CELL BIO FINAL

Chromatin consists of__ and __.

DNA and associated proteins

The primary structure of a protein includes

peptide bonds

Enzymes work with at least 3 mechanisms. Which of the following is NOT a mechanism by which enzymes function?


1. putting reactants in close proximity to each other
2. altering the free energy (deltaG) of the reaction
3. altering the immediate environment of the reactants to promote reactant interactions
4. orienting the reactants so they are positioned to favor the transition state
5. lowering the activation energy

altering the free energy (deltaG) of the reaction

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Which of the following is FALSE about chaperone proteins?


1. they assist protein folding by helping the folding process follow the most energetically favorable pathway
2. they can isolate proteins from other components of the cells until folding is complete
3. they can interact with unfolded proteins in a way that changes the final fold of the protein
4. they help streamline the protein-folding process by making it a more efficient and reliable process inside the cell
5. all of the above are true statements about chaperone proteins

they can interact with unfolded proteins in a way that changes the final fold of the protein

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The potential energy stored in high-energy bonds is commonly released when the bonds are split by the addition of ______ in a process called _______.

**water; hydrolysis**

DNA polymerase catalyzes the joining of a nucleotide to a growing DNA strand. This process can only proceed in the _______ direction because _________.

5’ to 3’; a hydroxyl group is needed

Telomeres serve as caps protecting the ends of linear chromosomes. Which of the following is FALSE regarding the replication of telomeric sequences?

a. The lagging-strand telomeres are not completely replicated by DNA polymerase.

b. Telomeres are made of repeating sequences.

c. Additional repeated sequences are added to the template strand.

d. The leading strand telomeres are not completely replicated by DNA polymerase.

e. all of the above are true

 The leading strand telomeres are not completely replicated by DNA polymerase.

Sometimes, chemical damage to DNA can occur just before DNA replication begins, not giving the repair system enough time to correct the error before the DNA is duplicated. This gives rise to mutation. If the adenosine in the sequence TCAT is depurinated and not repaired, which of the following is the point mutation that you would observe after this segment has undergone two rounds of DNA replication?

 TCT

Which of the following statements is NOT an accurate statement about thymine dimers?

a. Thymine dimers can cause the DNA replication machinery to stall.

b. Thymine dimers are covalent links between thymidines on opposite DNA strands.

c. Prolonged exposure to sunlight causes thymine dimers to form.

d. Repair proteins recognize thymine dimers and cut them out.

e. Thymine dimers are covalent links between thymidines on a single DNA strand.

Thymine dimers are covalent links between thymidines on opposite DNA strands.

A ribosome is made of

rRNA

What directly supplies the energy for ATP synthesis in oxidative phosphorylation?

the proton gradient

From where do the electrons for oxidative phosphorylation originate?

glucose

Glycolysis, pyruvate oxidation, and the citric acid cycle all have this molecule in common as one of their products.

NADH

What is oxidative phosphorylation?

the synthesis of ATP by ATP synthase, using a proton gradient.

Where do the electrons from NADPH go in the Calvin cycle?

They are added to 3PGA

The advantage to the cell of the gradual oxidation of glucose during cellular respiration compared with its combustion to CO2 and H2O in a single step is that

energy can be extracted in usable amounts

What are steps of the Methods of Science in order?

1. observe
2. Inferring
3. hypothesis
4. testing
5. conclusion

Observe

making an observation on a testable thing

inferring

ask further questions about testable thing

hypothesis

form a testable prediction based on observation

testing

conduct an experiment to confirm or deny hypothesis

how should testing be conducted?

conducted with a control and varying amounts of data

what are the two types of experiment

1. controlled experiment
2. correlation study

controlled experiment

in this there is a independent and dependent variable in order to accurately get results. this often has a control and experiment group

independent variable

what we are controlling

dependent variable

what we are watching for

correlation study

study the correlation between two variables in order to see how closely they are linked

statistically significant

a result that is unlikely to have happened by chance

P-value

if the result’s p-value is 0.05 or lower it is deemed significant

hypothesis

a prediction that has to be testable and falsifiable

Theory

an explanation of some aspect of nature that has been well-tested. may describe how a phenomenon happens.

Law

law describes and generalizes how that world works, usually using a mathematical equation

What do membrane receptors do?

Bind to a signal and relay a cellular response.

what are the 4 types of cellular signals

1. endocrine
2. paracrine
3. neuronal
4. contact-dependent

endocrine

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Broadcasting a wide signal that will impact multiple cells. Ex. hormones that travel through the bloodstream and impact many target cells

Paracrine

Produced in one area and that signal will bind to nearby cells

what’s another example for paracrine?

autocrine

What does autocrine do?

self-signaling. The signaling cell will release and will bind to the same cell

neuronal

this is what happens in neurons (nerve cells) and a signaling cell (neurotransmitter) is signaling to a specific target cell at the end of the nerve.

contact dependent

the signaling will come into contact with the target cell

ex. immune system

signal transaction (signaling)

external signals that bind to a receptor and a behavior emerges

how do cells limit which signals they respond to

* Each cell type in our body will produce a limited set of receptors-limiting which signals they can respond to. (surface or inside is specific to the cell)


* The same signal molecule can induce different responses in different target molecules.

what are the two types of receptors

1. Cell surface receptors
2. intercellular receptors

what are the three main classes of cell-surface receptors

* ion-channel-coupled receptors
* g-protein-coupled receptors
* enzyme-couple receptors

what determines whether a cellular response is fast or slow

* Fast pathways indicate that the responses are already there (altered protein function)
* Slow responses indicate gene expression

the functions/steps of an intracellular signaling pathway

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1. Signaling molecule must bind to its receptor which makes a conformational change
2. We must relay (relayed through intracellular proteins) the signal from the receptor to the rest of the pathway.
3. The signal will be transducer and amplified.
4. The signal will be integrated to achieve all the tasks needed
5. Distribute to the appropriate effector proteins.
6. Cellular response

3 main classes of cell-surface receptors

1. ion-channel-coupled receptors
2. G-protein-coupled receptors
3. enzyme-coupled receptors

extracellular signaling

hormones, neurotransmitters, cytokines growth factors call all influence the signaling and are able to bind the receptors to initiate changes in cell function

receptors

they can be inside or on the surface of a cell and receive a signal

intracellular signaling molecules

they bind to receptors which are expressed by their target cells

effector proteins

they can serve as ligands that decrease or increase enzyme activity, cell signaling, and protein function

target-cell responses

they can respond to hormones and display receptors that hormones can bind to

what is feedback

* feedback can be negative or positive.
* Feedback regulation within an intracellular signaling pathway can adjust the response to an extracellular signal
* If y is inducing a positive feedback you will get more y’s, opposite for negative feedback

positive feedback

positive allows the hormones to continue. Activation of more enzymes

negative feedback

negative allows organisms in the body to maintain homeostasis

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what are the 2 types of molecular switches

1. phosphorylation
2. GTP-binding proteins

most common example for phosphorylation

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* Protein kinase
* serine/ threonine kinase
* Tyrosine kinase
* Protein phosphatase
* Breaks off a phosphate group from a protein. (70% us this)

most common example for GTP-binding proteins

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* G-proteins/ g-proteins-coupled receptors. 
* GTP is guanine triphosphate
* Instead of directly hydrolyzing GTP, you exchange GTP and GDP. 
* More of a nucleotide
* In a GTP molecular switch, what does it do? 
* In the off position, there is a GDP attached to it. When a signal comes in the signal exchanges GDP with GTP turning it on. 

what are the 3 classes of cell-surface receptors

1. ion channel receptors
2. G-protein-coupled receptors
3. enzyme-coupled receptors

how do ion channel receptors function

functions like a gated channel. When ions bind to an ion channel it will open. It opens due to a conformational change

how do G-protein-coupled receptors function

when the signaling molecule binds to the receptor it will recruit and activate making the activator receptor bind them to the G protein

what are the three components that make up G-protein-coupled receptors

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1. Inactive receptors (squiggle in the cell membrane) transmembrane protein with multiple membranes
2. G-protein (in its inactive state)
3. Enzyme (in its inactive state

how do enzyme -coupled receptors function

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1. When the signal binds the two domains are brought together and activated. 
2. Sometimes they can phosphorylate each other or other things. 

what are the steps of GPCR signaling

1. Signal binds receptor triggering a conformational change in G protein
2. G protein exchanges GDP for GTP (exchange, not hydrolysis)
3. GTP binding triggers a conformational change
4. Beta/gamma subunits bind to target proteins (relaying the signal) causes molecule to break apart

* The G protein a subunit switches itself off by hydrolyzing its bound GTP to GDP.

How G-proteins-couple receptors work

* Often times they involve secondary messenger molecule
* The cyclic AMP signaling pathway can activate enzymes and turn in genes

Steps for turning on cellular response using G-proteins-couple receptors

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1. GPRC turns on Adenylyl cyclase
2. Adenylyl cyclase produces cyclic AMP (concentration can rapidly increase)
3. Cyclic AMP can induce many kinds of cellular responses

structural characteristics of Intermediate Filaments

rope-like fibers made up of proteins, they are bigger than actin but smaller than microtubules.

functions of Intermediate Filaments

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providing tensile strength. Help the cell sustain/resist mechanical stress, so the cell doesn’t get squished.

structural characteristics of microtubules

largest of cytoskeletal elements, hollow tubes.

functions of microtubules

Act as the highway system of the cell. Separate and organize our chromosomes during mitosis.

structural characteristics of actin filaments

Thin and flexible

function of actin filaments

Not that strong but helps with the shape. Found throughout the cytoplasm. 

where can intermediate filaments be found

* the nuclear envelope
* lamins
* desmosomes
* keratin filaments
* neurofilaments

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what happens if there is a mutation that effects the way intermediate filaments do its job

Progeria: due to a genetic mutation that causes the nuclear lamins to not fold properly which doesn’t provide nuclear shape. The lamin with start collapsing in itself and over time will damage the DNA.

where do microtubules originate in animal cells

centrosome

what is involved in intracellular transport

motor proteins and microtubules

what is flagella powered by

microtubules

what are the individual units that make up microtubules

tubulin dimers

* 2 subunits: alpha and beta

what happens when many dimers come together

they make a protofilament and they are combined to make a tube shape

what will be the negative and positive end of the microtubule

alpha: negative

beta: positive

kinesin

moves toward the positive grade

dyneins

moves toward the negative end

How do motor proteins do their job?

* Each step that they take is a conformational change driven by ATP hydrolysis


* ATP bound to one foot and ADP bound to another. 

what cells undergo cell division

single-cell prokaryotic and eukaryotic, somatic cells and multicellular eukaryotic

under what circumstances do cells divide

* as long as environmental conditions allow


* In multicellular eukaryotes, cell division is under strict control to develop and maintain different subpopulations of cells

Cell cycle divided into 3 parts

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1. Interphase: cell growth and activity (doing its job( if it receives a signal to make a copy of itself it will replicate it dna (longest phase)
2. Nuclear division (mitosis)
3. Division of the cytoplasm (cytokinesis)

mitosis

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(a growth process): divides the replicated DNA equally and precisely, generating daughter cells that are exact genetic copies of the parent cell

meiosis

(a process of sexual reproduction): produces daughter nuclei with half the number of chromosomes of the parental nucleus - the arrangement of genes on chromosomes are different from those in the parent cell. (unique combinations of genes)

Why is it important to compact the chromosomes before we separate them? 

If you have long stringy chromosomes they will get tangled and broken. Compact chromosomes are easier to separate. 

homologous chromosomes

they have the same genes in the same order in the DNA of the chromosomes, but may have different alleles (versions) of a gene

sister chromatids

Sister chromatids are identical copies, you will only have sister chromatids in the DNA replication process

Centromere

the central region that holds together the sister chromatids

chromosome segregation

The equal distribution of chromosomes into each of two daughter nuclei

What are the phases of the cell cycle

1. G1
2. S
3. G2
4. M

what does G1 do in the cell cycle

where the cell is growing and doing its job

* If and only if the cell receives a signal to copy itself will it go into S phase

what does S do in the cell cycle

Where dna is replication (duplication of chromosomes)

* Once replicated it will go to G2

what does G2 the checkpoint do in the cell cycle

proofreading and checking for damage to DNA

If something has happened to the cell the cell will die. 

Steps of mitosis

* Prophase
* pro-metaphase


* Metaphase
* Anaphase
* Telophase
* cytokinesis

Which stage of mitosis is the most variable in terms of time depending on the cell type?

G1, the most variable because some cells will grow and do their job before they get the signal to divide.

prophase

chromosomes condense