Rutgers Biology Final (115) Study Guide

Nervous system

circuits of neurons and supporting cells

neuronal plasticity

the ability nervous system to change after birth. Changes to the number of connections between neurons that take place during an individuals lifetime

Embryonic neural development and neuronal plasticity

synapse formation involved in both

short term memory

information stored for a short time, released if not used

long term memory

activated when information needs to be retained. When needed info retrieved into STM

long term potentiation

lasting increase in the strength of synaptic transmission -physiological changes, facilitated memory and retrieval, activity dependent
failure to retrieve from long term memory would affect LTP but not LTM OR STM

LTP (long term potentiation)/memory formation facilitated by

chunking

Encoding

transfer from STM to LTM forms a memory

emergent properties

result from the arrangement and interaction of parts within a system

emergence

the whole is more than just the sum of its parts

Levels of organization(Low to High)

molecule, organelle, cells, tissues, organs/organ systems, organisms, populations, communities, ecosystem, biosphere

reductionism

reduction of complex systems to similar components that are more manageable to study

hypothesis

testable explanation for observations based on available data; an educated guess

theory

broad explanation with significant support, leads to new hypothesis and accurate predictions

law

statement of what always occurs under certain circumstances, observable pattern, not explanatory

atoms made up of

protons, neutrons, electrons

potential energy

energy that a material possess due to its location or structure. can be used to do work

valence electrons

outermost shell

molecule

a compound of 2 or more atoms held together by chem bonds

Electronegativity

measure of an atoms affinity for e in chem bonds

covalent bonds

sharing of a pair of valence electrons by two atoms. STRONGEST BOND
Non-polar: electrons shared equally
polar covalent: unequal sharing causes partial + or - charge

Ionic Bond

highly unequal electronegativity. bond between cation (+) and anion (-)

Van deer Waals interactions

short lived, weak interactions due to electron position and motion

Hydrogen Bonds

When H bonds with O or N type of van der waals but stronger

1st emergent property of water

1) Hydrogen bond: water is a polar molecule

2nd emergent property of water

cohesive (stick together due to H bonds) (causes surface tension: measure of how difficult it is to break the surface of a liquid)/adhesive (stick to other stuff) behavior

3rd emergent property of water

Moderate Temperature: high specific heat (amount of energy it takes to raise 1g of a substance 1 degree Celsius) (takes a lot of energy to raise temp of water)

4th emergent property of water

expansion upon freezing (ice floats freezes top to bottom)

5th emergent property of water

versatility as a solvent: hydrophilic: loves water has affinity for it, will dissolve, can form H bonds with water. Hydrophobic: non polar and non ionic cannot for H bonds, no affinity for water

Carbon Backbone variation

Length
Branching
Double bonds
Rings

Hydrocarbons

Compounds composed of only carbon and hydrogen
Nonpolar, Uncharged (non ionic)=hydrophobic= insoluble in H2O

functional groups

key to molecular function dictate functions of molecules, affect chem properties

7 functional groups

1) hydroxyl (OH) polar, hydrophilic
2)carbonyl (C=O) 2 types: carbonyl at the end: aldehyde/carbonyl in middle: keytone, polar, hydrophilic
3)carboxyl (COOH) C double O and single OH, polar hydrophilic, IMPORTANT PART OF AMINO ACIDS
4)amino group (NH2) proton acceptor: basic IMPORTANT PART OF AMINO ACIDS 5)sulfhydryl (SH) important in some protein structures, thiols compounds with sulfhydryl groups, polar, hydrophilic
6)phosphate group (PO4H2) acidic hydrophilic
7)methyl (CH3) nonpolar Hydrophobic. in dna effects gene expression

Macrmolecules

large molecules formed by thousands of atoms

Polymers

Large compound formed from combinations of many monomers.

Monomer

The subunit that serves as the building block of a polymer.

dehydration reaction

synthesizing a polymer, removes a water molecule forming a new bond. enzymes:dehydrogenase

Hydrolysis

Breaking down a polymer by adding water, enzyme: hydrolase

4 classes of macromolecules

carbohydrates, lipids, proteins, nucleic acids

Carbohydrates

classified by location of carbonyl and #of carbons
Monomer, Polymer, Disaccharide

A Carbohydrates the architecture/function determined by

its sugar monomers and the positions of its glycosidic linkages

A Monomer is a ___________, ____________ is the most common one

monosaccharide, glucose

A disaccharide is made up of __________ formed via ____________ linkage.

2 monos, glycosidic

These two carbohydrates are used for storage

starch and glycogen

These two carbohydrates are used for striation

cellulose and chitin

A Polymer is also known as _________, its function is ________,______ and __________.

Polysaccharide; fuel, structure and storage

Lipids three important families are...

Three important families: fats, phospholipids, steroids

Steroids differ in ________________ groups
EX:________________

functional , cholesterol

Phospholipids are made up of

glycerol, 2 fatty acids tails and a phosphate group

Trans Fatty Acid has __________ bonds. Linear Fatty Acids have fewer ____packed _______ than saturated fats.

double, H, together

In Unsaturated Fats there are double bonds in the

CH chain

In saturated fats, each C is bonded to the ______ possible number of __. Saturated Fats are _______ at room temp.

highest, H, solid

Fats are the most abundant ______. Their structure is......

lipid, glycerol and 1-3 fatty acid chains

Lipids are NOT ________ or _________.

Polymers or Monomers

Lipids are Hydro______. mostly hydro_____ that dissolve in _______ solvents

phobic, carbon, non polar

Lipids are formed by

ester linkages

Lipids functions are

Storage, structure, signaling

A Fatty acid is made up of

carboxyl group + unbranched hydrocarbon tail

Proteins

Monomer: amino acids
polymer:polypeptide
Structure: carboxyl group, amino group, R side chain (determines functions, acidity, polarity), H atom
20 common amino acids
9 essential A.A that we get from diet
Formed by Peptide Bonds between carboxyl and anime group via dehydration reaction
Primary structure: a sequence of amino acids joined by peptide bonds in polypeptide chain
Secondary Structure: hydrogen bonds, R groups do not participate. local folding
Tertiary Structure: interrelationships of R groups fold into 3D shape
Quaternary Structure: two or more polypeptide chains form one macromolecule
Denaturation: loss of a proteins native structure. biologically inactive. due to pH, salt concentration, high temperature
protein function: structure, signaling, enzymes, defensive, transport

Nucleic acids

monomer: nucleotides
polymer: polynucleotides
Phosphodiester linkage
DNA: deoxyribonucleic acid
RNA: ribonucleic acid
transmit hereditary info and determine protein production

Abiogenesis/Abiotic synthesis

first life developed from non living organic molecules/ those molecules had to form spontaneously

4 requirements for Abiotic Synthesis to Occur: Conditions of Early Earth

1) Low Oxygen. oxygen breaks bonds, not conductive to building
2) Energy Source: to form biological molecules.
3) Presence of Chem building blocks: Water, dissolved inorganic minerals (ions), Atmosphere (CO2 H2O vapor CO H2 and N2) maybe NH3 H2S AND CH4
4) Time: spontaneous chemical reactions are slow

2 hypotheses as to how life started

1) prebiotic soup hypothesis: Oparin-Haldane
life formed near earths surface and conditions of early earth favored spontaneous formation of simple organic molecules
Stanley Miller and Harold Urey Experiment: stimulate early conditions of early earth. Found amino acids and other organic compounds (macromolecules)
2) Iron Sulfur Hypotheses: life formed at cracks of ocean floor-hydrothermal vents
Hot H2O CO and minerals such as iron and nickel sulfides released. Today these hot springs produce precursor to biological molecules

4 Steps of Abiogenesis

1) Abiotic synthesis of monomers
2) Formation of organic macromolecules
formation of polymers from monomers (protein or RNA)
can form on clay or rock surfaces
negative ions bind monomers
Zn2+ and Fe2+ catalyze polymerization
3) Formation of Protocells. In water lipids and other organic molecules spontaneously form vesicles (fluid filled compartments surrounded by membrane like structure)
organic polymers exhibit attributes of living cells 1)osmosis, 2) homeostasis, 3) divide is large enough. But NO mechanism of heredity
4) self replicating RNA. RNA first nucleic acid in protocells. RNA capable of: replicating itself, Catalyze protein synthesis: ribozymes. DNA: Double stranded, more stable

geological time scale

Established by study of fossils, radioisometric dating. Based on major geological, climate, and bio events
strata: sedimentary rocks deposited into layers.

Geological record

standard time scale divided into 4 eons
Hadean- oldest
Archean- first cells
Proterozoic- first eukaryotes
Phanerozoic includes 3 eras
Between eras: major extinction events
Periods and epochs-smaller divisions
Eons>Era>Period>Epoch (an age is the # of years ago)

Early life on earth

stromatolites: column composed of layers of dead cells

3.5 billion years ago just heterotrophic bacteria

prokaryotes 1st heterotrophs, used fermentation (anaerobic)
2nd photosynthetic autotrophs E from sunlight
cyanobacteria: released O2 caused rise of atmospheric oxygen
3rd aerobes: use (O2) lead to more ATP

endosymbiotic theory

Ancestors of mitochondria and plastids was prokaryotes thatcame to live in a host cell.
Serial endosymbiosis: mitochondria entered first. plastids after

Evidence for Endosymbiosis

Mitochondria and Plastids have double membrane, similar size, enzymes, ribosomes, DNA, undergo binary fission which is all similar to prokaryotes

Origin of Multicellularity

oldest fossils 1.2-1.8 bya
Ediacaran period-600 mya-eukaryotes:soft bodied
Cambrian Explosion: 535-525 mya: Fossils appear resembling modern animal, rapid evolution new animal body plans

Colonization of land

larger forms of life on land: fungi plants and animals
Adaptations for life on land-prevent drying out (desiccation)

Domains of Life

3 domains of organisms diverged from a common ancestor
Bacteria-prokaryote
Archaea-prokaryote
Eukaryotes: protists, plants, animal, fungi

cell

smallest unit that carries out all activities associated with life, can do everything or be specialized, all share common features and evolutionary history

Magnification

ratio of size of image to actual size of specimen, higher mag. = see smaller objects

Resolution

measure of clarity, minimum distance between two objects at which they can be seen separately

Light Microsope

uses visible light, 1 or more lenses

Electron Microscope

focuses beam of electrons through the specimen
2 Kinds: Transmission: specimen embedded in plastic, cut into very thin slices, electron beam passes through, stained with heavy metals improves contrast
Scanning: used to study surfaces, electron beam does NOT pass through specimen, specimen coated with gold film, emits electron when struck

Electron Microscopy Drawbacks

cells are killed, cant study living things or procedsses
many alter specimen structure
expensive
tedias preparation

Cell Fractionation

Separates Major organelles
Centrifuges fractionate cells into their component parts
Used to determine the functions of organelles
Helps correlate cell function with structure

Prokaryotes

Before nucleus
domains bacteria and archaea

Eukaryotes

"true nucleus:
domain eukarya
includes protists, fungi, animals, and plants

Common features in ALL cells

Surrounded by plasma membrane
Distinct internal enviroment
store, replicate gen info
divide, reproduce
metabolism
interact with and respond to external environment
(generally) limited in size
1)Plasma membrane- phospholipids
2)Cytosol- semifluid substance
3)Chromosomes- carry genes, DNA
4) Ribosomes- make proteins, RNA

Limits to cell size

1) plasma membrane- all materials must pass to enter cell, surface area limits rate at which they enter
2) advantages to maximize surface area to volume ratio

Components of Prokaryotic Cells

No nucleus Nucleoild: DNA in an unbound region
No organelles
they have nucleoid
plasma membrane
cell wall
ribosomes
capsule
chromosomes (DNA)
flagella

Components of Eukaryotic Cells

Nucleus: contains most DNA, often visible. DNA organized into chromosomes. DNA+ PROTEIN= CHROMATIN
Nuclear envelope: double membrane, separates nucleoplasm from cytoplasm, nuclear pores (regulates passage between cytoplasm and nucleus) is lined by nuclear lamina:composed of proteins, maintains shape of nucleus
Nucleolus: region of ribosome production within nucleus, dense in RNA and proteins
Ribosomes: Structures responsible for protein synthesis, NOT membrane bound, NOT considered organelle, made of protien and Ribosomal RNA (rRNA), found in the cytoplasm (free) and Rough ER (bound)
Endomembrane System includes: Nuclear envelope, plasma membrane, ER, Golgi Apparatus, Lysosomes, Vacuoles
ER: ER membrane continous with the nuclear envelope, Two regions: smooth ER: lacks ribosomes, lipid synthesis, metabolizes carbohydrates, detoxifies drugs and poisons, stores calcium ions. Rough ER: surface studded with ribosomes (bound) so make proteins. Proteins made--tract through translocation--into lumen (internal space). Proteins are folded and modified. Secretes glycoproteins, distributes transport vesicles, membrane factory for the cell
Golgi Apparatus: shipping and recieving center, Cisternae, NOT continuous from ER, cis face: receiving side from ER, trans face: shipping side. Modifies products of ER, Manufactures certain macromolecules, sorts and packages materials into transport vesicles, shipping product out of golgi using vesicles
Lysosomes: Digestive Compartments, sacs of hydrolytic (digestive) enzymes produced. Primary Lysosome: buds off golgi, Secondary lysosome: when digesting and fused with food vacuole, break down complex molucules- make fuel, degrade foreign molecules
Vacuoles: diverse maintenance comparments
Structure: Large vacuoles derived from the ER and Golgi App.
Functions: Variety functions in different cells. food vaculoles are formed by phagocytosis, contractile vacuoles: pumps excess water out of cells, Central vacuoles:storage in plant cells, organic compounds and water

Membrane Structure: Important features

Fluid Mosaic model
Phospholipids
Proteins
Carbohydrates

Membrane

contains a phospholipid bilayer that forms spontaneously due to shape and amphipathic nature (hydrophopic fatty acid tails) (hydrophilic head)

Membrane Protiens

Peripheral (hydrophilic)
Integral: Amphipathic trans membrane: span membrane

Fluid mosaic model

lipids,proteins, and carbs can move side to side (laterally) within one layer of the membrane .
Fluidity depends on: temperature, chain length of tails (and bends in tails), saturation (pack together less fluid), amount of cholesterol ( acts as a spacer. at moderate temperature it reduces membrane fluidity but at low temp it hinders solidification)

membrane protiens

proteins can move side to side (laterally) but cannot flip back and forth within membrane
Functions: Transport, enzyme acitivity, signal transduction, cell to cell recognition, intercellular joining, attached to the cytoskeleton and extracellular matrix

Carbohydrates in cell membrane

polysaccharide attached to protein (glycoprotein) or lipid (glycolipid) primarily cell identification (blood types)

Plasma membrane

selectively permeable
2 Basic types of transport:
Passive: doesnt use metabolic E (ATP) moves with the gradient
Active- DOES use metabolic E (ATP) moves against the gradient from a low to high concentration

Passive Transport

Includes Simple diffusion, osmosis, facilitated diffusion
Net movement is down concentration gradient
No ATP required
Results in dynamic equilibrium
Diffusion: tendency for molecules of a substance to fill available space
What can diffuse: small gasses (o2 CO2 N2), Small nonpolar molecules-includes hydrocarbons, small polar uncharged molecules- including H20
Osmosis: diffusion of water across selectively permeable membrance
[solvent: a substance capable of dissolving other substances (water) solute: a substance being disovles
Water moves towards higher concentration of solute. Always about water moving
Osmosis Tonicity: ability of a solution to cause a cell to gain or lose water
Isotonic (equal) amount of solute same outside and inside cell no net H20 MOVEMENT. Inside PLANTS: FLACCID
Hypertonic: solute outside cell bigger than solute inside the cell. H20 leaves cell causing cell to shrivel: IN PLANTS PLASMOLYZED (DRIED OUT) (plasma membrane detaches from cell wall)
Hypotonic: solute inside the cell is bigger than solute outside, H20 enters the cell causing it to LYSE (Burst) PLANT CELL BECOMES TURGID THIS IS THE NORM
Simple Diffusion is not enough (large molecules to big to get through , polar molecules cant get through hydrophobic area, ions- charged)
Facilitated Diffusion: Passive transport through a transport protein
Doesnt require ATP
2 Types channel and carrier protein

Active Transport

Transport through carrier protein/integral membrane protein that changes shape. Requires ATP
works against gradient
Sodium potassium pump- 3 Na+ out, 2 K+ in against gradient requires atp. establishes electrical
Bulk transport: transport of a large number of molecules at once
types of active transport but doesnt use Carrier proteins
Exocytosis: vesicle containing waste or secretory products fuses with plasma membrane
releases contents from cell
Adds lipids to Primary mechanism for growing plasma membrane
Endocytosis: Material taken into cell by forming vesicles derived from plasma membrane
3 Types
Phagocytosis: cellular eating, cell engulfs large particle, non specific. fuses with primary lysosome
Pinocytosis: cell drinking, ingestion of fluid and dissolved material
forms vesicle, slowly transferred to cytoplasm nonspecific
Receptor mediated Endocytosis: Specific, receptor proteins, form coated pits, fold inward to form vesicles, main mechanism for uptake of macromolecules

metabolism

sum of all chemical reactions and energy tranformations in in organism-maintaines homeostasis, emergent property of life

metabolic pathway

begins with a specific molecule (reactants) and ends with a product, each step is catalyzed by a specific enzyme

Anabolic Pathways

synthetic (build complex molecules from simpler ones) requires energy, dehydration

Catabolic

breaking bonds, releasing potential energy, hydrolysis (ex:cellular respiration)

Free energy change in chem reactions

Capacity to cause change OR DO WORK (supply heat)