EK BIO #1
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1. How many amino acids are there?
2. How many AAs are essential in humans?
3. What are the bonds involved in tertiary structure & quaternary structures?
- 1. ~20
- 2. 10
- 3. Ionic interactions (acidic & basic side chains), covalent disulfide bonds, van der waals forces, hydrophobic interactions, hydrogen bonding.
Which bonds are affected by:
2. Salt/Change in pH?
3. Organic solvents?
- 1. Hydrogen bonds
- 2. Electrostatic bonds
- 3. Hydrophobic forces
- 4. All.
1. What is the basic structure of a nucleotide?
2. Which are the pyrimidines? Which are the purines?
3. How many bonds between nucleotides?
4. How is DNA written by convention? In what direction is it read? In what direction is it synthesized?
- 1. Pentose, N base, and phosphate group
- 2. PYrimidines (thYmine and cYtosine & uracil); purines (adenine and guanine)
- 3. A2T, C3G
- 4. 5'-->3'. 3'-->5'. 5'-->3'
What are 3 functions of minerals?
- 1. Assist in transport of substances into/out of cell.
- 2. Can combine and solidify to give strength to a matrix (i.e., hydroxyapatite in bone)
- 3. Cofactors in enzyme and protein function
1. Can enzymes be structural?
2. How do enzymes affect the eq of a rxn?
3. What are the two theories of enzyme specificity? (2)
- 1. No - always globular
- 2. They don't.
- 3. Lock & Key and Induced fit
What is the structure of a virus? 3 in all, 4th optional
- 1. Capsid (protein coat)
- 2. Genetic material (DNA or RNA but not both)
- 3. Lipid-rich envelope
- (4) In bacteriophage, there is a base plate and tail fibers
Are viruses living organisms? Give 4 reasons why or why not.
- 1. Can only reproduce through host's reproductive machinery
- 2. Has DNA OR RNA, but not both.
- 3. Cannot oxidize macromolecules for energy, uses ATP from host cells
- 4. In active form, viruses are not separated from external environment by barrier.
Which organisms are immune from viruses?
None. All organisms are subject to viral infection.
What is the basic mechanism of action of a how a virus enters a cell? (3)
- 1. Virus adsorbs to specific chemical receptor site on host.
- 2. Nucleic acid of virus penetrates cell (in bacteriophage, nucleic acid is injected through tail after viral enzymes digest a hole in cell wall).
- 3. Endocytosis of virus.
What are the two types of viral infection? What happens after a virus enters a cell? How can you tell if it's lytic or lysogenic?
- Lytic and Lysogenic.
- 1. DNA is incorporated into host DNA (if RNA virus, will have reverse transcriptase)
- 2. When host cell replicates it's DNA, virus's DNA is replicated too.
- 3. If the virus lies dormant, it's lysogenic. If it fills the cell with viruses and the cell lyses unaccording to schedule, it's lysis.
How does the body defend against viral infection? 3 ways.
- What type of virus is least susceptible to antibodies?
- 1. Antibodies bind to viral protein and destroy infected cells with cytotoxic T cells
- 2. Spike proteins encoded from viral nucleic acids are recognized by antibodies when fighting the infection.
- 3. Vaccine - injections of antibodies or nonpathogenic virus with same capsid or envelope.
RNA viruses, because RNA polymerase does NOT have proofreading, so can easily mutate its spike proteins.
1. What does prokaryotic DNA look like?
2. Do prokaryotes have organelles?
3. What is the nucleoid?
- 1. Single, circular ds molecule of DNA
- 2. YES, but not complex, membrane-bound organelles
- 3. DNA, RNA, and protein complex in prokaryotes
What names correspond with the following bacterial shapes?
- 1. Cocci
- 2. Bacilli
- 3. Spirilla
What is the fluid mosaic model?
1. What does it describe?
2. Best overall description?
3. What 2 types of proteins are embedded into membranes?
4. What moderates membrane fluidity in eukaryotes? Prokaryotes?
- 1. Describes cell plasma membrane
- 2. Phospholipid bilayer (phospholipids are amphipathic with hydrophilic heads pointing outwards and hydrophobic heads pointing inwards)
- 3. Integral (intrinsic) - traverse membrane from inside to outside and peripheral (extrinsic) - situated entirely on surface of membranes.
- 4. In eukaryotes - cholesterol. In prokaryotes - hapanoids.
1. What types of molecules are difficult to transport through membrane? (2)
2. What does the bacterial envelope consist of?
3. What is the function of the bacterial envelope?
4. What is the cell wall made of? Do archaea have these?
- 1. Larger and more polar molecules
- 2. Cell wall
- 3. Prevents protoplast (everything inside bacterial envelope) from bursting, since most bacteria are hypertonic.
- 4. Peptidoglycan (disaccharide) - no.
What is the difference between gram-positive and gram-negative bacteria?
2. Thickness of wall
3. Outer membrane
- When stained:
- gram-positive bacteria (purple) have a thick peptidoglycan cell wall that prevents stain from leaking out.
Gram-negative (pink) have thin peptidoglycan wall allowing most of stain to be washed off. Additionally, gram-negative bacteria have their phospholipid bilayer OUTSIDE of cell wall.
1. What is eukaryotic vs. prokaryotic flagella and cilia made from?
2. What propels flagella?
3. What directions can flagella propel bacterium/eukaryotes?
- 1. Eukaryotic flagella & cilia (microtubules), prokaryotic flagella (flagellin - globular protein) and prokaryotes don't have cilia.
- 2. Propelled by ATP gradient
- 3. Single direction or can change direction.
1. Define a denatured protein
2. For a nucleotide, is phosphate or OH on the 5' or 3' end?
- 1. A protein who has had its conformation disrupted.
- 2. Phosphate: 5' and OH: 3'
What are the differences between RNA and DNA? (4)
Where is rRNA synthesized?
- RNA is
- (1) SS
- (2) Not deoxygenated
- (3) Has uracil instead of thymine
- (4) Can move outside of nucleus.
In the nucleolus.
1. What are the differences between transcription and replication? Name 3
2. How many RNA polymerases do prokaryotes have? Eukaryotes?
- 1.In transcription RNA is produced where as in replication DNA is produced.
- 2.New strand dissociates from the template in transcription where as in replication it doesn't.
- 3.Transcribes only at distinct palces where as in replication the entire gene is copied.
- 4.Transcription is unidirectional where as replication is bidirectional.
- 5.Transcription requires promoter whereas replication requires a primer.
- 6.In transcription a single stranded copy is produced where as in replication doble stranded copy is produced,
- 7.Transcription is less accurate where as replication is more accurate.
- 2. 1 vs. 3
1. Genetic unit consisting of operator, promoter, and genes that contribute to a single prokaryotic mRNA.
How are primary transcripts processed? (3)
Which molecular compounds are responsible for forming which enzyme to excise introns and splice together exons?
- 1. Addition of nucleotides
- 2. Deletion of nucleotides
- 3. Modification of nitrogenous bases
snRNPs form a spliceosome
Which blots correspond with which macromolecules? How are fragments separated? What is the purpose of the radioactive probe?
- 1. Western - detects protein with antibodies
- 2. Northern - RNA
- 3. Southern - DNA
RNA and DNA fragments are separated using gel electrophoresis by size. Radioactive probe hybridizes with and marks target fragment.
What is PCR?
- PCR - much faster method of cloning - (1) Target DNA is denatured and
- mixed with complementary primers (2) Primers hybridize with DNA
- fragments (3) Specialized polymerase to amplify (replicate)
- complementary strands doubling DNA.
What is RFLP?
What is recombinant DNA
Identifies individuals instead of identifying specific genes (DNA fingerprints - used to identify criminals).
What are characteristics of the genetic code? (3)
- 1. Degenerative - more than one series can code for a single nucleotide
- 2. Unambiguous - each series will only code for one nucleotide
- 3. Universal - used by all forms of life.
1-->2-->4 Mutations in DNA
1. Where does translation begin?
2. What directs beginning of translated polypeptide to attach to ER?
- 2. Free floating ribiosome
- 2. Signal recognition particle (SRP)
1. What are oncogenes?
2. What is the organization of a chromosome by level?
- 1. Genes that cause cancer
- 2. DNA --> histones --> nucleosomes --> chromatin --> chromosomes
Describe overall cell cycle (not including mitosis)
1. What happens in prophase? (4)
2. Metaphase (1)
3. Anaphase/Cytokinesis (1 each)
4. Telophase (2)
- 1. Prophase: condensation of chromatin into chromosomes, centrioles move to opposite sides of cell, nucleolus and nucleus disappear, spindle apparatus forms.
2. Metaphase - align
3. Anaphase - split (disjunction); cytokinesis - cytoplasm splits
4. Telophase - nuclear membrane reforms and chromosomes decondense into chromatin.
Describe the stages of meiosis!
- 1. Prophase I: DNA strands thicken and homologous chromosomes pair, centrioles form and move to opposite sides of cell, tetrads form, nuclear membrane disintegrates, recombination occurs.
- 2. Metaphase I - tetrads attach to spindle fibers at their centromeres and line up.
- 3. Anaphase I - tetrads separate and paired chromatids move along the spindle to their respective centrioles
- 4. Telophase I - nuclear membranes enclose separated chromatids.
- Product: 2 cells, each with the same number of chromatids as parent cell.
- 1. Prophase II - homologous chromosomes do not duplicate, they just separate
- 2. Metaphase II - alignment
- 3. Anaphase II - now-separated chromatids approach respective poles
- 4. Telophase - now 4 cells with half the number of chromosomes of the parent cell.
Draw spermatogenesis (5 stages) and oogenesis (4):
1. Name of cell
2. Number of chromosomes
3. Haploid or diploid
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