinetochores attach to the chromosomes

• metaphase: chromosomes are lined up at the cell’s equatorial plate

• anaphase: sister chromatids are separated, cell begins to cleavage furrow

• telophase: two new nuclear envelopes start to form around separated chromatids, and chromosomes start to decondense, cleavage furrowing is prominent

• cytokinesis: cell divides

• kinetochores microtubules: help with aligning and assisting chromosomes, the non-kinetochores microtubules elongate cell, kinetochores are the spots on the chromosome the microtubules connect to

chromosome (and its types) vs chromatin vs chromatid vs centromere

• chromatin: long, thin strands of DNA

• chromosomes: where chromatin condenses to form two identical copies of each other

  • autosomes: carries genetic info (22 pairs)

  • sex chromosomes: sex determination (1 pair)

• chromatids: what each of the singular copies are from a chromosome

• centromere: area where the two sister chromatids join together

explain the regulation of the cell cycle (cell growth check point, DNA synthesis checkpoint, metaphase check point, cancer + transformation, apoptosis)

• cell growth checkpoint: at the end of G1 phase, determines if cell has enough resources, is in a good health, and if there are growth factors

  • if not good: will go into 0 phase or apoptosis

• DNA synthesis checkpoint: at the end of G2 phase, sees if DNA has been accurately replicated and if there is damage

  • if not good: will go into 0 phase or apoptosis

• metaphase checkpoint: at metaphase, sees if chromosomes are aligned properly and attached to microtubules accurately

  • if not good: will go into 0 phase or apoptosis

• cancer: due to failure of the checkpoints, genes are lost and out of control from cell division

  • transformation: where cells behave like cancer cells

• apoptosis: programmed cell death in times of conflict. Cell will be notified from signaling, then will go into shrinkage and kill itself

mitosis vs meiosis (purpose, process, daughter cells + genetic loids, chromosome number, crossing over?, location)

mitosis:

• used for cell growth, repair, and asexual reproduction

• will only go through IPMATC

• creates two daughter cells identical to each other (diploids)

• will have the same number of chromosomes as parent (2n → 2n)

• no crossing over, completely identical

• in somatic cells (body cells)

meiosis:

• used for reproduction and genetic variety (sexual rep)

• will go through IPMATPMATC (meiosis I and meiosis II)

• creates four daughter cells different from each other (haploids)

• has half the number of chromosomes as parent (2n → n)

• crossing over occurs (in prophase 1)

• in reproductive cells

what are polar bodies? what’s the difference between male and female gamete formation?

• polar bodies: small cells produced during oogenesis to ensure ovum receives the majority of the cytoplasm for nourishing the cell after fertilization

• male: begins at puberty, produces tons, equal distribution of cytoplasmic division

• female: begins before birth, only one egg produced, unequal division of cytoplasmic division

explain crossing over and independent assortment

exchange of genetic material between homologous chromosomes, creates new combinations of alleles on chromatids (during prophase 1)

1. homologous chromosomes (maternal and paternal) are aligned together: synapsis

2. a protein called synaptonemal complex forms between homologous chromosomes

3. enzymes break DNA strands and exchange genetic material

4. chromatids break off and then chiasmata is shown to represent the exchange as evidence

• independent assortment: random distribution of maternal and paternal chromosomes into gametes (metaphase 1)

incomplete dominance, complete dominance, codominance, multiple alleles, pleiotropy, epistasis, polygenic inheritance

• incomplete dominance: one allele isn’t completely dominant over the other (intermediate phenotype- mixed alleles)

• complete dominance: one allele is fully expressed

• codominance: both alleles are present and neither is dominant

• multiple alleles: when there can be more than 2 alleles for a gene possible (we can only have 2 alleles for gene since one comes from each parent, ex: ABO)

• pleiotropy: when one gene influences multiple phenotypic traits (sickle cell)

• epistasis: how a gene can mask or modify the effects of another gene (retriever)

• polygenic inheritance: multiple genes contributing to a single trait, makes a range (skin color)

what is nondisjunction and what can it result in?

• nondisjunction: failure of homologous chromosomes to separate during cell division

• aneuploidy: having an abnormal number of chromosomes

  • trisomy: extra chromosome (trisomy 21, down syndrome)

  • monosomy: missing chromosome (turner syndrome)

explain structure of DNA

• n a double helix- 5’ and 3’ on opposite ends antiparallel of the two strands

• nucleotides: phosphate group, deoxyribose/sugar (middle), nitrogenous base

• DNA is wrapped around proteins called histones, forms a structure called the chromatin

DNA replication (state all enzymes and proteins)

• occurs in the nucleus (for eukaryotes), purpose is to create more DNA before it divides (interphase- s phase)

1. Initiation: beings at origin replication, helicase will unwind DNA to create replication fork by breaking H bonds. Single Stranded binding proteins keep strands apart to add new nucleotides, and topoisomerases relieve strain on helix (prevents supercoiling)

2. Primer Binding: Primase makes primer to allow DNA polymerase to attach to 3’ (when it should start to work).

3. Elongation: DNA polymerase adds nucleotides in 5’ to 3’ direction on a 3’ to 5’ strand, only new nucleotides are added to 3’. In a 5’ to 3’ strand, primers would have to be added continuously to allow DNA polymerase to replicate (okazaki fragments)

4. Termination: after replicating, forks meet, and RNA primers are replaced with DNA. then it proofreads

5. Result: two identical DNA molecules, parental (old) and daughter (new), which is called semi-conservative

leading and lagging strand

• leading: always the 3’ to 5’ strand because it makes 5’ to 3’ in one go

• lagging strand: always in the 5’ to 3’ strand because it makes a 3’ to 5’ strand in pieces, will have to keep placing primers and DNA polymerase. Ligase seals strands together

explain protein synthesis

transcription: in nucleus

• initiation: RNA polymerase binds to DNA were promoter

• elongation: RNA makes the growing strand of mRNA

• termination: continues until stop codon

• mRNA will then have to process

  • capping: guanine (5’) cap will be added

  • polyadenylation: poly-A-tail is added for stability

  • splicing: introns are cut out

translation: in cytoplasm

• initiation: rRNA binds to mRNA to start codon.

• elongation: tRNA will carry anticodons with amino acids to enter ribosome to make the protein

  • A site: tRNA enters in ribosome

  • P site: holds growing chain of amino acids

  • E site: where tRNA will exit out of ribosome

• termination: it will reach stop codon

what is “wobble”, peptidyl transferase, aminoacyl-tRNA synthase

• wobble: where tRNA can recognize the same amino acid with different codons, susceptible to mutations

• peptidyl transferase: in translation (P site), forms peptide bonds for amino acids

• aminoacyl-tRNA synthase: puts correct amino acid to each tRNA to form aminoacyl-tRNA