BIOLOGY 151: EXAM 2
57 Cards in this Set
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Proto-oncogenes
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Promote cell growth
Normal genes
When mutated – they have a gain-of-function mutation
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Tumor-Supressor genes
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supress cell growth and division. when mutated they undergo a loss of function and yield tumor formation
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Gain of Function
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a mutation that causes something in the cell to always be active
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Loss of Funtion
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mutation in the cell that turns something inactive
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G1 Phase
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Cell’s enter the cell cycle
- Growth phase (G stands for
gap)
- Duplicate and synthesize
nucleotides (as many as
needed) and organelles
- Proteins and histones
Figure 3: Explanation of cancer genes and normal genes.
Figure 4: The Cell Cycle DNA is always coated with proteins
- …
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G1 Checkpoint
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Is the cell big enough?
Sufficient nutrients?
Social signals/growth cues present?
DNA undamaged?
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S Phase
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DNA replication/synthesis
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S Phase Checkpoint
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ensure synthesis was successful/no DNA damage
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G2
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growth and prep for MPhase
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G2 Checkpoint
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Replicated fully?
Any damage?
Ready for M-phase?
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M Phase
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Chromosome segregation; separations of duplicated DNA
- Prophase, Metaphase, Anaphase, Telophase
- Spindles made with help of microtubules (MTs)
- All of the chromosomes line up along the metaphase plate (middle)
- MTs from each end (attached at poles)
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M Phase Checkpoint
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Are all the chromosomes lines up correctly?
- They are then pulled apart
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Cytokinesis
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Final separation into two identical daughter cells
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Checkpoints
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they will repair or apoptosis
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p53 pathway
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Tumor suppressor and TF on chr17p
DNA damage → p53 upregulates p21 → cdk-cyclin inhibitor expression → binds cdk-cyclin complexes, preventing RB1 phosphorylation → cell cycle arrest
Can also initiate apoptosis
Associated w/ AD Li-Fraumeni syndrome
Causes t/s of GADD45 DNA repair enzym…
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Proteins
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It is important to note that structure fits
function; the shape of a protein determines its
function or job
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Central Dogma
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: DNA RNA Protein (Amino
Acid Sequence)
- RNA Polymerase makes the mRNA from
DNA
- Ribosome is what reads the mRNA to
make the protein
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Amino Acid Structure
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All amino acids are similar in their central
carbon with an H; they also all have a
carboxyl and amino group
- They differ in their R group
- Most proteins are anywhere from 100 to
2000 amino acids
- Each amino acid has a different R group (i.e.
side-chains)
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N-Terminus
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the amino group on the
first amino acid
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C-terminus
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the carboxyl group of the last amino acid in a polypeptide chain
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Keep in mind
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Keep in mind the next amino acid binds to the carboxyl end of the
previous
- We number amino acids starting from the N-terminus with one all the
way to the C-terminus; goes in numeric order
- Often, the first amino acid is Methionine (start codon)
- Noncovalent bonds include hydrogen…
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Peptide Bonds
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what hold amino acids together; they are
also covalent bonds
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Chemistry of Amino Acids
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Determined by the
chemistry of the R-groups
because the backbone is
the same for all amino
acids
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Non-Polar
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Hydrophobic
inside, or in membrane
Hydrophobic dislike
water (water hating)
A lot of carbons and
hydrogens
C-C bonds; C-H
bonds
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Polar
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Hydrophilic (soluble
proteins), outside
Hydrophilic like
water (water loving)
Nitrogen and Oxygen are common here
Figure 1: Twenty Essential Amino Acids. The Nonpolar and Aromatics are
hydrophobic. The Polar and Charged are Hydrophilic. C-O bonds;
C-N bonds;
O-H bonds;
N-H …
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Positive Charged
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Bind negative
molecules (lysine
in histone proteins)
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Negative Charged
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Bind positive
molecules
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Covalent Bonds
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formed
due to dipole moments
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Hydrogen Bonding
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can occur with water, amino acids, etc.
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Phospholypid Bilayer
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The polar heads are exposed to water (because they are highly
hydrophilic)
- The tails are highly hydrophobic and thus form a hydrophobic
environment
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Primary Structure (1°)
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The linear amino acid
sequence.
- The beginning of this structure is always the
amino end while the end of the structure is
always the carboxyl end
- The amino end always adds onto the carboxyl
end of the previous amino acid
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Secondary Structure (2°)
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The alpha helices
and beta sheets of the protein.
- Alpha helices and beta (pleated)
sheets are formed by hydrogen
bonding with the backbon
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Tertiary Structure (3°)
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he 3D structure of the protein. - Four types of bonds that you will find
Recall tertiary structure was the formation of the 3D structure due to folding
- This folding occurs due to interactions between R-groups
- Keep in mind that the bonds you can see in this level of structure …
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Tertiary Structure-Hydrogen Bonds
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Between R groups; between an R group and a backbone
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Ionic Bonds
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Bonds between those amino acids that are polar charged (a
positive with a
negative)
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Van Der Waals
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Form between hydrophobic amino acids
Also called hydrophobic interactions
Just keep the idea that hydrophobic clumps with
hydrophobic; don’t worry about the mechanism
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Disulfide Bonds
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Only covalent bond among these;
found only with cysteine
Stabilizes tertiary structure
Typically strong bonds
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Quaternary Structure (4°)
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Formation of higher structures; multiple
polypeptides
- Dimers, trimers,
etc.
- i.e. hemoglobin
or collagen
- We can view proteins
using the backbone
model (showing the
backbone), ribbon model (shows secondary structure, not the R-groups), wire model, and the space-…
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Denaturation
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Protein unfolding
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Renaturation
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Protein refolding
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Aggregation
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when proteins stick together when they aren’t supposed to
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Protein Synthesis
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in the cytosol
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Signal Sequences
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Import into the ER: Hydrophobic path at
the N-terminus
- Retention in the ER: KDEL at the C-
terminus
- Import into the mitochondria: R/K
spaced 3-4 apart
- Import into the Nucleus: Patch of R/K
- Import into the Peroxisomes: SKL
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Substrate
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Compound acted up by the enzyme.
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Products
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Compound formed by the enzymatic reaction.
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Enzyme-Substrate Complex
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Physical association of the enzyme with the substrate that facilitates the reaction.
- Substrates bind into the active site of the enzyme
- When an enzyme is used, it speeds up the chemical reactions;
- It lowers the activation energy, which is the amount of energy required to ha…
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Initiation
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Reactants bind to
the active site in a specific
orientation
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Transition State
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Interactions
between the enzyme and substrate lower the activation energy required
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Termination
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Products have lower affinity for the active site and are release; enzyme is unchanged at the end
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Vmax
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tells us how quickly the enzyme can turn over product
- This is the asymptotic line at the top
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Km
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Michaelis constant)
is the substrate concentration at 1⁄2 vmax
- So, find your Vmax and then go half-way there; then draw out a line until it hits the curve
The amount of substrate at this point in the curve is your Km
A lower Km means higher affinity/efficiency
- It is an …
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Cofactors
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nonprotein helpers; are inorganic (lack carbon) molecules, such as zinc, iron,
or copper
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Coenzymes
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organic
(contain carbon) molecules and are often vitamins and/or minerals
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Competitive Inhibitors
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compete to block the active site so the substrate can’t bind.the Vmax isn’t affected, but km is
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Noncompetitive Inhibitors
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bind enzymes with or without substrate and affect the rate of reaction (Vmax)
This does not affect
km, which is the affinity of substrate or enzyme
the km is not affected, but the Vmax is
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Transcription Process
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Initiation: DNA is opened up; one strand is used to make RNA
- Elongation: RNA Polymerase runs along the strand and makes the
RN transcript
Figure 2: The Central Dogma. Source: http://www.ncbi.nlm. nih.gov/Class/MLACou rse/Modules/MolBioRe view/central_dogma. html
- Terminatio…
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DNA strands connected
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Remember that hydrogen bonding between the bases
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BIOLOGY 151: EXAM 2