General Biology 115 Final Exam

How does long term memory work?

Activated when needed => pulled into short term (working) memory

Long term potentiation

use of information is like a sorting process

T/F: If information is not used, then it is discarded

True

LTP is facillitated by

Chunking

Emeregnce

The whole is greater than the sum of the parts

Emergent Properties

Results from the arrangement and interaction of parts within a system

Reductionism

Reduction of complex systems to simpler components that are more manageable to study

Scientific Method

Make an observation

Do background research

Make a hypothesis

Create an experiment

Evaluate the results of the experiment

If the predictions are wrong, make a new hypothesis and start over from step 3

Revise predictions

Repeat and verify

4 most abundant elements

C, H, O, N

Ionic bonds

Between atoms => the more electronegative elements steals an electron

Van der Waals Interactions

-Develop because electrons are in constant motion

-single interaction is weak but multiple are strong

Hydrogen bonds

-very strong dipole-dipole interaction

-H + F, O, N

Cohesive behavior

-polar molecules side with different charges are attracted to each other

-surface tension is a measure of how hard it is to break the surface of a liquid

Hydrophillic

Ions, salts, polar, "water loving"

Hydrophobic

Lipids, nonpolar, "water hating"

Organic compounds

-carbon based compounds

-carbon bonded to another carbon or hydrogen

Hydrocarbons

-only hydrogen and carbon

-nonpolar, uncharged, hydrophobic

Hydroxyl group

-alcohol

-polar

-form hydrogen bodns with water

-hydrophillic

Ketone

-internal carbonyl group

-polar

-hydrophillic

Aldehyde

-terminal carbonyl group

-polar

-hydrophillic

Carboxyl group

-polar

-hydrophillic

-very acidic

Amino group

-proton acceptor => basic

-hydrophillic

Sulfhydryl group

-structure of some proteins

-less polar than a hydroxyl group

Phosphate group

-contributes a negative charge

-acidic

-hydrophillic

-phospholipids & nucleic acids

Methyl group

-nonpolar hydrocarbon

-hydrophobic

-control of gene expression

-shape and function of sex hormones

Macromolecules

-large complex molecules that are formed by thousands of atoms

-carbohydrates, lipids, proteins, nucleic acids

Enzymes

speed up chemical reactions

Hydrolysis

-"to break with water"

-using water to break polymers

-regulated by hydrolyses

Dehyration synthesis

-synthesizes monomers together

-removes water

regulated by dehydrogenase

Carbohydrates

-fuel & building material

-hydrophillic

-polysaccharides attached to proteins = glycoproteins or lipids

-cell identification (ex: blood types)

Lipids

-not true polymers

-hydrophobic

-dissolve in nonpolar solvents => nonpolar

-3 important families: fats, phospholipids, steroids

Fats

-highly concentrated energy

-consists of one glycerol (3 carbon alcohol with 3 -OH) & 1-3 fatty acids

Fatty Acids

-carboxyl group with a long, unbraided hydrocarbon tail

-added to glycerol during dehydration synthesis

-form a covalent bond => ester linkage

-triglyceride = main storage of fat

Phospholipids

-glycerol & 2 fatty acids (hydrophobic)

-phosphate group (hydrophillic

-polar

-acidic

Steroids

-3 rings with 6 carbons & 1 ring with 5 carbons

-differ in side chains or functional groups attached

Proteins

-made of amino acids

-monomers are bound together with peptide bonds through dehydration synthesis => becomes polypeptide

-primary structure => secondary structure => tertiary structure => quatinary structure

Primary structure of proteins

sequence of amino acids joined by peptide bonds in a polypeptide chain

Secondary structure of proteins

-hydrogen bonds

-R groups do NOT participate

-alpha helix = coil

-beta pleated sheet

Tertiary structure of proteins

-interrelationships of R groups fold into particular 3D shapes

-can have all types of bonds (hydrogen, ionic, covalent, disulfide)

Quatinary structure of proteins

-two or more polypeptide chains

-no more folding

Denaturation

-a loss of a protein's native structure

-biologically inactive

-pH, salt concentration & temperature are all factors that can cause denaturation

-low temperature slows down an enzymatic reaction

-even a short exposure to a high temperature can denature a protein

Nucleic acids

-monomers are nucleotides

-transmit hereditary information & determine protein production

4 factors of abiotic synthesis

1) little / no free oxygen

2) source of energy

3) presence of chemical building blocks

4) time

Miller & Urey experiment

-simulated early conditions of early Earth

-formed amino acids & other organic molecules

Iron-Sulfur World Hypothesis

-life formed at the cracks of the ocean floor => hydrothermal vents

-hot water, carbon monoxide, and mineral such as iron & nickel sulfide released

Steps of abiogenesis

1) abiotic synthesis of monomers

2) synthesis of macromolecules

3) formation of protocells

4) self-replicating DNA

Synthesis of macromolecules

-formation of polymers from monomers

-monomers polymerize on hot sand or on rock

-negative ions bind monomers

Formation of protocells

-in water, lipids and other organic molecules spontaneously form vesicles

-organic polymers exhibit attributes of living cells (osmosis, homeostasis, division)

-no mechanism of heredity

Self-replicating DNA

-RNA first nucleic acid in protocells

-RNA is capable of replicating itself & catalyzing protein synthesis: ribozymes

-DNA evolved later (double-stranded, more stable)

Order of geologic time

Eons => Eras => Periods => Epochs

Stromatolites

ancient bacterial mats on sedimentary layers

Order that life was formed in

Prokaryotes => Photosynthetic Autotrophs => Aerobes

Endosymbiotic theory

-mitochondria and plastids were initially small prokaryotes

-now are organelles of eukaryotic cells

Cambrian explosion

-535~525 million years ago

-fossils appear to resemble modern animals

-rapid evolution => new animal body plans

Cell theory states that

-all organisms are made up of cells

-all cells have 4 common features and a common evolutionary ancestor

Light microscope

-can see things the size of about 2um

-stains or dyes increase contrast

-you can see nucleus but not smaller organelles

Scanning electron microscope

electrons bounce off the outside of the object

Transmission electron microscope

-electrons go all the way through the object

Why aren't electron microscopes used all the time?

-cells must be killed (sliced / covered in gold)

-may alter their structure

-expensive

-tedious preparation

Features of all cells

-plasma membrane: phospholipids

-cytosol: semifluid substance

-chromosomes: carry genes and make DNA

-ribosomes: make proteins & RNA

Prokaryotic cells

-NO nucleus (there is a nucleoid form => DNA in an unbound region)

-NO organelles but have flagella, plasma membrane, fimbriae & cell wall

Eukaryotic cells

-DNA in nucleus

-membrane bound organelles

-10x the size of prokaryotic cells

Why are cells so small?

-plasma membrane acts as a selective barrier

-surface area to volume ratio (the bigger it is, the more places there are for things to enter / leave the cell)

Endosymbiosis

-both mitochondria and chloroplasts once were prokaryotes

-both mitochondria and chloroplasts have inner membranes, enzymes, their own DNA, their own ribosomes, undergo binary fission and are small

Nucleus

-DNA is organized in chromosomes

-DNA & proteins = chromatin

-RNA is the only thing that leaves the nucleus

Nucleolus

-RNA & proteins

-No membrane

Nuclear envelope

-made of 2 membranes => both are bilipid bilayers

-nuclear pores regulare entry & exit of the molecules

-is lined by nuclear lamina, which is composed of proteins & maintains the shape of the nucleus

Ribosomes

-site of protein synthesis

-not membrane bound => ribosomes are not considered organelles

-free ribosomes => float around in the cytoplasm (both prokaryotes and eukaryotes)

-bound ribosomes are bound on the endoplasmic regulation (only eukaryotes)

Endomembrane system

-made of a lipid bilayer

-separates internal contents from external environment & separates cell into many compartments

-function is to regulate protein traffic & performs metabolic functions in cell

-consists of: nuclear envelope, plasma membrane, endoplasmic reticulum, Golgi apparatus, lysosomes & vacuoles

Plasma Membrane

-encloses cell contents

-controls material that goes in & comes out of cell

-selectively permeable

-no cell wall

-phospholipid bilayer

Endoplasmic reticulum

-continuous with nuclear envelope

-smooth ER has no ribosomes & rough ER has ribosomes

-lumen = internal space

Functions of the Rough Endoplasmic Reticulum

-has bound ribosomes => makes proteins

-proteins are folded and modified

-secrete glycoproteins (proteins that are covalently bonded to carbohydrates)

-distributes transport vesicles

-is a membrane factory for the cell

Functions of the Smooth Endoplasmic Reticulum

-synthesize lipids

-metabolizes carbohydrates to break down glycogen and regulate blood glucose

-detoxifies drugs and poisons

-stores calcium ions

Golgi Apparatus

-cis face is the receiving side of the endoplasmic reticulum

-trans face is the shipping side

-modifies products of the endoplasmic reticulum

-manufactures certain macromolecules

-sorta & packages materials into transport vesicles

-shipping product out of Golgi apparatus using vesicles

Lysosomes

-digestive components

-sacs of hydrolytic or digestive enzymes

-primary lysosomes: buds off Golgi

-secondary lysosomes: primary lysosome fused with another structure

-breaks down complex molecules

Vacuoles

-diverse maintenance compartments

-food vacuoles are formed by phagocytosis

-contractile vacuole: plant cells, organic compounds & water

Membrane Proteins

-tend to be amphipathic

-integral or peripheral

-can move but can't be flipped

-hydrophobic => fold inside the protein

-hydrophilic => fold outside the protein

Functions of Membrane Proteins

-transport

-enzymatic activity

-signal transduction

-cell cell recognition

-intercellular joining

-attachment to the cytoskeleton & extracellular matrix

Fluid Mosaic Model

-membrane components can move laterally within one layer of the membrane

-fluidity depends on temperature, chain length / bends in tail, saturation, and amount of cholesterol

Passive Transport

-doesn't use ATP

-moves with the gradient

-spontaneous

-results in dynamic equilibrium

-cells prefer passive transport

Diffusion

-tendency for molecules of a substance to fill available space

-small gases like oxygen gas, carbon dioxide and nitrogen gas can pass through

-small nonpolar molecules like hydrocarbons can pass through

-small polar uncharged molecules like water can pass through

Osmosis

-diffusion of water across selectively permeable membrane

-water diffuses form a lower to a higher concentration

Solvent

a substance capable of dissolving other substances

Solute

a dissolved substance

Osmosis Tonicity

ability go a solution to cause a cell to gain to lose water

Isotonic solution

-concentration outside = concentration inside

-no net water movement

Hypertonic solution

concentration outside cell is greater than the concentration inside the cell

Hypotonic solution

concentration outside cell is less that the concentration inside the cell

Facilitated diffusion

-facilitated = to make easier

-larger molecules can be transported

-transport using transport proteins

-channel proteins

-some carrier proteins

Active Transport

-uses ATP

-moves against the gradient

-low concentration => high concentration

-not spontaneous

-not carrier mediated

-formation of vessicles

-exocytosis = "out"

-endocytosis = "in"

-phagocytosis = "eat"

-pinocytosis = "drink"

Exocytosis

-waste, proteins, & secretory products

-vesicle fuses with plasma membrane

-releases contents from cell

-vesicle fuses with plasma membrane (PM) => primary mechanism for growing plasma membrane

Endocytosis

-material taken into the cell by forming vesicles derived from the plasma membrane

-3 types: phagocytosis, pinocytosis, receptor mediated endocytosis

Phagocytosis

-"cell eating"

-cell engulfed large particle

-non-specific

Pinocytosis

-"cell drinking"

-ingestion of fluid & dissolved material

-non-specific

Receptor-Mediated Endocytosis

-receptor proteins in plasma membrane bind specific macromolecules outside the cell

-form coated pits

-fold inward to form vesicles

-fold inward to form vesicles

-main mechanism for uptake of macromolecules

Metabolism

-sum of all chemical reactions of an organism -> maintains homeostasis

-an emergent property of life

Catabolic Pathway

-breaking down complex molecules into simpler ones

-releases energy => exergonic

-ex: cellular respiration, hydrolysis

Anabolic Pathway

-build complex molecules from simpler ones

-uses energy => endergonic

-ex: synthesis of proteins from amino acids, dehydration synthesis

Energy

capacity to cause change

Potential Energy

stored energy that hasn't been used yet