Exam 3 Principals Of Biology

Front 1

Prokaryotic cells have many infoldings of their membrane and some have specialized structures:

Back 1

Respiratory membranes in an aerobic prokaryote and thylakoid membranes in photosynthetic prokaryote (folds of the plasma membrane)

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The theory of endosymbiosis

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1. Ancestor of eukartotic cell (host cell).

2. Engulfing of oxygen (respiration) using non-photosynthetic prokaryote which becomes a mitochondrion.

3. Photosynthetic prokaryote with chloroplast and mitochondrion. (can perform photosynthesis after engulfing mitochondrion)

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Endosymbiosis: Occurred via endocytosis – movement into a cell

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Heterotrophic bacteria with respiratory membranes became mitochondria.

Phototrophic bacteria with thylakoid membranes became chloroplasts

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How could one cell end up within another?

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Endocytosis: taking in a matter by a living cell by invagionation (folding) of its membrane to form a vacuole (the cell takes things in from the environment).

Endosymbiosis: one organism live inside the cell or cells of another organism (the host). Two cells are working together with one inside the other (mutualism)

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Evidence for endosymbiosis - both chloroplasts and mitochondrion have

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Double membranes, separate DNA and they both replicate/reproduce independently from the cell

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Eukaryotic cells have unique characteristics that prokaryotic cells do not have

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Internal membranes (membrane enclosed organelles) and nuclear envelope.

Linear Chromosome.

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Mitochondria (Heterotrophic prokaryote)

Internal membrane performs a lot of respiration and helps product ATP (the mitochondrial complex itself)

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Structure: Criste inner membrane - little folding (no longer a part of plasma membrane) and mitochondrial mix which is where the cytosol use to be. It has two membranes, inner (respiration) and outer.

Function: site of cellular respiration, metabolic processes that use oxygen to drive generation of ATP by extracting energy from sugars, fats, and other substances

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Mitochondria

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Have own DNA.

Manufacture their own ribosomes.

Replicate independently of the cell

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Chloroplasts (similar to photosynthetic)

Have green color because they are full of chloroplasts and they can perform photosynthesis

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Structure: 2 main sets of membranes

- inside thylakoids (extra spare) is the stroma, granum and the stacks in the inter membrane perform photosynthesis

-Outer membrane because it was engulfed

Function: Convert solar energy into chemical energy by absorbing sunlight and using it to drive the synthesis of organic compounds such as sugars from CO2 and water

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Chloroplasts

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Have their own DNA,

Manufacture their own ribosomes.

Replicate independently of the cell

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What do plant cells have that animal cells do not?

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

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Endomembrane system

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Endo = inside, system of internal membranes that can intermix.

They are either directly connected or vesicles transport between them.

Membranes have different structures, functions, and molecular composition

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Nuclear envelope

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Structure: 2 layers - inner and outer (which is continuous with the ER). The nucleus is connected to the cytoplasm by pores - has pores across both layers to allow molecules in and out of the nucleus. Proteins can go in and out
Function: Collect and protect DNA, keep in one area. Can be advantageous for efficiency - collected into much smaller space

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Endoplasmic Reticulum (ER)

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Has rough ER - dotted with ribosomes - and the smooth ER.

These two sections are parts of the plasma membrane that have folded in on itself and these folds are near the nucleus (inward of plasmic folds)

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Ribosomes

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Make proteins and are the site of protein synthesis.

Ribosomes can be free in the cytoplasm or docked on the rough E.

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Golgi apparatus (connected by vesicles)

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Vesicles carry material between the ER and Golgi. They arrive from the ER at the cis side of the golgi, it sorts and organizes molecules that pass through and sens vesicles to many destinations from the trans side.

To exit the cell - exocytosis (hormones, secretion proteins).

To lysosomes - only 1 possible location

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Also apart of the system are lysosomes and vacuoles

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The lysosomes join with vacuoles to digest materials from phagocytosis.

Phagocytosis is cellular eating (how the cell eats)

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What are some secreted products from the ER and golgi?

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1. Ribosomes deposit protein into the ER.

2. The protein exits the ER.

3. Protein enters golgi for processing.

4. protein exits the golgi.

5. protein exits the cell

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Nucleus

Nuclear envelope: two layers of membrane around the nucleus (contains DNA). The inner layer and outer layer which is continuous with the ER.Nuclear pores: cross both membrane layers and allow molecules in/out of nucleus. Transcribed RNA goes out and gets translated to protein. Protein can go in and out.

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Contents: DNA and protein.

Site of ribosomal RNA synthesis, usually dense structure in the nucleus. DNA is tightly packed within the nucleus

Function: protects DNA, packages DNA for storage, and keeps it in one place to make replication and transcription more efficient

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Howdo we store so much DNA in a small space?

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The nucleus keeps the DNA packaged/bundled in very tiny membranes. The DNA is wrapped around a cluster of proteins called histones and when coiled together they are called nucleosomes.

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Rough ER

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Series of membranes that are covered with ribosomes which synthesize proteins. This structure is closest to nucleus and it is the continuous with the nuclear envelope. The rough ER can detect misfolds in proteins and withholds or retains them. The function is it is the site of protein synthesis. It manufactures 3 types of proteins: secreted, integral membrane and soluble proteins that stay in the endomembrane system

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Smooth ER: There are no ribosomes present and it is also connected to the nuclear envelope

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Long folded tube like structure. The interior is called the lumen and is enclosed by a phospholipid membrane. It functions as a storage organelle and creates/stores lipids, steroids and calcium ions. It distributes products throughout the cell and other places and it aids in detoxification of drugs/harmful chemicals. It can also make and secrete hormones

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Gogli Apparatus

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It is composed of sack like folding structures called cisternane which are full of vacuoles proteins to be transported. The cisterna are polar (two opposite end charges) and the membranes at each end are different structurally. The cis side is closest to the nucleus and the trans is the side away from the nucleus. Plant cell have golgi vesicles called Dictyosomes.

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Lysosomes.

Membrane is made by rough ER and then transferred to the golgi. It is a single layered membrane, it works best in low pH (acidic) conditions and they are only present in animal cells. There are hydrolytic enzymes within the cell that are used to digest macromolecules and recycle the material.

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Phagocytosis is the process of engulfing smaller organisms which are passed to the cytosol and become nutrients for the cell. Autophagy is self eating meaning the hydrolytic enzymes recycle the cells own organic material. Tay-Sachs disease is when the lipid-digesting enzyme is missing or inactive and the brain becomes impaired due to accumulation of lipid cells.

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Vacuoles

Found in both plants and animals and made from the golgi or ER.

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There are large vesicles and single membrane organelles. Their function is storage (liquid other than cytosol like water and enzymes), hydrolysis of waste products and macromolecules. maintain acidic pH and constant ion concentration in the cell by pumping excess water out of the cell. They can contain pigments and they occupy up to 90% of a cells volume.

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Mitochondria: the two membranes are specialized for respiration

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Inner cristae membrane and a smooth outer membrane. Intermembrane space is area between the two membranes. The matrix contains enzymes and ribosomes and is space inside the inner membrane. The function is making ATP by maintaining strong proton gradient, respiration and pumping protons into the intermembrane space. Mitochondria move, change shape, fuse and divide.

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Chloroplasts

Contain pigments that are found in the thylakoid.

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Stroma is where the chloroplast DNA, ribosomes and enzymes exist and it is the fluid inside the organelle. The thylakoid is the interior membrane system make up of stacks called grana (singular is granum). They convert solar energy into chemical energy (photosynthesis). The two most common are chlorophyll A (green) and chlorophyll C (brown-gold)

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Peroxisomes carry out oxidation reactions and break down fatty acids and amino acids. Structure is similar to lysosomes and are found in both animal and plant cells.

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Peroxisomes are small vesicles around the cell and include a single membrane containing mostly enzymes and oxidases. The digestive enzymes break down toxic material in the cell. The function in animal cells it to protect against peroxide and in plant cells it breaks down fatty acids. They contribute to the biosynthesis of membrane lipids known as plasmalogens

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Cell wall (varies by species)

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Cellulose (calvin cycle) is made of complex polysaccharide. Plasmodesmata are pores that allow nutrients in and waste out. The function is support the cell shape, acts as gate keeper, prevents water loss, and prevents the cell swelling from too much water.

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Cytoskeleton:

Works with motor proteins and plasma membrane molecules to allow whole cells to move along fibers outside cell

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Structure is microtubles (tublun polymers) - hallow tubes -, microfilaments (actin filaments) - thin solid rows with 2 strands -, and intermediate filaments (keratin) - fibrous proteins coiled into cables. It maintains cell shape, aids in cell mobility (cillia and flagella) and in cell division it pulls apart chromosomes. The centrosome is the region near nucleus.

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Multiple linear chromosomes advantages/disadvantages

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Multiple chromosomes are able to store more genetic information.

Independent assortment of genes on separate chromosomes = more diversity.

Very easy to get tangled/damaged if not stored properly.

Difficulty replicating ends of DNA (results in a3 prime overhang once the primer is removed, and no 3 prime OH to add new nucleotides to)

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Telomeres

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Regions at the end of linear chromosomes. Consists of many repeats of a short sequences of nucleotides. It does not encode for a gene/protein to prevent the telomeres from fusing to the chromosomes and deteriorating. They are also disposable buffers that prevent the chromosome from being removed during replication/cell division

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Telomerase - enzyme that extends the 3 prime overhand at the end of chromosomes.

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It carries an RNA template and adds DNA nucleotides to the end of the template strand. It makes space (nucleotides) for an additional okazaki fragmanes on the lagging strand so that none of the origional DNA information is lost. The synthesis of new okazaki fragments uses standard replication machinery.

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Chromosome organization

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DNA needs to be tightly packaged to fir in the nucleus and prevent tangling between chromosomes.

Histones, nucleosomes and chromatin

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Histones

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Set of proteins that provide the spool for DNA packaging (like a spool of thread)

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Nucleosomes

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One nucleosome is DNA wrapped 1 and a half times around a cluster of histones. There will be many nucleosomes on a single chromosome - resemble beads on a string

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Chromatin

DNA packaged in nucleosomes and organized into a series of tightly coiled loops.

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1. Made up of both DNA and proteins (histones)

2. Very dense packaging of DNA

3. Density of packages increases during the cell cycle (visible in a mircoscope)

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Organelle highlights (protein trafficking) Proteins can be synthesized in the cytoplasm or at the membrane of the rough ER. (the ER does not make proteins - ribosomes do. Proteins pass from the ER to the golgi (cis face) then through to the trans face where they are sorted (secreted proteins carried to cell surface and hydrolytic enzymes to the lysosomes).

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Posttranslational modifications are small modifications added to proteins in the golgi (after translation) - proteins with same modification go to same site. Receptors in golgi for one modification cluster and bind to other proteins destined for the same site. The cluster region develops into a vesicle and carries all of the protein to the correct site (this speeds up protein sorting)

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Cytoskeleton

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Three types of filaments: intermediate filaments, microfilaments and microtubules they often serve as the anchor for organelles like mitochondria and chloroplasts

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Intermediate filaments:

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Relatively stable/sturdy and made from many types of materials (Keratin) and they do not change size or shape. An example is the nucleus that sits in a cage of keratin filaments

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Microfilaments (actin filaments):

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Thin solid rods, very dynamic - can be assembled or broken down very quickly - they are important for cell shape and mobility. The polymers are build from actin monomer (protein)

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Microtubules (tubulin)

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They are hallow rods made of tubulin (protein), can grow in length by addition of more tubulin and maintain cell shape. Important for movement of things within the cell (vesicles) - form the highway of the cell. And very important in cell division (clustered by nucleus)

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Motor proteins: Use energy from ATP to move/carry molecules along filaments.

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Myosin motors are actin filament associated motor (example is involvement in muscle contraction).

Dynein are microtubule motors (power movement along microtubules). It has 2 feel that walk along microtubules as ATP is hydrolyzed and it is responsible for a large part of vesicle movement in the cell

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Prokaryotic photosynthesis:

1. Light reactions – at plasma membrane.

2. Calvin cycle – cytosol.

3. Proton gradient – low concentration of protons(H+) inside cell, high

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Eukaryotic photosynthesis is entirely in chloroplasts (different location).

1. Light reactions – in thylakoids.

2. Calvin cycle – in stroma.

3. Proton gradient – low concentration of protons (H+) inside stroma, high concentration in thylakoid space

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Why are there so many stacks of thylakoids?

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Increases surface area for light reactions and harvesting energy from light

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Why pump protons into thylakoid space?

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Small space leads to a higher concentration of H+ which generates more potential energy which can be used for ATP synthesis

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Why are there are many types/colors of pigment?

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To increase the possible wavelengths of light (and light energy) that a plant can absorb. Pigments can also serve other protective functions by absorbing light that might otherwise damage DNA

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Light cycle (photo part)

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Converts solar energy into chemical energy. ATP + NADPH (electron carrier) are produced and is reducing agents

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Calvin cycle (Dark reaction) - synthesis part

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Products from light reactions used in carbon fixation. CO2 is incorporated into carbohydrates and Carbon becomes reduced.CO2, ATP + NADPH used to produce sugars

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Photosystem

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Light harvesting complex (pigment molecules bind to protein) and they collect energy from light, transfer them to the reaction center. Reaction center contains chlorophyll and a primary electron receptor (surrounded by light-harvesting complexes).

Photosystem 1 and photosystem 2 (first in light reactions)

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Linear Electron Flow

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Electrons are passed through photosystem 2 and to cytocrome complex, producing ATP, then to photosystem 1 and finally to NADP+.The products are ATP and NADPH

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Cyclic Electron flow

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Electrons from photosystem 1 are passed back to cytochrome complex, producing ATP and is then returned to the reaction center of photosystem 1.This produces ATP but no NADPH

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Calvin cycle (dark reaction) - Used energy from NADPH and ATP.One G3P molecule is the final product of 3 cycles of the Calvin Cycle

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Carbon fixation: Carbon from CO2 is attached to the redox reaction and it is a anabolic reaction. NADPH and ATP from light reactions used as reducing agents (energy coupling with light reaction).

Produces (G3P) – 3 carbon chain.

Cycle must occur 3 times– 3 CO2 needed to produce one G3P

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Phase 1 – Carbon Fixation (x 3)

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One CO2molecules is added to (RuBP).

Catalyzed by RubisCO.

Yields an unstable intermediate which breaks into two molecules of 3-PG.

6 total molecules after 3 reactions

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Phase 2 – Reduction

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The 3-PG molecules are phosphorylated by ATP and reduced by NADPH.
Uses energy from 1 ATP and 1 NADPH for each 3-PG (6 for each).
Produces 1 molecules of G3P per 3PG of starting material.
6 total molecules of G3P produced

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Phase 3 – regeneration

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5 molecules of G3P are used to regenerate 3 molecules of (RuBP) so that cycle can start again.

Hydrolyzes 1 ATP per RuBP molecule

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Glycolysis

Input: glucose, 2 ATP and 2 NAD.

Output: 2 pyruvate, 4 ATP (2 used), 2 NADH.

Location is in the cytosol

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Pyruvate Oxidation

Input: 2 NAD, coenzyme A

Output: 2 NADH, 2 CO2, 2 Acetyl CoA

Location is in the mitochondrial matrix

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Citric Acid cycle

Input: 2 ADP, 6 NAD, 2 FAD.

Output: 2 ATP, 6 NADH, 2 FADH, 4 CO2, oxalocate acetyl. The CoA is removed at the CAC.

Occurs in the mitochondrial matrix.

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Electron transport chain is a series of oxidation-reduction reactions. Electrons come from the CAC and are NADH and FADH2. FADH2 is more electronegative than NADH but NADH has more energy. In the inner mitochondrial membrane, pump H+ into intermembrane space (between two mitochondrial membrane). Low H+ concentration in mitochondrial matrix

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The pyruvate junction

If O2 is present - pyruvate moved into mitochondria. In O2 is absent - pyruvate stays in cytoplasm for fermentation

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Alcohol fermentation:
Input - 2 pyruvate, 2 NADH.
Output - 2 CO2, 2 NAD, 2 Ethanol.

Lactic Acid Fermentation:
Input - 2 pyruvate, 2 NADH.
Output - 2 NAD, 2 Lactate (lactic acid)

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Mitochondria

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Major structures - inner and outer membrane, intermembrane space, cristae, matrix - (cristae of the inner membrane increase the surface area for respiration). The number of mitochondria in a cell is related to the energy needs of the cells - the more energy needed, the more mitochondria needed.

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Comparison of Mitochondria and Chloroplasts

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Electron transport chains and ATP synthase in inner membrane. Low H+ concentration inside (matrix and stroma) and high H+ concentration between inner and outer membranes

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Cellcycle- 5 stages: (G1, S, G2 phases are apart of interphase - accounts for 90% of the cycle)

G1 gap phase: cell grows and prepares to replicate DNA,Organelles replicate.S synthesis phase: DNA is replicated DNA replication machinery is the same as prokaryotic, Telomerase is needed to prevent shortening of ends of linear chromosomes.

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G2 second gap phase:more cell growth and double check that DNA is replicated correctly.

M mitotic phase:The process by which cells reproduce (asexual reproduction),Results in clones(daughter cells) of parent cells.

G0: Cell is not progressing in cell cycle, not preparing to divide Leaves the cell cycle briefly or indefinitely Example: most neuronal cells

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DNAduring the cell cycle

The number of unique chromosomes = (n). Humans have 2 copies of each chromosome (one from each parent).- Diploid (2n)- One pair of every chromosome- Pairs are not identical,but they are similar = Homologous.

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DNA doubles during synthesis phase (4n).

Chromatin condenses during prophase into sister chromatids (both copies of a chromosome).

- Connected at point on chromatid called centromere (will also be the site of spindle attachment).

After cell division, the number of chromosomes is (2n)

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Mitosis

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Prophase.

Prometaphase.

Metaphase.

Anaphase.

Telophase.

Cytokinesis.

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Prophase: chromosome coil and condense, spindles form

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Chromosomes finish condensing.

Mitotic spindle forms.

- Aster: structure of centrosomes and microtubules.

Nuclear membrane breaks down

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Prometaphase: nuclear envelope breaks down

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Centrosomes reach opposite poles of cell.

Spindle microtubules attach to centromeres.

Kinetochore is structure of microtubule attached to centromere

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Metaphase: Chromosomes line up at equator (metaphase plate).

Anaphase: – away Chromosomes separate and move toward spindle poles.

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Telophase: Chromosomes arrive at spindle poles.

Mitotic spindle disassembles.

Nuclear membranes begin to reform

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Cytokinesis:

If no Cell Wall: Cleavage furrow forms. Contractile ring of actin filaments and myosin.

If there is a cell Wall: Cell plate forms. Cellulose and phospholipids. Grows until it meets parent cell walls. Cell is divided

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How do chromatids move? Motors in kinetochore pull chromatids along microtubules

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Cell Cycle Control: Checkpoints:

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Places where cell cycle arrest may occur.Important to prevent major problems (ie. cancer).

G2: checking that S phase went correctly.

G1: checking that enough proteins and enough cellular material.

M: checking that the chromatids were separated correctly

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What might happen of a cell skipped the G2 phase? No proteins needed to carry out Synthesis, cells wont be able to survive.

What might happen if a cell skipped the S phase? 1 Cell with DNA and 1 cell with out DNA What

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What might happen if a cell skipped the G2 phase? Not enough cellular material for both cells to survive (rough ER, golgi).

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What might happen if a cell skipped cytokinesis? Resulting cell with multiple nucleus

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Why does a cell need to regulate its progression through the cell cycle? You could get tumors (cells wont stop dividing) and metastasize = cancer (malignant spreading tumor)

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Types of ATP Phosphorylation

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Substrate-level: Phosphate group is transferred from substrate to ADP to make ATP.

Oxidative: Loose phosphate group from cytoplasm is connected to ATP using energy from H+ gradient created by redox reactions of electron transport chain.

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The central Dogma

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DNA to RNA to Protein

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Road map of molecular biology: In eukaryotes

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Replication= DNA synthesis: occurs in nucleus, Can also occur in mitochondria and chloroplasts.

Transcription= RNA synthesis: occurs in nucleus, Can also occur in mitochondria and chloroplasts. RNA processing – only occurs in eukaryotes, only in nucleus.

Translation= Protein synthesis: occurs in cytoplasm Can also occur in mitochondria and chloroplasts

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Synthesis of RNA

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Catalyzed by RNA pol II.

Adds RNA nucleotides complementary to template of DNA.

Same complementary base-pairing as in prokaryotes

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Transcription—Initiation

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Initiation begins at promoter which includes

- TATA box: Located ~25 nts before initiation start site.

- Binding sites for transcription factors =regulatory proteins.

TATA binding protein and other transcription factor bind to TATA box.

RNA polymerase II binds with more transcription factors.

RNA pol II begins synthesis at start point

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Transcription - Elongation.

continues 5 prime to 3 prime.

- Complementary base pairs are added (A=U, G=C)

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Transcription—Termination.

RNA polymerase transcribes polyadenylation signal (AAUAAA).

Transcript is cleaved 10-35 nts downstream of polyadenylation signal.

Transcript is referred to as pre-RNA ( requires processing to become mRNA)

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Components of the pre-RNA transcript

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5 prime and 3 prime UTR – untranslated regions, found upstream and downstream of protein coding sequences, will be modified.

Exons– contain nucleotides that will encode for amino acids/proteins.

Introns– nucleotides that do not code for proteins, will be removed via splicing

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RNA Processing

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Splicing, 5 prime cap, Poly A tail.

Processing reactions take place in nucleus during transcription

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Splicing- mRNA Splicing

Removes introns

- Intervening sequences

- Splices exons together: Sequences that encode for proteins.

Alternative splicing: can produce more than one protein from the same primary RNA transcript by selecting different exons to include.

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Spliceosome: Composed of RNA and protein

- Recognizes upstream splice site (exon 1)

- Cuts exon/intron boundary and hangs on.

- Recognizes downstream splice site (exon 2).

- Cuts and splices 3 prime end of exon 1 to 5 prime end of exon 2

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5 prime-cap:

Aids in mRNA export from nucleus.

Aids in translation initiation.

Helps prevent degradation

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Poly A tail:

Transcript is cleaved 10-35 nts downstream of polyadenylation signal.

Asare added to 3 prime end of transcript to create poly-A tail.

Helps prevent degradation

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Transcription and translation

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Eukaryotes are separated by time and space, mRNAs are synthesized and processed in the nucleus and then transported to the cytoplasm for translation by ribosomes.

Multiple ribosomes attached to an mRNA form a polyribosome which form in the cytosol

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What is translation?

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The process of going from nucleic acid to amino acid sequence (tRNA). Occurs in the cytoplasm and also in chloroplast and mitochondria.

Ribosomes catalyze translation of mRNA sequences into amino acid sequences.

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Translation initiation and genetic code (how to translate nucleic acid to amino acid)

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Where does the ribosome bind?

5 prime cap (UTR - no translation) small rRNA binds first

Where does translation start?

Start codon (AUG - amino acid methionine met)

Where does translation end?

Polyadenylation tail ( 3 stop codons UUA, UAG, UGA - no tRNA bind to these)

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Translation ingredients

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mRNA (fully processed).

aminoacyl-tRNAs - tRNA with amino acid attached.

Ribosomes (rRNA) - Small subunit and Large subunit

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Small subunit of ribosome binds

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mRNA, recognizes 5 prime G-cap in eukaryotes, scans 3 prime until it finds AUG, this sets the reading frame, and then the anticodon of tRNA MET base-pairs with AUG

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Large subunit attaches (initiation complex is complete)

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3 tRNA binding sites

A = aminoacyl-site, where tRNA with amino acids first enter.

P = peptidyl site, location of growing polypeptide chain.

E = Exit site, tRNA without amino acid is released

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Translation elongation
The first AA starts at the p site, then comes in through a site
Codon recognition = anticodon on tRNA binds codon on mRNA in A site, tRNA is carrying the correct AA

Peptide Bond Formation = a new peptide bond is formed between the growing polypeptide chain and the AA attached to the tRNA in the A site.

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Translocation = mRNA/tRNA shift sites, so that tRNA with attached polypeptide chain is now in the P site, a new codon is exposed in the A site,tRNA from P site is moved to E site and is released.

Requires energy in the form of GTP (guanine tri-phosphate).

Order of sites is A P E

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Translation termination

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Reaches stop codon (no tRNAs to bind).

Release factor enters A site

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Targeting proteins

translation always begins on free ribosomes in the cytoplasm.

Signal sequence = short amino acid sequence in growing polypeptides (signal sequence is recognized by Signal-recognition peptide (SRP) which escorts ribosomes/growing polypeptide to ER for translation

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Translocation complex allows growing polypeptide chain to pass directly into ER as synthesized.

Signal sequence is cleaved off, and protein finishes folding in ER lumen

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General Steps

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Translation begins in cytoplasm.

Signal sequence is recognized by SRP.

Ribosomes associate with translocation complex.

Polypeptide synthesis (translation) continues and growing chain passe sinto ER lumen as it is formed.

Signal sequence is cleaved (cut) off Polypeptide folds in ER lumen

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Post translational modifications of proteins is responsible for increasing the diversity of proteins.

AA, sugars, lipids, phosphate groups can be added and a single polypeptide can be cleaved into multiple polypeptides

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Serve as markers for targeting proteins to specific locations, or with specific functions.

There are many types of post translational modifications

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Mutations

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Silent – change in nucleic acid sequence, but no change in amino acid sequence.

Missense – change to both nucleic acid and amino acid sequences and Nonsense – change which produces an early stop codon.

Frameshift – the addition or deletion of a nucleotide which results in a shift in the reading frame of codon, tends to have severe consequences

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Eukaryotic Gene regulation

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Cells need to turn genes on and off as needed.

In multicellular organisms, all cells have the same DNA, but not all are identical. Differences are due to expression of different genes (ie. Differential gene expression)

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Transcriptional regulation - effects rate and production of mRNA transcript

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Operon.

Chromatin modification.

Control elements.

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Operon: a cluster of functionally related genes that can be coordinately controlled by a single on/off switch - segment is called an operator and is positioned within the promoter

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a gene or series of genes under transcriptional control.

Monocistronic – mRNA from operon only encodes for one protein.

Polycistronic – a long mRNA transcript from operon carries the information for multiple proteins. Separate start and stop codons for each protein

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Chromatin modifications

Change accessibility of DNA to transcription factors and RNA polymerase II by loosening or tightening association between DNA and histones.

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Modification of histone tails – addition of functional groups to tails of histone to change DNA-histone interactions. Can loosen or tighten interaction between DNA/histones. An example of a post-translational modification.

DNA methylation – leads to tighter interactions, less accessibility, and less gene expression

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Control elements

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Non-protein coding DNA sequences that can bind transcription factors and help in gene expression.

Enhancers are an example – they are usually located very far away from gene, but DNA looping brings enhancer region close to promoter

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Post-transcriptional regulation – effects rate and production of proteins from mRNA

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You can get more than one copy of a protein from each mRNA.

Need to control how many copies of the protein are made.

Control often occurs through non-coding RNAs which interact with the mRNA. Can either: Block translation by being in the way (prevent initiation of translation) or Promote degradation of mRNA (mRNA is less stable.

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Post-translational Regulation – affect protein function after it is made

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Post-translational modifications can turn protein function on and off.

Proteins can be targeted for degradation. Catalysts do not get used up in a reaction, so if we want to turn off a reaction, one possible way would be to degrade the catalyst

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Asexual reproduction:

Produces clones of parents Mitosis produces new cells

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Sexual reproduction

Meiosis produces new combinations of parent alleles in gametes (haploid cells) - Sperm and Egg.

Combinations of two gametes produces offspring which are unique from parents.

The process of combining two gametes (sperm + egg) is called fertilization

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Genetic Information

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Parental traits are passed on in the form of genes. Sequences of DNA on a chromosome. Different forms of the same gene = alleles. Each form of the gene is an allele.

Humans have 23 unique chromosomes, but two copies of each for 46 total chromosomes.

One version from each parent, so copies are not identical

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Homologous Chromosomes (Homologs) – pairs of chromosomes that carry genes controlling the same traits (ie. hair color, eye color, etc).
May carry different alleles of a gene (ie. blue eyes vs. brown eyes)

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Sex chromosomes – chromosomes involved in determining sex of an organism In humans – X, and Y chromosomes.

Autosomes– chromosomes which are not involved in sex determination

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Karyotype – a layout of all of the chromosomes in a cell.

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Ploidy – the number of copies of a chromosome from unique sources.

DNA synthesis does not increase ploidy.

n = the total number of unique chromosomes in an organism

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Haploid (n) One copy of each unique chromosome.

Human gametes are haploid.

Fertilization produces a diploid zygote

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Diploid (2n) Pairs of homologous chromosomes From 2 unique sources – mother/father.

Polyploidy – 3 or more copies of each unique chromosome

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Meiosis

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Two division in meiosis.

DNA replication still occurs in S (interphase) phase, prior to the start of meiosis)

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Meiosis I

Sister chromatids from homologous chromosomes pair in prophase I.

Tetrad – all four copies of a chromosome together.

Non-sister chromatids – chromatids of homologous chromosomes.

Homologous chromosome may recombine (cross-over) in late prophase I.

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Non-homologous chromosomes line up independently of each other in metaphase I.

Homologous chromosomes separate in anaphase I.

Sister chromatids remain paired.

Daughter cells are formed in telophase I.

Daughter cells are NOT identical and are Haploid

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Meiosis II

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New set of spindles form in prophase II.

Non-homologous chromosomes line up as in mitosis in metaphase II.

Sister chromatids separate in anaphase II.

Daughter cells are formed in telophase II.

Daughter cells are Haploid gametes.

From 1 diploid cell, 4 haploid cells are produced

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The key difference between the two processes is that homologs pair in meiosis, but do not in mitosis. Because homologs pair in prophase of meiosis I, they can migrate to the metaphase plate together and then separate during anaphase of meiosis I, resulting in a reduction division.

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Meiosis produces four genetically different daughter cells with half the genetic material of the parents, while mitosis produces two daughter cells that are genetically identical to the parent cell and each other.

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Genetic diversity: Meiosis generates gamete diversity through

Independent assortment:

Mixes up maternal and paternal chromosomes.

2n possible combinations (n=haploid chromosome #) is random!

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Recombination (crossing over)

Physical exchange of DNA – swap alleles of same gene.

Produces new combinations of alleles on one chromosome.

Occurs between homologous chromosomes.

Occurs when homologous chromosomes pair in prophase I

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Mistakes in meiosis:

If a mistake occurs during meiosis I and the chromosomes from the parent cells are not properly distributed to each daughter cell, the resulting gametes will contain an abnormal set of chromosomes.

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Nondisjunction– chromosomes do not separate correctly in Meiosis

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Aneuploidy – having an abnormal number of chromosomes

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Usually does not result in viable offspring.

Trisomy – 3 copies of a chromosome (after fertilization).

Downs Syndrome is the result of a chromosome 21 trisomy.

Monosomy – 1 copy of a chromosome (after fertilization) One gamete did not have a copy of the chromosome

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Mendelian Genetics:

Interested in heredity of traits.

Heredity – passing from one generation to another.

Traits – physical characteristics, encoded by different versions of a gene

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Used peas because:

They were easily cross- or self-pollinated, ie. he could control crosses.

Many either/or characters were available.

True-breeding varieties available ( homozygotes)

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Gene: section of DNA encoding for a specific characteristic, may have multiple alleles/trait. example: gene for eye color or flower color

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Allele: different forms of a gene, encoding for a specific trait. example: brown eyes, purple flowers

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Homozygous (for a gene): having two copies of the same allele

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Heterozygous (for a gene): having two different alleles for the same gene

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Dominant trait: A trait that is expressed regardless of the presence of other alleles.

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Recessive trait: a trait that is hidden by the presence of a dominant trait. It will only be visible if the organism has two copies of the recessive trait

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Genotype: the combination of alleles for a specific gene

Phenotype: the appearance of a trait due to the present alleles

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Genotype determines phenotype but phenotype does not determine genotype unless if a recessive trait is visible, them both copies must be recessive and the genotype can be determined.

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Mendel's model

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Alternate versions of genes (alleles) account for variations in inherited characters. Gene: flower color and Alleles: purple and white.

For each character,an organism inherits two alleles (one from each parent).

If two alleles at a locus differ (a heterozygote), then the dominant allele determines the organisms appearance (phenotype); the other allele is termed recessive

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A typical cross

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Cross two true-breeding varieties (homozygous): Parental (P) generation (true-breeding homozygous parents) are the Generates F1 generation (heterozygous)

Self-crossing F1 Generates F2 generation and results are a 3:1 phenotypic ratio

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Results from a typical monohybrid cross

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Purple flowers - self cross (progeny is all purple).

White flowers - self cross (progeny is all white).

Purple times white (F1 progeny is all purple).

F1 - self cross (F2 progeny 3/4 purple flowers and 1/4 white flowers - 3:1 phenotypic ratio)

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Genotypic and phenotypic ratios from a monohybrid cross

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Phenotypic3:1 (or 3/4 : 1/4) purple : white (or dominant : recessive).

Genotypic1:2:1 (or 1/4 : 1/2 : 1/4) homozygous dominant : heterozygous : homozygous recessive

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Law of segregation: two alleles for a gene segregate (separate)during gamete formation and end up in different gametes

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This happens in anaphase 1 of meiosis when homologous chromosomes are separating and each gamete (egg or sperm) receives only one of the two alleles present in an organism.

The punnett square: The resulting products of meiosis goes into the punnett square

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The testcross

How do we know if a dominant phenotype is the result of a homozygote or aheterozygote?

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Cross with homozygous recessive.

If all results in the punnett square are dominate, then parent was homozygous dominate.

If results in punnett square are dominate and recessive then parent was heterozygous recessive

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The Law of Independent Assortment: each pair of alleles segregates independently of each other pair of alleles during gamete formation.

(Alleles for different genes segregate independent of each other)

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Example: traits on separate chromosomes split into gametes regardless of how genes on other chromosomes segregate.

This occurs during anaphase 2 of meiosis

This applies only to genes on nonhomologous chromosomes.

Alternately, genes located near each other on the same chromosome tend to be inherited together

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Results from a typical dihybird cross:

Dependent assortment would result in the 3:1 phenotypic ratio,

Independent assortment would result in the 9:3:3:1 phenotypic ratio

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F1 progeny: Phenotypic ratio - all yellow and round, displays both dominant phenotypes.

Genotypic ratio: all YyRr (receiving genetic material from homozygous parents results in heterozygous)

(YYRR X yyrr)

Self F1 Phenotypic ratio:

9/16 yellow, round. (Y_R_)

3/16 yellow wrinkled. (Y_rr)

3/16 green, round. (yyR_)

1/16 green, wrinkled (yyrr)

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The product rule: the probability of two events both happening isthe product of the probabilities of independent events

Multiplication rule: The probability (p) of both A and B happening = p(AB)p(AB)=p(A) X p(B). (multiply probability of each event)

In Genetics Phenotypic ratios If AaBbDd x AaBbDd Then p(aabbdd) = p(aa) X p(bb) X p(dd) =1/4 X 1/4 X 1/4 p(A_B_dd)=3/4 X 3/4 X ¼

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The Addition Rule: the probability that multiple exclusive events occur (OR) is the sum of the probability of the independent event. (Add probability of each event).

Example: What is the probability that the seeds will be round OR the seeds will be yellow?

p(P or G) = p(P) + p(G)

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Not all alleles are either dominant or recessive.

Incomplete dominance: When the heterozygote is intermediate between both homozygotes.

Phenotypic and genotypic ratios in monohybrid cross are both 1:2:1 because heterozygotes have separate phenotypes

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Codominance: visible phenotype of more than one allele. Many genes have more than two alleles and an example is blood type!

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Polygenic inheritance:

More than one gene may affect a single trait. (contributes to a single characteristic)

Results in a spectrum of phenotypes.

Examples: height, skin color, hair color

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Pleiotrophy: A single gene may affect more than onetrait. (some genes can influence many traits - these genes are said to be pleiotropic) Proof: Marfan syndrom.

Individuals exhibit a wide array of phenotypic effects: increased height, limb length and severe heart problems.

Other factors can affect phenotype such as age, nutrition, and environment factors

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Pedigrees: following a trait through a family tree (usually disease)

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Symbols – square for males, circles for females.

Filled/shaded symbols for affected individuals.

Partially filled/shaded symbols for carriers (often heterozygotes).

Drawing a pedigree- Horizontal Lines between two symbols indicate parents.

Vertical lines indicate progeny from parents.

Each row represents a new generation.

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Autosomal recessive traits

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Phenotype due to an autosomal recessive allele.

Individual with the trait must be homozygous.

Heterozygous carriers have the allele and transmit it without exhibiting the phenotype

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Autosomal dominant trait

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Expressed in any individual with at least one dominant allele.

Individuals who are homozygous or heterzygous for the trait with display the dominant phenotype.

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Law of Segregation: the two alleles for each gene separate during gamete formation

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Law of Independent Assortment: Alleles of genes on non-homologous chromosomes assort independently during gamete formation.

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Gene linkage:

The law of independent assortment does not applyto traits on the same chromosome. Traits on the same chromosome can be separated by recombination between the genes. The closer two genes are, the lower the frequency of recombination (ie. the chance that they will be separate intodifferent gametes) and more likely will be inherited together

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The highest possible recombination frequency is 50%.

When genes are very far apart or on separatechromosomes.

If traits are always inherited together the recombination frequency is 0% - Only occurs in cases where the genes are very close together or overlapping

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Sex-linked genes

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Found on either X or Y chromosomes.

Y-linked genes are not required for life, primarily expressed in testes.

Transmission of sex-linked genes: X-linked recessive diseases will be found more often in men.

Men only have one X chromosome, so recessiveallele is expressed.

In woman, must have 2 recessive allele X-chromosomes to see disease

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X-inactivation

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To avoid over-expression of X-linked genes, females inactivate one copy of the X chromosome. (dose of x genes is the same in females and males).

Inactivated form is called Barr body (compact objects within nucleus).

Selection of which copy to inactivate is randomfrom one cell to another.

Inactivation occurs by addition of methyl groups to A chromosomes (DNA methylation)

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Is the trait autosomal or sex-linked?

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If a trait appears equally often in males and females, it is likely to be autosomal. If males are much more likely to have the trait, it is usually X-linked.

Hemophilia and color blindness are examples of X-linked traits resulting from a recessive allele

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Genome size:

Bacteria + Archara: 1-6 Mb (million base pairs)

Eureka genomes are larger

General rule: There is no true relationship between genome size or gene density and organism phenotype

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Gene Density: In eukaryotic genomes, most of DNA does not code for protein or known RNA molecules.

Humans have 10000 times more noncoding DNA than bacteria

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Prokaryotes: Most DNA codes for protein.

Eukaryotes: Only 1.5% codes for proetins, rRNA or tRNA

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Most non-coding DNA is made up of introns, gene-related regulatory sequences (enhancers, promoters and the UTRs regions), Unique non-coding DNA (pseudogenes which are former genes that no longer make proteins), repetitive DNA such as telomeres and centromeres

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Transposable genetic elements are not really genes, they move over organisms, generations and can have recombination in meiosis

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Regions of DNA that can move a copy of themselves to another location within the genome. sometimes called jumping genes and there are two types:

Transposons (DNA intermediate) and retrotransposons (RNA intermediate).

Can lead to incorrect recombination events

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Transposoms: move within a genome by means of a DNA intermediate. They copy-and-paste their DNA to a new location (leaves a copy behind)

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Retrotransposoms encode for RNA, whcih is reverse transcribed into DNA which is inserted into a new location on the genome.

1. make use of an RNA intermediate.

2. Synthesis of a single-stranded RNA intermediate.

3. RNA transcriptase to DNA stands.

4. mobile copy of retrotransposon

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Multiple copies of a transposon may lead to incorrect recombination or crossing over events.

Transposons may have arisen from ancestral viral genomes that incorporated gene families

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Gene Families: Unequal crossing over leads to gene duplication or may create a pseudogene. Duplicated gene can mutate into a new gene.

Could lose genes, could occur in non-homologous chromosomes and recombination between non-homologous chromosomes.

Matching based on similar sequences and occurs in the wrong spot.