exam 1 (notes version) Flashcards
1
Q
cells
A
compartments of all living things
2
Q
1665
A
Hooke looks at bark and coins the term “cell” (cell means little room)
3
Q
1673
A
Leeuwenhoek looks at different organisms and finds different looking cells
4
Q
cell theory has two parts
A
o Cells are composed of cells
o And all cells come from preexisting cells
5
Q
in cell theory all cells came from
A
a primitive cell
6
Q
• There are three domains of cells
A
o Bacteria
o Achaea
o Eukarya
7
Q
shapes of cells vary relating to
A
function
8
Q
shared universal characteristics of cells
A
- All cells enclosed by a membrane
- Store genetic information in DNA
- Use that DNA as a template
- Used as transcription
- Used genetic info to protein
- Use proteins as catalysts (enzymes)
- 4 macromolecules (proteins, carbs, lipids, nucleic acids)
9
Q
what experiment is responsible for chemical evolution?
A
• Miller-Urey experiment
10
Q
where did cells come from?
A
- Small to large molecule
- Light and head energy used
- Small molecule (hydrogen, methane, ammonia) heated and used light and created small molecules
11
Q
what was the first life form?
A
was a self replicating RNA (a ribozyme) and had catalytic ability
12
Q
when did the first cell come about?
A
3.5 – 4 billion years ago (and after the ribozyme) most likely a ribosome surrounded by a membrane
13
Q
sections of cell biology
A
- Cytology
- Biochemistry
- Genetics
14
Q
cytology
A
- Describes cell structure
* Relies on microscopy and staining techniques
15
Q
biochemistry
A
- Describes chemistry of cellular functions
- Pathways of synthesis and breakdown of compounds
- Energy generations and usage
- Enzyme catalysis
- Relies on many techniques
16
Q
genetics
A
• Describes the flow of information in the cell
• Central Dogma
o DNA transcribed to RNA and RNA is translated to protein and protein creates traits (gene expression)
o All cells contain the entire genome of DNA
o Different cell types express different sets of genes
Some genes are transcribed continually = constitutive expression (house keeping)
o Some genes are transcribed when the cell has a need for a specific protein
Regulated expression – specific need for specific genes
17
Q
central dogma
A
DNA transcribed to RNA and RNA is translated to protein and protein creates traits (gene expression)
18
Q
elements
A
substance that cannot be broken down or converted into other substances
19
Q
atoms
A
smallest particle of an element
20
Q
molecule
A
combination of atoms
21
Q
polymer
A
combination od repeating monomer units. A molecule you make from repeating monomer units
22
Q
critical elements
A
– carbon, hydrogen, oxygen, nitrogen
o Makes up 96.5% of living organisms
23
Q
oxygen
A
= highly electronegative O>N>C ~H
24
Q
dna is
A
polar molecule
25
amphipathic
• Polar + nonpolar areas
26
• Macromolecules of living organisms
o Proteins
o Carbohydrates
o Lipids
o Nucleic Acids
27
• Polymerization
o Monomers and polymers
o Proteins, carbohydrates, nucleic acids (not lipids)
Atoms
28
• Atomic weight (mass number)
protons + #neutrons
29
atomic number
#protons
30
• Neutral atoms =
#protons = #electrons
31
viruses
* Technically not alive – can’t replicate themselves
* Obligate intracellular parasites
* Composed of genetic material (DNA (RNA)) and a capsule
* Gain entry into cells by binding to protein receptors
32
bacteria
* Single celled
| * Prokaryotes – no nucleus
33
archae
* Single celled
* Prokaryotes – no nucleus
* Extreme environments – EX: thermophiles, halophiles etc
34
Eukaryotes
```
• Multi-cell
• Membrane bound nucleus
• Have unique cell features
1. Compartmentalization
2. Specialization
```
35
compartmentalization
a. Protection of genetic information
| b. Increased surface area of membrane
36
specialization
a. Organelles – membrane bound intracellular structures
b. Specialized for a particular function
c. Includes nucleus, mitochondria, chloroplasts (plants) endoplasmic reticulum, Golgi apparatus, lysosomes, peroxisomes, secretary vesicles
37
Cellular Specialization
• Most eukaryotic cells are specialized
| cells to tissue to organs
38
Extracellular Matrix (ECM)
• Bacteria, archae, the cell wall sometimes surrounds the membrane – protection because it’s susceptible to the environment
39
Cellular Specialization
• Cell to cell connections
o Plant cells are connected to each other with cytoplasmic bridges plasmodesma = which helps pass things back and forth between the cell wall
40
cell to cell connections
• Animal cells have different types of connections
41
gap junctions
like a tunnel. Allows passage between cells
42
tight junctions
prevents passage between cells “sewn shut”
43
o Adherin Junctions
connect plasma membrane to microfilament of cytoplasm
44
o Desmosomes
– connects plasma membrane to intermediate filaments of the cytoskeleton
45
cytoplasm
cytosol + cytoskeleton
46
cell walls in plants
• Cell wall can be primary (around the cell)
• Plant cells have rigid cell walls
• In complex plants, you have secondary cell walls
o Around tissue
o Lignin (wood)
• The more layers of the wall the more rigid it is, the more rough it is
• Cytoplasm = cytosol + cytoskeleton
• Cytosol is permeated by 3D array called cytoskeleton
47
domain differences
1. Presents/absence of nucleus
2. Unique Organization of DNA
3. Unique Expression of DNA
4. Cytoskeleton
5. Exocytosis and Endocytosis
6. Internal Membranes
48
1. Presents/absence of nucleus
• Eukaryotic cells contain membrane bound nucleus
49
2. Unique Organization of DNA
• Bacterial DNA – circular with few associated proteins
• Archael DNA – circular with moderate amounts of protein
• Eukaryotic DNA – multiple, linear, many associated proteins called histones
• Archael have few histones. Moderate amounts of protein.
o Also have circular chromosomes
50
3. Unique Expression of DNA
• Replication/synthesis (during cell division)
51
cytoskeleton
```
• Cell Shape, movement, division
• Proteinaceous
o Microtubules
o Microfilaments
o Intermediate filaments
```
52
5. Exocytosis and Endocytosis
* Only eukaryotes
* Moves things in and out of cell
* Membrane fusion events
* Endo = in and Exo = release
53
internal membranes
• Most bacteria, archae don’t contain internal membranes
• Cellular functions occur at the plasma membrane in cytoplasm
• Exception – cyanobacteria
o Photosynthetic
o Extensive internal membrane
54
organelles
little organs, membrane bound and highly specialized
55
mitochondria
site of aerobic respiration and relatively large
56
chloroplasts
relatively large, site of photosynthesis
57
Endoplasmic Reticulum
```
• Rough ER – associated with ribosomes
o Protein synthesis
• Smooth ER – no ribosomes
o Synthesis of lipids and steroids
o Drug detoxification
```
58
Golgi Apparatus (Golgi complex)
o Stack of flattened sacs and vesicles
o Processing/packaging secretory proteins
o Synthesize of complex polysaccharides
o Compounds in vesicles bud off of trans face other parts of cell
59
The Lysosome
• Stores enzyme (acid hydrolases) for digesting/degrading
60
Peroxisome
• Generate and degrade hydrogen peroxide (h20)
o Highly toxic
o Converted to H20 and O2 by catalase
o Role in oxygen regulation? Aging?
• Detoxify methanol, ethanol, formaldehyde
• Degrade unusual substances (d-amino acids)
• Especially prominent in liver and kidney
61
Vacuole
* Plant organelle
| * Maintains turgor pressure to prevent wilting
62
function of membranes
o Defines boundary of cell – surround organelle
63
structure of membranes
o Lipid bi-layer w/ associated proteins
o Amphipathic – contains hydrophilic and hydrophobic regions – both polar and non-polar
o Assembles spontaneously in an aqueous environment
Polar regions interact with water
Non polar regions remain protected from water
64
• Phospholipids
o Most abundant membrane lipid
| o Phosphate + glycerol (+/- small molecules) = “head”
65
• Glycolipids
o Carbohydrate around it
| o Cerebrosides and gangliosides (two groups found in nervous system)
66
• Antigenic
glycosphingolipids on RBC’s
o EX: Tay-Sachs disease
o Lysosomal storage disease
67
sterols
Maintains and stabilizes membranes
| Building block of steroid hormones
68
o Permeability
a measure of abaility to allow substances to pass through
69
o Singer + Nicholson
Described fluid mosaic model of the membrane
• Fluid nature of lipids
• Mosaic scattering of proteins
70
o Unwin and Henderson (1975)
Used bacteriorhodospin as a model (archaea spp protein pump)
Described transmembrane segments (7)/hydrophobic; connecting hydrophilic “loops”
71
lipid rafts
Areas of homogeneity within a monolayer
Especially prominent in outer monolayer
• Tend to have:
o Increased cholersterol
o Increased saturation
o Increased glycosphingolipids (glycosphingolipids are find in the membrane of the red blood cell)
72
Fluidity –
state of viscosity of the lipids in a membrane
73
membrane fluidity
* Increased temp – membrane too fluid; doesn’t hold together
* Decreased temp – membrane begins to gel, eventually becomes solid (death of organism)
* Transition temperature – where solid membrane becomes fluid – WE ARE HOMEOTHERMIC
74
o Homeoviscous adapation
– ability to alter lipid composition to maintain membrane fluidity on different temperatures
o Methods
Shorten/elongate fatty acid length
Add/remove double bonds in fatty acids to alter saturation
75
• Categories of membrane proteins
o Integral
Integral monotopic – cross one monolayer
Transmembrane – cross entire bi-layer
• Single pass – cross through one time
• Multipass – in and out of membrane and move around – looping
o Peripheral
Weak electrostatic interactions
o Lipid Anchored
Covalent bonds to lipids within bi-layer
76
simple diffusion
o Direct and unaided
| o Does NOT require energy
77
concentration gradient
difference in the concentration of solutes in a solution between two regions (across a membrane)
78
polarity
– measured by partition coefficient (oil/water)
Non polar = increased coefficient = more permeable
Polar = decreased coefficient = les permeable
79
osmosis
movement of water across a semipermeable membrane
80
• Facilitated Diffusion
```
o Similarities to simple diffusions
Spontaneous; no energy required
Moves down a concentration gradient [high] [low]
o Requires transport proteins
Channel proteins
Carrier proteins
```
81
hypertonic
water out (cell shrivels)
82
hypotonic
water in (cell ruptures
83
isotonic
nothing changes
84
o Active Transport
```
Proteins called membrane pumps
Directional
Movement is against a concentration gradient (up the gradient)
[low] t [high]
Requires energy
• Hydrolysis of ATP (ATP ADP+Pi)
• Coupled movement/hydrolysis
```
85
steps of transcription in bacteria
* Initiation of Transcription (step 1)
* Sigma binds core and binds promoter region on DNA (35 and 10 boxes common)
* Helix Opens
* RNA Polymerase
* Elongation (Step 2)
* Termination (Step 3)
86
Transcription in Eukaryotes
* More complex process
* Diverse array of promoters
* Diverse array of basal transcription factors that replace sigma
* Genes divided into exons and introns
87
• The DNA molecule
o Contains all the information to make all the RNA and all the proteins needed to construct a new organism
88
gene
o Contain sequences of base pairs that encode for proteins
One gene, one protein
o Contain sequences of base pairs that regulate expression of genes
Turn gene “on” and gene “off”
• Induction = express gene; or increase expression
• Repression = don’t express gene; or decrease expression
89
the central dogma
o DNA is transcribed to produce RNA
o RNA is translated to produce protein
o Protein creates traits
90
there are two distinct uses for DNA
```
o Replication/synthesis (DNA used to make more DNA)
o Transcription (DNA is used to make RNA)
```
91
• Wraps around histone proteins
nucleosome
92
dna excists as a
double stranded protein in the cell
93
• Cells have different functions
o Only genes that code for proteins needed by that cell will be transcribed, only when needed
94
house keeping genes
o Code for proteins needed by all cells, all the time (except for Y Chromosome)
95
• Heterochromatin
tightly packed, transcriptionally inactive
96
• Euchromatin
loosely packed, exposed nucleosomes actively transcribed
97
• Global regulation of Transcription
getting to Euchromatin
98
2. SWI/SNF enzymes
a. Rearrange nucleosomes
99
3. Histone Acetylation Transferase Enzymes (HAT)
a. Place acetyl groups on histones
b. Removes (+ charge) less tightly bound to (-) charge on DNA
c. Helps heterochromatin euchromatin
100
4. Methyl Transferase Enzymes
a. Target CpG regions in promoters of genes
| b. Place methyl groups helps euchromatin heterochromatin
101
Gene Transcription
• Other regulatory proteins bind regulatory regions around gene itself
o Repressors bind to operators downstream from promoter regions
o Activators bind to enhancer region upstream from promoter regions (sometimes bend DNA)
o Can work together for fine control
102
Gene Expression
• Regulation of Gene expression = pile one!
o Heterochromatin euchromatin
o Repressors/operators, Activators/Enhancers
o Basal transcription factors bind to promoters
• Leads to building of very complex machinery to enhance or suppress transcription
103
promoter
a region of DNA that initiates transcription of a gene; located upstream (100-1000bps)
104
enhancer
a region of DNA that becomes bound with protein activators (transcription factors) to activate transcription; located upstream (50-1500 bps)
105
operator
region of DNA that becomes bound with protein repressors (transcription factors) to inhibit transcription’; located upstream between promoter and the gene
106
Control of Eukaryotic Gene Expression
1. Transcriptional control is only the beginning
2. RNA processing control
3. RNA transport and localization control
4. Translational control
5. mRNA degradation control
6. Protein activity control
107
• In many diseases, the cause is the overexpression of
a particular gene
108
• Microarrays
o Measures the total* amount of mRNA (transcription product) in a diseased cell and compare it to the amount of mRNA in a healthy cell
o Looks for where the two cells differ; where transcription is unregulated in diseased cell
