Repressors:
Transcription factors:
Activators:
5th step
4th step
3rd step
2nd step
can also occur in
can also occur in
can also occur in
can occur in
6th step
5th step
4th step
3rd step
2nd step
1st step:
example
Protein destination
Termination:
Elongation:
Initiation:
Cytoplasm:
which forms
which forms
to
adds
Energy associated with H+ membrane called
H+ go back in down their concentration gradient (facilitated diffusion) through membrane transport protein called ATP Synthesis
pump H+ to
Use released energy to pump H+ gradient against concentration gradient
8th step
creates
7th step
6th step
5th step
4th step
3rd step
2nd step: forms
Producing with the loss and gain of an H20 molecule
occurs in
starts with Acetyl CoA
formed
electrons transferred to
10th step
9th step
8th step
7th step
6th step: First sequential reactions
5th step
4th step
3rd step
2nd step
1st step
complexes of ETC
location of components of
occurs in
Occurs in
Occurs in
Protein binds to Active Tyrosine
Protein binds to Active Tyrosine
Phosphate groups transferred to each Tyrosine
Require ATP to phosphorylate and activate
Come Together to Form
Phosphate Added from ATP
Phosphate Added from ATP
Phosphate Added from ATP
Protein Kinase Adds Phosphate from ATP
Hydrolyzed by Adenylyl Cyclase
Turns from GDP to GTP by adding 1 inorganic Phospahte from ATP
Ligand Binds to Site
Ligand Binds to Site
Binds to a specific receptor
Small and nonpolar can diffuse through the phospholipid bilayer
Large and polar cannot diffuse through the phospholipid bilayer
Produced by Organs
1 G3P leaves to become an output:
6 carbon compound splits into 2, 3 carbon compounds:
5, G3P are recycled to regenerate the RuBP acceptor (uses ATP):
ATP and NADPH are used to convert 3 PGA into 6 G3P
C is fixed into RuBP through rubisco:
Producing sugar from CO2 with the help of the NADPH and ATP is called the:
Only temporary when the cell has enough NADPH and does not want to make more.
makes:
special pair of chlorophyll molecules get excited and goes to the primary e- acceptor which the goes to Fd --> cytochrome complex --> Pc --> primary acceptor:
special pair of chlorophyll molecules get excited and goes to the primary e- acceptor which then goes to Fd --> NADP+ reductase:
Energy is used to add a phosphate to ADP to make:
energy is released and is used to pump protons against their concentration gradient:
Is split to provide a constant supply of e-:
Is released:
Energy from light excites a chlorophyll molecule which is transferred to another until it reaches the special pair of chlorophyll a molecules (700nm):
E- go down Pq, cytochrome complex, Pc, and Fd::
Energy from light excites a chlorophyll molecule which is transferred to another until it reaches the special pair of chlorophyll a molecules (680nm):
Converting solar energy into chemical energy is called a:
Second stage occurs in the:
First stage occurs in the:
Connected By:
Can either be:
Can either be:
One function is:
One function is:
One function is:
One function is:
One function is:
One function is:
A component Located in the hydrophilic head is called:
Located in hydrophilic head; The component that joins the head and tail is called:
One tail is:
One tail is:
In the inner portion of the bilayer, away from water, are the:
One side is hydrophilic making the bond:
One side is hydrophobic making the bond:
contain two different parts making it:
The most abundant type in membranes are:
Selective:
An attraction between oppositely charged atoms where valence electrons are "taken" is
The relation between a non polar molecule and water is called a:
An interaction between a highly electronegative atom and a hydrogen atom is called:
An attraction between an ion and a neutral molecule that has a dipole is an:
A reaction between SH side chains in two cysteine residues is called a:
In amino acids, R groups have certain orientations:
Creates Bent Tail
Semi-Straight Tail to Create Solid
C-H Chain for Tail
Animals
Plants
Bacteria
Animals
Plants
Gene Expression
Genetics
Long-Term Energy
Short-Term Energy
After translation, when proteins are made, they begin their destinations:
If they are non polar, they are hydrophobic meaning they bury themselves inside away from water.
Are a part of Amino acid:
Attaches through Dehydration Synthesis
Connection between eukaryotic cells and Proteins:1.) Proteins are necessary for the functionality of eukaryotic cells. The protein “tubulin” (alpha-tubulin and beta-tubulin) makes up hollow rods present in microtubules. Microtubules support the maintenance of cell shape and movement. So, the concept of proteins connects to eukaryotic cells, specifically the cytoskeleton in eukaryotic cells because it provides a support system and without proteins, eukaryotic cells can die since organelles won’t have a rigid structure. As mentioned, microtubules also need proteins for movement. The protein Kinesin protein binds to a receptor on the vesicle and allows movement on the vesicle on the microtubule using ATP as an energy source.
Bonds with Adenine in DNA
First type of ribosomes
Absence of O2, leads to anaerobic process of
Free ribosomes present in cytosol
As you go down the ETC
If they are acidic, they are hydrophilic so they are on the surface:
Along with cholesterol determines:
Nucleus stores eukaryotic cells DNA
If they are polar, they are hydrophilic so they are on the surface of the protein:
Can take place in the Quaternary level, but between two tertiary chains:
Pyruvate Oxidation happens then
WIth fatty acids make up a:
Electrons transferred down ETC end up
Bonds with Adenine in RNA
Bonds with Thymine in DNA
Bonds with Uracil in RNA
High if it is small and non polar molecule
Ribosomes are in Proteins:
Peroxisomes are pinched from the ER
Gene Regulation most commonly occurs at transcription (but can occur at any point during teen expression):
Second type of ribosomes
Special pair of chlorophyll molecules reach an excite state and go to the primary e- acceptor which then go down the:
Unless cholesterol is present, it does not allow things to move across which in certain cases can be bad for:
movement
Can take place in the Tertiary level:
Either removes or adds when needed in the process:
Act as delivery vectors to introduce foreign DNA in bacterias nucleoid
Rough ER contains ribosomes
Bonds with Guanine in DNA and RNA
Smooth ER synthesizes lipids
Chromosomes attached to cell membrane
Lysosome Autophagy uses lysosomes to recycle cells
1st step: Acetyl CoA adds two- carbon groups to
When you change the r group from one to another it will also change the structure and function:
Stage after transcription is:
The nucleic acid biomolecules allow for the replication of DNA and allows the body to carry out processes such as mitosis which allow the cell to be able to assemble nucleotides together to form double-stranded DNA. All the nucleic acids are made up of nitrogenous bases, phosphate groups, and deoxyribose sugars, and once assembled can then be used to add onto the chain of replication of DNA. This allows bonds to form between the two strands and for the monomers of DNA to be completed in full and to allow DNA replication to carry on seamlessly.
Intermediate filaments are made of proteins called keratin
Movement
Transmembrane proteins included in the fluidity of membranes in things such as animal cells. The fluid mosaic model contains many membranes such as channel, ion, gated, etc. Transmembrane proteins will remain within the membrane if it becomes fluid or viscous depending on temperature. These allow the cell to function despite temperature fluctuations as large molecules can be activated or facilitate diffusion of large biomolecules into the cell during times in which they are needed.
If they are basis, they are hydrophilic so they are on the surface:
Components of the cytoskeleton are made of proteins
Major phase
Eukaryotes and prokaryotes differ in structure and therefore the process in transcription. Due to prokaryotes not having a nucleus they are able to carry out transcription and translation almost immediately. Although, eukaryotes have a nucleus which is the site of transcription which must be passed through in order to begin translation causing a delay or a barrier in order to finish translation. The nucleus contains all of the instructions for transcription and is the genetic code/programming of every single cell in the body.
Links in Amylopectin from Starch
Vacuoles derived from Golgi and give rise to vacuoles
One type of transport:
Lysosome Phagocytosis uses lysosomes to help break particles, bonds, food, organelles and absorb bacteria
Microfilaments provide support to the plasma membrane
Along with cholesterol determines:
Bonds with Cytosine in DNA and RNA
With glycerol make up a:
Cytoskeleton maintain cells shape and is an anchorage for eukaryotic cell organelles
Nucleoid contains bacterial DNA
Made of Beta Links
1. Amino acids are needed to attach to appropriate tRNAs so they can enter an active site of a specific synthase so translation can eventually occur.
Connected By:
Movement
Transcription Factors Are Part of Gene Regulation
Movement
First stage of cellular respiration (aerobic)
Hold Together Nitrogenous Bases
The electron transport chain and chemiosmosis connect to ATP. Energy is used to pump protons in the thylakoid space (against their concentration gradient) and since there are a lot of protons it’s acidic so they will want to leave down their concentration gradient through ATP synthase by going through the stroma in which energy is associated. The movement of protons down the concentration gradient creates energy which is used to add a phosphate group to add ADP to form ATP, which is chemiosmosis (concept). Through these two processes, ATP is made in the cyclic electron flow
ATP Supplied by Respiration and Fermentation
e- that went down the electron transport chain supply the special pair of chlorophyll a molecules in:
Contain 3 groups of phosphate:
Glycolysis happens then
Backbone of Lipids:
Third stage of cellular respiration (aerobic)
6th step: Second sequential reaction
Makes proteins
Major phase
Serves as a Template for Transcription
Low if it is an ion:
Has binding site that fits the chemical messenger:
Golgi Apparatus is responsible for the formation of lysosomes
Rough ER produces proteins
Cell wall outside of Cell membrane
Bacterial chromosomes inside the nucleoid
Nucleus contains DNA
Transmembrane Receptor
Mitochondria generates the eukaryotic's cells energy
Plasma membrane provides protection to eukaryotic cells
Allows for cell to move things across which is good for:
Low if it is a large and polar molecule:
The cell wall of many bacteria is surrounded by the Glycocalyx
Made of Beta Links
Polypeptides folds through interactions of R groups to form a final 3-D shape at the Tertiary level:
Attaches through Dehydration Synthesis
Transport vesicles from ER to Golgi Apparatus
Smooth ER metabolizes carbohydrates
3.) Mitochondria connects to mutations because they contain enzymes that make ATP and if they are absent, such as the enzyme of pyruvate dehydrogenase, they can cause diseases in this case the absence of pyruvate dehydrogenase can cause Leigh’s disease which causes mutations in the mitochondria DNA and can be fatal to individuals.
Second stage of cellular respiration (aerobic)
some organisms in absence of 02, pyruvate from acetaldehyde, is reduced to form ethanol, CO2 is released and in process of reduction electrons from NADH are transferred to Acetaldehyde recycling NAD+ so glycolysis can occur
Contain a:
2. Proteins are needed in photosynthesis for many reasons. In the electron transport chain ferodoxin (a protein) is used whether in a cyclic or a noncyclic electron flow. Also, not to mention photosystem I and II are both large pigment protein complexes.
Cytoplasm helps with chemical reactions and supports eukaryotic cells.
R groups are interacted with here:
Occurs between Phosphate Groups and Nitrogenous Bases of Other Nucleotides
movement
Pyruvate is reduced to form lactate and recycling back NAD+ so glycolysis can continue. No CO2 produced
One type of transport:
On the higher end if it is small, uncharged polar molecule
3. DNA is located in the nucleus and because of it repressors and/or activators are able to bind to DNA sequences to regulate gene expression in either or manner.

Biomolecules

Carbohydrates

Polysaccharides

Storage

Starch

Amylopectin

Glycogen

Dextran

Branched

Straight

Structure

Cellulose

Chitin

Lipids

Fat Molecule

Triaglycerol

Glycerol

Fatty Acid (Palmitic Acid)

Hydrophobic (C-H Bonds. Nonpolar)

Saturated

Solid

Unsaturated

Liquid

Trans

Alternating H

Cis

Same Side H

Phospholipids

Polar/Hydrophilic Head

Hydrophobic Tail

Create C Double Bonds (Kink)

Nucleic Acids

Deoxyribonucleic Acid (DNA)

Directs Own Replication

Allows as Base for mRNA Synthesis

mRNA

Gene Expression (Protein Synthesis)

Complementary Base Pairing (Double Strand)

Ribonucleic Acid (RNA)

Nucleotides

r

ar

Phosphodiester Bond

Phosphate

Deoxyribose Sugar

Base

Pyrimidines

Thymine (T)

Cytosine (C)

Uracil (C)

r

r

RNA Only (Replace Thymine)

Purines

Guanine (G)

Adenine (A)

Ribose Sugar

Proteins

Enyzmatic

Defensive

Storage

Transport

Structural

Contractile/Motor

Hormonal

Receptor

CELLS

Prokaryotic Cells

Alpha Glucose

Beta Glucose

Plant

Animal

Alpha 1-6 Glycosidic Linkage

Branch Point

Alpha 1-4 Glycosidic Linkage

Beta 1-4 Glycosidic Linkage

Ester Linkage

Link

Nucleoside

DNA Bond

DNA Bond

RNA Bond

Hydrogen Bonds

Amino Acid

Main Chain

Amino Group

Carboxyl Group

Ionized

Side Chain

R Groups

Nonpolar

H, CH, CH2, CH3, H2C, H3C

Polar

OH, NH2, SH, CO

Acidic

Negative Charge

Basic

Positive Charge

R Group

Interactions

Disulfide

Ion Dipole

Hydrogen Bonding

Hydrophobic

Ionic

Orientation

Nucleus

c1r

ConnectionsNucleus Relationship to Eukaryotic Cells: The relationship between the nucleus and eukaryotic cells is that all eukaryotic cells contain a nucleus where they store their DNA and control gene expression. Nucleus Relationship to the nucleolus, nuclear envelope/membrane, chromatin, centrioles, and nuclear lamina (TEM)The nucleus connects to the nucleolus, nuclear envelope/ membrane, chromatin, centrioles, and nuclear lamina (TEM) because the nucleus has inside all of these organelles. Nucleolus Relationship to Nucleus: The relationship between the nucleolus and nucleus is that the nucleolus is located in the nucleus and assembles ribosomes in the nucleus.Nuclear Envelope/ Membrane Relationship to Nucleus: The relationship between the nuclear envelope and the nucleus is that it is a structural framework/ support system for the nucleus. Nuclear Envelope/ Membrane Relationship to Nuclear Lamina (TEM)The relationship between the nuclear lamina and the nuclear envelope is that the nuclear lamina provides support to the nuclear membrane so it won't collapse and die. Chromatin Relationship to Nucleus: The relationship between chromatin and the nucleus is that the DNA of the nucleus helps make up chromatin which helps make chromosomes when cells divide. Centrioles' Relationship to Nucleus: The relationship between centrioles and the nucleus is that the centrioles determine the position of the nucleus. Centriole's Relationship to Chromatin:The relationship between centrioles and chromatin both help the process of cell division in the nucleus.

Ribosomes

c1r

Free Ribosome's relationship to Ribosomes:Free Ribosome's relationship to ribosomes is that its one type of ribosome based on its location in the cytosol.Bound relationship to Ribosomes:Bound Ribosome's relationship to ribosomes is that its the second type of ribosome that is based on being in the Rough ER and the nuclear membrane.

Free Ribosomes

c1

Bound Ribosomes

c1

Cytoplasm/ Cytosol

c1r

Cytoplasm/ Cytosol Relationship to Eukaryotic Cells:The cytoplasm is present in all eukaryotic cells that carry out complex metabolic reactions and provides support to the organelle's structures.

Peroxisomes ^

c1r

Peroxisomes' relationship to the Endoplasmic Reticulum:Peroxisomes' relationship to the Endoplasmic Reticulum is that peroxisomes emerge from the ER.

Mitochondria

c1r

Mitonchondria Relationship to the Eukaryotic cell: The mitochondria' relationship to the eukaryotic cell is the powerhouse of the cell because they generate energy (ATP).

Plasma membrane

c1r

Plasma Membrane relationship to Eukaryotic Cells:The plasma membrane's relationship to eukaryotic cells is that it provides protection.

Golgi Apparatus

c1r

Golgi Apparatus relationship to the Endoplasmic Reticulum:The Golgi Apparatus' relationship to the Endoplasmic Reticulum is that it receives proteins and lipids (fats) from the ER.

Cilia

c1r

Cilia's relationship to the plasma membrane : Cilia's relationship to the plasma membrane is that cilia extend from the plasma membrane.

Flagellum

c1r

Flagellums' Relationship to the plasma membrane:The Flagellums' relationship to the plasma membrane is that it also extends from the plasma membrane.

Lysosomes

c1r

Lysosomes' relationship to Golgi Apparatus: Lysosomes' relationship to Golgi Apparatus is that the Golgi Apparatus receives protein enzymes from the ER, which are packed in a vesicle in the Golgi Apparatus, processed, and then pinched off as a lysosome.

Lysosome Autophagy

c1

Lysosome Phagocytosis

c1

Vacuoles

c1r

Vacuoles Relationship to Golgi Apparatus:Vacuoles' relationship with the Golgi apparatus is that it is derived from the Golgi and gives rise to the organelle. Vacuoles' Relationship to the Endoplasmic Reticulum: Vacuoles' Relationship with the ER is that it is derived from it and membrane/ proteins produced by the ER move via transport vessels.

Food vacuoles

c1

Contractile vacuoles

c1

Central Vacuoles

c1

Endoplasmic Reticulum (ER)

c1r

Smooth ER relationship to the Endoplasmic Reticulum (ER):The Smooth ER's relationship to the endoplasmic reticulum is that its part of the ER and helps with lipid synthesis modification.Rough ER relationship to the Endoplasmic Reticulum (ER):Rough ER's relationship to the endoplasmic reticulum is that its part of the ER and helps with protein synthesis.

Smooth ER

c1

Rough ER

c1

Cytoskeleton

c1r

Cytoskeletons' relationship to eukaryotic cells:The cytoskeleton's relationship to eukaryotic cells is that it maintains the cell's shape and it is the anchorage for many organelles.

Intermediate Filaments

c1

Microfilaments ^

c1

Microtubules

c1

Membrane

Lipids

Phospolipids

Amphipathic

Nonpolar

Fatty Acids

Saturated

Unsaturated

Polar

Glycerol

Phosphate Groups

Proteins

Transport

Signal Transduction

Intercellular Joining

Enzymatic activity

Cell-Cell Recognition

Attachment to cytoskeleton and the ECM

Permeability

Fluidity

Fluid

Viscous

Function

v

c1

Capsules or Slime Layers

c1

Plasma/ Cell Membrane

c1

Cell Wall

c1

Flagellum

c1

Plasmid

c1

Chromosome

Nucleoid

c1

Cilia

c1

Hydrophilic (Charged)

Ionic Bond

SH Forms Disulfide Bonds with other SH R Groups (Only Covalent Bond in R Groups)

Primary Structure

Amino Ends Connect to Carboxyl Ends

Secondary Structure

Alpha Helices

Tertiary Structure

Quarternary Structure

Non-Covalent Bonds Between Hydrophilic and Hydrophobic Surface Units

Hydrogen, Ionic, Dipole-Dipole

Beta Pleated Sheets

Hydrogen Bonds

Hydrophobic Interactions and van der Waals interactions

Membranes

Plasma Membrane

Phospholipid Bilayer

Transmembrane Proteins

Transport

Passive Transport

Diffusion

No Energy Input

Facilitated

Aided by Proteins

Carrier

Channel

Hydrophilc Inside

Hydrophobic Outside

Osmosis

Water from Higher to Lower Concentration

Active Transport

Sodium/Potassium Pump

Open Sodium Pump

Depolarization

Open Potassium Pump

Hyperpolarization

Ion Channels

Gated

Stretch

Ligand

Voltage

Ungated

Concentration Gradient

Concentration from Low to High

Requires Energy Input

Cotransport

Indirect Transport of Other Molecules

Bulk Transport

Exocytic

Endocytic

Phagocytosis

Pinocytosis

Receptor-Mediated Endocytosis

Enzymatic

Signal

Cell Recognition

Intercellular Joining

Attach to CS and ECM

Alpha Helix

Extracellular N-Termiinus

Cytoplasmic C-Terminus

Selective Permeability

Electrogenic Pumps

Generates Voltage (Membrane Potential)

Store Energy for Cellular Work

Proton Pump (H+)

Peptide Bonds

Floating topic

Photosynthesis

Thylakoid Membrane

Light Reaction

Photosystem II

O2

H20

Electron Transport Chain

Chemosmosis

ATP

Photosystem I

Noncyclic

NADPH:

Cyclic

No NADPH

Stroma

Calvin cycle

Carbon Fixation (Phase 1)

3 phosphoglycerate

Reduction (Phase 2)

G3P (Sugar)

Regeneration of the CO2 Acceptor (Phase 3)

Cell Signaling

Membrane Receptors

Accepts Polar Ligands

Intracellular Receptors

Accepts Nonpolar Ligands

Ligand/Signal Molecule

Receptor

G Protein Coupled Receptor

Activated GPCR

Binds to G Protein

Activates G Protein

GTP

Binds to Adenylyl Cyclase

Active Adenylyl Cyclase

Converts ATP to cAMP (Second Messenger)

Activates Protein

Cellular Response

Hydrolyzed to GDP

Active Relay Molecule

Active Protein Kinase 1

Active Protein Kinase 2

Phosphorylated Protein

Cellular Response

Active Protein Enters Nucleus

Binds to Gene as Transcription Factor

mRNA Transcribed

Leaves Nucleus for Ribosome

Ribosome Creates Protein as Response

Tyrosine Kinase Receptors

Forms Dimer

6 ATP Activate Tyrosine Kinase Receptors

Phosphorylated Dimer

Active Relay Protein 1

Cellular Response 1

Active Relay Protein 2

Cellular Response 2

Epinephrine

Beta Receptor

Liver Cell

Glycogen Breakdown

Glucose Release

Blood Glucose Increase

Beta Receptor

Smooth Muscle Cell

Cell Relax

Blood Vessel Dilation

Increased Blood Flow to Skeletal Muscle

Mitochondria Supply ATP

Cellular Respiration and Fermentation^

Pyruvate Oxidation

c1

In the mitochondrial matrix

Glycolysis

c1

Cytoplasm outside mitochondria

c1

Oxidative Phosphorylation

c1

Inner mitochondria membrane

Electron Transport Chain

Complexes I,II,III,IV and Q

Energy Investment Phase

c1

Addition of phosphate from ATP to glucose6P using the enzyme of Hexokinase

Glucose 6 phosphate converted to fructose 6-phosphate

Uses enzyme PFK (Phosphofructokinase) to convert fructose6phosphate to fructose1,6 bisPhosphate by transferring a phosphate group from ATP to the opposite end of the sugar, investing a second molecule of ATP^

Aldolase cleaves the sugar molecule into two different three-carbon sugars

6 carbon sugar splits into two molecules of 3 carbon each forming DHAP and G3P. Eventually DHAP converts G3P , so at the end we have 2 molecules of G3P from 1 molecule of glucose

Energy payoff phase

c1

(1) G3P is oxidized by the transfer of electrons to NAD+ , forming NADH

Phosphate group is transferred to ADP (substrate-level phosphorylation) in an exergonic reaction. The carbonyl group of G3P has been oxidized to the carboxyl group (-COO-) of an organic acid (3- phosphoglycerate)

Enzyme relocates remaining phosphate group

Enolase causes a double bond to form in the substrate by extracting a water molecule, yielding phosphoenolpyruvate (PEP) , compound with high potential energy

Phosphate group is transferred from PEP to ADP (second example of substrate- level phosphorylation) forming pyruvate

(2) Using energy from this exergonic redox reaction a phosphate group is attached to the oxidized substrate , making a high-energy product

Pyruvate oxidized

NAD+ to form NADH

Acetyl Coenzyme A

Citric Acid Cycle/ Krebb's Cycle

c1

inside mitochondrion

Oxaloacetate

Citrate

Isocitrate

Redox reaction: Isocitrate is oxidized; NAD+ is reduced

Redox reaction: After CO2 release, the resulting four- carbon molecule is oxidized (reducing NAD+), then made reactive by addition of CoA

There is an addition of a phosphate to Succinyl CoA which causes GTP to be released and bind with ADP which forms Succinate

Redox reaction: Succinate is oxidized; FAD is reduced

Addition of H20 to Fumarate

Malate

Redox reaction: Malate is oxidized, NAD is reduced

Energy released

Complexes I,II, and IV

intermembrane space

ATP Synthesis

Proton motive force

Pi

ADP^

ATP

Chemiosmosis

c1

Water, H20

Fermentation

c1

Alcohol Fermentation

c1

Lactic Acid Fermentation

c1

DNA Structure & Replication

Nucleotides

Phosphate Group

Nitrogenous Base

Purines

2 Nitrogen Rings

Adenine

Guanine

Pyrimidines

1 Nitrogen Ring

Thymine (DNA)

Uracil (RNA)

Cytosine

Deoxyribose (DNA)/Ribose (RNA) Sugar

Double Stranded

Replication Bubble

Replication Fork

Separate Double Strand of DNA

Helicase

Unwinds and Separates Parental DNA

Topoisomerase

Breaks, Swivels, and Rejoins DNA Ahead of Replication Fork Relieving Strain from Unwinding

SSB

Stabilize Unwound Parental Strands

Primase

Synthesize RNA Primers 5' Leading Strand

Form Okazaki Fragments of Lagging Strand

DNA Polymerase III

Bonds Nucleotides to Polymer

Removes 2 Phosphate from Nucleotide

Forms Phosphate Group/Backbone

2 Inorganic Phosphate Produced

Bind to RNA Primer

Polymerization 5' --> 3'

Also has DNA Polymerase I in Bacterial Replication

Remove RNA Nucleotides from Primer and Replaces with DNA Nucleotides at 5' End

Origin of Replication

Complementary Base Pair in DNA/RNA

Complementary Base Pair in RNA

Complementary Base Pair in DNA

Hydrogen Bonds

2 Hydrogen Bonds

3 Hydrogen Bonds

Sliding Clamp

Aids DNA Polymerase III

Leading Strand

Elongated Continuously

Lagging Strand

Okazaki Fragments

DNA Ligase

Seals Gaps Between Fragments

Transcription

RNA Synthesis

Prokaryotes

mRNA

Immediately go to Translation Because of No Nucleus

Eukaryotes

Nuclear Envelope

Pre-mRNA

Goes Through RNA Processing

mRNA

5' Cap

Modified Guanine Nucleotide Added to 5' End

Protein Coding Segments

Start/Stop Codons

Polyadenylation Signal

50-250 Adenine Nucleotides Added to 3' End

Poly-A Tail

RNA Splicing

Introns Cut Out/Exons Spliced Together

Exons = Coding Segment

Alternate Splicing

Splice Together Exons But Can Leave Out 1 or More to Produce Different Proteins During Translation Through Different Exon Sequences

Start Point (+1)

Upstream (Left = Negative)

Downstream (Right = Positive)

Direction of Transcription

Read/Template in 3' --> 5'

Can Be In or Directly After Promoter

Initation

RNA Polymerases

Binds to Promoter

DNA Unwinds and RNA Synthesis Begins

Prokaryotes

RNA Polymerase (RNAP)

Eukaryotes

RNA Polymerase II - pre-mRNA, snRNA, microRNA

snRNA + Spliceosome + Other Proteins

Spliceosome Components

mRNA

Cut-Out Intron

Splice Together Ends of Introns to Form a Ring and Join Exons Together, Introns Form Ring Separate from mRNA

Promoter Includes Nucleotide Sequence TATA Box

About 25 Nucleotides Upstream from Transcription Start Point

Transcription Factor Must Recognize Before Binding of RNA Polymerase II

Additional Transcription Factors Bind with RNA Polymerase to Form Transcription Initation Complex

Elongation

Moves Downstream Unwinding DNA

Elongate RNA Transcript 5' --> 3'

In Wake DNA Reforms Double Helix

Termination

RNA Transcript Releases

Polymerase Detaches from DNA

mRNA is Released

Cleavage by Ribonuclease at 3' End

Poly-A Polymerase Adds 100-200 A's to 3' End Using ATP

Poly-A Tail

Translation

Occurs in the cytoplasm for both eukaryotes and prokaryotes. However, in eukaryotes it is spatially separated from transcription while in prokaryotes it is coupled with it.

Prokaryotes: First tRNA carries formyl methionine; 30s and 50s = 70s ribosome; Has shine dalgarno. Eukaryotes: First tRNA carries methionine; 40s and 60s = 80s ribosome; Binds to 5' end until start codon. Both: Initiator tRNA binds to start codon and large ribosomal subunit joins to form initiation complex.

Polypeptide chains get longer; Ribosomes have 3 binding sites; First tRNA starts at the P site (anticodons of tRNA with codons of mRNA). The A site next to it allows for a tRNA to bind to matching codon forming a peptide bond and then shifting mRNA forward by a codon allowing the empty tRNA to exit through the E site.

Translation comes to an end; Occurs when a stop codon in the mRNA enters the A site. Proteins called release factors recognize stop codons (fit into p site).

Endomembrane System

Secretory Pathway: path taken by a protein in a cell on synthesis to modification and then release out of the cell (secretion)

Targeting Proteins to the ER

Polypeptide synthesis begins on free ribosomes in the cytosol

An SRP binds to the signal peptide, halting synthesis momentarily

r

SRP is a signal recognition particle and is made of RNA and proteins.

The SRP binds to a receptor protein in the ER membrane, part of a protein complex that forms a pore.

The SRP leaves, and polypeptide synthesis resumes, with simultaneous translocation across the membrane

The signal peptide is cleaved by an enzyme in the receptor protein complex

The rest of the completed polypeptide leaves the ribosome and folds into its final conformation.

2 ways

r

-Both processes synthesis is completed on free ribosomes

1st way: ER (inside of cell "cytoplasm")

r

Summary: mRNA--> ribosome-> rough endoplasmic reticulum-->Golgi apparatus--> Lysosome--> Exocytosis

go through organelles

Mitochondria

chloroplasts

peroxisomes

nucleus

The nuclear envelope is connected to the rough ER which is also continuous with the smooth ER.

Membranes and proteins produced by the ER move via transport vesicles to the Golgi

The Golgi pinches off transport vesicles and other vesicles that give rise to lysosomes, other types of specialized vesicles, and vacuoles.

The lysosome is available for fusion with another vesicle for digestion.

A transport vesicle carries proteins to the plasma membrane for secretion

Examples of secreted proteins

-Digestive enzymes: Amylase

Peptide hormones:Insulin

Milk proteins: casein

Serum proteins: albumin

Extracellular matrix proteins: collagen

Gene Regulation

Promote gene expression; positive regulation.

Regulate the transcription of genes; Bind to the promotor or enhnacer area of DNA.

Turns off or reduces the expression of one or more genes by binding to the operator.

Bacteria

Eukaryotic Cells