Fundamentals of Cellular and Developmental Biology - Exam 1

Are viruses alive?

Sometimes! Viruses cannot replicate on their own but can replicate inside a cell. When they are inside a cell, they can be considered living. However, they are not living when they just exist as virus particles.

Why are cells considered alive?

They maintain organization and structure, harvest energy from the environment, and replicate or reproduce.

Describe the common features of a cell.

- Enclosed by membrane

- Shares most essential components of cell metabolism

- Nucleic acid = genetic material

- Information transcribed into RNA

- RNA translated into proteins

- Proteins are biochemical catalysts

Explain the evolution of cells. Is this certain?

We guess that cells evolved from a common ancestor, but this is not 100% certain. During cell division, mutations may occur. If this mutation has a selective advantage, it will be selected for across many generations, providing diversity.

How do cells differentiate? Is the DNA in the cells the same or different?

Cell differentiation occurs through changes in gene expression, not the actual genetic code. Expression of a gene means converting the information into something functional.

What is confocal microscopy and how does it work? What is the significance of this?

Confocal microscopy uses two pinholes to focus the illumination and detection on a single point in space. This can help detect fluorescent dyes. These dyes are illuminated by one wavelength of light and emit a second wavelength, which is seen. Confocal microscopy allows us to see images without seeing other scattered light.

List the organelles in the eukaryotic cell and their functions.

Nucleus - information store of the cell

Mitochondria - generate usable energy from food

Chloroplasts - capture energy from sun

Internal membrane - create intracellular compartment with different functions

Cytosol - concentrated aqueous gel of large and small molecules

Cytoskeleton - responsible for directed cell movements

What happens to DNA as the cell starts to divide?

DNA condenses and becomes visible

Explain the structure of mitochondria.

Mitochondria are enclosed in two separate membranes. Inner membrane is folded into finger like structures. They have their own DNA. They generate ATP using glycolysis and oxidative phosphorylation.

How were mitochondria formed?

Hypothesized to derive from bacteria through symbiosis. Mitochondria was essentially engulfed by bacteria.

What are chloroplasts and how do they work?

Chloroplasts use sunlight and CO2 to store energy. Contain their own circular DNA. Enclosed in two separate membranes with a third inner membrane forming internal stacks.

Peroxisome

compartment for specialized reactions, like oxidation

Why is the cytoskeleton important?

Required for cell motility, division, and structural organization of cell.

What is the difference between actin filaments, microtubules, and intermediate fillaments?

Thinnest are actin filaments which are used to move things around. Microtubules also move things around and are the thickest filaments. Intermediate filaments do everything else.

What is the significance of microtubules in mitosis?

Condensed chromosomes are separated into daughter cells using mitosis. Chromosomes attach to microtubule spindle at the centromere.

Explain the model organisms and why they are model organisms.

Drosophila - fruit fly, first proof that genes carried on chromosomes, short life span and rapid reproduction

C. elegans - worm with simple body structure and few cells, every cell is mapped and named, genome fully sequenced

Zebrafish - model of vertebrate development, easy and cheap to breed, embryo is clear to allow observation of cells during development

Rodents - mice inbred and rats outbred. use recombinant DNA tech to interrupt (knockout) or alter (transgenic) genes

What are the two organizations that oversee ethical research on humans and animals?

Institutional Animal Use and Care Committee (IACUC)

Institutional Review Board (IRB)

What are human cell lines?

a clonal, immortalized cell that survives and reproduces under laboratory conditions

first was HeLa derived from a patient with cervical cancer

Explain the term similarity implies function in terms of evolution and dendrograms.

organisms with similar features will be closer together evolutionarily, and closer together on the dendrogram

What do all organic compounds contain?

Carbon

What are polymers? Name some examples.

Polymers are large molecules made up of monomers. They include proteins, fats, carbohydrates, and nucleic acids.

True or false. Aqueous reactions take place in lipid environments.

False. They take place in water usually, except when they are in a lipid environment.

Why do hydrogen bonds often form linearly?

When a hydrogen bond donor and acceptor interact, the most strong conformation is when they are in a straight line.

Identify the donor, acceptor, polar covalent bond, hydrogen bond, more electronegative atom, and less electronegative atom.

Acceptor - bottom O

Donor - top O

Polar Covalent - solid

Hydrogen - dotted

More electronegative - O

More electropositive - H

What are the most common hydrogen bond donors in cells?

O and N

List the intramolecular forces and bond types in order of strongest to weakest.

Covalent

Noncovalent ionic

Noncovalent hydrogen

Hydrophobic force

Noncovalent van der Waals

What is recognition in biology? Why is it important?

Recognition is the interaction of complementary shapes in space through usually weak forces. The forces allow tho shapes to recognize each other and bind together. Recognition is fundamental to information transfer, catalytic activity, and cellular structure.

Explain how van der Waals forces work

they are due to transient shift in charges due to fluctuations in distributions of electrons. (iow: when electrons move around, they may create temporary dipoles which are attracted to another dipole on another molecule)

List the four polymers and their monomers

Sugars -> polysaccharides, glycogen, and starch

Fatty acids -> fats and membrane lipids

Amino acids -> Proteins

nucleotides -> nucleic acids

Why are fats not technically considered polymers?

It takes more than one type of molecule to create a full fat polymer

Around what percent of the cell weight is composed of macromolecules? Why is this significant?

24%, macromolecules clearly make up a large portion of the cell.

What are the four was to visualize sugars and what are the two isomeric forms?

Structural formula, chair configuration, ball and stick, space filling

D and L

Name the most common formulas for glucose that are studied in class.

C3H6O3, C5H10O5, C6H12O6

Describe and name the process for making and breaking a glycosidic bond.

Monosaccharides are condensed into disaccharides and give up a water

Disaccharides are hydrolyzed to monosaccharides and consume a water

Describe the structure of fatty acids and the difference between saturated and unsaturated fatty acids.

Unsaturated fatty acids have double bonds, whereas saturated fatty acids don't. This gives unsaturated fatty acids lower melting/boiling points. Fatty acids are a combination of nonpolar carbon chains with a polar head.

What are triacylglycerols? What is their significance?

The are three fatty acids covalentl bound with a glycerol. They are a highly concentrated energy source.

What are phospholipids? What is their significance?

Glycerol bound to two fatty acids. Third OH bound with a phosphate group and small hydrophilic molecule. Amphipathic. Form the lipid bilayer

Explain the structure of an amino acid. Identify the carboxyl group, amino group, alpha carbon, and side chain.

What are the four groups of amino acid side chains? Name an example from each one.

Acidic - aspartic acid

Uncharged polar - asparagine

Nonpolar - alanine

Nonpolar with reactive side chain - cysteine

Explain how peptide bonds are formed. How does this cause directionality in amino acids?

Condense amino with carboxyl groups. There is now a carboxy terminus and amino terminus.

What are nucleotides? What is the difference between ribose and deoxyribose?

nucleotides are 5 carbon rugars with a nitrogenous base and phosphate group. Ribose has an OH group on 2'C but deoxyribose only has an H group.

What is the significance of ATP and GTP/GDP?

ATP important for energy metabolism. GTP and GDP important in signal transduction.

Name the purines and pyrimidines.

Purine - AG

Pyrimidines - CTU

Describe the structure of a polynucleotide. Why is the bond called a phosphodiester bond?

Phosphodiester bond because an acid and alcohol combine to form an ester. Mononucleotides are condensed into polynucleotieds when two phosphates split off the 5' end and the remaining phosphate combines with alcohol group.

What type of bond is present between monomers? Covalent or ionic?

Covalent

The ____ is the central code of life. Explain the significance of this statement.

The order of assembly

Order of DNA makes you who you are

How do noncovalent bonds specify shape and chemical properties of polymers?

Through intermolecular forces and ionic bonds.

True or false. Epigenetic changes involve a change in the genetic code.

False - no change in sequence but rather a chemical modification to the physical structure.

Explain the Griffith experiment and what they concluded about DNA.

Studied streptococcus pneumoniae. Used smooth strain (deadly) and rough strain (not deadly). S strain made ineffective with heat. HOWEVER, combining inactive S strain with living R strain kills mouse by producing the S strain.

Heat inactivation did not destroy genetic material in bacterial, and it could transform R strain into S strain.

Explain the Avery experiment and what they concluded.

Different biochemical materials were extracted from the S strain and each were tested for their ability to complement the R strain. The only thing that could transform the R strain into S strain were DNA. Therefore, DNA must contain genetic material.

What is Chargaff's rule?

A = T, G = C

Identify the 3' and 5' end of this DNA molecule.

What is the name of the bond that links nucleotides together?

phosphodiester

What are nucleotides made up of?

5 carbon sugar, nitrogenous base (A,C,G,T), and phosphate group

How many hydrogen bonds are in an AT and GC pair?

GC have 3

AT have 2

Can the DNA molecules easily wind and unwind? Why?

No because of forces holding the strands together. Energy is required to break hydrophobic and hydrogen interactions to change the shape or bend DNA.

Define genome.

complete set of information in organism's DNA

Define chromatin.

complex of linear DNA and protein

What is karyotyping and how is it useful?

karyotyping is a map of the chromosomes in your cells. They are useful for detecting developmental defects or sex differences

Describe DNA packaging during interphase of mitosis.

DNA is dispersed throughout the nucleus during interphase. However, they condense during mitosis.

What is required of linear DNA molecules to function as chromosomes?

Replication origin - site where replication begins

Telomere - repeated sequence generated or extended by an enzyme. protect ends from degradation

Centromere - binding site for spindle proteins. Handles separating paired chromosomes during mitosis

What is the nucleolus?

An aggregation of ribosomal RNA genes in the nucleus

Where are chromosomes found?

Inside the nucleus, physically attached to the nuclear envelope

What is the fundamental unit of a chromatin? What is this unit made up of?

Nucleosome. DNA wrapped around a basic protein structure called an octamer core

Which histone is not part of the octameric core? Which ones are?

H1 is not. H2A, H2B, H3 and H4 are

How does salt concentrations affect the appearance of chromatin?

Low salt concentration = thicker fiber because of more protein DNA interaction

High salt concentration = thinner fiber or beads on a string

Explain chromatin looping

Chromosome loops occur when matching DNA sequences line up. The rest of the DNA is looped out. These genes are usually active or inactive as a group. Chromosome loop forming clamp proteins keep the areas looped.

Provide a summary of chromatin structure.

Each level of structure adds more organization.

double helix -> beads on a string chromatin -> chromatin fiber of packed nucleosomes -> chromatin fiber folded into loops -> entire mitotic chromosome

When chromosome loops are tightly packed after mitosis, the genes are turned off. When chromatin is loose, the genes are turned on.

Define epigenetics.

Heritable changes in an organism that do not affect DNA sequence

Explain some chromatin modifications.

Histone protein tails (N regions) can have a chemical group added.

Ex. adding 3 methyl groups to 9th lysine on histone 3 inhibits gene expression by promoting heterochromatin formation

Replacing trimethyl with acetyl group removes heterochromatin and increased gene expression

What is the function of ATPase in chromatin remodeling?

Chromatin remodeling proteins use ATP to move DNA relative to nucleosomes

What are Barr bodies?

one of two x chromosomes in females is silenced by condensing the entire chromosome into heterochromatin.

choice of which x chromosome to silence is made early in differentiation

How do mutations in somatic cells and reproductive cells differ?

Mutations in reproductive cells results in evolution or genetic disease. Mutation in somatic cell results in cancer or may not be noticed.

Explain semiconservative replication.

Each old strand of DNA serves as a template for a new strand. Replication preserves one original strand.

What was the Meselson and Stahl experiment?

they used 15N isotopes to trace the fate of the parental strand. After replication, they found that the new DNA was of an intermediate density, which showed either semi-conservative or dispersive replication. When they melted the DNA and reran the experiment, only heavy or light strands were seen, proving that it had to be conservative.

What are the steps of the scientific method?

Background, hypothesis, experiment, conclusion

How is DNA melted to start replication?

energy is added to break non-covalent bonds using ATP. Lots of energy is required because of the hydrogen bonds and hydrophobic interactions making DNA very stable.

Explain the replication origin.

Usually a region rich in A-T because that is easier to melt (less H bonds). A short region is melted, which is where DNA replication starts. Helicase is used to split the DNA open. Replication proceeds bidirectionally using two replication forks.

What are the requirements for DNA synthesis by DNA polymerase?

1. Template strand

2. Primer, base paired with template, containing 3' OH

3. Deoxynucleotide triphosphates (includes source of energy for making phosphodiester)

In what direction does nucleic acid synthesis occur?

5' to 3'

Explain how the incoming nucleoside triphosphate binds.

The incoming nucleic acid loses two phosphate groups (pyrophosphate). The nucleoside triphosphate cleaves pyrophosphate into two phosphoric acid residues to make polymerase irreversible in the cell.

If DNA replication is only 5' to 3' , how are both DNA strands replicated at the same time?

One strand is called the lagging strand that is made in fragments and joined together.

Explain the function of a primer and its requirements.

Primers must be base paired to templates and contain a 3'OH group (meaning it can also be made of RNA). Primase starts primer synthesis. The DNA polymerase will then take over after the primer is created. The 5' exonuclease on DNA polymerase will destroy the primer.

Primase -> primer -> DNA polymerase

What is used to join okazaki fragments?

DNA ligase. It requires ATP to form phosphodiester linkages.

How is DNA able to proofread?

DNA polymerase cannot continue if there is an error because the new base cannot base pair with the template. The DNA polymerase 1 has 3' exonuclease activity which will cleave the wrong base and leave a 3'OH group.

What are the 3 enzyme domains of DNA Polymerase 1?

DNA polymerase

5' exo (destroys RNA primer)

3' exo (proofreading)

What properties of replication does proofreading depend on?

All DNA synthesis is 5' to 3'

DNA pol requires base-paired primer with 3'OH

Energy to create phosphodiester comes from dNTP

What is the function of:

single stranded biding protein

DNA topoisomerase

Sliding clamp

bind to ssDNA exposed by helicase to prevent base pairs from reforming

produces nicks in the DNA backbone to relieve tension built up by unwinding

keeps DNA polymerase attached to the template, allowing the enzyme to move along without falling off

Be able to identify the parts of replication machinery

Explain telomerases.

Termini of linear DNA cannot be completely replicated due to requirement of a primer.

Telomerase uses RNA template to extend the 3' end. DNA polymerase can then complete the sequence.

How do errors in DNA come about?

depurination/deamination - guanine or amine removed

thymine dimers due to UV exposure - two adjacent thymines crosslink and cause a distortion of the shape of dsDNA.

Double-strand breaks - most difficult to correct because there isn't a template. Can be corrected through non-homologous end joining or homologous recombination.

What are the types of repair mechanisms?

Mismatch repair - wrong base cut out and right one added

Excision repair

End joining or homologous recombination

What are the four steps of repair?

Recognition of error (surveilling of the genome)

Nuclease or base removal (enzymes break phosphodiester linkage)

Polymerase to correct error (DNA pol)

Ligation to seal nick (DNA ligase)

What is non-homologous end joining and homologous recombination?

NHEJ - causes insertion or deletion of small number of base pairs. Can cause mutations in protein-coding sequence. Causes loss of nucleotides at repair site

Homologous recombination - use sequence of recently replicated chromosome as scaffold to repair break and fill in missing sequence

Go into further detail about homologous recombination and the steps in how it repairs breaks.

1. Nuclease digests 5' ends of broken strands

2. Strand of paired chromosome is used as template and it invades by complementary base pairing

3. 3' end base-pairs with the template and is extended using polymerase

4. Invading strand is released and complementary base pairing allows broken helix to reform

5. DNA synthesis continues using complementary strands from damaged DNA

6. DNA ligation

What is the difference between eukaryotic mRNA and bacterial mRNA?

Eukaryotic is capped, spliced, and polyadenylated.

What is the central dogma of molecular biology?

DNA -> RNA -> Protein

How is gene expression regulated?

Genes can be transcribed at different rates

Stability of RNA can be changed (rate of degradation)

RNA translation can be regulated

How is RNA different from DNA?

Ribose instead of deoxyribose, uracil instead of thymine, mostly single stranded,

RNA folds into 3D structures using internal base pairing

How is RNA strand specific?

RNA transcribed from template strand and matches the DNA coding strand. Direction of transcription determined by choice of template strand (always 5'->3')

RNA can be transcribed from one or both strands, giving different RNA products