AP Biology

Hell pls help im gonna fail

Covalent bond

When atoms share electrons

Ex: Hydrogen and Oxygen in H2O, Hydrogen and Oxygen share 2 atoms.

Valency

The number of electrions in an atom’s outer shell

Characteristics of CHON

96% of us

• Carbon: acts as molecular glue because of 4 valence electrons- can bond in four different directions

• Hydrogen: very reactive, hydrogen in = energy in, implies energy

• Oxygen: oxygen in = energy out

• Nitrogen: good for storing energy

Essential elements

Potassium, Iron, Calcium… (4% of us)

Ionic bonding

When a metallic atom gives an electron to a non-metal atom for a complete octet (8 valence electrons)

Saturated fats

A type of lipid with only single covalent bonds

Trace elements

Arsenic, Zinc… (0.0001% of us)

Unsaturated fats

A type of lipid with double covalent bonds

Hydrophobic

Doesn’t have affinity for water

Hydrophilic

Has affinity for water

Molarity

Molecules of solute per solution

Moles of solute divided by liters of solution

Emergent properties

Properties because of structure

Hydration shell

Water molecules surrounding a substance to form a shell around it

3 main properties of water

Cohesion: bonding between same molecules

Adhesion: bonding between different molecules

Surface tension: greater hydrogen bonds at the surface of water

Typers of isomers

Different bonds = structural isomer

Mirror image = enantiomers

Other = cis-trans isomer

Dehydration synthesis

Create covalent bonds (peptide bonds between amino acids in a protein) between molecules, where the reaction takes out H and OH from functional groups

Proteins

• Proteins (made from peptide bonds)

  • Made up of amino acids which form a polypeptide

  • Primary structure: chain of amino acids, polypeptide

  • Secondary structure: alpha helix, beta sheet

  • Tertiary structure: 3D shapes where the different bonds of the R groups of amino acids determine form

  • Quaternary: proteins interacting with each other

  • Functions:

    • Enzymatic: catalyzed chemical reactions

    • Defensive: respond and act against invading pathogens

    • Storage

    • Hormonal: regulates the organism

    • Receptive: receives signals

    • Motor: movement

    • Structure

Carbohydrates

• Carbohydrates (made from glycosidic linkages)

  • Properties: can dissolve water

  • Functions: storage of energy, production of energy, structure

Lipids

Lipids:

• Triglyceroids

  • Properties: hydrophobic

  • Stucture: made up of glycerol and fatty acids

  • Function: store energy, transport fat for cell

• Phospholipids

  • Structure: phosphate group, glycerol, fatty acids

  • Properties: phosphate head is hydrophillic and fatty acid tails are hydrophobic

  • Functions: stores energy, makes cell membrane

• Steroids

  • Structure: 4 rings

  • Properties: hydrophobic

  • Functions: stores energy, helps with blood flow

Nucleic acid

DNA

• Structure: double strands, nitrogenous bases (ACGT), sugar deoxyribose, directionality from 5’ to 3’

• Function: storing hereditary information

RNA

• Structure: single strands, nitrogenous bases (ACGU), sugar ribose, directionality from 5’ to 3’

• Function

  • mRNA: translate information from DNA to ribosomes for protein synthesis

  • tRNA: link between mRNA molecule and growing chain of amino acids

  • rRNA: directs the catalytic steps of protein synthesis

How were cells formed

Elements formed lipids in water, which became more complex and became cell membranes

Endosymbiosos

Theory that organelles in eukaryotic cells are prokaryotic cells compartmentalized (inside). Two prokaryotic cells (archaebacteria, eubacteria) marged and formed eukaryotic cells

Cell theory

All living organisms are made up of cells and all cells originate from one cell

Nucleus

Has a nuclear envelope connected to ER. Stores chromosomes (chromatin- the entirety of genetic information stores in nucleus)

Ribosomes

Protein synthesis (not membrane-bound)

Golgi apparatus

Modifies proteins, synthsis of plysaccharides, releases stuff in vescicles

Lysosomes

Only in animal cells, sack of enzymes which break down macromolecules and damaged organelles, digestion

Central vacuole

Only in plant cells, for digestion, storage, wast disposal

Mitochondrion

Generates chemical energy, ATP to power the cell

Chloroplast

Only in plant cells, for photosynthesis

Cytoskeleton

Microfilaments, microtubules, intermediate filaments, helps support

Plasma membrane

Made mostly of phospholipids, some proteins and cholesterol, is selectively permeable

Endomembrane system

1. Vescicles bud off from ER

2. Vescicle fuses with golgi

3. Golgi modifies vescicular content

4. Vescicles bud off from golgi

5. Fuses with plasma membrane, or forms lysosome, which then fuses with endosome

Endoplasmic Reticulum

Smooth ER

• Synthesis of lipids, metabolism of carbohydrates, stores calcium ions

Rough ER

• Has ribosomes attached, aids in synthesis of proteins

Types of transport transmembrane methods

Ion channel

• Passive transport

• Gates which open and close to allow for diffusion

• High concentration to low concentration

Sodium Potassium pump

• Active transport

• Sodium binds on protein which then releases it outside the cell

• Outside cell, potassium binds on the proteins, which is then released inside cell

• Energy to do this used from ATP hydrolysis (ATP = ADP + P, P used)

Proton pump

• Active transport

• Uses energy from ATP hydrolysis (ATP = ADP + P, P used) to move H+ inside the cell to outside the cell

• From low concentration to high concentration

Cotransport

• Facilitated diffusion

• 1st step, proton pump to move H+ out of cell

• 2nd step, H+ pulls sucrose into cell through a carrier protein

Exocytosis

• Substance goes into cell, membrane forms around the substance and creates a vescicle

Endocytosis

• Opposite of exocytosis, substance in vescicle moves out of cell, vescicles meges into plasma membrane

Metabolism

Change in energy

2 types of metabolism

Anabolism (A+B=AB)

• Engergonic (requires energy)

• Making molecules from smaller elements

• Anabolic pathway - rises uphill - change in gibbs free energy is greater than 1

Catabolism (AB=A+B)

• Exergonic (releases energy)

• Breaks molecules down into smaller elements

• Catabolic pathway - falls downhill - change in gibbs free energy is smaller than 1

Energy coupling

Usage of energy from one chemical reaction power to another: the energy produced by one reaction powers another

Enzymes

Biological catalysts, speeds up chemical reactions, reusable

Affected by pH, temperature, salinity = causes protein to change shape

Denature

Enzyme that has difficulty working because of shape change

Renature

Return to original shape of enzyme

Enzyme Substrate Complex

• Active site: where the substrate binds

• Allosteric: outside the active site of enzyme

• Inducer: molecules that can also bind to an enzyme, can be competitive and non-competitive

Activation energy

Energy needed to start a reaction

Word endings

OSE - carbohydrate

ASE - enzyme

IN - protein

Null hypothesis

Variables do not cause each other

Alternate hypothesis

Variables cause each other

Proof of evolution

1. Homology (ancestral, analogous structures)

2. Cladistics / molecular biology

3. Fossil record

4. Biogeography

5. Embryonic development (resembes “mini-evolution”)

Ancestral structures

Homologous structures as a result of divergent evolution

Ex: black bears and pandas having round ears

Analogous structures

Homologous structures as a result of convergent evolution

Ex: bats and birds having wings

Convergent evolution

Two different species that develop similar traits due to their environment or other pressures

Ex: dolphins and fish looking similar because of onvironmental pressure of the water

Divergent evolution

When a species have similar traits because they have a common ancestor with those traits

Ex: chimpanzees and humans looking alike because of a common ancestor

Homologous

Having similar / the same structures or characteristics

Cladistics

The study of genetics

Cladogram

Diagram that shows the genetic relationships between organisms

Four steps of evolution

1. Overproduction

2. Struggle to survive

3. Variation

4. Reproduction

Philogenetic tree

A diagram that represents evolutionary relationships between organisms

Punctuated equilibrium

Features in a species quickly changing

Ex: moths turning black due to pollution in trees

Graduation

Slow, uniform, and gradual speciation / changing features

Ex: chimpanzees slowly starting to walk and become humans

Intermittent species

All of the soecies in between the evolution of one species into another

Hardy-Weinberg formulas

Microevolution

Changing small feature of a species, no speciation happening

Ex: blue eyed group of humans becoming black eyed

Macroevolution

A species becoming another, speciation

Ex: chimpanzees becoming humans

Linnaean classification system

Domain (Eukarya), Kingdom (Animalia), Phylum (Chordata), Class (Mammalia), Order (Primates), Family (Great Apes), Genus (Homo), Species (Sapien)

Paraphyletic

Some organisms from one group and some from another

Ex: fish with pink flesh

Monophyletic

All the organisms of a group

Ex: Mammals

Polypheletic

All the organisms of multiple groups

Ex: Insects and spiders

Taxonomy

Putting things into groups; classification

Clade

A node point and all of its descendents on a cladogram

Derived structure

A structure that an organism has as a result of diverence from another species

Ex: having five fingers is a derived structure of primates

Homoplasy

Used to do the same thing

Ex: bird wings and bat wings

Non-homoplasy

Not used to do the same thing

Ex: penguin wings and seagull wings

Types of selection

Niche

A job that a specific organism does; role or function of an organism in their ecosystem

Ex: a graden spider’s niche is to hunt prey in plants

Adaptive radiation

An event in which a lineage rapidly diversifies with multiple new lineages evolving different adaptations. Usually happens after periods of mass extinction, where new niches have to be filled and there are new opportunities for evolution

Ex: mammals after the extinction of dinosaurs

Cline

A slope

The domains of life

1. Eukaryotes

2. Eubacteria

3. Archaebacteria

Eubacteria and Archaebacteria are more closely related to Eukaryotes than with themselves, which suggests the theory of endosymbiosis is true

The story of Darwin’s finches

An example of adaptive radiation. Their common ancestor arrived to the Galapagos around 2 mya. During the time that has passed, Darwin’s finches have evolved into 18 different species with different characteristics and structures due to the environmental conditions of each island. The islands are also geographically isolated, which prevented genetic information flowing between the archipelago. This is also an example of natural selection

What is cellular respiration

A metabolic pathway that uses glucose to produce adenosine triphosphate (ATP)

Where do the 4 stages of cellular respiration occur

• Glycolisis: in the cytoplasm of the cell

• Pyruvate oxydation: starts outside of the mitochondria, then inside the mitochondria

• Citric acid cycle (Kreb’s cycle): in the mitochondrial matric

• Oxidative phosphorylation: inner mitochondrial membrane and intermembrane space

Aerobic

With oxygen- in cellular respiration, allows for procession into Kreb’s cycle

Anaerobic

Without oxygen- in cellular respiration, Kreb’s cycle will not happen

Glycolysis

Investment phase

• Turns glucose into two G3P

• Process uses two ATP (turns into two ADP)

Payoff phase

• Turns two G3P into two Pyruvate

• Process uses NAD+ (turns into NADH) and two ADP (turns into two ATP) for each G3P turned into Pyruvate

Pyruvate oxydation

Pyruvate is turned into Acetyl COA

Process uses O2 (turns into CO2) and NAD+ (turns into NADH)

Acetyl is transported into the mitochondria by the coenzyme A (COA)

Citric acid cycle (Kreb’s cycle)

Acetyl COA is turned into Oxaloacetote, which helps turn Acetyl COA into Oxaloacetote (reason why it’s a cycle)

COA leaves the Acetyl once it arrives in the mitochondria

Process uses NAD+ (turns into NADH), GDP+P (turns into GTP which then turns into ATP), and FAD (turns into FADH2)

Another product of the process is CO2

Oxydative phosphorylation

Uses NADH+H+, and 2H+ to pump protons into the intermembrane system

This causes the intermembrane space to have a high concentration of H+

H2 from FADH2 (which turns into FAD) and ½O2 is turned into H2O

H+ from the intermembrane space can only escape through ATP synthase, which causes a turbine to turn, which in turn synthesizes ADP and P into ATP

Conclusion: uses products of the other phases of cellular respiration to synthesize ATP

Photosynthesis

Happens in chloroplast

The conversion process that transforms the energy from the sunlight into chemical energy stored in sugars and other organic molecules

Hypotonic

Solutions having lower osmotic pressure (lower solute concentration and higher water concentration)

A hypotonic red blood cell will shrink because of this

Hypertonic

Solutions having higher osmotic pressure (higher solute concentration and lower water concentration)

A hypertonic red blood cell will expand because of this

Isotonic

Solutions having equal osmotic pressure

Osmosis

The movement of molecules of solute through a selectively permeable membrane from a region of low solute concentration to a region of high solute concentration

Water moving from high concentration to low concentration

The amount of solute in water decreases its concentration

Autotrophs

Organisms that can produce their own energy without having to consume other organisms

Ex: plants

Heterotrophs

Organisms that cannot produce their own energy, so they have to consume other organisms in order to get their energy

Ex: humans

What are the components of Chloroplast

Outer membrane

Inner membrane

Stroma: fluid inside the chloroplast

Thylakoid: disc-like structures in the chloroplast

Granum: a column of thylakoids stacked on each other

Lumen: thing inside the thylakoid

Where do light reactions happen

Inside the thylakoid and along its membrane

Carbon fixation

Biological process where carbon dioxide from the environment is converted into a biological compound

Phosphorylation

Attaching a phosphate group to an ion or molecule

Photosynthesis in thylakoid

Light reactions and water cause electrons to move across the thylakoid membrane and to help the synthesis of NADPH

The high proton concentration from the breakup of H2O in the Thylakoid causes H+ to move through the ATP synthase, which synthesizes ATP

ATP and NADPH is then used in the Calvin cycle

Calvin cycle

Happens in the stroma after photosynthesis in thylakoid

Takes CO2 from the atmosphere and utilizes the ATP and NADPH generated from photosynthesis in thylakoid to generate G3P which is used to synthesize glucose

The entire process recycles the molecules and repeats over and over again

Absorption spectrum

If you wear a green shirt, the shirt is absorbing

This means that whatever an object’s color is, it is reflecting that color, while absorbing all of the others

Signal

Sending information to other cells or components