Unit 2 Test

Proteins are made up of

Amino Acids

How many types of amino acids are there?

20 amino acids

Amino acids are made up of 4 main things:

A carbon atom bonded to H

An amino group

A carboxyl group

An R group

1° primary structure of a protein

Amino acid sequence

2° secondary structure of a protein

Spirals or folds

3° tertiary structure of a protein

Complex 3-D shape that gives protein its function

4° quaternary structure of a protein

Some proteins need more than one piece to make the final protein

Enzyme

A type of protein that speeds up the rate of chemical reactions

Steps of how an enzyme works

1. Bring substrates together in a precise orientation at the active site
2. Binding to the active site

Destabilizes bonds in the substrates, allowing new bonds to form

R-groups that line the active site form temporary covalent bonds that assist with transfer of atoms from one reactant to another
3. A final product is formed and released

Induced Fit

The substrate induces a slight change in the shape of the enzyme that it can fit perfectly

Competitive inhibition

Occurs when a regulatory molecule directly blocks the active site

Blocks the active site so that the substrate can’t bind

Allosteric regulation

Occurs when a regulatory molecule binds somewhere other than the active site

Changes the shape of the enzyme so that the substrate can’t bind

How to reverse competitive inhibition

An increase in the substrate concentration can return enzyme activity to 100%

How to reverse allosteric inhibition

An increase in the substrate concentration can increase enzyme activity but it will not reach 100% unless there is no longer a regulatory molecule present

Metabolic pathway

A specific molecule is altered in a series of steps that results in a final product

Inside a cell what are 3 jobs of proteins

* Enzymes facilitate chemical reactions inside the cell.
* Cytoskeleton (microfilament protein) gives the cell its shape.
* Microtubules facilitate chromosome movement during cellular division.

Between cells what are 3 jobs of proteins

* Insulin relays a message to other cells.
* The Na/K pump transports sodium out of the cell and potassium into the cell.
* Hemoglobin carries oxygen to cells all over the body.

Primary structures of all proteins are manufactured by

ribosomes

Signal sequence

either the first few amino acids, or the last few amino acids in the chain

Chemical label

A chemical group added to a protein after it’s completely finished being manufactured, folded, and specialized

Endoplasmic Reticulum

formed from invaginations of the nuclear envelop

Proteins travel through __ and then bud off in __

Proteins travel through RER and then bud off in VESICLES

Vesicles fuse to the _

Golgi Apparatus

Proteins leave GA for the _ or bud of GA in _

Proteins leave GA for the CELL MEMBRANE or bud of GA in VESICLES

When proteins bud off GA in vesicles that become _

lysosomes

The endomembrane system_

The endomembrane system folds, specializes, packages, transports and receives (lipids and) proteins which have an ER signal sequence

Steps of Protein manufacture, specialization, packaging, transporting and receiving in the endomembrane system

1. A ribosome begins protein manufacture (in the cytoplasm)
2. The first few amino acids serve as the ER signal
3. The ER signal sequence binds to the signal recognition particle which pauses translation
4. The SRP binds to a receptor on the rough endoplasmic reticulum
5. The amino acid chain is threaded through the receptor into the RER
6. SRP detaches. Ribosome completes the primary structure . The amino acid chain is released

What happens in the RER (4 things)

* After the SRP leaves, the ribosome completes the primary structure while its attached to the RER membrane
* Once primary structure is completed the amino acid chain is released into the interior (lumen) of the RER
* Proteins are folded inside the RER
* Enzymes produce glycoproteins

Glycoproteins

Proteins with added carbohydrate side chains

What happens in the GA? (8 things)

* Proteins bud off in vesicles composed of the ER membrane.
* They fuse to the cis side (closest to the nucleus). Proteins flow inside.
* Proteins are moved along the \n membranes of the GA, encountering different groups of enzymes at each step.
* Proteins are modified and specialized by enzymes encountered in each cisternae (membrane section).
* Many receive chemical labels.
* Once proteins reach the trans side those with chemical labels bud off in vesicles.
* Vesicles carrying lysosome proteins develop into lysosomes
* Proteins without chemical labels are released from the GA and travel to the cell membrane

What happens in the lysosome? (3 things)

* Vesicles that have budded off from the GA and are carrying lysosome proteins develop into lysosomes
* Lysosomes digest foreign materials that have been brought into the cell.
* The resulting macromolecules are recycled to make new materials.

The Cell Theory

All life is composed of one or more cells...the cell is the basic unit of life. \n All cells arose from other cells

Prokaryote

Unicellular organisms (bacteria, archaea)

No membrane bound organelles Contain ribosomes

Non-membrane bound nucleoid

Does not have mitochondria

DNA is circular and can be arranged in one chromosome

Small size

Some have flagellum which helps it move

Some have fimbriae which help it attach

Eukaryote

Multicellular organisms (animals, plants, fungi, protists)

Membrane bound organelles in cell (ER, GA, lysomes)

Membrane bound nucleus

Mitochondria/chloroplast

DNA is linear and arranges in multiple chromosomes

Large size

Desmosomes (animals) and plasmodesmata (plants)

How are prokaryotes and eukaryotes related?

Eukaryotes and Archaea share more distinct features suggesting they inherited them from a recent common ancestor

The Theory of Endosymbiosis

A bacteria got inside of an archaea cell and that bacteria evolved into the mitochondria and chloroplast

Development of The Theory of Endosymbiosis

* First proposed in 1905 but was ignored for several decades
* In 1967 Lynn Margulis published a paper about it and was net with intense criticism
* Her idea that cooperation (between the proto-eukaryote and engulfed prokaryote) could be a driving force of evolution was counter to the prevailing ideas of the time that only competition was important.
* Regardless of the opposition, evidence for her hypothesis began to mount

Are prokaryotic cells compartmentalized?

No

Meaning that there are no organelles. \n Everything is just floating around inside the cell without any separation

Are eukaryotic cells compartmentalized?

Yes

Meaning that there are organelles.

Most things are separated from each other

Cell Attachment

* Molecules that attach one cell to another are often proteins that span \n the cell membrane and extracellular matrix.
* Cells attach to each other temporarily to perform a function or attach \n semi-permanently to form a tissue

The extracellular matrix (of animal cell)

* Surrounds the outside of the cell membrane
* Composition of extracellular matrix is unique to cell type

Composition of the extracellular matrix (of animal cell)

* Proteoglycans-proteins with lots of cards attached. Protects cell
* Collagen-rope-like protein. Provides strength and form
* Integrins-span the cell membrane. Connects the inside of the cell to the ECM
* Specifics of the composition unique to the cell type

Cell Communication

* A signal sent from one cell has to recognize and bind to the correct receiving cell
* Signals (hormone or neurotransmitter) can be proteins or other molecules
* Receptors are proteins that are on or inside the cell membrane of receiving cells
* The signal will fit perfectly into the receptor

Neurotransmitters

Travel through nerve cells in the nervous system to reach their destination.

Fast response

Hormone

Travel in blood to reach their destination

Slow response

Nucleic aicids consist of

nucleotides

Nucleotides are…

polar

Nucleotides are composed of (3 things)

* Phosphate group
* Nitrogenous base
* Sugar: deoxyribose in DNA and ribose in RNA

RNA

* Sugar is ribose
* Single stranded96

DNA

* Sugar is deoxyribose
* Double Stranded
* Double helix

RNA is __ reactive than DNA

RNA is _MORE_ reactive than DNA

DNA sequence

* the order of nucletides
* dictates the order of amino acids for the resulting protein

5’ end

phosphate attached to the 5’ carbon on the sugar

3’ end

3’ carbon on the sugar

Antiparallel

* 2 nucleotides are arranged opposite in orientation to each other
* When 2 nucleotides are bonded

Mitosis

* Cell replication to create identical cells
* One cell divides into 2 diploid daughter cells
* dealing with a nuclear membrane & multiple chromosomes require mitosis to have more steps than binary fission

Meiosis

* Cell replication to create haploid gamete
* One cell divides into 2 daughter cells and then the 2 daughter cells each divide
* The result is 4 haploid daughter cells

Replication bubble

forms during DNA synthesis

Replication fork

* Y-shaped region where the parental strands are separated


* where active DNA synthesis takes place

Steps of DNA replication

1. DNA helicase breaks the hydrogen bonds between the nucleotides in that location & opens the double helix so that the two strands separate at the replication fork. \n The unwinding of DNA strands should create twists further down the helix, but \n topoisomerase binds to relieve twisting forces.
2. Single-strand DNA-binding proteins attach to the separated strands to prevent them from snapping back into a double helix
3. Primase lays down primer on both strands

An RNA strand about 10 ribonucleotides long

Forms complementary base pairs with the DNA template strand
4. DNA polymerase α or ε synthesizes the leading strand by attaching nucleotides to the 3’ OH ends of the primer and extending it

DNA polymerase δ synthesizes the lagging strand and replaces primers with \n deoxyribonucleotides

DNA helicase

breaks the hydrogen bonds between the nucleotides in that location & opens the double helix so that the two strands separate at the replication fork

Topoisomerase

binds to relieve twisting forces

Leading strand

strand that is synthesized towards the fork

synthesis is straightforward

Lagging strand

strand that is synthesized away from the fork

causes gaps in synthesis

Direction of synthesis

3’ to 5’ on template strand

5’ to 3’ on daughter strand

Primase

lays down primer on both strands

Why primase adding primer is necessary

DNA polymerase can only \n add nucleotides to a free OH \n group, it can only extend a \n pre-existing strand... but when DNA strands are separated there are no free OH groups

Primase provides the free 3’ OH \n group that DNA polymerase \n needs to start adding nucleotides

DNA polymerase α or ε

synthesizes the leading strand by attaching nucleotides to the 3’ OH ends of the primer and extending it

DNA polymerase δ

synthesizes the lagging strand and replaces primers with deoxyribonucleotides

Ligase

seals the gaps between the Okazaki Fragments

endonuclease

Removes the RNA when DNA pol δ gets to the end of its new \n daughter strand and bumps up against the older daughter strand, thus dislodging the old primer

Okazaki Fragments

Fragments of new daughter \n DNA

Lagging strand

Proofreading

* Fixes mistakes in DNA synthesis.
* DNA polymerase fixes its own mistakes


1. A newly added base that is not paired correctly creates misalignment.
2. DNA polymerase’s active site can identify misalignment. Once detected, DNA polymerase will pause.
3. DNA polymerase has exonuclease activity – it will remove the mismatched nucleotide. Then replace it with the correct one.

Mismatch Repair

* Fixes mistakes in DNA synthesis not repaired by proofreading


1. A mismatch is detected \n immediately after DNA synthesis is finished.
2. Proteins and enzymes cut out the mismatch
3. DNA polymerase returns to add the correct nucleotides.
4. DNA ligase seals the breaks.

Nucleotide excision repair

* Fixes DNA damaged by UV light


1. UV light from the sun or tanning beds can cause a covalent bond to form between adjacent pyrimidine bases within the same strand. This causes a kink.
2. Protein complexes detect the \n kink, remove the section of DNA containing the kink.
3. DNA polymerase adds in the \n nucleotides and ligase seals the breaks.

Binary Fission

* Cellular cloning
* asexual reproduction by a separation of the body into two new bodies

Cell Cycle

1. Interphase (G1, S, G2)
2. Mitosis (PMAT)
3. Cytokinesis

PMAT

Prophase (DNA condenses into chromosome)

Prometaphase (The nuclear envelope disintegrates)

Metaphase (The chromosomes are lined up in middle)

Anaphase (Sister chromatids pulled apart)

Telophase (2 nuclei form)

G1

DNA is uncondensed (chromatin). The cell is fulfilling its function. It is \n “deciding” to replicate (longest phase)

S phase

DNA replicates

G2 phase

The cell grows to prepare for M phase

Sister Chromatids

Homologous chromosome and identical copy

Made through replication

Homologous Chromosomes

A chromosome pair

Prophase

* DNA condenses into compact chromosomes
* The spindle apparatus forms - produces mechanical forces that move replicated chromosomes during early mitosis and pull sister chromatids apart in late mitosis. It is composed of microtubule proteins.

Prometaphase

The nuclear envelope disintegrates.

Kinesin and dynein motor proteins attach to the kinetochores at the centromere and walk the chromosomes up and down the microtubules, until they reach the middle of the spindle.

Metaphase

The chromosomes are lined up at the metaphase plate. \n The microtubules overlap in the middle of the cell creating a pole-to-pole connection

==Anaphase==

* The cohesion that holds sister chromatids together splits.
* Sister chromatids are pulled apart by the depolymerization of the \n microtubules.
* Because sister chromatids are pulled apart, homologous \n chromosomes end up together in the new cells.
* The two poles of the spindle are pushed and pulled farther apart by specialized proteins.

Telophase

The spindle microtubules are fully depolymerized to remove the spindle. Sister chromatids reach the opposite poles. \n The nuclear envelope re-forms around each set of chromosomes. \n Once two independent nuclei have formed, mitosis is complete.

Cytokinesis

Cytoplasm is divided equally between the two new cell regions.

Then, cytoskeletal fibers form the contractile ring which pinches the cell into two new cells

G1 Checkpoint

* Cell size is adequate


* Nutrients are sufficient
* Social signals are present
* DNA is undamaged

G2 Checkpoint

* Chromosomes have replicated successfully
* DNA is undamaged
* Activated MPF is present

M-phase checkpoints

* chromosomes have attached to spindle apparatus
* chromosomes have properly segregated and MPF is absent

Regulator molecule

* active at checkpoints
* prevent the division of cells that are damaged or are in poor condition

Apoptosis

Programed death of cell (dignified)

Cyclins

* work by binding enzymes called cyclin dependent kinases
* prompt the movement of cells from one phase to the next

When cyclin binds to Cdk

* Cyclin activates Cdk


* Guides it to a specific set of proteins for phosphorylation.

M phase promoting factor

* Composed of Cdk and M cyclin.
* When the concentration of M cyclin is high enough it causes the formation of MPF.
* Then, the kinase subunit catalyzes the phosphorylation of other proteins to start M phase.

Anaphase-promoting \n complex/cyclosome

* MPF activates APC/C during anaphase.
* APC/C adds a small protein tag, ubiquitin, to its targets.
* Molecules tagged with ubiquitin get destroyed.
* Thus, APC/C destroys proteins, stopping their function