BIOL 1101: Unit 2 Vocab

Endomembrane system,

Endomembrane System

Collection of interconnected, membrane-bound organelles in eukaryotic cells that work together to synthesize, modify, package, and transport proteins and lipids

Topological Equivalence

The idea that the ER, golgi, lyosomes, and endosomes share the same internal environment, allowing the molecules to move between them without crossing a membrane

Nucleus

Contains nuclear envelope, nuclear pore complex, nuclear lamina

Control center of eukaryotic cell, acts as storage for cell’s genetic material, protects and manage instructions necessary for cell growth, survival, and reproduction

Nuclear Envelope

Highly-regulated double-membrane barrier separating the nucleus from the cytoplasm. Continuous with rough ER.

Nuclear Pore Complex

Channel of 50-100 different polypeptides allowing RNA and proteins to travel between the nucleus and cytosol

Nuclear Lamina

Provides structural support to the envelope and a point for chromatin to attach during interphase

Endoplasmic Reticulum

2 distinct regions with 2 different functions: Smooth and rough

Smooth ER

No ribosomes

Synthesizes lipids (steroids), metabolizes carbs (glycogen), stores calcium ions, detoxifies poisons and drugs

Rough ER

Bound ribosomes, synthesizes proteins destined for secretion or the endomembrane system, syntehsizes integral membrane proteins, performs initial protein modifications and membrane assembly

Golgi Apparatus

Acts as the cells receiving, shipping, and modification center

Modifies proteins produced in the ER and pinches off vesicles to give rise to lysosomes and vacuoles

Vesicles

Move cargo between organelles using specific protein “coats” that designate their direction of travel

COPII-Coated Vesicles

1/3 coat proteins, goes from ER—>Golgi, pathway type: anterograde (forward)

Carry new proteins and lipids

COPI Coated Vesicles

1/3 coat proteins

Golgi—>ER

Pathway Type: Retrograde (recycling/backward)

Recycles ER resident proteins

Clathrin Coated Vesicles

1/3 coat proteins

Plasma Membrane—>Inside

Pathway Type: Endocytosis/Receptor mediated

Moves material (digestive enzymes that will break down things in the lysosomes) from the plasma membrane inward (endocytosis) or from the golgi to the lysosomes

Lysosomes

Membrane-bound sacs containing digestive enzymes acting as the cell’s destructive and break down forces and recycling center and digestive system

Main functions include: phagocytosis, autography, and waste processing

Phagocytosis

Digestion of food or foreign particles taken in from outside the cell into a large vacuole called the phagosome, which then fuses with the lysosome for digestion

Autophagy

Recycling the cell’s own damaged organelles

Endocytosis

Taking material into the cell

Includes Phagocytosis, pinocytosis, and receptor-mediated endocytosis

Phagocytosis

Cell eating, large particles are engulfed

Pinocytosis

Cell drinking, nonspecific uptake of extracellular fluid

Receptor-Mediated Endocytosis

Highly specific uptake using receptors and clathrin coated vesicles (LDL or cholesterol uptake)

Receptors on the cell surface bind to specific ligands, and once bound the clathrin proteins coat the membrane to form a vesicle and pull the material inside

Exocytosis

sending material out

Includes Constitutive secretion, regulated secretion

Constitutive Secretion

Continuous Release of materials, supplies the plasma membrane with new lipids and proteins constantly (mucus secretion in the gut)

Regulated Secretion

Materials are stored in vesicles and are released only in response to a specific signal (insulin in pancreas, or neurotransmitters from neurons)

Cytoskeleton

Network of protein fibers that give the cell its shape, hold organelles in place, and allow for movement

Consists of the microtubules, microfilaments (actin), and intermediate filaments

Microtubules

Structure: hollow tubes (tubulin)

Protein: tubulin

Diameter: largest

Key Functions: cell motility (cilia/flagella), chromosome movement, organelle tracks, ATP and movement, mainly involved in moving things like vesicles and DNA

Motor Proteins: kinesin and dynein

Dynamic? Yes (grows and shrinks)

Microfilaments

Structure: 2 intertwined strands

Protein: actin

Diameter: smallest

Key Functions: muscle contractions, cell shape (cortex), cytoplasmic streaming, ATP and movement, mainly involved in cell shape and contraction

Motor Proteins: Myosin

Yes (grows and shrinks)

Intermediate Filaments

Structure: fibrous proteins coiled into cables,

Protein: keratin and fibrous ones

Diameter: middle

Functions: anchorage of nucleus, formation of nuclear lamina, strength, permanent structure, mainly involved in permanent support and anchoring

Motor Proteins: none

No (permanent and stable)

Motor Proteins

The guiders of the cytoskeleton to allow intentional movement of the organelles and vesicles

Microtubule Motors

Kinesin and Dynein

Kinesin

Microtubule motor

moves cargo towards the “plus” end (usually towards the cell edge)

Dynein

Microtubule motor

Moves cargo towards the “minus” end (usually towards the nucleus or centrosome)

Actin/Microfilament Motors

Myosin

Myosin

Actin/Microfilament Motors

Responsible for muscle contraction and pinching the cell during cell division (cleavage furrow)

Glycoproteins

proteins with carbs attached, carb tags that help with protein folding, stability, and cell-to-cell recognition

Glycolipids

Lipids with bound sugars, important in the membranes of nerve cells, sugars attached directly to lipid head groups, on the outlet side of the plasma membrane

Function as ID tags, receptors for cell signaling, help cells stick together to form tissues, carbs can form hydrogen bonds with the surrounding water, helping to stabilize the membrane structure

Gangliosides

Most complex type of glycolipids, found in the highest concentration in the central nervous system, help in electrical signaling between neurons and involved in cell-cell recognition with the brain

Metabolism

Sum of biochemical processes in the cell

Includes catabolic and anabolic pathways

Catabolic Pathways (energy, example)

Break down complex molecules into simpler compounds

Release Energy (exergonic)

Example: cellular respiration: breaking down glucose to CO2 and H2O

Anabolic Pathways (energy, example)

Building complex molecules from simpler ones

Consume energy (endergonic)

Example: protein synthesis (building a polypeptide from amino acids)

Kinetic Energy

energy associated with motion

Potential Energy

Energy that matter possesses because of its location or structure

Example: chemical energy

Chemical Energy (example)

Type of potential energy stored in chemical bonds that is available for release in a chemical reaction

Example: ATP has high potential energy due to the arrangement of its phosphate groups

First Law of Thermodynamics

Energy can be transferred and transformed, but it cannot be created nor destroyed

Second Law of Thermodynamics

Every energy transfer/transformation increases the entropy (disorder) o the universe

Gibbs Free Energy Equation

DeltaG=DeltaH-TdeltaS

Exergonic Reactions

Spontaneous (energetically favorable)

Energy Released

Products have less free energy than reactants

DeltaG<0

Spontaneous

Exergonic, energetically favorable

Endergonic Reaction

Nonspontaneous (energetically unfavorable)

Energy required/absorbed

Products have more free energy than reactants

DeltaG>0

Nonspontaneous

Endergonic, energetically unfavorable

Energy Coupling

Making endergonic nonspontaneous reactions possible by pairing them with exergonic ones

ATP

Adenosine Triphosphate, cell’s energy currently

ATP Hydrolysis

ATP + H2O —> ADP + P (highly exergonic)

Enzyme

Biological Catalysts (usually proteins) that speed up metabolic reactions

• Increase Reaction Rates

• Lower Activation Energy to provide an alternative pathway with a lower energy barrier

• Transition State Stabilization: enzymes work by binding to the substrate and stabilizing the high-energy unstable transition state to make it more favorable to create relative to before

Active Site

A specific pocket or groove where the substrate binds

Induced Fit

The idea that when the substrate enters the active site, the enzyme changes its shape slightly to grip the substrate more tightly, favoring the transition state

Competitive Inhibition

1. Inhibitor mimics the shape of the substrate to compete for the enzyme’s active site

2. Blocks the substrate from entering the active site

3. To overcome, you can add more substrate as opposed to inhibitor

Allosteric Site

Distinct spot on an enzyme from the active site where molecules can bind to change the protein’s shape and activity

Noncompetitive Inhibition

1. Inhibitor binds to a different site (allosteric site) on the enzyme

2. Effect: binding causes the enzyme to change its shape, making the active site

3. Substrate Level: adding more substrate doesn’t help because the inhibitor and substrate aren’t fighting for the same spot

Stabilization Rule

Enzymes always favor and stabilize the transition state, not the substrate or product

Gene

a heritable unit of information

example: flower color

Allele

alternative versions of a gene (subject of heritable info, like color of flower) (purple vs. white)

Genotype

Genetic makeup of a gene (letters, like Pp)

Phenotype

Physical Appearance (what we see, like the color purple)

Homozygous

Having two of the same allele in one gene (PP or pp)

Heterozygous

Having two different alleles (Pp)

Mendel’s First Law

Law of Segregation

Mendel’s First Law: Law of Segregation

The two alleles for a heritable character segregate (separate) during a gamete formation and end up in different gametes during anaphase I of meiosis when homologous chromosomes separate

Result: an egg/sperm gets only one of the two alleles present in the aromatic cells

Monohybrid Cross

3:1 Ratio

Cross 2 heterozygotes (Pp x Pp)

Genotypic Ratio: 1:2:1 (1 PP, 2 Pp, 1 pp)

Phenotypic Ratio: 3:1 (3 Purple, 1 white)

Testcross

Performed using the principles of a monohybrid cross

Used to determine if a dominant looking plant is PP or Pp

Cross the dominant looking plant with a homozygous recessive (pp), and if any fo the offspring are white (recessive trait), the parent was Pp

Mendel’s Second Law

Law of Independent Assortment

Mendel’s Second Law: Law of Independent Assortment

Law: Each pair of alleles segregates independently of any other pair during gamete formation (ones splitting does not impact the others), occurring during Metaphase I of meiosis, based on how the chromosomes line up on the plate

Constraint: only applies to genes on different chromosomes or very apart on the same chromosome

Dihybrid Cross

9:3:3:1 ratio

Crossing two double heterozygotes (YyRr x YyRr)

Phenotypic Ratio: 9:3:3:1

• 9 of both dominant traits

• 3 of one dominant one recessive

• 3 of other one dominant and other one recessive

• 1 shows both recessive traits

Multiplication Rule

AND, to find the probability of two independent events happening together, multiply them by their individual probabilities from a monohybrid cross

Example: (probability of getting pp and rr from a PpRr x PpRr cross?) ¼ x ¼ = 1/16

Addition Rule

Find the probability of any one of two or more mutually exclusive events, add their individual probabilities

P Generation

True-Breeding parents (one is homozygous dominant, other is homozygous recessive)

Example: Purple x white flower

F1 GEneration

First generation of offspring from the P parents, every single offspring is a heterozygote Pp, so you see 100% of the dominant phenotype (purple, the white trait completely disappears)

F2 Generation

Second generation of the P generation. Created by crossing two of the F1 plants together Pp x Pp, or self pollinating just one of the F1 plants.

Recessive white trait reappears.

Creates 3:1 rule (monohybrid cross), where even though both parents were purple, about 75% of the offspring will be purple and 25% will be white

Independent Assortment

Genetic Linkage

When two alleles on the same chromosome do not separate during meiosis because they are on the same chromosome. (even if two different traits are on one chromosome, they cannot be separated)

Crossing Over

If two genes are on the same chromosome but are very far away from each other, crossing over can occur, where during meiosis in prophase I, homologous chromosomes (one from mom and one from dad) swap chunks of DNA. If the distance is large enough, the swap happens so frequently between the two genes that they behave as if they were on different chromosomes

Increases genetic diversity

Allows genes on the same chromosome to eventually follow the law of independent assortment if they are far enough apart

Chiasma

Where chromosomes swap DNA pieces in prophase I for crossing over