Exam 2

Lecture 14: Mutations

Defects in DNA that change gene function

Mutations can be from three different things: ***

1. change in template for rRNA or tRNA

2. change in coding region for protein

3. change in recognition sites for protein binding

Homologous genes

ancestral gene. Humans and other animals have genes that evolved from this ancestral gene.

Frameshift mutation ***

loss or gains of anything other than 3ⁿnucleotides

Frameshift causes... ***

extensive missense. It shifts the reading frame.

How does change in recognition sites for protein binding cause mutation?

DNA change in operator might block binding of repressor protein. It screws up the expression of the genes, not only the coating.

Mutations can change the...

promoter, regions that bind transcription factors. Ex: splicesome binding

Big mutations rearrange chromosomes: 1)

Can recombine coding regions of different genes-exon "shuffling" to make new gene

Function is not always changed by coating region, but mostly by

expression

Marty Chalfie, Roger Tsien, Osamu Shimomura

Fuse enhancer promoter DNA to coding regions of Green Flourescent Protein (GFP) from jellyfish. Get regional expression of GFP.

Homology

similarity by descent from common ancestor

Bioinformatics

Important field, computer predictions of the sequence of DNA

How do cells generate variation in heredity needed for variation of evolution?

Mutations and individuals can swap DNA

How can individuals swap DNA?

Eukaryotes-mostly via sex

Prokaryotes-not real sex, but can exchange parts of DNA

Why swap DNA?

b/c of environment: selection pressure, need variation, swapping DNA gives an advantage

Prokaryotic cell division

fission into 2 daughter cells. replicate circular chromosome DNA. Only differences are from mutations or errors.

Bacteria exchange parts of DNA 3 different ways:

transformation, conjugation, or transduction

transformation ***

Take up DNA from outside and incorporate into chromosome

What is an example of transformation?

Griffith's experiments with Smooth and rough pneumonia bacteria

What do you need for transformation?

Cell surface proteins and transport proteins for uptake of DNA (DNA is polar and won't go through lipid bilayer by itself).

Conjugation ***

Direct transfer of DNA from another bacterium

How is DNA passed in conjugation?

long extensions of membrane called pili. This makes a bridge.

Conjugation can pass plasmids:

small circular DNA, not part of the chromosome

Other kinds of conjugations can pass part of...

chromosome. Can recombine DNA between plasmids and chromosomes

Plasmids passed during conjugation can carry...

valuable info. Ex. R plasmids carry mutant genes that make bacteria resistant to antibiotic drugs. Huge medical problem.

Transduction ***

transfer DNA via a bacterial virus (bacteriophage or phage)

virus

infectious agent smaller than bacterium. reproduce in host. contain mostly protein and nucleic acids.

Capsid

protein that wraps up a viruses nucleic acid, sometimes with membrane lipid envelope

Uses host cell to make more virus in the...

lytic cycle

Ribozyme

perform enzyme-like catalytic functions

Lecture 15: What does Viral DNA do?

takes over DNA replication and make viral mRNA. Protein and virus assemble together to make macromolecular complex

alternative lysogenic life cycle ***

virus DNA recombines into and out of host chromosome. Like a storage stage for the virus; not making more virus.

transduction

(accidental) Virus takes fragment of bacterial DNA from old host, incorporates it into chromosome of new host.

species

group of physically similar organisms that can interbreed in nature

Are there seperate species in bacteria?

Yes and sometimes. It''s possible to make single stranded DNA or double stranded DNA.

Bacterial genomes are...

mosaics

Viruses for Eukaryotic hosts

Can be RNA or DNA, double stranded or single.

Retrovirus RNA is converted to DNA by...

Reverse transcriptase. ex: HIV virus, causes AIDS

Viral diseases

can take over and disrupt tissues by producing more virus. can import and abnormally express genes from humans and others.

Occasional viruses pick up...

host DNA

Difficulties with primordial soup

synthesis problems, clutter and diffusion problems, chirality (most sugars are right handed, most AA are left handed)

chiral

mirror images. cannot be superimposed

Miller's Freeze experiment ***

can create organic molecules. they can convert molecules to one chiral form.

What could you get self-replicating polymers with?

RNA

Lecture 16: RNA can be... ***

an enzyme and a template.

"RNA World" hypothesis

RNA is the only thing that does this. Acts like ribozymes

Two step self-replication

one acts like template for complimentary strand. The complimentary strand makes original enzymes that make the process more efficient.

Chemical natural selection

ribozyme replication not accurate. Select for ribozyme variants that are better at linking nucleotides.

This is better with RNA because

RNA is better at linking phosphate backbone. Made efficient by picking enzymes that make more of themselves.

Ancient cells?

Have short polypeptide-can bind to selective DNA or RNA sequence. RNA acted as a template for forming proteins and the protein then aided in replication of RNA

Modern hypothesis

RNA does not self replicate. DNA does. DNA is much more stable then RNA, better storage of nucleotides

Primitive membranes

fatty acid membranes, instead of phospholipid membranes. Much more permeable. No active transport of diffusion.

Order of process ***

DNA to RNA to protein

Eukaryotes

have membrane bound organelles including nucleus containing the DNA

Eukaryotes made metabolic processes to be...

more efficient. Greater complexity=specialized. Allows cells to get bigger.

Semi autonomous organelles

act like small organisms. capable of replicating and dividing. can move. remnants of bacteria

DNA to RNA to proteins: Pro vs. Eu

Pro is all together

Eu is all in different parts

Chromatin ***

strands of chromosomes

nucleoulus ***

site of rRNA synthesis from chromosomes, assembly of large and small ribosomal subunits. Assemble rRNA and proteins

Nuclear envelope

two lipid bilayers. (2 membranes for each lipid bilayer)

Can mRNA pass through a lipid bilayer?

No.

Can proteins pass through a lipid bilayer?

It depends of kind of protein. Ones that have hydrophilic and hydrophobic parts are hard to get completely through

Nuclear pores

complex of proteins, filter. active transport pore. in inner and outer nuclear envelopes

Nuclear "pore"

active transport complex of about 30 kinds of proteins. selectively recognizes proteins through lock and key

mRNA sorting ***

binds adaptor and export proteins that interact with pores. Machine recognizes specific proteins

What do you need to recognize adaptors?

5' cap, poly A tail and splicing

protein sorting by signal sequence

AA sequence that allows binding to nuclear import protein by lock and key

Lecture 17: Endoplasmic Reticulum

Network of membrane enclosed tubes, discs

rough er vs. smooth er

rough has ribosomes(translates proteins) and smooth does not

ER membrane is continuous with

the outer nuclear envelope

Smooth ER ***

no protein synthesis. Site of phospholipid and steroid (cholesterol) synthesis. Also a process storage (of Ca²⁺) and others.

The endomembrane system traffics...

transmembrane proteins that are exported, or secreted, from the cell

What do the proteins do that were made by rough ER?

Either make transmembrane proteins or get proteins out of the cell by exocytosis

"Pulse-Chase" experiment with radioactive amino acid

Use cell that secretes lots of protein

Pulse

add radioactive AA to tag something for a short period of time

Chase

Add lots of non-radioactive AA

What did this verify? ***

movement of radioactive proteins from the rough ER to the Golgi and eventually outside of the cell

ER signal sequence

allows insertion through ER membrane.ribosomes are slightly attached to the membrane and allow protein to float around inside of ER

Secreted proteins move from ER to...

golgi apparatus

Golgi apparatus

stack of flattened membrane bound discs. There are diff enzymes in diff stacks for processing proteins

Processing of proteins

some cleaved to make smaller polypeptides, some linked to other proteins, and some linked to other molecules, like carbohydrates

Glycosylation ***

when proteins covalentely link to carbohydrates

central vacuole

in plant and fungal cells for digestion, processing and storage. membrane wrapped

Vesicle formation and trafficking

can fuse with or pinch off from cell membrane or intracellular membranes. endo, pinch and bring in. exo, fuse and bring out

How are proteins secreted?

via transport vesicles in the ER and secretory vesicles in the golgi

Trafficking of vesicles

end in "somes." endosomes, exosomes, etc

lysosomes ***

contain digestive enzymes and reduce AA

What is the correct order for protein secretion? ***

ER, transport vesicle, Golgi, secretory vesicle

What happens to the lipids in a secretory vesicle?

They wind up in the cell membrane

Cytoskeleton

intracellular rods and fibers that support the cell

Movement of vesicles

Attach to cytoskeleton and move with motor proteins. (change shape, grab vesicle and walk along the cytoskeleton)

Prokaryotes vs. eu.

Pro-diffusion would work

Eu-diffusion won't work because they're bigger

Microtubules

thickest diameter

microfilaments

finest diameter

intermediate filaments

intermediate. stable "girders."

What is the major role of these?

to move things inside and move proteins around in the cell

More on microtubules ***

helical polymer made of individual dimers of alpha and beta tubulin proteins. (polymer made of proteins). Dimer is a polymer of 2. Can be stable "girders" but can also move things

Lecture 18: More about intermediate filaments

mostly stuctural meshwork under membranes. many diff types. Same family as nuclear laminin (thick cloth). gives shape

Microtubules can move things three different ways: ***

1)push or pull things by rapid lengthening or shortening

2)using attached motor proteins

3) slide past each other via motor proteins

In animal cells, microtubules often emerge from

centriole in the centrosome-made in microtubules, made of 2 centrioles.

centrosome ***

microtubule organizing center. two cylinders, each with a ring of 9 microtubule "triplets". 1 centrosome in animal cells

Movement by motor proteins: kinesin

"walks" vesicles along microtubule. Require E. E stored in phosphate bonds in ATP

Sliding microtubules move

cilia-short and many- and flagella-long and few. Fine bendable projections from cell, enclosed by cell membrane.

How do the cilia and flagella work?

they can either move by pushing water or stay still in membrane and create a flow for other things to move

Cilia ***

contain mictotubules organized into ring- 9 pairs in ring plus 2 central("9+2") Pairs connected by dynein=motor protein

More about microfilaments

narrow, double helix made of actin proteins

How do microfilaments move? ***

1) shortened or lengthened by removal or addition of actin

2) slid pass each other with motor proteins=myosins

Both drive actively changing extensions of cell membrane

end with "podia" blobby=pseudopodia. fine=filopodia.

What does the movement of microfilaments do? ***

shortens muscles, other changes in cell shape and cytoplasmic "streaming" in plants (circulate cytoplasm)

Does endocytosis require energy?

Yes. any shape change needs E.

Does waving cilia require E?

Yes

Semi-autonomous organelles

mitochondria and chloroplasts. where most of the ATP comes from in eukaryotic cells

Mitochondria

produce chemical E from sugars and other compounds. machine for making ATP. lots in cytoplasm. has 2 membranes, inner and outer

chloroplast

in plants and some protists. site for photosynthesis=site for production of E from sunlight. also has 2 membranes

"Semi-autonomous?" ***

mito and chloro contain some of their own DNA, mRNA and ribosomes. They reproduce in cells by fission. Resemble free-living bacteria. have transcription and translation

symbiosis

organisms living together in direct and intimate contact. endosymbiont theory

Lecture 19: Win win situation

endosymbionts get nutrients from the host cell. mitochondria, like endosymbionts, make ATP for host cell.

Bacteria has diff kinds of metabolism

pro has more than eu but eu is good at specialization

Mitrochondria produce ATP in the

2nd and 3rd steps of respiration

C₆H₁₂O₆(glucose) + 6O_2------->6CO₂ + 6H2O + ATP (energy)

spontaneous, but you'd have to wait a long long time

Respiration of the monosaccharide glucose via

a series of enzyme-catalyzed reactions. this lowers the Ea for the reaction to make it go

Glycolysis ***

in cytoplasm(not in mitochondria). 6 carbon glucose lysed into 2 3-carbon pyruvates, get ATPs and electrons

Pyruvate then enters the...

Kreb (Citric Acid) cycle in mitochondrial matrix

Kreb Cycle

Broken into CO2's, get ATPs and electrons

Oxidative phosphorylation

in mitochondrial matrix, electrons + O2 ---> ATP

Reduced ***

atom that gains electrons (reduces charge)

Oxidized

atom that loses electrons (gains charge)

Reduction-Oxidation (REDOX) reaction

when one is reduced and one is oxidized. A + B ----> A- + B+. Product has more electrons than what it started with

Electron carriers are reduced by

high energy electrons

NAD+ + 2e- + H+ ----> NADH

FAD + 2H+ + 2e- ---->FADH2

NADP+ + H+ + 2e- ----> NADPH

What does this do?

Grabs electrons and stores in high energy state or builds intermediates

Every step in glycolysis and Kreb cycle is..

catalyzed by a seperate protein enzyme

More about glycolysis

1) initial steps require phosphate from ATP

2) More ATP is produced than initially used

3) electrons are captured in NADH

Yields: 2ATP + 2NADH

Could glycolysis occur if there was no ATP?

No

Pyruvate

organic, polar, needs transportation protein

After Pyruvate enters the mitochondrion matrix...

3 carbon pyruvate loses 1 carbon as CO2 as it binds to Coenzyme A to make Acetyl-coA.

Acetyl CoA adds its...

2 carbons to a 4 carbon oxaloacetate, making a 6 carbon citric acid (citrate)

The cycle then takes the 6 carbon and

produces the 4 carbon again. Two carbons are lost as CO2 (needs to run twice for one glucose)

Yield of Kreb cycle: ***

1 ATP, 3 NADH, 1 FADH2

Glycolysis: glucose (6C) --->

2 pyruvates (3Cx2), yields 2ATP, 2NADH

Binding Coenzyme A (x2): 2 pyruvates--->

2 acetyl coa's (2C) + 2CO2, yields 2NADH

Kreb cycle (x2): 2 acetyl coA's----->

4CO2, yields 2 ATP, 6 NADH, 2 FADH2.

Per glucose, glycolysis and Kreb cycle give...

2 ATP Each, 4 total (pathetic)

But, convert electrons to energy via

Oxidative phosphorylation

substrate level phosphorylation

glycolysis and kreb cycle make ATP by taking phosphate from high energy subtrate molecule and binding ATP.

Lecture 20: 2 parts of oxidative phosphorylation ***

electron transport chain and ATP synthase

Electron transport chain

uses electrons to pump H+ into space between mitochondrial membranes (H+ needs to be pumped because it's too polar to diffuse)

Where are the pumps?

in the inner membrane. uses energy from electrons. Three different pumps in a row. Each grab electrons in diff. E states. O2 grabs electrons at the end to make H2O.

Electrons in the chain are often carried by ***

metal atoms, iron or copper, surrounded by protein

Heme

iron-containing ring. similar to heme that carries O2 in blood. stores E. imbedded in transport proteins.

Second step is ATP synthase

uses diffusion of H+ back across membrane to make ATP. uses a turbine (backwards pump). goes from high concentration of H+ to low concentration

Inner and outer membrane

acidic environment because of H+

How efficient?

Total per glucose is about 32-38 ATP. 40% efficient. rest of E is lost as heat.

Evolution? Some prokaryotes have electron transport chains. Why?

Reduces acidity of the cytoplasm and drives co-transport (get H+ concentration high on outside to drive other molecules in)

What if there is no oxygen? ***

The electron transport chain will quickly stop pumping H+ ions and the cell will start to run out of NAD+.

What will happen to glycolysis and Kreb cycle if there is no oxygen?

they will quickly shut down

Aerobic=

Anaerobic=

with oxygen

without oxygen

If there is no NAD+,

no glycolysis or Kreb cycle. (There is a limited pool of NAD+)

What is the solution?

Add steps to regain NAD+ from NADH by fermentation

Fermentation

to get NAD+ back if there in no O2.

What are the two types of fermentation? ***

Lactic acid, used by us. pyruvate---> lactate. Needs 2NADH and get 2 NAD+.

Ethanol fermentation, used by yeast. Pyruvate---> take C off to get CO2.

Can the products of fermentation enter the Kreb cycle?

No. No NADH for oxidative phosphorylation. You do get 2 ATP per glucose with Fermentation

Lecture 21: Respiration can use _____ feedback... ***

negative, for allosteric control of enzyme activity. EX: ATP or citric acid inhibit glycolysis. keep cell at homeostasis. Too much ATP slows it down

Where do animals and fungi get E?

From many organic molecules, not just glucose. From eating other animals and fungi and photosynthesis in plants

A tree gets most of its non-water mass from

the atmosphere

chloroplasts

surrounded by 2 membranes

stroma ***

space inside inner membrane

thlakoids ***

membrane-bound discs in stroma. They are stacked into grana

Light reactions ***

Use light energy to make ATP, electrons in NADPH and O2. happens in the thylakoid membranes.

Dark reactions ***

use ATP, electrons in NADPH and CO2 to make sugar. happens in the stroma

Calvin cycle

Dark reactions. Carbon fixation, reduction, and regeneration.

Carbon fixation ***

3 ribulose biphophate (RuBP) + 3 CO2 ---> 6 3 carbon chains (short-lived), using Rubisco enzyme

Reduction ***

produces 6 G3P's, 1 of which is removed from the cycle and is used to make sugars.

Regeneration of RuBP ***

Remaining 5 G3Ps + ATP regenerate 3 5-carbon RuBP's (starting Material)

How many times do you need to run? ***

Three times to harvest an organic molecule. Use 9 ATP's, and 6 NADPH's. get 3 CO2's

Pigments absorb

light energy. Chlorophyll a and b. Magnesium containing ring. Light excited electrons in ring to higher, unstable energy.

Carotenoids

accessory pigments. Absorb diff. wavelengths of light, protect chlorophylls from bleaching. This is the color you can see in leaves because the chloroplasts are dying

Pigments in photosystems

use light to excite and donate electrons to electron acceptor. Water is the electron donor.

Photosystem II is first

gives high energy electrons to H+ pumping electron transport chain.

What does Photosystem II do? ***

Pumps H+ into the thylakoid and uses the H+ gradient to drive ATP synthase. Again, uses electrons from H2O.

Then Photosystem I

get and excites electrons from H+ pumping electron transport chain.

The excited electrons can go one of two directions: ***

1) donated to NADP+ to make NADPH

2) Go back to H+ pumping electron transport chain to make ATP

Choice after photosystem I creates two different schemes. 1) Non cyclic (the Z scheme) ***

makes both ATP via H+ pumps and NADH after PSI. Creates NADPH

2) Cyclic ***

Makes ATP via H+ pumps, but no NADPH

Lecture 22: Why would you chose to do the cyclic scheme instead of the non-cyclic? ***

The non-cyclic scheme makes about equal amounts of NADPH and ATP. The calvin cycle needs 9 ATPs and 6 NADPH. Use the calvin cycle to make more ATP

Plants get almost all their energy from

sunlight

plants get almost all their carbon from

CO2

Differences in: carbon source-

Organic(heterotroph) or inorganic(autotroph)

Differences in: energy source

molecules(chemotroph) or sunlight(phototroph)

Plants get almost all their electrons from

H2O

Electron donors and acceptors: Plants- ***

H2O is donor and oxygen is acceptor

In animals and fungi ***

Reduced organic molecules is the donor and oxygen is the acceptor

Electron donors and acceptors in bacteria... ***

have lots of possiblities, eu. are limited. this is why pro. can live in diff. environments

protists

single celled eu. first eu. to evolve

colony

collection of individuals. some protists and pros. form colonies

"true" mulitcellular life

fungi, plants and animals

Plants and fungi have

cell walls outside cell membrane. allows cells to stick together. There are breaks in the cell walls that allow for direct contact between cells

Cell wall is made of

polysaccharides and proteins

Fungi

single celled or multicellular. Cell wall is made of chitin polysaccharide.

hyphae

"cells" in long tubes

septa

cells often seperated by wall and membrane by these

Pores in walls

connects membranes, big enough for nuclei, organelles and metabolites to pass through

syncytium

fused cells

Plants

cell walls mostly made of cellulose polysaccharide.

plasmodesmata ***

pores in cell walls that connect cell membranes. Can pass RNA, proteins, nucleic acids and small organic molecules, but too small for nuclei and organelles

What does plasmodesmata connect? ***

The smooth ER of two cells

Animals

no cell was, but jelly-like extracellular matrix. mixture of proteins and polysaccarides. flexible

Collagen

long protein fibers, connective tissure

chondroitin sulfate

large polysaccharide. make jelly coat

what happens when you age?

extracellular matrix begins to break down

Most animal cells are not_____, but can be connected by ***

syncytial, gap junctions: small pores between some(not all) animal cells. Ex: sponges, muscles.

What can pass though gap junctions? ***

Monomer, ions, small monosaccharides, not macromolecules

Animal cells also adhere using

Cell Adhesion Molecules (CAMs) in membranes. Protein with carbohydrate in membrane. Use lock and key binding to protein on adjacent cell

Binding: homophilic-

bind cell adhesion molecule to identical molecule on other cell

Binding: heterophilic-

bind to different molecule

binding also by...

indirect binding by linker molecule

Lecture 23: Animal cells can be arranged in many different ways. Connective tissue:

cells relatively loose

Epithelium

Tightly attached cells organized into flat sheet. ex: organs and skin

Epithelia are

polarized. Two sides: apical and basal

Basal Lamina

extracellular matrix that underlies the basal side (collagen)

Junctions between epithelial cells

specialized CAMs (homophilic adhesion molecules) at each. ex: Cadherin. Little room for diffusion, seals it up

Junctions from epithelial cells to extracellular matrix

EX. connection to basal lamina uses integrin: binds to cytoskeleton and collagen

How do cells signal?

1) cytoplasmic connections

2) without cytoplasmic connections

Via cytoplasmic connections

syncytieal cells can pass everything. Plants use plasmodesmata and animals use gap junctions (Take a long time to signal)

Signals without cytoplasmic connections: Signaling molecule= ***

ligand. Either membrane bound (short range) or secreted (short or long range).

Signal binds and activates specific

receptor by changing it's shape

What is a diffusible signal that can go through membranes? ***

Steroids. Hydrophilic and hydrophobic parts. lipids, testosterone, and estogen, etc. All molecules can signal

Steroid transduction

steroid binds receptor protein in cytoplasm and nucleus.

Receptor-steroid complex is a ***

transcription factor that binds to DNA. It turns on transcription of genes with matching enhancer DNA

Other than lipids and gasses,

most signal cannot diffuse through lipid bilayer. ex. proteing and AA. Receptor is usually transmembrane protein.

Range within cell: whole cell example:

signals that turn on (or turn off) transcription

Range within cell: local:

Signal affects part of cell near receptor. EX. Signal changes assembly of nearby microfilaments or response to food.

No amplification if... ***

activated molecule only activated one target molecule (protein-protein binding)

Amplification if... ***

activated moleucule is an enzyme

Example of no amplification

Activated G protein binds and activates single target protein

Activated enzymes amplify signal

protein kinases: enzymes that add phosphates to specific proteins, activating or inactivating them.

Cascades of kinases can... ***

amplify weak signals

Positive feedback ***

can amplify or lengthen time of signal (Goes back to receptor and makes more)

Negative feedback ***

can decrease or shorten time of signal (Doesn't make more receptor). Nervous system and light sensors

Lecture 24: Steroid summary

go through membranes, activates cytoplasmic receptor that becomes a transcription factor

Some signal transduction pathways use...

small, non protein messengers=second messengers. inside the cell.

big examples of second messengers ***

lipids from membrane lipids, cyclic AMP (cAMP) from ATP, and CA2+ from outside cell or storage in ER

cAMP

major component of transduction pathways. ATP---> cAMP + 2P. cAMP stimulates protein kinase.

can a second messenger also be a signal between cells? ***

Yes

Second messengers through gap junctions?

Yes. Ca2+ wave via gap junctions and positive feedback.

Do all multicellular eukaryotes have sexual reproduction?

NO

Asexual Reproduction

From single parent. in pro. or multicellular eu.

Sexual reproduction

From two different parents, eggs and sperm of germ line

Eggs are...

immobile and usually larger. Most contain yolk that serve as nutrients (we don't have yolk because of placenta)

sperm are...

mobile and usually smaller. swims by flagellum. DNA in nucleus. Big mitochondria

Fertilization

combining genetic info. sperm membrane fuses with egg membrane. sperm has enzymes that digest extracellular matrix of egg.

First steps, fertilized egg... ***

divides to form embryo

Cleavage

first divisions. can occur without growth, forms blastula

blastula

many cells indistinguished from one another.

Cells mover to make germ layers in

gastrulation in the gastrula

ectoderm ***

outermost, makes skin, nervous system

mesoderm ***

middle, makes muscles and internal organs

endoderm ***

innermost, makes digestive system (stomach, esophagus, etc.)

Organogenesis

Each germ layer subdivides into specific organs (skin brain heart, liver, muscles, intestines, etc)

Organogenesis: neurulation: ***

formation of central nervous system in vertebrates.

in neurulation, the ectoderm ***

pinches off a long tube=neural tube. the neural tube forms brain and spinal cord.

Do differentiated cells have different DNA? ***

No, mostly have the same DNA

Differentiated cells all contain the same ***

DNA

cloning

making an embryo that contains the DNA from a differentiated adult cell

If cell is limited,

If cell allows for making of all cell types,

DNA is lost,

DNA is not lost

Process of cloning

take differentiaeted cell and take out nucleus, take unfertilized egg and take nucleus out. Sub nucleus into egg.

what makes differentiated cell diff? ***

Same DNA, but diff. gene expression (mRNA and protein).

Why are they diff?

Diff signals from diff parts of embryo or diff. determinants inherited during cell division

Lecture 25: Signals form one set of cells can change differentiation of adjacent cells example

Dorsal mesoderm from amphibians signals to dorsal ectoderm to make neural tube. cells incorporated into host by induction

Cytoplasmic determinant

molecule inherited from one parent cell by only one daughter cell, makes that cell diff.

Example of cytoplasmic determinant ***

gray crescent in frog embryo. if daughter cell inherits gray crescent, they are normal. if they do not, they only develop belly tissue.

What is a cytoplasmic determinant? ***

Not known yet. Proteins or mRNA

Cytoplasmic determinants vs. cell-cell signaling

most embryos use both

potency ***

can make more than one cell type

Early in development, most cells are.. ***

pluripotent-can make several cell types. ex. stem cells

Later in development,

most cells lose potency, and become determined as a specific cell type

But we retain some stem cells

undetermined cells capable of forming a wide range of tissues in response to signaling

growth ***

change in cell size

proliferation ***

increase in cell number

Synthesis or S phase

DNA replication

Mitotic or M phase

Division

Gap 1 (G1)

period between M and S phases

Gap 2 (G2)

period between S and M phases

Cell cycle checkpoints

control proliferation. 3 big checkpoints

G1 checkpoint ***

cell large enough, nutrients, signals? If it fails, it goes to G0.

G2 checkpoint ***

Happy, DNA duplicated

Example of checkpoint: MPF

complex of two proteins, drives cell through gap checkpoint. spikes at mitosis

The cyclin concentration

Increases as the cell matures

Binds and activates... ***

cyclin dependent kinase (CDK) to create active MPF. allowed to move on to G1

Failure in CDK

can cause cancer. Rb protein normally stops cell cycle at G1

What happens with CDK?

normally inhibits Rb protein. Rb mutation are common. lose inhibitor of checkpoint.

Pro. cell division

circular chromosome. Make a copy of chromosome, divide cell by fission into two daughter cells

eu. chromosomes

linear DNA in a complex of proteins. Different chromosomes contain genes.

What is the order for a cell based on pluri and totipotent? ***

stem to pluripotent to determined

Every cell is totipotent untill... ***

it gets signals from other cells

In gastrulation, cells are

In organogenesis, cells are

pluripotent

determined

T/F. The egg differentiates into 3 germ layers

False, the blastula does

The egg contains yolk and is mobile

F, sperm is mobile

Can Ca2+ diffuse through the membrane>

No, but can be transported

Lecture 26: Mitosis ***

Daughter cells have same DNA as parent

Meiosis ***

Daughter cells have half the DNA of the parent before fertilization

Sister chromatids

DNA is not joined, proteins are joined. Joined at the centromere=center of the chromosome

Mitosis

Seperate sister chromatids to make seperate chrmomosomes

The center of a chromosome is a ***

centromere

A chromatid has ***

one double helix

A chromosome has ***

it depends. 1 helix before replication and 2 helixes after.

Chromatids ***

double stranded. attache into single chromosome at centromeres, ends are telomeres

Microtubules are organized by ***

centrosome with two centrioles

2 sister chromatids together = ***

1 centromere

Mitotic spindle

arranges and moves chromosomes. Some attach to centromeres others attach to nothing

How does the mitotic spindle work?

kinetochores

Kinetochore

proteins surrounding centromere, control movement by shortening and sliding using motor proteins

What about the nuclear envelope?

Remains in a few protist and yeast, in most eu. it is lost during mitosis and remade after seperation

What happens in G2?

the centrioles are duplicated

Prophase

chromosomes condense, spindle forms, nuclear envelope breaks down

Metaphase

Chromosomes line up along metaphase plate

anaphase

chromatids seperate, move to poles

telophase

reform nuclei

The cell cycle

Interphase (G1, S, G2) 90%

Mitotic phase 10%

cytokinesis

subdivision of the cytoplasm into two cells

Animal cells form...

cleavage furrow. Requires microfilaments and myosin

Cytokinesis is diff if there is a cell wall

Plants form a new membrane from vesicles fusing in the middle of the cell=cell plate

In meiosis, daughter cells have

half the number of chromosomes (and half as much DNA) as the parent

2n

n

diploid

haploid (gametes)

Fertilization combines

haploid gametes to make diploid zygote. Meioses converts diploid cells back to haploid gamete

In animals,

mitosis is only in diploid cells

in other organisms,

haploid cells can undergo mitosis to produce more haploi cells, multicellular haploid stages in life cycle

Diploid cells have pairs of

homologous chromosomes (with exception of sex chromosomes). Homologues contain same genes and transcriptions units

Homologues are not ***

copies. Each is inherited by a diff. parent

Lecture 27: The women have a total of 46 chromosomes. How many homologue pairs do they have? ***

23

The men have 46 chromosomes. How many homologue pairs do the sperm have? ***

0. They are haploid

How many chromosomes do the sperm have? ***

23

Haploid

one of each homologue

diploid

two of each homologue, one from sperm and one from egg

Homologues have... ***

same genes, but can have different versions (alleles)

Different alleles of gene have diff...

coding or regulatory DNA. diff. functions.

Mitosis ***

Seperate sister chromatids (copies) for all chromosomes. You seperate homologous chromosomes

Meiosis

Four haploid cells from one diploid cell via two rounds of cell division

Meiosis I ***

Homologous chromosomes seperate, sister chromatids stay together. Replicated into tetrad

Meiosis II ***

Second division to halve the amount of DNA, no DNA replication, sister chromatids are separate

segregation ***

gametes only get one of two possible alleles

Mendel crossed pea plants because

he could control which ones mated with which. used self pollination. and pea plants had heritable differences

phenotype

the physical traits the individual has

genotype

what genetic info the individual can pass on. Can't see.

Homozygous

both alleles of a gene are identical (AA, aa)

Heterozygous

One of the two alleles of that gene is diff (Aa)

Dominant

control the phenotype even if only one homologue has that allele

Recessive

Control phenotype only if both homologues have that allele

Mendels law of segregation ***

The two alleles in the parent segregate from each other during formation of gametes

Lecture 28: Segregation of alleles during meisosis

homologues go to different cells. They get different versions of the gene.

Dihybird cross

assume that the two genes are on different (non-homologous) chromosomes.

Independent assortment ***

of non homologous chromosomes. have four different combinations in gametes

2ⁿ if n=

number of homologue pairs being considered

with peas

round and yellow are dominant

How do you determine which trait is dominant?

mate homozygotes

Heterozygotic (RrYy) genes on non homologous chromosomes: After replication, metaphase Meiosis I:

RRrr

YYyy

These are sister chromatids and need to have the same version of the allele

For punnet squares

put all four combos on top and sides. they need to be on seperate chromosomes

one complication with mendelian inheritance

what if a gene is on a sex chromosome (sex linked)

Autosomes ***

not sex chromosomes

sex chromosomes ***

not paired, non homologous. In human, the X is larger and the Y is smaller. XX female, XY male

sex linked

genes on sex chromosomes. no versions of x linked gene on y chromosome, vice versa

This is why

males are more likely to get a disease that is carried on the x chromosome because they don't have another x chromosome (like females) to help it out.

X linked diseases in humans ***

320. hemophilia, color and night blindness, muscular dystrophy, high blood pressure

baldness

not sex linked, but sex influenced

Barr bodies ***

inactive/condensed X chromosomes. become inactive at blastula stage. Random X chromosome inactivation blocks transcription and creates genetic mosaic.

Lecture 29: Incomplete dominance: ***

Heterozygote has phenotype that is intermediate between that of homozygotes. neither are dominant. Ex: pink flowers

co-dominance ***

different alleles give different dominant traits. Get both traits. EX: blood groups-diff carbs on blood cells

Blood example ***

A can't get B or AB, but can get O

Things can get complicated when...

different genes control the same phenotype. EX: mouse coat color is controlled by B and C, c wins over b

What is two genes are on the same chromosome? ***

lots of genes on chromosomes, physically linked to each other. Thomas Hunt Morgan

If genes are on the same chromosome..

show heterozygotes

b+vg+

b vg

Crossing over ***

recombines parts of homologous chromosomes. Meiosis I=tetrad from prophase and metaphase

Chiasma ***

different arms can recombine here. adds more variability to offspring

Male flies

can't do crossing over

Frequency of crossing over is determined by...

distance between genes

Between adjacent genes, ***

crossing over rarely occurs

Between distant genes, ***

crossing commonly occurs

Distance in centimorgans

% of offspring with non parental genotype

Nondisjunction ***

errors in chromosome assortment during meiosis

Genes in mitochondria and chloroplasts

sperm do not donate organelles, so purely inherited maternally

Imprinting ***

reversible change in gene expression (transcription) passed on to offspring

Prions ***

self replicating protein shape. Some shapes cause disease, others don't

Exam 2

Biology 151 with Blair at University of Wisconsin - Madison

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