cells and genes final Flashcards
1
Q
- Define central dogma
A
-central dogma defines a central idea that all living things use DNA to encode RNA to encode protein
2
Q
membrane
A
defines cell (structure of the cell, outline)
3
Q
nucleus
A
largest organelle, where DNA replication, transcription, and RNA processing take place
4
Q
cytoskeleton
A
determines cell shape, organizes cell contents, contributes to cell movement
5
Q
mitochondria
A
synthesizes energy, powerhouse of the cell
6
Q
chloroplast
A
large green organelles only found in plant cells, perform photosynthesis. Reproduce by dividing into 2
7
Q
Endoplasmic reticulum
A
site of protein synthesis, rough ER:ribosomes bound, smooth ER:no ribosomes
8
Q
Ribosome
A
molecular machines that make protein, complexes of RNA and protein, critical to protein formation
9
Q
golgi apparatus
A
modifies translated proteins, stacks of flattened membrane enclosed sacs
10
Q
lysosomes
A
membrane bound, break down macromolecules, responds against foreign substances
11
Q
peroxisomes
A
membrane enclosed, isolate reactions where hydrogen peroxide is made
12
Q
small vesicles
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membranes form involved in transport of materials between organelles, exchange materials between ER, golgi apparatus, lysosomes, and the outside
13
Q
Eukaryotic
A
has a nucleus and organelles enclosed in a cell membrane
14
Q
prokaryotic
A
don’t have a membrane bound nucleus or organelles
15
Q
light microscope
A
used to make small things appear bigger by using light
16
Q
electron microscope
A
uses beam of electrons rather than light
17
Q
fluorescent microscope
A
dyes used to image only labeled portions of specimens
18
Q
confocal microscope
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high resolution version of fluorescent microscopy
19
Q
- Define the term model organism and provide 4 general traits that may make for a good
model organism
A
-a species that offers an advantage to study a process, behavior, or disease
Characteristics:high reproductive rate, large population, behaviorally interesting, morphology
20
Q
describe atoms generally and chemically
A
Atoms make molecules using covalent bonds and molecules can combine to form cells that make up tissues which make up organs. Atoms contain protons and neutrons and make covalent bonds which are super strong
21
Q
protein
A
monomer=amino acid, they form polypeptide chains, polymer=protein, helps with cell shape and organization
-proteins control cell division and flow of materials and information in and out of the cell
22
Q
carbohydrates
A
monomer=monosaccharides, they produce and store energy, polymer=polysaccharide, they provide structural support and energy storage
-carbohydrates act as an energy source and help control blood glucose and metabolism
23
Q
lipids
A
monomer=fatty acid, they influence cell and tissue metabolism, polymer=nothing
-lipids help move and store energy and absorb vitamins
24
Q
nucleic acids
A
monomer=nucleotides,they carry out metabolic functions, polymer=nucleic acids, DNA is genetic instructions
-nucleic acids carry genetic information which is read in cells to make RNA and proteins
25
primary
sequence of amino acids joined by peptide bonds (long string of amino acids)
26
secondary
alpha helix or beta sheet formed by hydrogen bonds (helices are swirly, beta sheets are folded squares)
27
tertiary
folding and coiling due to interactions among R groups and between R groups and surrounding water (helices and beta sheets intertwine together)
28
quaternary
association of two or more polypeptide chains with each other (the structure of helices and beta sheets joins together with other structures of helices and beta sheets)
29
* Describe how both shape and R-group characteristics together influence protein function
-The nature of the R groups found in the amino acids involved can counteract the formation of the hydrogen bonds which creates the 3D tertiary structure of protein
30
phosphorylation
chemical process of adding a phosphate group to an organic compound
31
kinase
group of enzymes which add phosphate
32
phosphatase
enzyme that removes a phosphate group from a protein
33
* Describe the 4 characteristics of enzymes (PRES)
-Proteins- Reusable- lower activation Energy- Selective/Specific
34
Chromosome
has many genes, many chromosomes in a cell, they are dynamic
35
Histone
family of proteins which help to package, half of total mass of chromosome, tend to be positively charged
36
nucleosome
DNA wound around a core of histone proteins, beads on a string, 8 histone protein octamer
37
Replication origin
area of DNA where replication process begins
38
Centromere
region of DNA towards center of chromosome, used during replication to separate pairs
39
Telomere
area of repetitive DNA at the end of chromosome, corrects for issue faced during replication
40
Junk DNA
genomic DNA that does not encode protein, unknown function, 99% to 20% of human DNA
41
* Describe the relationship between DNA, chromosomes, genes, and the genome
If the DNA code is a set of instructions that's carefully organized into paragraphs (genes) and chapters (chromosomes), then the entire manual from start to finish would be the genome.
42
* Describe the Meselson and Stahl experiment, including general methods and results, actual and potential
1.Grew bacteria in 14N or 15N media
2.spun bacteria in density gradient
3.heavier bands moved to the bottom
They compared bands
Experiment demonstrated that DNA replicated semi-conservatively
43
* Generally describe the process of DNA replication using the terms
Replication origin, replication fork, lagging strand, leading strand, Okazaki fragments
Replication origin is in the middle, initiator proteins help open double stranded helix, each replication origin results in 2 replication forks. Lagging strand= DNA strand that is made discontinuously, leading strand= DNA strand that is being made continuously. Okasaki fragments=term for small chunks of DNA made on the lagging strand
44
Bacterial transcription
RNA polymerase scans the DNA until it finds the promoter region. Sigma factor recognizes promoter from outside of helix, sigma factor dissociates, transcription proceeds until terminator sequence is rerached, both polymerase and RNA molecule are released, sigma factor re-associates with RNA polymerase
45
Eukaryotic transcription
3 RNA polymerases, transcription factors replace sigma factor, transcription factor binds to TATA box
46
mRNA
transfers genetic information from genes to ribosomes to synthesize proteins
47
tRNA
transfers amino acids to mRNA for protein synthesis
48
rRNA
provides structural framework for ribosomes
49
* Define RNA processing and describe ways mRNA is processed or regulated)
RNA processing=making changes to the RNA molecule that will affect the final protein product, RNA capping=special nucleotide added to 5’ end of mRNA, polyadenylation=series of adenine added to 3’ end of mRNA, RNA splicing=removal of portions of mRNA, mRNA degradation=one mRNA can be used to make many proteins
50
RNA capping
special nucleotide added to 5’ end of mRNA
51
polyadenylation
series of adenine added to 3’ end of mRNA
52
* Describe the general steps in protein translation, including how it is initiated and terminated: A site, P site, E site, small subunit, large subunit, tRNA, start codon, initiator tRNA, release factor
1. tRNA carrying the next amino acid
binds to A-site on ribosome
2. C-terminus of amino acid in P-site is
uncoupled from tRNA and joined to
amino acid in A-site
3. Large subunit moves down the mRNA
* Moving P site tRNA into E
* Moving A site tRNA into P
4. Small subunit moves down the mRNA
* tRNA in E site is ejected
* Cycle starts over again
53
DNA polymerase
replication (DNA to DNA), requires DNA template and primer
54
RNA polymerase
transcription (DNA to RNA), does not require a primer but requires transcription factors to bind to promoter and enhancer regions
55
Ribosome
translation (RNA to protein), translates encoded messages from mRNA to synthesize proteins from amino acids
56
* Describe how the structure of phospholipids and how their properties lead to bi-layer formation and the ability to self-heal a break
the hydrophilic heads face the water at each surface of the bilayer, and the hydrophobic tails are shielded from the water in the interior. They spontaneously form bilayer when faced with water and self healing tears in the the sheet expose non-polar region
For a protein to embed in a membrane, it needs a covalent attachment of a lipid
Membrane domains are functionally specialized regions of a membrane created by restricting particular proteins to an area
57
Diffusion
solution consists of a solvent and solute, molecules in solution are always in motion, passive (no energy used)
58
Osmosis
water slowly crossing the membrane, can cross more rapidly through membrane channels (aquaporins), net movement of water= from side with more water (more dilute), to the side with less water less dilute)
59
Carrier mediated transport
molecules that are large or polar cannot diffuse across membrane, carrier proteins within plasma membrane move these molecules across, require formation of non-covalent bonds, facilitated diffusion (passive, high to low, requires carrier-mediated proteins, transport proteins always exist in plasma membrane), active transport (low to high, requires ATP, coupled transporters, ATP-driven pumps, light driven pumps
60
Electrochemical gradient
determines the direction that ions will flow through an open ion channel, has two components: concentration gradient=difference in the amount of one molecule on either side of the membrane, and electrical gradient=difference in total charge on either side of the membrane. Gated ion channels are not continuously open, specific stimulus triggers to open, open briefly and then close
61
* Describe how proteins enter the nucleus, using (and defining) the following terms:
Nuclear pore, nuclear localization signal, nuclear import receptor
Nuclear pore:large, elaborate complex of about 30 proteins, anything entering or leaving must go through a nuclear pore
Nuclear localization signal:NLS, 1 or 2 short sequences of amino acids containing several positively charged, such as lysine or arginine
Nuclear import receptors:recognize NLS, direct protein to pore by interacting with tentacle-like fibrils on rim
62
* Describe the process in which soluble proteins are brought into the ER using (and defining)
the following terms:
Translocation channel, ribosome, ER localization signal, signal recognition particle (SRP), SRP
receptor, chaperone proteins
Ribosomes start to translate in cytosol and move to ER membrane after signal sequence is recognized. SRP binds growing peptide signal sequence and ribosome. SRP receptor reognizes SRP. release SRP and guides threads forming protein into ER through protein translocator tunnels. Signal sequence opens translocation tunnel. Proteins are unfolded to cross. C-terminus passes through the membrane and protein is released into lumen if soluble. Chaperone proteins inside the organelle help pull the protein across and refold it when its inside
63
* Describe the process of formation of a clathrin-coated vesicles, using (and defining) the
following terms: Cargo receptors, adaptins, clathrin, and dynamin
Cargo receptors bring cargo molecules to the cargo receptors connected to the adaptins. The dynamin brings up the bottom part to help form the ball shape of the coated vesicle(pinches it off). While this happens, a clathrin coat is created and forms the ball fully
64
* Describe how Rab proteins and SNARE proteins determine and cause vesicle fusion with the
target membrane
Rab proteins: on surface of vesicle and recognized by tethering proteins on cytosolic surface of target membrane
SNARE: transmembrane proteins after tethering, captures vesicle
-v-SNARES interact with complementary t-SNARES on target membrane docking the vesicles
65
* Describe the 3 potential fates of substance undergoing endocytosis
1.most return back to same PM that they came from
2.some go to lysosome to be degraded
3.some go to different domain of PM
-transfers cargo across the cell called transcytosis
66
* Describe the overall pathway of a glucose molecule being converted to
ATP with or without oxygen present
Steps 1-3:energy investment, glycolysis
Steps4-5:cleavage of six-carbon molecule into two three-carbon sugars
Steps 6-10:energy generation
67
* Describe the role of fermentation in supporting glycolysis
-Allow ATP to be produced in absence of O2
-NADH is oxidized to NAD to go back into glycolysis
68
* Describe the requirement for oxygen for the Kreb’s cycle to occur
Oxidative phosphorylation is required to refresh NAD and FAD
69
Chloroplast
organelle found in plants in which photosynthesis occurs
-surrounded by 2 membranes called chloroplast envelope, outer membrane=highly permeable, inner membrane=selectively permeable
70
Stroma
large inner space
71
Thylakoids
third membrane forms flattened disc-like sacs, they contain chlorophyll
72
Chlorophyll
molecule which is capable of absorbing light
73
Photosystems
large multiprotein complexes involved in the light reactions which capture and convert light energy into chemical energy
74
Light reactions:
-occur in thylakoid membrane
-goal is to make ATP to power dark reactions
inputs=light,H2O,ADP,NADP
outputs=ATP,O2,NADPH
75
Dark reactions:
-occurs in stroma
-goal is to fix/reduce CO2 to produce organic molecules
inputs=ATP,NADPH,CO2
outputs=sugars, amino acids, fatty acids
76
* Describe the similarities and differences between the electron transport chain and light
Reactions
-Like with mobile electron carriers moving electrons between respiratory centers in electron transport chain, mobile electron carriers shuttle electrons between photosystems
-goal of both is to make a H gradient
