McSharry Intro to Biology Test #2

Cell Size Problem

As proportions increase in organisms, their volume grows much faster than their surface area.

Universal Cell Features (4)

plasma membrane, cyotoplasm, DNA, ribosomes

Peptidoglycan

Makes up prokaryote cell walls.

Made of a sugar backbone connected with cross-linked peptides.

Gram Negative

Prokaryotes with a secondary outer membrane composed of phospholipids which block the intake of a certain pigment.

Make up 70% of prokatyotes.

Prokaryote Cell Wall

Made of peptidoglycan.

Required for growth, reproduction, and maintaining structural integrity.

90% of prokaryotes have it

Eukaryote Cell Wall

Made of cellulose.

Mostly in plants, not in animals.

Nucleoid

Region (NOT organelle) in prokaryote cells that contain most of the genetic material.

Prokaryote DNA

Genetic information stored in a circular chromosome in the nucleoid of certain organisms.

Prokaryote

Single celled organisms that have no membrane bound organelles or nucleus.

Usually smaller (1-10 μm)

Ex: bacteria, archaea

Eukaryote

Organisms with membrane-bound nucleus and other organelles like mitochondria and chloroplasts.

Usually larger (10-100 μm)

Ex: animals, plants, fungi, protists

Prokaryote Ribosome

Protein synthesizing machinery with smaller 70s complexes made of 30s and 40s subunits, only in cytoplasm of certain organisms.

Outer Membrane

A secondary layer of phospholipids and proteins for cell to cell communication, adhesion, and nutrient uptake.

Found on the outside of the cell wall in Gram negative prokaryotes.

Gram Stain

Test using a specific pigment to differentiate between prokaryotes with and without outer membranes.

Nucleus

Membrane-bound organelle in eukaryotes containing the nucleolus, cellular DNA, and the proteins to transcribe it into RNA.

Nucleolus

Part of the nucleus dedicated mostly to creating ribosomes.

Mitochondria

Oval shaped organelle that produces ATP from sugars.

Contains its own DNA seperate from the cell.

Chloroplast

Lens shaped organelle that absorbs light energy in the pigment chlorophyll to produce sugars from photosynthesis.

Contains its own DNA seperate from the cell.

Vacuole

Large, mostly empty organelle which helps provide rigidity, hold pigment, aid in digestion, and store water and waste.

In plant cells, it can take up to 90% of the cell’s volume.

Smooth Endoplasmic Reticulum

Organelle with layered structure in the cytoplasm between nucleus and plasma membrane.

Synthesis for steroids and lipids (eg. cholesterol), detoxifies harmful substances, breaks down glycogen into sugar (liver cells), stores calcium ions.

Rough Endoplasmic Reticulum

Organelle in cytoplasm near nucleus with layered structure embedded with ribosomes.

Synthesis, modification, and folding (primary, secondary, & tertiary) for many proteins.

Adds tags to proteins to signal final destination before sending to golgi apparatus.

Golgi Apparatus

Organelle with layered structure in cytoplasm near nucleus and ER. Cis-face near ER, trans-face near plasma membrane

Center of sorting, modifying, and packaging proteins; then sends proteins to outside of cell, lysosome, or plasma membrane.

Lysosome

Spherical organelle in cytoplasm containing hydrolase and other digestive enzymes in acidic environment to break down macromolecules.

Primary Lysosome

Organelle originating in golgi and has inactive digestive enzymes.

Phagosomes

Vesicle in cytoplasm formed from ingestion of particles/molecules in phagocytosis.

Immunoflorescence

Technique for visualizing multiple cell structures by using fluorescent dyes connected to antibodies which target and attach to parts of cells and can be seen in microscope.

Sulphation

Addition of sulphate to protein/hormone while in golgi.

Glycosylation

Addition of oligosaccharide to protein/hormone while in golgi.

Can also start in the ER before golgi.

Oligosaccarides in membrane often used as intercellular identification.

Microtubule

25 nm filament in cells made of molecule tubulin (α or β).

Associated with motor proteins kinesan and dynein.

Kinesan

Motor protein in cells that uses microtubules as ‘railroad tracks’ to carry molecules.

Uses ATP to move, only goes towards plus end of microtubule.

Dynein

Motor protein in cells that uses microtubules as ‘railroad tracks’ to carry molecules.

Uses ATP to move, only goes towards minus end of microtubule.

Microfilaments

7 nm filament in cells made of molecule actin.

Associated with motor protein myosin and integrins.

Used to move cells via contraction, divide cells in two, and maintain cell shape by resisting tension.

Intermediate Filaments

8-12 nm filament in cells made of molecules like keratin, nuclear lamins, etc.

Used to resist tension and anchor cell structures.

Cilia

0.25 μm hairlike membrane bound projection in large numbers sticking out of eukaryotic cells for movement.

Made of axonemes with motor proteins (dynein) and anchored to cytoskeleton.

Move together in sync to push fluid and particles past cell surface.

Flagella

0.25μm membrane bound projection sticking out of eukaryotic cells like a tail that undulates to move cell.

Made of axonemes with motor protein base anchored to cytoskeleton.

Prokaryote Flagella

Simple structure used for movement in certain organisms made of only one protein and disconnected from the cytoskeleton with motor protein and base between cell membrane and wall.

Pili & ‘Sex Pili’

Short, hairlike filaments mostly on outside of Gram-negative bacteria.

Specialized versions are instrumental in transfer of genetic material between bacteria.

Axoneme

Filament structure in eukaryote structures (flagella & cilia) made of 9 microtubules in circle surrounding 2 other microtubules.

The Central Dogma of Biology

DNA contains genetic data to define RNA which then codes for amino acids needed to make proteins. Process cannot go backwards.

Transcription

In nucleus, protein RNA polymerase reads DNA and makes complementary RNA molecule.

Template Strand

Strand of DNA read by RNA polymerase during transcription.

Complementary and antiparallel to RNA molecule produced.

Coding Strand

Strand of DNA that complements template strand read by RNA polymerase during transcription.

Identical and parallel to RNA molecule produced, but has thymine in place of uracil.

Translation

In the cytoplasm or ER, ribosomes make a protein from reading the sequence of nucleotides in the codons of mRNA strands.

RNA to mRNA

Introns are removed from unprocessed strand.

Cap (methylated guanine) added to 5’ end.

Poly-adenine (~200 adenine) tail added to 3’ end.

Intron

Section of DNA or unprocessed RNA that interferes and doesn’t contribute to protein synthesis and so it’s removed during processing from RNA into mRNA.

Exon

Section of DNA or unprocessed RNA that contributes to correct protein synthesis when translated.

Codon

Three-base triplet sequence in mRNA that specifies one amino acid when translated.

Start Codon

Specific three-base triplet (AUG) that codes for Methionine which when read by a ribosome signals beginning of translation.

Redundancy in Genes

All amino acids in proteins (except Methionine and Tryptophan) have multiple different codons that translate to them.

Conservatism in Genes

When there are several codons for the same amino acid, the first 2 bases are almost always the same.

Example: ACU, ACC, ACA, & ACG all code for Threonine

Eukaryote DNA

Genetic information stored in a linear chromosome in the nucleus of certain organisms.

Eukaryote Ribosome

Protein synthesizing machinery with larger 80s complexes made of 30s and 50s subunits in cytoplasm and rough ER of certain organisms.

Secondary Lysosome

Organelle with active digestive enzymes formed from lysosome and phagosomes combining.

Eukaryote Flagella

Membrane bound intracellular structure in certain cells containing axonemes for structure and proteins to cause undulating movement.

Unambiguity in Genes

A single codon NEVER codes for more than ONE amino.

Universal in Genes

ALL organisms have the same way of translating mRNA (With few exceptions).

Example: 5’-AUGUGUAAAUGAGU-3’ would code for the same peptide in a human or E. Coli.

mRNA

Oligoribonucleotide chain that has been processed in nucleus and is translated by ribosomes to make proteins.

tRNA

Structure composed of oligoribonucleotide in cytoplasm, used by ribosomes.

One side has the anticodon complentary to a specific mRNA codon,

other side has the corresponding amino to the codon.

Anticodon

Three-base sequence in tRNA complementary to specific codon in mRNA.

rRNA

Structure composed of non-coding oligoribonucleotide in ribosome.

Makes up 80% of cellular oligoribonucleotides.

Endosymbiotic Theory

Mitochondria and chloroplasts evolved from bacteria which were consumed by ancient eukaryotes and have their own DNA.

Eukaryotic Endomembrane System (5)

Nucelar envelope, ER, golgi, lysosomes, plasma membrane.

Secretion

Process of golgi sending proteins out of cell.

COP II (2)

Proteins travelling from ER to golgi are covered in this protein.

Required to for proteins to navigate/dock at golgi.

COP I (1)

Proteins travelling from golgi to ER are covered in this protein.

Required to for proteins to navigate/dock at ER.

Phospholipid

Amphipathic molecule made of 2 fatty acid chains and a phosphate group attached to a glycerol.

Phosphate head is hydrophillic, tail is hydrophobic.

Amphipathic

Describing a molecule with both hydrophillic and hydrophobic interactions.

Example: phospholipid

Selective Permeability

The ability of certain barriers/membranes to allow certain molecules or ions to pass through while restricting others.

Molecules that can Pass Cell Membrane

Most permeable: small nonpolar molecules (O₂, CO₂, N₂)

Second most permeable: small uncharged polar molecules (H₂O, glycerol)

Molecules that cannot Pass Cell Membrane

Least permeable: large uncharged polar molecules (glucose, sucrose)

Second least permeable: small ions (Cl^-, K⁺,Na⁺)

Membrane Fluidity

Describing the flexibility and seperation of parts of a barrier.

In cells, unsaturated fatty acids in the lipid bilayer increase this factor due to their bent tails taking up space.

Permeability

Describing the ability of a membrane to let through molecules and ions.

Directly related to the fluidity of the membrane.

Diffusion

When solute molecules move from regions of high concentration to regions of low concentration.

Can happen through (semi) permeable membranes

Diffusion at Equilibrium

Even when there is no difference in concentration between regions, solute molecules continue to move between them at uniform rates.

Molarity (mol/L)

Unit of concentration for solutes dissolved in solutions.

Concentration

The number of a given particle in a given volume.

Concentration Gradient

Gradual difference in the amount of solutes in a given volume of solution between two regions.

Directly related to diffusion rate.

Decreases during the process of diffusion as solute amount equalizes.

Diffusion Rate Factors (5)

Direct relation to:

concentration gradient and temperature.

Indirect relation to:

size and mass of particles, density, and distance.

Example: high conc. grad. + high temperature + small light particles + thin solution + small space = highest rate of particle movement

Osmosis

Diffusion of water across a membrane.

Hypertonic

High solute concentration outside cell relative to inside.

Water diffuses out of cell and cell shrinks.

Hypotonic

Low solute concentration outside cell relative to inside.

Water diffuses into cell and cell swells.

Isotonic

Equal solute concentration inside and outside cell.

No major movement of water in or out of cell.

Passive Transport

Powered by diffusion.

Requires NO additional energy.

Molecules move WITH concentration gradient.

Simple Diffusion

Movement from high to low concentration.

Form of passive transport.

Facilitated Diffusion

Process using channel proteins (passive transport) to speed up transfer from high to low concentration.

Form of passive diffusion.

Aquaporin

Channel protein (passive transport) which allows water to cross the membrane.

Has positively charged structure to help repel water through.

Ion Channel

Gated channel proteins (passive transport) that allow charged particles through membrane.

Can be opened or closed by ligands, electrical charges, or mechanical signals.

Carrier Protein

Channel protein (passive transport) that physically binds to polar molecules and uses concentration gradient to change conformational shape and move it across membrane.

Active Transport

Powered by ATP.

Requires additional energy (ATP).

Molecules move AGAINST concentration gradient.

Primary Active Transport

Process using energy from ATP hydrolysis to power special pumps which move molecules across the membrane.

Example: sodium potassium pump.

Secondary Active Transport

Process of moving a solute against its gradient through membrane using energy from another solute’s gradient to push it through.

Other solute’s gradient created by pumping with ATP.

Example: glucose transporter moving glucose into cell using diffusion of sodium after it was pumped out.

Symporter

Transport Protein (active transport) which moves 2 substances in same direction through membrane.

Example: glucose carrier protein letting through sodium and glucose.

Antiporter

Transport Protein (active transport) which moves 2 substances in Different directions through membrane.

Example: sodium potassium pump moving sodium out of cell and potassium into cell.

Uniporter

Specialized carrier protein (passive transport) which moves 1 substances in 1 direction by facilitating.

Gating Signals in Ion Channels (3)

Ligands, electrical charges differences, & mechanical changes.

Channel Saturation

Transporter proteins can only move so much solute so fast, as concentration of solute increases rate of diffusion reaches approaches a maximum plateau.

Phagocytosis

Process of other cells/molecules being engulphed into the cell in the form of phagosomes.

Endocytosis

Active transport process where cells absorb molecules, particles, or fluids from surroundings by engulfing them in a pocket of the plasma membrane.

Pinocytosis

Form of active endocytosis where cells engulf extracellular fluid and dissolved nutrients by forming small vesicles.

“Cell drinking”.

Example: endothelial cells do this all the time.

Receptor-Mediated Endocytosis

Active transport process where cells use special membrane proteins to absorb specific molecules into vesicles.

Example: cholesterol being brought into cell.

Fluid Mosaic Model

Description of the plasma membrane as being a liquid-like bilayer in which proteins “float” like in a lake.

Proteins can move laterally around membrane freely.