Cell Biology and Biochemistry Review Flashcards

Comprehensive set of vocabulary flashcards covering key topics in cell theory, biological molecules, protein structures, cell organelles, bioenergetics, enzyme kinetics, membrane dynamics, and cellular transport mechanism concepts.

Cell Theory

1) All living organisms consist of one or more cells;

2) The cell is the most basic unit of structure for all organisms

3) Cells arise from pre-existing cells only.

Limit of Microscopic Resolution

$\text{Wavelength} / 2$ .

Tetravalent Carbon

4 valence electrons

Water Polarity

polar molecular structure with a 105 bond angle,

partial positive and negative ends that allow hydrogen bonding,

heat sink

cohesiveness

Biopolymer Directionality

ends are not interchangeable

5’-3’

N end and C end

Polypeptide vs. Protein

polypeptide - simple chain of amino acids,

protein - one or more polypeptides folded into a functional 3-D shape.

Primary Structure Bonds

Covalent peptide bonds that connect amino acids sequentially in a polypeptide chain.

Secondary Structure Bonds

H-bonds that form folding patterns such as alpha helices and beta pleated sheets.

Tertiary Structure Interactions

Bonds and interactions stabilizing 3-D structure

including h-bonds, ionic bonds, hydrophobic interactions, and disulfide bridges.

Quaternary Structure Interactions

Interactions between multiple polypeptide subunits

involving h-bonds, ionic bonds, hydrophobic interactions, and disulfide bridges.

L-Isomer

specific stereoisomer form used for AA subunits in proteins

Hydrophobic Amino Acids

Nonpolar amino acids including

Glycine (Gly), Alanine (Ala), Valine (Val),

Leucine (Leu), Isoleucine (Ile), Methionine (Met),

Proline (Pro), Phenylalanine (Phe), Tryptophan (Trp).

Polar Uncharged Amino Acids

Hydrophilic

Serine (Ser), Threonine (Thr), Cysteine (Cys),

Tyrosine (Tyr), Asparagine (Asn), Glutamine (Gln).

Acidic Amino Acids

Negatively charged

Aspartate (Asp) and Glutamate (Glu).

Basic Amino Acids

Positively charged

Lysine (Lys), Arginine (Arg), Histidine (His).

Peptide Bond

Condensation covalent bond between carboxyl N and A amino group to form proteins.

Protein Termini

amino end ("N") and the carboxy end ("C").

Prions

Misfolded proteins that act as infectious agents by converting similar normal proteins into abnormal shapes.

Endosymbiont Theory

mitochondria and chloroplasts evolved from prokaryotic cells engulfed by early ancestral eukaryotic cells,

supported by the presence of their own circular DNA.

DNA vs. RNA Structure

DNA is double-stranded, contains deoxyribose sugar and thymine, and stores genetic info;

RNA is single-stranded, contains ribose sugar and uracil, and uses genetic info to make proteins.

Antiparallel and Complementary DNA

DNA consists of two strands running in opposite directions (antiparallel)

with matching base pairs $A\text{-}T$ and $G\text{-}C$ (complementary).

Informational Macromolecules

Macromolecules such as DNA and RNA that store and transmit genetic information, unlike polysaccharides and lipids which function in structure and energy storage.

Glycosidic Bond

The covalent bond characteristic of carbohydrates. Alpha glycosidic bonds are directed away from the $\text{CH}_2\text{OH}$ group,

whereas beta glycosidic bonds are directed on the same side as the $\text{CH}_2\text{OH}$ group.

Ester Bond

covalent bond connecting components in lipids.

Phosphodiester Bond

covalent bond linking nucleotides in nucleic acid chains (DNA and RNA).

Sugar

An aldehyde or ketone with 2 or more $-OH$ groups attached to a carbon backbone that is 3 to 9 carbons long.

Classes of Lipids

Fatty acids (building blocks and energy),

triglycerides (energy storage),

phospholipids/sphingolipids (cell membranes),

steroids (hormones and membrane regulation),

terpenes (vitamins, signaling, and defensive compounds).

Fatty Acid Saturation

Degree of h-bonding on carbon chains; saturated fats contain no c-c double bonds, whereas unsaturated fats contain one or more double bonds.

Nucleus

Double membrane-bound organelle that stores DNA and makes/processes RNA.

Mitochondria

Double membrane-bound organelles that produce ATP from sugars, fats, and proteins.

Chloroplasts

Double membrane-bound organelles containing thylakoids that perform photosynthesis and produce sugars.

Peroxisomes

Membrane-bound organelles that detoxify harmful compounds and break down fatty acids.

Rough Endoplasmic Reticulum

Membrane network studded with ribosomes that synthesizes and processes proteins.

Smooth Endoplasmic Reticulum

Membrane network without ribosomes that synthesizes lipids/steroids, detoxifies compounds, and stores calcium.

Golgi Complex

Stacks of flattened membranes that modify, package, and transport proteins.

Lysosomes

Single membrane-bound organelles containing digestive enzymes used to digest and recycle materials.

Vacuoles

Single membrane-bound organelles involved in storage, transport, and maintaining turgor pressure in plant cells.

Cytoskeleton

The internal framework of a cell composed of three classes of protein elements: microtubules, microfilaments, and intermediate filaments.

Microtubules

Hollow cytoskeletal tubes composed of $\alpha/\beta\text{-tubulin}$ used for cellular movement and intracellular transport.

Microfilaments

Thin cytoskeletal filaments composed of actin used for movement and cell shape maintenance.

Intermediate Filaments

Rope-like protein fibers in the cytoskeleton that provide structural support to the cell.

Cytoplasm vs. Cytosol

Cytoplasm includes everything inside the cell except the nucleus; cytosol is specifically the semi-fluid material surrounding organelles where metabolic reactions occur.

Viruses

Genetic material (DNA or RNA) enclosed in a protein coat

are not considered alive because they cannot reproduce or carry out metabolism without a host cell.

Compartmentalization

Eukaryotic organizational strategy that increases efficiency by concentrating enzymes and substrates, separating incompatible reactions, and expanding membrane surface area.

Enthalpy ($H$)

The heat or total energy content of a thermodynamic system.

Entropy ($S$)

A measure of the disorder or randomness in a system.

First Law of Thermodynamics

E cannot be created or destroyed, only transformed.

Second Law of Thermodynamics

every energy transformation increases entropy and loses usable energy

Third Law of Thermodynamics

Law stating that molecular motion stops completely at absolute zero.

Calorie

amount of E required to raise the temperature of $1\,\text{g}$ of water by $1\,^\circ\text{C}$.

Exothermic Reaction

Rxn that releases heat into its surroundings,

negative change in enthalpy ($-\Delta H$)

Endothermic Reaction

Rxn that absorbs heat from its surroundings,

positive change in enthalpy ($+\Delta H$)

Free Energy ($G$)

E that is available to do work

Exergonic Reaction

spontaneous chemical Rxn that releases free energy,

negative free energy change ($-\Delta G$).

Endergonic Reaction

Nonspontaneous Rxn requiring energy input,

positive free energy change ($+\Delta G$)

Equilibrium Constant ($K_{eq}$)

ratio of product concentrations to reactant concentrations at chemical equilibrium

Standard State Conditions

pressure= $1\,\text{atm}$

Temp= $25\,^\circ\text{C}$ ($298\,\text{K}$)

$$\text{pH } 7$$

$1\,\text{M}$ reactant/product concentrations

R= 1.987 cal/molK

Ribozyme

RNA molecule capable of acting as an enzyme/catalyst

Active Site

Specific spot on an enzyme where substrate binding occurs, lined with charged or polar amino acids that directly facilitate the reaction

Activation Energy ($E_A$)

The minimum energy threshold required to initiate a chemical reaction.

Metastable State

state in which high-E molecules are unstable but do not have enough E to surpass Ea

Crucial because it keeps the rxn’s from happening too quick

Prosthetic Group

metal ion or small non-protein organic molecule required by an enzyme to assist in electron/proton transfer during catalysis

Induced Fit Model

how substrate binding induces a conformational change in the enzyme to catalyze the reaction, returning to original form after product release

Bond distortion

Enzyme proton exchange

Enzyme electron exchange

Lineweaver-Burk Plot Parameters

Double-reciprocal kinetic plot where Y-intercept = $1/V_{max}$, X-intercept = $-1/K_m$, and slope = $K_m/V_{max}$.

Competitive Inhibitor

Inhibitor that competes with substrate for the active site

increasing $\text{K}_m$

$\text{V}_{max}$ unchanged.

Noncompetitive Regulator

Regulator that binds to a site other than the active site

decreasing $\text{V}_{max}$

$\text{K}_m$ unchanged.

Allosteric Regulation

Regulation of an enzyme caused by a molecule binding at a non-active site, inducing conformational changes that either activate or inhibit function.

Feedback Inhibition

Regulatory mechanism where the final product of a pathway binds allosterically to an early enzyme to decrease pathway activity

Fluid Mosaic Model

The membrane is a dynamic mixture of lipids and proteins capable of lateral diffusion within the membrane layer

Homeoviscous Adaptation

The capability of cells to adjust their membrane lipid composition (e.g., increasing unsaturated fatty acids at cold temperatures) to maintain stable membrane fluidity

Membrane Asymmetry

lipids are distributed unequally between 2 monolayers

Lateral vs. Transverse Diffusion

Lateral diffusion is the frequent side-to-side movement of lipids/proteins within the same layer

transverse diffusion (flip-flop) is the rare movement across the bilayer requiring flippase

What are N and O linked glycosylation?

proteins w/ sugars covalently bonded

N-linked Glycosylation

$\text{NH}_2$ on the side group of an asparagine used for sugar linkage

O-linked Glycosylation

$-OH$ group of serine, threonine, hydroxylysine, or hydroxyproline on a protein, used for sugar linkage

Simple Diffusion

Passive transport of substances directly across the membrane down their concentration gradient without transport proteins

Facilitated Diffusion

Passive transport of substances down their concentration gradient using membrane channels or permeases.

Active Transport

E-requiring movement of substances across a membrane against their concentration or electrochemical gradient

Saturation?

tightly packed H-bonds

Channels vs. Permeases

Channels are pores that: small, selective, fast

permeases undergo conformational changes to move small polar mc’s

Alternating Conformation Model

Transport mechanism where solute binding to a permease causes a structural shift, opening access to the opposite side of the membrane

Symport vs. Antiport

Symport transports two solutes across a membrane in the same direction

antiport transports two solutes in opposite directions

P-type ATPase

reversible phosphorylation to transport ions such as

$\text{Na}^+$, $\text{K}^+$, $\text{H}^+$, and $\text{Ca}^{2+}$

V-type ATPase

proton pumps that use ATP to pump $\text{H}^+$ ions into vacuoles to acidify them

F-type ATPase

pumps that utilize $\text{H}^+$ gradients to synthesize ATP

ABC-type ATPase

pump family that utilizes ATP energy to move a wide variety of solute molecules across cellular membranes

Sodium-Potassium Pump (Na+/K+ Pump)

An active transport pump that consumes $1\,\text{ATP}$ to pump $3\,\text{Na}^+$ ions out of the cell and $2\,\text{K}^+$ ions into the cell.