Exam 2 Flashcards
What gives DNA its helical shape?
Plate stacking and Hydrogen bonding
In what way does a DNA strand grow?
5’-3’
In what way does the complimentary strand grow?
3’-5’
What are the steps in DNA replication for a leading strand?
- the DNA is unwinded or “unzipped” at an origin (replication fork)
- a short segment of RNA (primer) synthesizes and acts as a starting point for the enzyme DNA polymerase to attach to
- DNA polymerase then goes down the strand and replicates the strand with its matching base pair
- once replication is done RNA primers are then replaced with DNA by DNA polymerase
- any gaps left are then sealed together with enzymes
What are the steps in DNA replication for a lagging strand?
- the replication fork starts so that the DNA polymerase can bind and start replication
- a segment of RNA (primer) acts as a starting point for the DNA polymerase
- the DNA polymerase then has to keep unattaching and reattaching because it is moving away from replication fork instead of with the replication fork
- RNA primers have to continuously bind to act as starting points for replication, seeing as the polymerase keeps having to unattach and reattach, leaving it needing a new place to start
- once the lagging strand is replicated DNA polymerase then goes back and replaces the primers with DNA
- topoisomerase goes through and seals any nicks made to the strand during replication
What does topoisomerase’s function?
makes nicks in the double helix ahead of the replication fork to prevent it from getting too tightly wound up as the DNA is opened (releases tension), after replication it goes back and seals those nicks in order to avoid permanent damage
What keeps DNA polymerase 1 from floating away on the lagging strand whenever it has to reattach?
a protein known as the sliding clamp that holds DNA polymerase 3 molecules in place as DNA is synthesized, keeps the polymerase from floating away as it starts a new Okazaki fragment
What is an Okazaki fragment?
short sequences of DNA nucleotides which are synthesized discontinuously and later linked together by enzyme DNA ligase
What is DNA ligase’s function?
to replace the RNA primers with DNA sequences
What is a phosphodiester bond?
result of a condensation reaction between a hydroxyl group of two sugar groups and a phosphate group
Where is a phosphodiester bond found in the DNA strands?
5’ end phosphate group attaching to a 3’ end sugar
Why is the major groove where most contact is made in DNA rather than in the minor groove?
the minor groove is too narrow
What causes the DNA backbone to be highly charged and polar?
the phosphate groups
What gives the DNA helix its stability?
base stacking and Hydrogen bonding
How many rings do purines have?
2 rings
How many rings to pyridines have?
1 ring
A G-C pair is stabilized through how many Hydrogen bonds?
3
An A-T pair is stabilized through how many Hydrogen bonds?
2
What is a sequence of nucleotides on a single strand there for?
to code for the RNA which then codes for the primary protein
Do all RNA’s code for proteins?
no
What does ribosomal RNAs code for?
formation of the structure of the ribosome
What do tRNAs do?
deliver amino acids to translation, they DO NOT synthesize proteins
What are the non used regions between genes referred to as?
untranslated regions (UTR)
Describe what untranslated regions (UTRs) do.
they are sites where the enzymes will assemble to transcribe the gene
Is eukaryotic DNA packaged into a single chromosome or multiple chromosomes?
multiple chromosomes
What are specialized DNA sequences (regions) needed for?
DNA replication and chromosome segregation
True of False, the DNA chromosome is always highly condensed.
True
What are histones?
group of proteins found in chromatin
Are histones controlled?
yes, they are controlled
Are coding regions always continuous?
no, they can be fragmented
Why won’t molecular methods let the RNA out of the nucleus until it is fully correct?
because of the RNA’s nonlinear coding regions
Why would nonlinear coding regions mess up the whole DNA sequence?
there would be many regions where sequenced would be present that were not needed and that would make many unneeded amino acids
Is the process of duplication and segregation of chromosomes highly regulated? Why?
yes, because lack there of can be dangerous and could lead to many unwanted problems
What are the discreet sites where DNA replication starts called?
origin of replication
Do interphase chromosomes randomly occupy regions or are they in their own distinct regions?
own distinct regions
What causes premature aging in children?
the lamith protein
What is found in an interphase nucleus?
euchromatin
heterochromatin
nucleolus
How is the nucleolus formed?
by interaction of DNA, RNAs, and Proteins
What was the significance of beads on a string?
was an argument on how the basis of DNA has something to do with this specific formation
What is a histone octamer?
DNA wrapped around a protein core of 8 histone proteins
How many nucleotide pairs forms the histone octamer?
147
What happens on the tails of histones?
they are the site of post translational modification
What are the three forms of post translational modification?
acetylation, phosphorylation, and methylation
What causes the DNA to be 10,000 folds shorter than the full length?
Chromosome packing
What allows access to DNA in the regulation of chromosomes structure?
changes in the nucleosome structure
Do interphase chromosomes contain both highly condensed and more extended forms of chromatin?
yes
What else, other than changes in nucleosome structure, allows access to the DNA?
methylation and/ or acetylation of histone proteins
What makes heterochromatic and euchromatic regions change in the cell?
outside signals to the cell
What do histones control?
which regions of the chromatin are open for expression or not
Define Epigenetics.
control of expression that is not biases on the genetic sequences, rather it is based on heredity
What are polymerases 2 domains?
one goes down the strand lining up the template, the other finds mistakes and clips (edits) them
How many replication forks form at each replication origin?
2
What enzyme synthesizes DNA using a parental strand as the template?
DNA polymerase
Why does RNA have to prime the DNA before the polymerase can start replication?
because DNA polymerase can only bind to double stranded DNA
What enzyme replicates the ends of eukaryotic chromosomes?
telomerase
What acts as a replication machine during DNA synthesis?
a group of proteins
What enzyme unwinds the double stranded DNA to prepare it for replication?
helicase
What enzyme primes the single DNA strand with and RNA primer?
primase
How many times does the leading strand have to be primed for replication?
once
How many times does the lagging strand have to be primed for replication?
continually as it is being replicated
Do the two replication forks move in the same direction or opposite directions on the DNA strand?
opposite directions
What are the characteristics of DNA polymerase?
it polymerizes (replicates) and edits the strand it is working on
Where is one of the most common mutations that is involved in cancer?
P53
What enzyme joins the Okazaki fragments together on the lagging strand?
DNA ligase
What does ligase use to seal the nicks to give a continuous double strand?
ATP
What are telomeres?
short repeating sequences at chromosome ends
What does telomere shrinking raise the chances of?
cancer
What happens if the DNA is A-T rich?
the curve of the DNA is changed, it makes it more planar
What would happen without a special mechanism to replicate the ends of linear chromosomes?
some DNA would be lost during each cell division
Defects in telomerase can start allowing what to happen?
shorter DNA in turn wiping out genes after a period of time
What are some reasons for continual DNA damage in cells?
mutations, chemically induced errors, ionizing radiation induced errors
What is sickle cell anemia thought to be evolved for?
defense in certain areas of the world where malaria is prevalent
What enzyme requires general transcription factors in eukaryotes?
RNA polymerase
Where are mRNAs processed?
nucleus
Are the full DNA sequences transcribed into RNA or just portions of the full sequence?
portions of the full sequence
Define introns.
noncoding sequences between protein-coding genes
How are introns removed from pre-mRNA?
RNA splicing
Where are mRNA molecules eventually degraded?
cytosol
What are the chemical differences between RNA and DNA?
RNA uses ribose sugar while DNA uses deoxyribose sugar
RNA uses uracil while DNA uses thymine
What does RNA. polymerase do for DNA?
transcribes it into RNA
Can many molecules of RNA polymerase simultaneously transcribe the same gene?
yes
What are the different types of RNAs?
mRNA, rRNA, miRNA, tRNA, and other noncoding RNA
How does RNA polymerase know when to start and stop during transcription?
signals in the DNA
Where are promoter regions located?
upstream of gene sequence
Where are terminator regions located?
in the transcript
What is RNA polymerase 1’s transcribed genes?
most rRNA genes
What is RNA polymerase 2’s transcribed genes?
alll protein-coding genes, miRNA genes, and other noncoding RNA
What is RNA polymerase 3’s transcribed genes?
tRNA genes, 5S rRNA genes, and genes for many other small RNAs
What does RNA polymerase need in order to initiate transcription?
general transcription factors
Eukaryotic promoters contain sequences that promote what?
binding of the general transcription factors
Where are mRNAs processed?
in the nucleus
Where do processed mRNAs exit?
nuclear pores (arrows)
How are eukaryotic mRNA molecules modified?
5’ methyl capping and polyadenylation
Splicing is carried out by a collection of RNA-protein complexes called?
snRNPs (U1, U2, U6)
Do some pre-mRNAs undergo alternative RNA splicing to produce different mRNAs and proteins from the same gene?
yes
How are mRNA sequences decoded?
sets of 3 nucleotides
What does tRNA do in mRNA?
match amino acids to codons
Where are mRNA messages decoded?
on ribosomes
What signals the ribosomes to stop and start on the mRNA?
specific codons in the mRNA
What factors are used as antibiotics?
inhibitors of prokaryotic protein synthesis
What do ribosomes contain?
RNA, ribosomal RNA, and at least 40 different proteins
What are the 2 different parts of the ribosome?
small and large subunits
When do proteins start folding?
as they are synthesized
what reads the codons (nucleotide triplets) in transcription from RNA to protein?
anticodons
Why is the reading frame of nucleotides important?
the change or mutation of act reading Fram can cause the depletion of specific proteins needed, or make unneeded proteins
What is a point mutation?
where one nucleotide is added or removed
What shape do all tRNAs have?
L-shape
What do tRNAs couple with in order to correct the amino acids?
aminoacyl synthetase
Where are proteins produced?
on polyribosomes
What is the first amino acid on every protein?
methionine (Met)
How do ribosomes bind to the RNA for transcription?
the small subunits bind first, then the large subunit binds two the small subunit
What happens when a ribosome and protein reach the stop codon?
they disassociate from each other
Describe cytoplasmic proteins.
start initiation at the 5’ end of the RNA and codes for proteins then fall apart and disassociate
What happens to the translator?
it is either clipped by an enzyme or is kept as a protein
What are the 3 ribosomal binding sites?
E site, P site, and A site
What is the E, P, and A site(s)?
exit, polymerization, and addition
What does a hydrolysis reaction require?
energy from ATP
What are the 4 steps of the translation cycle?
shift, exit, open, repeat
Where does the shift happen?
between the large and small subunits, this opens an entry site and eliminates the exit site
What are the steps in tRNA processing?
- translation
- 5’-3’ end processing
- common nucleotide modifications
- addition of CCA to processed 3’ end
- nuclear export
How is tRNA made?
synthesized from tRNA gene through transcription by RNA polymerase
What are the steps in a polymerization reaction?
- denature template into single strands
- addition of primers to each strand for new strand synthesis
- extension of new DNA strand from primers
What is required for translation initiation?
small ribosomal subunit, initiation factor, and loaded tRNA methionine
What happens when a stop codon is reached?
it releases a factor
Can one mRNA encode several different proteins and have multiple protein signals available to it?
yes
True of false, mRNA can be degraded or translated.
true
What are the 3 post translational modifications?
acetylation, phosphorylation, and methylation
Many proteins require what in order to become fully functional?
post translational modifications
What cell component is selectively permeable and can selectively import and export molecules?
plasma membrane
What are the functions of the plasma membrane?
cell communication, cell growth, and cell motility
What are internal membranes?
compartments for specialized metabolic functions
What do internal membranes do?
import, export, and transport molecules
What two cell components have double membranes?
nucleus and mitochondria
What is the structure of a membrane?
lipid bilayer, embedded with proteins, and is dynamic
Cell membranes are selective and semi permeable, what does this mean?
they allow some molecules to pass while restricting others
What is the lipid bilayer?
flexible 2D fluid
Where does membrane assembly begin?
in the endoplasmic reticulum (ER)
What is an example of the lipid bilayer?
liposomes
What does the fluidity of the lipid bilayer depend on?
its composition
What is the fluid mosaic model of membranes?
describes cell membrane as a tapestry of types of molecules (phospholipids, cholesterols, and proteins) that are constantly moving
Membrane growth can only happen by addition of what?
addition of lipids to the pre existing membrane
certain phospholipids are confined to one side of the membrane, this results in what?
a resulting curvature that may assist in membrane budding
Do membranes retain their orientation during transfer between cell compartments?
yes
Are phospholipids and glycolipids symmetrically or asymmetrically distributed in the membrane bilayer?
asymetrically
True or false, cholesterol is evenly distributed in the bilayer?
true
A polypeptide chain usually crosses the lipid bilayer as a?
alpha helix
What is the plasma membrane reinforced by?
the underlying cell cortex
Can a cell restrict the movement of its membrane proteins?
yes
What is the cell surface coated with?
carbohydrates
What are the integral membrane proteins?
transmembrane proteins, monolayer associated proteins, and lipid linked proteins
What is the peripheral membrane protein?
protein attached
How can a transmembrane hydrophilic pore be formed?
multiple amphipathic alpha helices
What kind of carbohydrates is the cell surface coated with?
glycolipids and glycoproteins
What is an example of the reinforcement of the plasma membrane?
red blood cells (transmembrane, attachment, and spectrum-actin complex proteins)
What can the cell use to restrict movement?
cytoskeleton, extracellular matrix, and cell-cell
Define a tight junction.
junction that prevents molecules from passing through the intercellular space
Define a desmosome.
anchoring junctions bind adjacent cells together like a molecular “velcro” and help form an internal ten sion reducing network of fibers
Define a gap junction
communicating junctions allow ions and small molecules to pass for intercellular communication
What is the only way the cell membrane can moves things across it?
diffusion
Is the pH significantly lower of higher inside of the cell compared to the outside of the cell?
significantly lower
Is the ion concentration significantly higher or lower inside of the cell compared to outside of the cell?
significantly higher
How do cell signals come through?
ion exchange
What gives the membrane opportunity for a current to pass through?
the membrane potential, one positive pole and one negative pole
What to transporters do?
bind, change conformation, and move target from in to our or out to in
Lipid bilayers are impermeable to what?
ions and most uncharged polar molecules
What are the two classes of membrane transport proteins?
transporters and channels
How do solutes cross membranes?
either passive or active transport
What influences the passive transport of charged solutes?
the concentration gradient and membrane potential
What is the process of water moving across cell membranes down its concentration gradient?
osmosis
What allows an ion to pass through?
a pore, it travels highest to lowest concentration
What are aquaporins?
where water can move through
What doe the rate at which an ion passes through depend on?
size and solubility
Sodium is mostly where in reference to the cell?
outside of the cell
Potassium has a high concentration where in reference to the cell?
inside of the cell
What creates a membrane potential?
the difference in concentrations or inorganic ions across a cell membrane
Describe channels.
they open and allow flow
Describe transporters.
they can be energy dependent or independent and guide molecules across the membrane
Active transport is energy…
dependent
Inactive transport is energy…
independent
Do diffusion and electrostatic forces drive in the same direction or opposite directions?
opposite
What happens in a sodium potassium pump?
potassium goes in as sodium goes out
What are the two component forces of an electrochemical gradient?
the net driving force and a force from the membrane potential
_____ move a solute along its electrochemical gradient.
passive transporters
_____ actively transport a solute against its electrochemical gradient.
pumps
Where are H+ gradients used mainly?
plants and bacteria plasma membranes
What do electrochemical H+ gradients do?
drive the transport of solutes in plants, fungi, and bacteria
What do electrochemical Na+ gradients do?
drive the transport of glucose across the plasma membrane of animals
What mediates passive transport in a cell?
conformational changes
What are the characteristics of passive transport?
- reversible
- rate of transport is concentration dependent
- there’s no required energy
What is the Na+:K+ ratio in a sodium- potassium pump?
3 Na+ for every 2 K+
What is the sodium-potassium pump mediated by?
phosphorylated aspartate
What happens when Na+ binds to the transporter?
results in hydrolysis of phosphate and transporters is phosphorylated
What happens when K+ binds to a transporter?
results in the dephosphorylation of the transporter
Is there exchange present in a calcium pump?
no
Define symports.
transfer solutes in the same direction
Define Antiports.
transfer solutes in opposite directions
Define uniports.
facilitate the movement of a solute down its concentration gradient
Ion channels have what that control which inorganic ions it will allow to cross the membrane?
a selectivity filter
What is a voltage gated channel?
passage of current alters the membrane which alters the opening and closing of a particular protein complex
What are sterocilia?
oriented projections that allow for mechanical signals
What is the trigger zone in voltage gated channels?
axon hillock
What is a threshold?
the minimum voltage required to voltage regulated ion channels
What is absolute refractory?
start of action potential when it reverts back to resting
Can neurotransmitters be excitatory and inhibitory?
yes
What happens for a period of time in a voltage gated channel?
after a signal the nerve cell cannot react to other signals for a period of time
An electrical signal is converted into what at a nerve terminal in transmitter gated ion channels?
a secreted chemical signal
Most phsychoactive drugs affect what by binding to neurotransmitter receptors?
synaptic signaling
What does synaptic signaling enable us to do?
think, act, learn, and remember
What does glycolysis produce?
ATP & NADH
How does the citric acid cycle generate NADH?
by oxidizing acetyl groups to CO2
Many symbiotic pathways begin with what processes?
glycolysis or the citric acid cycle
Do all pathways have to enter the citric acid cycle?
yes
What does the inner membrane of the mitochondria contain?
electron transport proteins
Are most food molecules destined for the mitochondria for energy production?
yes
What are the 3 stages of food breakdown in animals?
Stage 1: mouth & gut
Stage 2: cell cytoplasm (glycolysis)
Stage 3: cell mitochondria (citric acid cycle, acetyl coA)
What is the only way fatty acids and proteins can enter the citric acid cycle?
through acetyl coA
What do simple sugars form into through glycolysis?
pyruvates
What are the net results of food breakdown in animals?
ATP
NADH
CO2
H2O
How does glycolysis extract energy?
splitting sugar
How do fermentations produce ATP with no oxygen present?
through the generation of NADH
Where are organic molecules converted into acetyl coA?
the mitochondrial matrix
What is pyruvate converted into?
acetyl coA and CO2
What is fat stored as?
triglycerides
The citric acid cycle generates NADH by oxidizing what groups to CO2?
acetyl groups
Wherever CO2 is generated ____ is also generated.
NADH
What are 3 high energy intermediates that contain nucleotides in their reactions?
acetyl coA, FADH2, and NADH
Where does the H+ gradient exist in animal cells?
matrix between the two membranes
Define catabolic.
breaking down molecules
Define anabolic.
synthesis of molecules
Plants store what in their chloroplasts?
starch and fats
Chloroplasts carry out the metabolism of what?
sugar
The mitochondria carries out what process?
oxidative phosphorylation
Energy converted from food is what process?
oxidative phosphorylation
energy converted from sunlight is what process?
photosynthesis
NADH brings what to the membranes?
high energy electrons
Chemiosmotic coupling is part of what?
symbiotic theory of eukaryotic evolution
What is chemiosmotic coupling?
links elctron transport chain to the production of ATP through molecular machine ATP synthase
Mitochondria divide like what through a Fischer process?
bacteria
Proton pumping produces a steep electrochemical proton gradient across what in the mitochondria?
the inner mitochondrial membrane
ATP has to get ___ of the mitochondria while ADP has to get ____ the mitochondria.
out; into
Cytostolic mitochondria proteins require what to enter the mitochondria?
membrane transporters
What does coenzyme-q (coQ) do?
its membrane soluble and accepts and transfers electrons within the electron transport chain
Mitochondria moves along where in the cells?
microtubules
What is associated with programmed cell death?
regulated changes impermeability of the mitochondrial membrane
Coupled transport system associated with both membranes form what?
pores and mechanisms for the proteins to get in
Where are electron transport chains located in the mitochondria?
inner mitochondrial membrane
The prevention of cell death leads to what?
tumors
Where is acetyl coA produced?
mitochondria
Polysaccharides go through wha steps before it can get to acetyl coA?
glucose steps (glycolysis to pyruvate)
What are the electron carriers in the citric acid cycle?
NADH, FADH2
The breakdown of carbon-carbon bonds yields what compound?
CO2
The movement of electrons is coupled with the…
pumping of protons
ATP synthase is a reversible coupling device that can drive both…
ATP synthesis and hydrolysis
What molecule absorbs light?
chlorophyll
Excited chlorophyll molecules funnel energy into where?
reaction center
Oxygen is generated by water splitting complex associated with what photosystem?
photosystem 2
Describe carbon fixation.
uses ATP and NADPH to convert CO2 into sugars
What happens in photo system 2?
action center, water hydrolysis, initiation of electron transport
What happens in photosystem 1?
electron is delivered here, enzymatic complex system take electron to get NADPH in the dark, carbon fixation uses NADPH to make sugars in the form of starch in plants
What are cyanobacteria?
microorganisms in stromatolites that carry out oxygen-producing photosynthesis changed Earth’s atmosphere
Where does photosynthesis take place?
chloroplasts
What can the thylakoid membrane system do?
able to capture light and turn water into oxygen
PS2
contains chlorophyll, absorbs light an donates an electron
PS1
carrier transports electron, generates NADPH, and uses hydrogen gradient to generate ATP
Describe the Calvin cycle
- carbon fixation
- reduction
- regeneration of the starting molecule
Do plants do photosynthesis AND phosphorylation
yes
What is the structure of the thylakoid?
resembles the mitochondria but has an extra compartment
What are the two stages of photosynthesis?
light dependent and light independent reactions
What kind of light do chlorophyll molecules absorb?
mostly blue and red light
What is in the middle of a Porphyrin ring?
magnesium
What is light harvesting?
where the reaction center is surrounded by a high density of chlorophyll molecules that are all absorbing light and pass it all to the chlorophyll special pair
What does photosystem 2 generate?
ATP and O2
What does photosystem 1 generate?
NADPH
What is a Plastoquinone?
a mobile electron carrier
Does photosystem 1 split the water?
no
Where does the special pair in photosynthesis 1 receive its electrons?
Photosystem 2
What is carbon fixation catalyzed by?
rubsico
ATP & NADPH from light dependent reaction is used in the cycle to form what?
glyceraldehyde 3-phosphate (from CO2 and H2O)
What is the only energy lost in the carbon fixation cycle?
heat from all of the reactions
Do plants store glucose?
no, starch
How do chloroplasts store sugar?
in the form of carbohydrates and fatty acids
Chloroplasts and mitochondria collaborate to supply cells with what?
metabolites and ATP
