Cell structure and Functions

Basic Unit of life

Cell

Common features of all cells

Cytoplasm

Genetic material

Plasma membrane

Phospholipid bilayer

Semi-permeable membrane

DNA

RNA

Ribosomes

r RNA

Prokaryotes VS. Eukaryotes

Prokaryotes

Eukaryotes

single-cell organisms made of prokaryotic cells.

both single-cell and multi-cell organisms made of eukaryotic cells

cell membrane

Cytoplasm

Ribosome

Nucleoid

a region in the cell where DNA is located (not surrounded by a membrane)

Cell wall

Capsule

Flagella

Locomotion organelles of some bacteria

Rigid structure outside the cell membrane

Jelly like outer coating of many prokaryotes

Organelle

Nucleus

Cytoplasm, cell membrane, and ribosome

Three domains of life

Taxonomy

Domain

Eukarya

Arachae

Bacteria

consist entirely of a eukaryotic organism, which can be single-celled or multi-celled.

Include four main types of organisms: animals, plants, fungi, and protists

include a group of prokaryotes that are mainly characterized by their ability to thrive in extremeenvironments

include a diverse group of prokaryotes that are most notably recognized for their role in disease, health, important ecological relationships with plants and animals, and decomposing dead organic matter

Animal cell vs. Plant cell

Animal cell

Plant cell

Both plant and animals are made of eukaryotic cells.

Animal cells have centrioles and lysosomes, which are absent in most plant cells

Plant cells have a cell wall, a large central vacuole, and chloroplast

Endomembrane system

Nucleus

Chromosomes

Nuclear envelope

Nucleolus

Nuclear pores

Endoplasmic Reticulum(Smooth vs. Rough)

Smooth

Rough

lacks ribosomes

embedded with ribosomes

synthesize proteins

build the polypeptide chain

then modified and the finished protein is wrapped in a membrane

a transport vesicle, which carries the protein to its next destination.

Bound ribosomes

Free ribosomes

contains many important metabolic enzymes

synthesize lipids

fats, steroids, and new membrane phospholipids

Golgi apparatus

where proteins are modified, stored, and then sent to other destinations in new transport vesicles

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cisternae

trans face

Golgi is made of flattened membranous sacs called cisternae

cis face

(receiving end) vesicles from the ER fuse with the Golgi membrane, giving the Golgi its content

(receiving end) vesicles from the ER fuse with the Golgi membrane, giving the Golgi its content

Lysosome

a vesicle containing hydrolytic enzymes that are used to digest (break down) macromolecules. Not usually found in plants

Lysosomes also play an important role in apoptosis, programmed cell death

Typically lysosomes fuse with food vacuoles to break down the contents into simple sugars, amino acids, and other monomers

Vacuole

are large vesicles created by the ER and Golgi that perform a variety of functions

Food vacuoles

Contractile vacuoles

formed by phagocytosis, which is a process in which a cell engulfs materials from outside the cell

found in many freshwater protists, pump excess water out of cells

large central vacuoles

A common type of vacuole found in plant cells

store water, nutrients, pigments, and waste products

Advantage(s) of having membrane bound organelles

Minimized competing reaction

Increased surface area for reactios to occur

Mitochondria

found in nearly all eukaryotic cells, including plants, animals, fungi, and protists.

double membrane

intermembrane space

mitochondrial matrix

cristae

The inner membrane contains foldings

Overview of aerobic cellular respiration

If oxygen is available, sugar molecules (like glucose) are completely broken down into carbon dioxide and water in the mitochondria.

If oxygen is available, sugar molecules (like glucose) are completely broken down into carbon dioxide and water in the mitochondria.

Overall Reaction: sugar + oxygen → carbon dioxide + water + ATP

Chloroplast

intermembrane space

thylakoids

granum

stroma

thylakoid space

endosymbiotic theory

an early ancestor of eukaryotic cells engulfed an oxygen-using, non-photosynthetic prokaryotic cell, which evolved into the mitochondria

Later on, one of these cells may have engulfed a photosynthetic prokaryote, which evolved into the chloroplast

Components of the plasma membrane

fluid-mosaic model

Functions

Separates the internal cytoplasm from the external environment of the cell

Controls the movement of substances in and out of the cell

Allows cells to communicate with one another and interact with their external environment

selectively permeable

Structures

Protein molecules

Float around like icebergs in a sea of phospholipids

Cholesterol

Peripheral proteins

Integral proteins

amphipathic

controls the fluidity of the membrane

Carbohydrate Chains

cell’s “fingerprint”

Glycoproteins

Glycolipids

Channel Proteins

Carrier Proteins

Carrier Proteins

Receptor Proteins

Enzymatic Proteins

Junction Proteins

Small, hydrophobic

Polar or charged substances

surface-area-to-volume ratio

a large surface area to adequately exchange materials with their surroundings, and a small volume for materials to quickly travel within the cell.

concentration gradient

A particle moving along (or down) its concentration gradients moving from an area of high concentration to an area of low concentration

A particle moving against (or up)its concentration gradientis moving from an area of low concentration to an area of high concentration

Molarity

osmolarity

Passive transport

the movement of substances across the cell membrane withoutthe input of energy

Diffusion

Osmosis

Facilitated transport

aquaporins

dynamic equilibrium

Molecules still move both ways, but at equal rates

Solute concentration is uniform –no concentration gradient

Gas Exchange

Diffusion allows gas exchange to occur between the lungs, blood, and cells

Isotonic Solutions

Hypotonic Solutions

Hypertonic Solutions

Solute and water concentrations are equal on both sides of cellular membrane

lyse (rupture)

turgor pressurein plants

plasmolysis, causing the plant to wilt and die

Channels Proteins

Follows concentration gradient, moving from high concentration to low concentration. No energy is required

Carrier Proteins

allow specific molecules or ions to quickly tunnel through the cell membrane.

specific solutes bind to the protein, changing the protein's shape, which results in the release of the solute on to the other side of the membrane

water potential

Formula for water potential: Ѱ = ѰP+ ѰS

pressure potential (ѰP)

solute potential (ѰS)

measures how much pressure is exerted by the cell wall (due to turgidity) on the water inside a plan

Solute Potential Formula: ѰS = -iCRT

i= ionization constant

C = Molar Concentration (M) (moles/liters)

R = pressure constant (R = 0.0831 L∙bar/mol∙K)

T = Temperature in Kelvin (K = °C+ 273)

Active transport

the movement of substances against their concentration gradient, which requires the inputof energy

sodium-potassium pump

use ATP to transport 3 Na+ ions out of the cell and 2 K+ intothe cell.

electrochemical gradient

Membrane potential

a measurement of the charge difference across a cell membrane and is measured in millivolts

cotransporter

a membrane protein that actively transports a solute against its concentration gradient by utilizing the concentration gradient of another solute

bulk transport

ransported into and out of cells by vesicles

Vesicles are pieces of a phospholipid bilayer that encircle and transport large cargo

exocytosis

intracellular vesicle fuses with the plasma membrane to secrete its contents out of the cell

endocytosis

cells take in substances by forming vesicles around the material

Phagocytosis

Pinocytosis

Receptor-mediated endocytosis

Large, solid material

liquid or very small particles

specific to a certain type of molecule

Cellular Energetics

Enzyme

Energy

Metabolic Pathways

Catabolic pathways

Anabolic pathways

break down complex molecules into simpler compounds

uild complex molecules from simpler ones

Kinetic energy

Potential energy

energy of motion

Thermal energy is random movement of atoms or molecules

Heat describes thermal energy in transferfrom one object to another

the energy that matter possesses because of its location or structure

Thermodynamics

The 1stlaw of thermodynamics

Energy can be transferred and transformed but cannot be created or destroyed

The 2ndlaw of thermodynamics

Every energy transfer or transformation increases the entropy (heat) of universe

Entropy

Releasing heat = Increasing entropyof the universe

a measure of disorderor randomness

Chemical reaction

exergonic (=energy outward)reaction

releases energy

endergonic (=energy inward) reaction

requires a net input of energy and yield products that are rich in potential energy

Cellular respiration

Photosynthesis

ATP

powers nearly all forms of cellular work

structure

Cells manage energy resources by energy coupling, the use of an exergonic process to drive an endergonic one

phosphorylation

transferring a phosphate group to some other molecule

the phosphorylation of reactants provides energy to drive the endergonic synthesis of products.

biological catalyst

a chemical agent that speeds upa reaction without being altered in the process

Enzyme speeds up the reaction by lowering the activation energy (EA) barrier,

Hydrolysis of sucrose by the enzyme sucraseis an example of an enzyme-catalyzed reaction

Enzyme Structure

enzyme-substrate complex

active site is the region on the enzyme where the substrate binds

induced fit

Environmental Impacts on Enzyme Function

Temperature

Chemicals

pH

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Cofactors

non-protein helpers of enzymes

coenzyme

Competitive inhibitors

Noncompetitive inhibitors

Enzyme regulation

Allosteric regulation

proteins function at one site is affected by binding of a regulatory moleculeto a separate site

Activator–stabilizes active site

Inhibitor–stabilizes inactiveform

Cooperativity–one substrate triggers favorable conformational changes in other active sites => Increase catalytic activity

feedback inhibition

the end product of a metabolic pathway shuts down the pathway

It prevents a cell from wasting chemical resources by synthesizing more product than is needed

Oxidation-Reduction (Redox) Reactions

The transfer of electrons from one molecule to another

Electrons

hydrogen atoms

As glucose is broken down during cellular respiration, hydrogen atoms and pairs of high energy electrons are taken away from glucose and given to electron carrier molecules, NAD+ and FAD

NAD++ H++ 2e-→ NADH
FAD + 2H++ 2e-→ FADH2

Aerobic (oxygen-using) cellular respiration

the complete oxidation/breakdown of glucose.

Glycolysis–breaks down glucose into two molecules of pyruvate

Pyruvate Oxidation and the Citric Acid Cycle–completes the breakdown of glucose

Oxidative Phosphorylation–ETC & Chemiosmosis

Glycolysis consists of 10 reactions (each with its specific enzyme) that split one molecule of glucose (6-carbon) into two pyruvate molecules (3-carbon)

does not require oxygen.

energy investment phase

two G3P

energy harvesting phase

oxidized into pyruvate

Acetyl CoA

1)2 carbon dioxide are released
2)2 NADH are formed
3)Coenzyme-A (CoA) is added to the molecules forming 2 acetyl CoA

The citric acid cycle or Krebs cycle

oxaloacetate

citrate

○4 CO2○6 NADH○2 FADH2○2 ATP through substrate-level phosphorylation

Oxidative Phosphorylation

Electron Transport Chain (ETC)

Chemiosmosis

a series of protein complexes embedded in the inner membrane of the mitochondria

The proteins use the energy released from the electrons losing free energy to pump protons (H+) out of the matrix into the intermembrane space

Oxygen acts as the final electron acceptor

proton-motive force

ATP Synthase

the use of energy in a H+ gradient to drive the production of ATP

Decoupling Oxidative Phosphorylation from ETC

Oxidative phosphorylation can be decoupled from the electron transport chain if protons are allowed to diffuse back into the mitochondrial matrix without going through ATP synthase.

Anaerobic cellular respiration

Fermentation

consists of glycolysis plus reactions that regenerate NAD+, which can be reused by glycolysis

Alcohol Fermentation

Lactic Acid Fermentation

pyruvate is converted to ethanol

The first step releases CO2

The second step regenerates NAD+ and produces ethanol

Regenerated NAD+ is needed for the continuation of glycolysis

pyruvate is reduced by NADH, which regenerates NAD+

Forming lactateas an end product, with no release of CO2

Autotroph vs. Heterotroph

Autotrophs sustain themselves without eating anything derived from other organisms

Photosynthesis occurs in plants, algae, certain other unicellular eukaryotes, and some prokaryotes

Heterotrophs are unable to make their own food and must rely on compounds made by other organisms

They are the consumers in ecosystems and eat producers (autotrophs) as well as other heterotrophs

Photosynthesis

6 CO2+ 6 H2O + Light Energy → C6H12O6+ 6 O2

The chemical change during photosynthesis is the reverse of cellular respiration

Photosynthesis is a redox reaction

Electrons are taken from water (oxidation) and given to carbon dioxide (reduction)

Sites of Photosynthesis

chlorophyll

stomata

thylakoids

grana

stroma

CO2enters the leaf and O2exits

An Overview of Photosynthesis

light reactions

Calvin cycle

Sunlight

Light consists of discrete energy particles called photons

Pigments are substances that absorb certain wavelengths of visible light

Chlorophyll

absorption spectrum

Accessory pigments, such as chlorophyll band carotenoids

synthesize ATP and NADPH

photosystem

The energy transferred to the chlorophyll amolecules is used to boost an electron to a high energy level

Happens in stroma

Cell Communication and Cell Cycle

Cell Communication

Cell Cycle

Interphase

Mitotic Phase

G1Phase

S Phase

G2Phase

cell grows in size and begins doubling its number of organelles

cells replicate their DNA, producing two copies of each chromosome. The two copies are attached to one another as sister chromatids

cell continues to grow and prepares for cell division (M phase)

Mitosis

Cytokinesis

Prophase

Prometaphase

Metaphase

Anaphase

Telophase

Structure of Chromosome

sister chromatids

Chromosome

Chromatin

thread-like structures located inside the nucleus of animal and plant cells

the identical copies (chromatids) formed by the DNA replication of a chromosome, with both copies joined together by a common centromere

the substance within a chromosome consisting of DNA and protein. The DNA carries the cell's genetic instructions

kinetochore

Protein structure found at each sides of the centromere

Centromere

Narrow region where sister chromatids are joined are called centromere

Eukaryotes

Animal

Plant

Prokaryotes

binary fission

cell plate

cleavage furrow

Daughter cell

produced after a single cell undergoes cell division. During mitosis, one pair of daughter cells is created after one round of DNA replication.

diploid cell (2n)

Somatic cells

contains two sets of chromosomes (one set inherited from each parent)

Reproductive cells

How’s cell division used in life?

Cell division serves as a means of reproduction in unicellular organisms through binary fission. In multicellular organisms, cell division aids in the formation of gametes, which are cells that combine with others to form sexually produced offspring.

Regulations of cell cycle

Three check points

Cyclins vs. cylin-dependent kinases

Density dependent inhibition

G0 State

Apoptosis

G1 checkpoint

G0 phase

nondividing state

G2checkpoint

Checks if the DNA is properly copied during S phase

Usually repairs if there is wrong part, but if cannot it goes through apoptosis

M checkpoint

checks to make sure that all the kinetochores are properly attached to microtubules of the mitotic spindle before beginning anaphase

cyclins

cyclin-dependent kinases (CDKs)

enzymes that phosphorylate (add phosphates to) other proteins

CDKs are only activated when bound to cyclins,

cyclin-CDK complex

When cells get too crowded, they signal each other to stop dividing by inhibiting the CDK-cyclin complexes at the G1checkpoint

Programmed cell death

Cancer

Proteins

Tumor suppressor genes

Mutations in either of these genes can lead to uncontrolled cell division and tumor formation

Proto-oncogenes

code for proteins which promote the cell cycle in various ways

code for proteins that inhibit the cell cycle and promote apoptosis in various ways

Cell Communication in single vs. multicellular organisms

In single-celled organisms, signal transduction pathways influence how the cell responds to its environment

In multicellular organisms, signal transduction pathways coordinate the activities within individual cells that support the functionof the organism as a whole

Similarities in signal transduction pathways in both prok and euk, organisms

Cell signaling, in both prokaryotes and eukaryotes, occurs via signal transduction pathways

signal transduction pathway

a series of steps by which a signal on a cell’s surface is converted into a specific cellular response

Three stages of cell signaling

Reception

Transduction,

Response

ligand

produces a response in a cell

target cells

Only cells with the necessary receptors (target cells) can respond to a signal

Intracellular receptors

Membrane receptors

Their ligands are smaller nonpolar and can diffuse across the membrane

large or polar ligands that cannot diffusethrough the membrane

Ligand-Gated Ion Channels

G Protein-Coupled Receptors

closed channel proteins that change shape and open when a ligand binds

A G protein-coupled receptor (GPCR) is a plasma membrane receptor that works with the help of a mobile membrane protein, called a G-protein

The binding of a ligand to a receptor will trigger the start of a signal transduction pathway within the cell

Like falling dominoes, the initial receptor protein activates another protein, which activates another, and so on, until the protein producing the response is activated

Phosphorylation

dephosphorylation

Protein kinases

transfer phosphatesfrom ATP to proteins, a process called phosphorylation

phosphorylation cascade

Protein phosphatases

Opening of ion channels

Alterations in gene expression

Regulation of enzyme activities

Examples of signal disruptions

Conditions where signal transduction is blocked or defective can have deleterious effects

The poison produced by anthrax bacteria binds and inhibits the function of adenylyl cyclase, the protein that converts ATP to cAMP

Anthrax

Diabetes

Types of Cell communication

Direct Contact Communication

Short Distance Communication

Long Distance Communication

juxtacrine signaling

autocrine and paracrine signaling

endocrine signaling

Quorum Sensing

Morphogens

Plaque

Insulin

Human Growth Hormone

Homeostaisis

Negative vs. Positive feedback Mechanisms

refers to the ability of an organism (or a cell) to maintain a stable internal environment despite changes in external conditions

dynamic homeostasis

Organisms use feedback mechanisms to maintain their internal environments and respond to external environmental changes

Negative

Positive

maintain dynamic homeostasis for a particular condition (variable) by regulating physiological processes, and returning the changing condition back to its target set point

Thermoregulation

amplifyresponses and processes in biological organisms

Childbirth

Ripening of Fruit