Cell Bio 2020 Exam 1: University of Utah

What is the cell theory? (3 parts)

1. All living things are made up of cells

2. Cells are the basic units of structure and function in living things

3. New cells are produced from existing cells

What are common cell features? (3)

1. Boundary

2. Metabolism

3. Mechanism of Inheritance

What are the steps of the central dogma?

replication, transcription, translation

Features of prokaryotic cells

- Circular DNA

- No membrane bound organelles

- No nucleus

- Double boundary

Features of Eukaryotic cells

- Linear DNA

- Membrane bound organelles

- Nucleus

- Single or Double boundary

Nucleus

A part of the cell containing DNA and RNA and responsible for growth and reproduction (Site of DNA replication and RNA transcription)

Mitochondria

Powerhouse of the cell, organelle that is the site of ATP (energy) production

Chloroplasts

Site of photosynthesis

Endoplasmic Reticulum

synthesizes proteins (rough) and lipids (smooth)

Golgi apparatus

processing and sorting

lysosomes

Uses chemicals to break down food and worn out cell parts

light microscopy

light lenses to magnify objects

scanning electron microscope

uses electrons to image the surface of dried gold-coated cells

confocal microscopy

optical sectioning and 3D reconstruction of cells or tissues

fluorescence microscopy

uses a fluorescent dye that emits fluorescence when illuminated with ultraviolet radiation

live cell fluorescence

watch living cells

Endosymbiosis theory

A theory that mitochondria and chloroplasts originated from bacteria that took up residence within a primordial eukaryotic cell.

What is the subunit of a polysaccharide

sugar

What is the purpose of a polysaccharide?

Energy source; cell structures

Sugars are linked via...

condensation

Sugars are split via...

hydrolysis

What is the subunit of a lipid

fatty acid

What are lipids used for?

long term energy storage; cell membranes

Amphipathic

A molecule that has both a hydrophilic region and a hydrophobic region.

A fatty acid hydrocarbon tail is

hydrophobic

A fatty acid carboxylic head is

hydrophilic

Saturated fats

have no double bonds

Unsaturated Fats

have double bonds

Phospholipid structure

2 fatty acids, 1 glycerol, 1 phosphate group

Subunit of Proteins

amino acids

side chains of amino acids

can be:

polar

non-polar

aromatic

nonaromatic

charged

uncharged

Proteins form in

linear chains

What bond joins amino acids?

peptide bonds

What process creates proteins

translation

Folding of proteins happens because of

non-covalent interactions (electrostatic attractions, hydrogen bonds, van der waals)

primary structure

linear sequence of amino acids

secondary structure

alpha helix and beta sheet

tertiary structure

three-dimensional shape of a polypeptide due to interactions of the R groups of the amino acids making up the chain.

quaternary structure

the shape resulting from the association of two or more polypeptide subunits.

What is the subunit of a nucleic acid?

nucleotide

Nucleotide bases

Adenine, Thymine, Guanine, Cytosine

Pyrimidines (3)

cytosine, thymine, uracil

Purines (2)

Adenine and Guanine

Nucleic acid sugars

deoxyribose and ribose

deoxyribose vs ribose

deoxyribose lacks an oxygen atom on the second carbon in the ring

what makes up a nucleic acid

The phosphates, the sugars and the nitrogenous bases

A favorable reaction has a ________ deltaG

negative

An unfavorable reaction has a _____ deltaG

positive

Favorability of a reaction depends on:

- concentrations

- intrinsic chemistry (enthalpy and entropy)

Enzymes

lower the Ea and don't affect delta G

Energetically unfavorable reactions must...

be coupled with energetically favorable reactions (via peptide bond formations)

Ways to damage DNA (3)

1- Depurination

2- Deamination

3- Thymine Dimers

Depurination

Chemical reaction that removes the purine bases from DNA

Deamination

the removal of an amino group from an amino acid

Thymine Dimers

two neighboring thymines attached to one another by covalent bonds bond together on a single strand of DNA

Ways to repair DNA (3)

1- DNA Polymerase

2- Mismatch repair

3- Double Strand breaks

Nonhomologous end joining

A quick-and-dirty mechanism for repairing double-strand breaks in DNA that involves quickly bringing together, trimming, and rejoining the two broken ends; results in a loss of information at the site of repair. (done by DNA Ligase)

Homologous recombination

uses intact chromosome as a template for error-free repair by nuclease

What does CRISPR do

makes it possible to change or remove a specific gene in living cells

What does CRISPR need to work

- Cas9 protein (cuts DNA)

- gRNA (guide RNA; finds target gene)

CRISPR process

1- gRNA binds to Cas9

2- Cas-9:gRNA complex finds matching DNA site

3- generates a double strand break

4- repaired by non homologous end joining

What direction is DNA synthesized

5' to 3'

Helicase

An enzyme that untwists the double helix at the replication forks

Topoisomerase

Enzyme that functions in DNA replication, helping to relieve strain in the double helix ahead of the replication fork.

Primase

synthesizes RNA primer

DNA Polymerase

principle enzyme involved in DNA replication

RNA polymerase

enzyme that links together the growing chain of RNA nucleotides during transcription using a DNA strand as a template

Transcription process (8)

1. TATA-binding protein (TBP) recognizes the TATA box.

2. TFIID (transcription factor II D) recruits TFIIB.

3. RNA polymerase II and the rest of the transcription factors assemble at the promoter.

4. Helicase opens DNA.

5. TFIIH phosphorylates RNA polymerase

6. Polymerase uses NTPs to begin synthesis.

7. Polymerase continues through the gene, generating an mRNA.

8. Eukaryotic terminator sequences cause the polymerase to release from the gene.

Prokaryote Transcription

1. One type of polymerase

2. Sigma factor

3. No nucleosomes

4. Transcript immediately available for translation.

Eukaryote Transcription

1. 3 types of polymerases

2. Many transcription factors

3. Must unpack chromatin structure

4. Transcript must be exported to cytoplasm before translation

RNA Processing (3)

1- Capping

2- Splicing

3- Polyadenylation

What do eukaryotes splice out?

introns

Alternative splicing

allows for a single gene to code for different proteins (opportunity for evolution)

snRNPs

RNA protein complexes that coordinate intron removal.

spliceosomes

Collection of snRNPs that remove introns from pre-mRNA.

ribosome

Makes proteins

What process makes proteins

translation

tRNA

transfer RNA; type of RNA that carries amino acids to the ribosome

A site

acceptor site

P site

holds the tRNA carrying the growing polypeptide chain. Generates the peptide bond

E Site

the exit site, where discharged tRNAs leave the ribosome

small ribosomal subunit

bound to initiator tRNA; Finds AUG

transcription regulator proteins

bind to DNA to switch genes on or off

transcription repressor

decreases transcription

transcription activator

increases transcription

Epigenetics

Heritable information that does not involve changes to DNA

Genetic Variation (6)

1- Mutation within a gene

2- Mutation in regulatory DNA

3- Gene duplication and divergence

4- Exon shuffling

5- Transposition

6- Horizontal transfer

Mutation within a gene

small changes to transcript or protein product

Mutation in regulatory DNA

Changes to expression level, timing, location

Gene duplication and divergence

Genes are copied, and then can evolve separately

Exon shuffling

rearrangement of exons to generate new coding regions

transposition

mobile elements of DNA that 'hop' in and out of genes

horizontal transfer

transfer of genes between organisms