Cell And Molecular Biology (Bi 314), Oregon State, Part 1

Front 1

1. ______ are the areas within a genome that are expressed through transcription and translation.

2. ______ are the areas that aren't expressed.

Back 1

1. Coding sequences (exons)

2. Non-coding sequences (introns)

Front 2

Name the mutation...

1. It causes negative effects and is typically eliminated quickly.

2. The mutation either doesn't change the amino acid, or the amino acid is changed, but the protein coded remains the same.

3. A slight phenotype change that can benefit the host.

4. A genetic change that has no effect on the hosts fitness.

Back 2

1. Deleterious mutation

2. Silent mutation

3. Useful mutation

4. Neutral mutation

Front 3

Where are the mutations occurring?

1. Lactase is never produced throughout a hosts lifetime.

2. At some point during the hosts life, the amount of lactase produced somehow changes.

Back 3

1. Mutation in coding sequences

2. Mutation in regulatory regions

Front 4

______ can create new genes by breaking sequences between genes (in an intron) and reconnecting the halfves.

Back 4

Exon shuffling!

Front 5

______ are short DNA sequences that can replicate and shift about the genome, potentially interrupting coding sequences or regulatory regions.

Back 5

Transposons!

Front 6

What is the main gist of:

Horizontal Gene Transfer

Back 6

Genes are exchanged between species/individuals.

A genetic exchange NOT between parent and progeny

Front 7

All regions of the genome have the same probability of becoming mutated...

Is the rate of change throughout the genome the same?

Back 7

Yes, BUT natural selection removes most of these changes because the organism requires most genetically-coded functions.

Front 8

What are the subunits of:

1. Polysaccharides

2. Protein

3. Nucleic acid

Back 8

1. Sugar (aka- carbohydrates, saccharides)

2. Amino acids

3. Nucleotides

Front 9

What are the 5 macromolecules abundant in cells?

Back 9

1. Phospholipids
2. DNA
3. RNA
4. Proteins
5. Polysaccharides

Front 10

______ are used to make biological membranes.

They are generally composed of two fatty acids, and have distinctly hydrophilic and hydrophobic ends.

Back 10

Phospholipids!

Front 11

What are the 2 major parts of an amino acid?

Back 11

1. An amino group (--NH2)

and 2. a carboxyl group

Front 12

What is cholesterol, and what is its function?

Back 12

A lipid molecule with a 4-ringed steroid structure.

Important component of the plasma membranes of animal cells.

Front 13

A lipid molecule with a 4-ringed steroid structure.

Important component of the plasma membranes of animal cells.

Back 13

Cholesterol!

Front 14

What is a side chain, where do they exist, and why is it important?

Back 14

They are the portions of amino acids that aren't involved in making peptide bonds.

They also give an amino acid its unique properties.

Front 15

They are the portions of amino acids that aren't involved in making peptide bonds.

They also give an amino acid its unique properties.

Back 15

Side chain!

Front 16

Describe:

Peptide bond

Back 16

Chemical bond between the carbonyl group (carbon double-bonded to oxygen) of one amino acid and the amino group (nitrogen bonded to hydrogens) of a second.

Front 17

How does a "family" of genes occur?

Back 17

Duplication and divergence

Front 18

Explain the function of the Histone Code

Back 18

Protein tails off histones provide the code which signals a change in the state (condensed/non-condensed) of chromatin.

Front 19

Differentiate the following:

1. Chromatin

2. Heterochromatin

3. Euchromatin

Back 19

1. Complex of DNA and histones wound up into chromosomes

2. Areas within chromosomes that are more tightly packed; unexpressed areas; typically seen in centromeres and telomeres.

3. Less tightly packed chromatin that is being expressed.

Front 20

Where does replication start along a chromosome?

Back 20

Replication origins!

Specific sequences within DNA strands (there are many!)

Front 21

Explain:

Helicase

Back 21

An enzyme that separates two parent strands using energy released by ATP hydrolysis

Front 22

Explain:

Topoisomerase

Back 22

Enzyme that relieves the torsional stress from the twisting & unraveling by DNA Helicase

Front 23

What are the functions of:

1. Clamp loader

2. Sliding clamp

Back 23

1. it marks the end of the RNA primer (that links to a template strand) and indicates where DNA synthesis should start

2. it keeps DNA polymerase on the template strand

Front 24

1. Explain the role of Telomerase

2. what would happen without it?

3. define the Hayflick Limit

Back 24

1. it elongates the template strand, allowing a primer to attach & complete the lagging strand.

2. Without telomerase, each replication would remove the ends of the strands. After enough replications, genetic material is lost and the cells become static.

3. The maximum number of cellular replications (without telomerase) where chromosomes become unreproduceable. (around 50 generations)

Front 25

Where does telomerase exist?

Back 25

In germ cells (sperm & egg)

NOT in somatic cells.

Front 26

How does DNA polymerase prevent mistakes when copying DNA?

Back 26

Proofreading!

> Polymerizing activity: checks WIDTH of helix; prevents purine-purine and pyrimidine-pyrimidine pairing.

> Exonuclease activity: before continuing to the next nucleotide, it checks to see that A:T and C:G

Front 27

How are mistakes corrected after DNA replication?

Back 27

Mismatch Repair!

Front 28

explain Mismatch Repair

Back 28

Proteins cut either side of the mistake & remove it. Polymerase fills in the removed section.

Front 29

How can DNA be damaged?

Back 29

-- UV radiation
-- Chemicals in car exhaust & cig. smoke
-- Spontaneous chem. reactions within the cell.

Front 30

What is a common result of UV radiation on DNA?

Back 30

Thymine Dimer:
a cross-linking of two adjacent thymine bases

Front 31

How can carcinogens (cig. smoke & car exhaust) damage DNA?

Back 31

Carcinogens can merge with guanine and thicken the sequence at that nucleotide

Front 32

What is a common spontaneous chemical reaction within the cell?

How is the damage repaired?

Back 32

Deamination:
cytosine loses an amino group and becomes uracil

Excision repair mechanisms:
intercellular mechanisms that repair genetic damage.

Front 33

What is a result of lacking functional excision repair systems?

Back 33

Extreme light sensitivity, and increased risk for skin cancer.

Front 34

Explain promoter regions with respect to RNA polymerase & transcription (in prokaryotes)

Back 34

Promoter regions have docking sequenecs around -10bp and -35 bp from transcription start site.

RNA polymerase docks onto these sequences to begin transcription

Front 35

RNA polymerase is assisted by the "Sigma Factor"

what is it and what is its purpose?

Back 35

It's a protein that assists RNAp in properly fixing to -35bp and -10bp.

It disengages once RNAp begins transcribing.

Front 36

Prokaryotic replication is fairly simple...

What are the 5 special considerations in eukaryotes that make replication more complex?

Back 36

1. Chromatin

2. 3 different RNA polymerases

3. Additional proteins are needed for initiation

4. Regulatory sequences can be far away from the gene being transcribed

5. Transcription (within nucleus) and translation (within cytosol) occur separately

Front 37

What are the 3 RNA polymerases and what RNA do they produce?

Back 37

RNAp1 = makes ribosomal RNA (rRNA)

RNAp2 = makes messenger RNA (mRNA)

RNAp3 = makes transfer RNA (tRNA)

Front 38

Prokaryotes use only the protein "sigma factor" to assist RNA polymerase during transcription...

What proteins are used in eukaryotes?

Back 38

General Transcription Factors
=
proteins that help RNAp's find transcription start sites and initiate RNA synth.

(i.e. TF2x helps RNAp2; TF1n helps RNAp1)

Front 39

What is the term used for the combination of transcription factors (TFs) and their RNAp?

Back 39

Basal Transctiption Complex

(aka- Transcription Initiation Complex)

Front 40

_____ are regions of DNA that initiates transcription of a particular gene.

Back 40

Promoters!

Front 41

Define:

1. TATA box

2. "Upstream elements" (give example)

Back 41

1. A eukaryotic promoter for transctiption located about 25bp before start site

2. Minor promoters (i.e. GC box) that appear within 100bp before the start site

Front 42

Several genes can be controlled by a single promoter in bacteria/prokaryotes...

______ is a group of genes expressed by the same promoter.

Back 42

Operon!

Front 43

When an operon isn't needed for expression or conditions aren't met for transctiption, a repressor binds to _______

Back 43

Operator sequence (-5bp, +21bp)

Front 44

In the case of the lac-operon...

Transcription is blocked by a repressor in the operator sequence when lactose is ABSENT.

What happens when lactose is PRESENT?

Back 44

Lactose binds to/distracts the repressor, deforms it, and allows transcription to occur.

Front 45

In the case of the lac-operon...

explain the CAP & CAP-binding site

Back 45

When glucose is ABSENT, transcription is helped by a CAP at the CAP-binding site (behind the promoter region)

Front 46

______ are short DNA sequences (outside of the promoter) that control transcription of genes.

Back 46

Enhancers!

Front 47

What is the protein that attaches to enhancer sites and interacts with the Mediator?

Back 47

Transcriptional activator (aka- Activator Protein)

Front 48

_____, _____, and _____ are all DNA sequences that are necessary for initiation and regulation of transcription.

Back 48

Enhancer, promoter, and operator

Front 49

"Primary transcript" is another name for...

Back 49

the newly made mRNA after transcription

Front 50

What happens to a newly made mRNA strand?

Back 50

5' capping and Polyadenylation (addition of adenines to 3')

Front 51

snRNP's are the structural unit for (1) ______ and are themselves made up of (2) _____ and _____

Back 51

1. Spliceosomes

2. RNA and protein

Front 52

What is the result of RNA splicing?

Back 52

Introns are separated from exons...

Exons form a 5'-3' chain, and introns form a 3' lariat with an adenine branch-point

Front 53

Define:

Alternative splicing

Back 53

Splicing of RNA transcripts from the same gene in different ways, each of which produces a distinct protein.