Types of cells | Mindomo Mind Map

Concept Map (Fall 2020)- Group #7

by Allison Schellenberg

The One and Only You - Genetics

by Jose Hernandez

Proteins

by Jenna Battle

Microbial Groups

by izzati zulkifli

Gene expression and G-Protein pathway, I found that the way RNA polymerase 2 binds into the promoter in order to activate gene expression is a lot like how a GTP binds to adenyl cyclase in the G protein pathway, the specific transcription factor, activator in this case, acts like the signal molecule, triggering high level expression.

I find that in gap junctions, molecules are easily permeating through it. We learned that molecules are transported through ion channels, therefore that means that gap junctions must have lots of ion channels as opposed to other junctions.

I find that cell signaling and cell expression have a lot of similarities regarding the way they can be stopped or “turned off”. The cell has a way of regulating itself so that if something goes wrong or if something is unneeded, it can easily make adjustments that can change or modify.

In cell communications, the way a cell signal transduction pathways are very similar to how phosphorylation cascades work. When a cell needs to communicate, it’s interesting how it relays a message whether it's close or far away and how it adapts to the distance.

Another connection I made was between glycolysis and photosynthesis as they are both important processes that are vital to energy production. They are both involved in the creation of ATP, and are both tightly regulated by the cell to balance energy production and demand, with photosynthesis using ATP and NADPH in the Calvin cycle to regulate, and with glycolysis using high levels of ATP or citrate to regulate itself when energy is sufficient.

One connection I made was between Gene expression and regulation and the Meselson-Stahl experiment. This is because in the Meselson and Stahl experiment, researchers demonstrated that DNA is semi-conservative, meaning that each new DNA molecule consists of one old strand and one newly synthesized strand, which is a process that is fundamental for maintaining genetic code during cell division, making sure that the information required for gene expression is accurately passed on to daughter cells.

Another connection I found was through entropy and the breaking of hydrogen bonds. If the hydrogen bonds in nitrogenous bases were to be broken apart, then this would mean that entropy or the amount of disorder would increase in the system. This would increase the entropy because by breaking the hydrogen bonds, they are less structured meaning that they have more freedom. More freedom = more entropy/disorder.

One of the connections I found was through archaea and enzymes, more specifically thermophiles. We know that thermophiles can survive in extreme conditions, like high heat. This has to do with enzymes because usually when enzymes are exposed to high heat, they begin to denature/break down since they can only work at an optimal temperature. There is no change to the enzymes even after being exposed to the conditions thermophiles live in, since thermophiles continue to live/survive. Even if there was change done to the shape of the enzyme, it would continue to work in these conditions as opposed to our enzymes, which would denature if exposed to the same conditions.

DNA structure, replication, expression, and regulation

Found in cells

Membranes, energy, and cell communication

Eukaryotic

Animal Cells

Has a Plasma membrane

Cell membranes are selectively permeable barries

cell transport

active transport

protein pumps

Na+ and K+ pump

establishes proton gradient

2 K+ in

3 Na+ out

ion channel

form pores in cell membranes, allowing ions to pass through

passive transport

diffusion

simple diffusion

small molecules move from high to low concentrations

facilitated diffusion

uses specialized proteins to move ions and molecules across membrane

osmosis

water molecules move with gradient

controls what goes in and out of cell

Has a Golgi Apparatus

Contains Lysosomes

Has a nucleus (nuclear envelope, nucleolus, and chromatin)

Contains Ribosomes

Contains Peroxisomes

Has a Mitochondria

Plant Cells

Has a Golgi apparatus

Contains both smooth and rough ER

Has a nucleus

Has a central vacuole

Has Plasmodesmata

Cell Respiration (Energy Making Process)

In plant

Photorespiration

C4 Plants

Use PEP carboxylase instead of rubisco cause it favors CO2 over oxygen

CAM Plants

Photosynthesis during the day

Takes in CO2 at night

in hot and dry conditions the stomata are partly closed due to which CO2 concentration is low in cells. Rubisco favors to bind O2 instead of CO2, so if CO2 concentration is low, Rubisco will bind whatever O2 is present, releasing CO2

Calvin Cycle

Phase 1: Carbon Fixation

3 CO2

Interacts with Rubisco

6 3-Phosphoglycerate

6 1,3-Bisphoglycerate

6 P

6 NADP+

Phase 2: Reduction

6 Glyceraldehyde-3-phosphate (G3P)

Phase 3: Regeneration ofthe CO2 acceptor (RuBP)

3 ATP is used

Ribulose bisphosphate(RuBP)

1 Glyceraldehyde-3-phosphate (G3P) leaves the chain to become sugar

6 ATP is released

Electrons are gained from the break down of H2O

Photosystems

Photosystem 2

P700

Accept light of wavelength 700nm

Photosystem 1

P680

Accept light of wavelength 680nm

Light Reaction

If excess NADPH

Start in PS1

Cyclic flow of electrons is used to make more ATP, not NADPH

If no excess NADPH

Starts in PS2

Photons go through stroma

Excites electron

Energy gets transfer through chain of stroma with each excitement of electrons

Energy reaches special pair of chlorophyll

Electron is grabbed by electron acceptor

Transfer down electron transport chain to PS1 chlorophyll, going through cytochrome complex on the way

1 ATP

Using ATP, H+ is pumped through the thylakoid spoce against their concentration gradient

Goes through ATP synthase

H+ goes to the stroma, down their concentration gradient

Same reaction happens as in PS2

Electron goes down second electron transport chain

Goes through NADP+ reductase

NADPH

Enter calvin cycle

In animal

Oxidative Phosphorylation

Oxidative Phosphorylation is Chemiosis coupled with ETC

Chemiosis

This happens with all the protons that were pumped against their concentration gradient

Goes through ATP Synthase

The energy released is used to add a Phosphate to ADP

Electron Transport Chain

This happens to all the electron carriers in the cells

Glycolysis

Starting organic molecule (Glucose) (C6H12O6)

NAD+ (already in cells)

Redox reaction happens, oxidation of gluclose (C6H12O6 + 6O2 -> 6 CO2 + 6 H2O + Energy)

Oxygen is reduced

Glucose is oxidized

Glucose

interacts with Hexokinase

Glucose 6 Phosphate

Interact with Phosphoglucoisomerase

Fructo 6 phosphate

1 ATP used

Interact with Phospho-fructokinase

Fructo 1,6-biphosphate

Interact with aldolase

Dihydroxyacetone phosphate (DHAP)

Glyceraldehyde 3-phosphate (G3P)

Prokaryotic

Is branched into:

Archae

Has ether bond for its Phospholipid

Can survive in extreme conditions

Methanogen can tolerate high acidity

Thermophiles can tolerate high heat

Halophiles can tolerate extreme saline environment

Has branching cell wall

Has Circular DNA

Bacteria

Has Peptidoglycan in cell wall

No membrane bound organelles

Has no circular DNA

No Nucleus

Has plasmid

Has nucleioud

Has fimbria or pili for DNA exchange

Has slime layer or capsule

Has ribosome

Read tRNA and translates it into amino acid chains

amino acid

comprised of:

amino group

carboxyl group

R group

monomer of protein

made of RNA and protein

used for protein syntehsis

Has Flagella for movement (the tail)

Can either be

Facultative Aerobic: can do both

Aerobic: can handle oxygen

Anaerobic: can't handle oxygen

Lipids

HDL vs LDL

low density pipoprotein ' bad cholesterol

sat and trans fat can increase LDL

High density lipoprotein 'good cholesterol'

Steroids

ex: cholesterol

precursor to other steroids

common component of membranes

found in animals

contain 4 fused rings

Phospholipids

form closed bilayers in waater

at 3rd OH another group is attached containing a phosphate group

polar

glycerol is linked to 2 fatty acids

amphipathic

hydrophobic parts gather together in H2O

hydrophilic polar head groups

contains both hydrophilic and hydrophobic parts

Unsaturated Fatty acids

common example: oil

Isomers of unsaturated fatty acids

cis fat

hydrogens on the same side of the carbon chain

the presence of double bonds in cis far causes the molecules to have a kink/slight bemd

trans fat

hydrogens on the opposite side of the carbon chain

do not have hydrogen atoms at every position

one or more double covalent bonds are found within the carbon chain

are liquid at room temperature

come from plant sources

Saturated fatty acids

hydrocarbon chains are tightly packed together by hydrophobic interactions

common example: butter

saturated with hydrogen atoms at every position

no double covalent bonds

solid at room temperature

Commonly found in animal

Major function is energy storage

Comprised of glycerol and 3 fatty acids

Have geometric isomers

Carboxylic acid group at the end of each chain

an ester linkage connects each fatty acid to an OH in glycerol

Formed by dehydration or condensation sysnthesis

Energy transfer

Anabolic Pathways

Pathways consume energy to build larger molecules.

Biosynthetic Pathways

Photosynthesis

Polymerization

Binding

Enzyme-substrate binding

Substrate enters site and changes shape of protein

Enzyme

Catalytic cycle of an enzyme

Enzyme-catalyzed reactions

Rate of reaction increases as substrate concentration increases

Substrates enter and change site

Substrates are not help very strong, there is weak interaction

Active site lowers energy and speeds up reactions

Substrates are converted to products

Products are released and active site is free for new substrates to enter again

pH can affect enzyme activity

pH affects enzyme activity by influencing the enzyme's shape and ability to bind to substrates. If the pH is too far from the enzyme’s optimal range, it can lead to reduced activity aka denaturation

Temperature can affect enzyme activity

Optimal temperatures

Temperature at which cell works just right

To low (temperature) will cause the cell to have a slow reaction

Too high (temperature) will cause for cell to denature

Can be used to speed up chemical reactions

Enzymes achieve this by lowering the activation energy

Thermodynamics

System + Surroundings = Universe

Laws of thermodynamics

Gibbs' free energy

Energy coupler in cells

Coupling

Exergonic + Endergonic

coupling allows cells to carry out complex and energy-demanding tasks by taking advantage of the free energy released by exergonic reactions (ex: ATP hydrolysis).

Transport work

ATP phosphorylates transport proteins when ATP is added to tranport proteins

Causes higher free energy

Unstable

Inorganic Phosphate + ADP + H20 = ATP with 7.3kcal of energy

Chemical reactions are powered by ATP

Can cause lower free energy

Can cause higher free energy

Free-Energy Change

Chemical Reaction

Enzymes can speed up chemical reactions in cells

Hydrolysis

Diffusion

the movement of molecules or ions from an area of higher concentration to an area of lower concentration

Gravitational Motion

Objects moving spontaneously from higher places to lower places

When there less free energy present then it is more stable

Less work capacity

Change in free energy during a chemical reaction

Change in energy can be calculated by doing G final state-G initial state

When more free energy is present then it is less stable

More work capacity

G= H-TS or H=G+TS

Non-spontaneous Process

Endergonic

Non-spontaneous process

Energy is needed

Change in free energy is positive

In equilibrium

Change in free energy is 0

No net changes occurs

Spontaneous Process

Catabolic

Exergonic

Spontaneous process

Energy isn't needed

Change in free energy is negative

2nd law: Every transfer of energy increases entropy in the universe

Entropy

Measure of disorder

1st law: Energy cannot be created or destroyed

Chemical Reactions

Surroundings

Matter in the rest of the universe and outside of the system.

System

Matter with a region of space, can either be an open or closed space.

Closed system: Only energy can come in and out of its surroundings, but not matter

Open system: Energy is free to come in or out in its surroundings

Catabolic Pathways

Pathways release energy by breaking down larger molecules and turning them into simpler, smaller compounds.

Occurs with the net release of energy

Cellular Respiration

DNA is a molecule of heredity in all organisms

Experiments involving DNA

Meselson and Stahl (1957)

Used density gradient centrifugation to track the replication of DNA, grew E. coli in heavy nitrogen and incorporated it into DNA, then centrigued with light nitrogen to receive their results.

Found that DNA was semi-conservative

Griffith (1928)

Injected rats with 4 different types of cells

S-cells: Pathogenic

R-cells: Non-pathogenic

S-cells (heat killed): Non-pathogenic

Mixture of heat killed S-cells and R-cells: Pathogenic

Found that even though cells are heat killed, they can still transfer their DNA.

Hershey and Chase (1953)

Utilized bacteriophage injected with radioactive protein and radioactive phosphorus

After letting the bacteriophage infect, they centrifuged the infected cells.

Radioactive phosphorus was found in the pellet, with the DNA.

They led to the conclusion that DNA is the genetic material

Radioactive protein was found on the outside and not inside the pellet, where all the concentration is at. Radioactive protein was not entering the cells.

DNA Replication

Dispersive

Both strands of daughter molecules contain old and new DNA

Conservative

Parental molecules reassociate

They both act as templates for the new strands, which restores the parental helix

Semi-Conservative

Parental molecules separate

They both become templates for a new and complementary strand

DNA's structure consists of: Phosphate group, nitrogenous bases, and a sugar backbone

Can be found going from 5' to 3'

Nitrogenous bases can be: Adenine, Cytosine, Guanine and Thymine

Chargaff's rule: Amount of Adenine = amount of Thymine, amount of Cytosine = amount of Guanine

Nitrogenous bases are held together by hydrogen bonds

Gene expression and regulation

At what step can the production of a protein be stopped?

Protein can be stopped at any of these steps

Protein processing

protein enters golgi apparatus through cis side

in Golgi, protein is modified with the addition of tags such as phosphate groups

protein is then exited through trans site, in which it has several destinations

Go back to the ER

Go to membrane protein

Gets secreted

Lysosome to be broken down

protein is regulated

Translation

mRNA

Gets attached free smaller subunit ribosome

it slides down and find the start codon (AUG)

tRNA with Met attaches to it

bigger subunit of ribosome sits on top

Translation starts

if signal sequence is reached

Signal Receptor Protein gets attached to it

translation stops

the entire complex enters ER membrane

translation starts

tRNA enters through A side

its Amino acid gets attached to the amino acid of the first tRNA using peptidyl transferase

exits through the E site

this continues until a stop codon is reached

Translation stops

protein is snipped off from tRNA

SRP protein is snipped off

Transportation out of the cytoplasm

Gene production can be stopped at this point

RNA Processing

pre-mRNA

using Poly A polymerase

Attaches a poly A tail to the sequence AAUAA in the 3'

After 3' and 5' end has been modified, mRNA gets modified by spliceosome

alternative splicing

exons are rearranged

some exons are removed

Exons stay

Introns are removed

gets attached to a G group, called a 5' cap

DNA Packaging

Chromatin modification

Nuclesomes

Formation of Nucleosome

Gene production can be stop here

Histone Proteins

H2B

H2A

Linkage protein

DNA

Transcription

Eukaryote

Proximal control element (promoter)

General transcription factors

RNA Polymerase 2 to activate gene expression

Distal Control Element (enhancer)

Prokaryote

Lac I

Constitutive production of repressor

Promoter

RNA Polymerase binds here to activates gene expression

Operator

Gets binded by

Activator

In presence of Glucose

Glucose blocks adenyl cyclase

No cAMP is produced

CAP is not activated

No Activator is made

Activates enhanced level gene expression

Repressor

In presence of lactose

Repressor binds to lactose instead of Operator

Reverts to baseline level or below gene expression

Lac Z

Lac Y

Lac A

Chemical bonds, biological molecules, cell structures, and functions

Cell Communications

Critical players in cell signaling

Phosphatases

enzymes that catalyze the removal of phosphate groups from proteins by hydrolysis

Kinsases

can take a phosphate from ATP and add something to it to activate it

additional/removal of phosphate groups to and from proteins is one way cells regulate protein functions -> can change the shape of a protein, and thus it's function

enzymes that catalyze the transfer of phosphate groups from ATP to proteins

Second messengers

5) cAMP, a second messenger, activates another protein, leading to cellular response

4) Activated adenyl cyclase converts ATP to cAMP

3) Activated G protein.GTP binds to adenyl cyclase. GTP is hydrolized, activating adenyl cyclase

2) Activated GPCR binds to G protein, which is then bound by GTP, activating the G protein

1) 1st messenger binds to GPCR, activating it

cAMP is a second messenger in a G protein signlaing pathway

relay molecules that carry the message from the first messenger (signal) inside the cell

Receptor

Two types of receptors

Intracellular receptors - In cytoplasm and nucleus

Membrane receptors

ex: Ion channel receptor

3) ligand dissociates from receptor, channel closes and ions no longer enter the cell

2) ligand binds to receptor, channel opens, specific ions can flow through the channel and rapidly change the concentration of that particular ion inside the cell, may directly affect the cell

1) channel remains closed until a ligand receptor binds to it

Ex: G protein linked reeceptor (GPCR)

Transmembrane protein - part is inside, part is outside of the cell

receptors in membrane

Signal molecule is hydrophilic

Present in a target cell that receives the signal molecule

Signaling molecule/signal/ligand

Molecule released by a cell which is received by another cell (target cell)

Local signaling (close proximity)

Synaptic signaling

Paracrine signaling

Stages of signaling

Response

Activation of cellular response

Transduction

Phosphorylation cascade

4) protein phosphatases catalyze the removal of the phosphate groups from the proteins, making the proteins inactive again

3) active protein kinase 2 phosphorylates a protein that brings about the cells response to the signal

2) active protein kinase 1 activates protein kinase 2

1) a relay molecule activates protein kinase 1

an example of signal transduction pathway that uses kinases and phosphatases

signal relayed in molecules in a signal transduction pathway

Reception

Signaling molecule binds to receptor

Long distance signaling

ex: Hormonal signaling

If the cell releasing the signal is far from the cell that has the receptor to receive the signaling

Endocrine signaling

Direct contact

These contacts allow molecules to pass from one cell to the other, allowing the recipient to respond

Plasmodesmata within the plant cell

Gap junctions within the animal cell

Proteins gets transported to golgi appartus through vesicle

no atp required

Enzymes that take part in DNA replication

These 2 convert back and forth before interacting with Isomerase

Isomerase

Converts all to Glyceraldehyde 3-phosphate (G3P)

G3P is oxidized

Energy is released

G3P interact with Triose Phosphate Dehydrogenase, adding a Phosphate to G3P

Forms 2 1,3-Biphosphoglycerate

Interacts with Phosphoglycerokinase

1,3-Biphosphoglycerate gets oxidized with Phosphoglycerokinase

2 Phosphates groups added to 2 ADP

2 ATP

2 3-Biphosphoglycerate

Interacts with Phospho- glyceromutase

2 2-Phospho- glycerate

Enolase, form Double bonds in the substrate through hydrolosis

2 Phosphoenol- pyruvate (PEP)

Interacts with Pyruvate kinase and 2 ADP

2 ATPs

2 Pyruvate

If there isn't oxygen

Fermentation

Pyruvate gets reduced

Lactate/Alcohol

The Cori Cycle

If there is oxygen

Pyruvate Oxidation

Starting Molecule (Pyruvate)

Goes through oxidation

Acetyl CoA

Enters citric acid cycle

Citric Acid Cycle

Starting Molecule: Acetyl CoA

Interacts with Oxaloacetate

Citrate

Attaches to an H20

Isocitrate

Gets Oxidized

alpha-ketoglutorate

Gets oxidized

Interacts with CoA-SH

Succinyl CoA

Interacts with succinyl CoA synthetase

CoA-SH

Succinate

Fumarate

Gets Hydrated

Malate

Oxaloacetate

FADH2

ATP

CO2 release

NADH

CO2

2 NADH formed

Altogether, this creates a strand of DNA

Fold together into a condensed chromatin

Fold into an X shaped chromosome

atp required

Gets reduced

Electrons

Complex Q is reduced

Energy released

Used to pump H+ against their concentration gradient in complex 1,3,4

Interacts with Oxygen

Forms water

NAD+

FAD+

Summary

In order to start replication we need:

Double Stranded DNA

DNA Polymerase

Helps form polymer of DNA and connects the nucleotides in polymer of DNA.

DNA Polymerase I

Found in bacterial replication

DNA Polymerase II

DNA Polymerase III

Lagging Strand

DNA Polymerase I helps remove RNA Primers and replaces them with nucleotides

DNA ligase helps from having the strand fall apart

Leading Strand

RNA Primer made and DNA Polymerase III makes the leading strand

Leading strand is elongated from 5' to 3' direction

RNA Primer

Uses parental strand in order to start replication.

Helicase

Unwinds and separates DNA strands.

Topoisomerase

Unwinds any DNA that may be stuck, makes sure that everything is not tangled.

SSB

Stabilizes the unwound DNA strands.