Cell Structure Final Exam

primary transcript

a newly produced RNA molecule

RNA processing

necessary chemical modification for newly produced RNA before it can function in the cell, generates a “mature” RNA product

mRNA processing in eukaryotes

involves capping, addition of Poly (A), and removal of introns

why bacteria are translated as they are transcribed

because there is no nuclear membrane

heterogeneous nuclear RNA (hnRNA)

very long primary transcripts that are usually 2000- 20,000 nucleotides, a mixture of mRNA and pre-mRNA

pre-mRNA

precursors to mRNA, processed by removal of sequences and addition of 5’ caps and 3’ tails

5’ cap

a guanosine that is methlated at position 7 of the purine ring, bound to the RNA by 5’ to 5’ linkage

contributes to mRNA stability by protecting the RNA from nucleases, plays a role in positioning the RNA on the ribosome for initiation of translation

poly(A) tail

ranges from 50 to 250 nucleotides long

protects the mRNA from nuclease attack, required for export of the transcript to the cytoplasm, may also help ribosomes recognize and bind to mRNAs

poly(A) polymerase

adds the poly(A) tail

AAUAAA

a signal for addition of the poly(A) tail, located just upstream of the polyadenylation site

exons

sequences that appear in the final mRNA

introns

present in most protein-coding genes of multicellular eukaryotes

RNA splicing

the process of removing introns and joining the exons

branch point

one additional sequence near the 3’ end of the intron, contains an A residue

splice sites

specific nucleotide sequences at the boundaries of introns and exons in a pre-mRNA that are recognizd by the splicing machinery to remove introns and join exons

spliceosomes

catalyze intron removal, consists of 5 types of RNA and more than 200 proteins

small nuclear ribonuclear protein complexes (snRNPs)

RNA-protein complexes in the cell nucleus that are the building blocks of the spliceosome

snRNA

non-coding RNA molecules in the nucleus of eukaryotic cells that primarily function in pre-mRNA splicing

spliceosome assembly

1. binding of U1 to pre-mRNA

2. U2 snRNP binds to pre-mRNA

3. U4/U6 and U5 snRNPs bind

4. RNA is cleaved at 5’ splice site and lariat structure is formed

5. RNA is cleaved at 3’ splice site, exons are joined, and an EFC is added

6. excised intron is degraded

they are assembled by sequential binding of snRNPs to pre-mRNA

lariat

formed from excised introns during RNA splicing

exon junction complex (EJC)

required for efficient export of the mRNA, influence regulatory events like degradation of mRNA

alternative splicing

a process where a single gene can produce multiple different proteins by joining different combination of exons from the initial pre-mRNA transcript

nuclear RNA export factor (NXF 1)

interacts with cap-binding complex and exon junction complex so the mRNA cargo can exit the nucleus and enter the cytosol

cap-binding complex (CBC)

proteins that bind to the mRNA 5’ cap

triplet code

combinations of three bases specify amino acids, the genetic code

degenerate code

particular amino acids can be specified by more than one triplet

nonoverlapping

the reading frame advances three nucleotides at a time

codons

RNA triplets, read and written in a 5’ to 3’ manner

start codon

AUG

stop codons

UAA, UAG, UGA

unambiguous

every codon has only one meaning

degenerate

multiple different three-nucleotide codons can specify the same single amino acid

ribosomes

carry out the process of polypeptide synthesis

tRNA molecules

align the amino acids in the correct order, an adaptor that binds both a specific amino acid and the mRNA sequences that specify the amino acid

each one is linked to its amino acid by an ester bond

aminoacyl-tRNA synthetases

attach amino acids to their appropriate tRNA molecules, the tRNA is called charged and the amino acid is called activated, there are 20 different ones in cells

mRNA

encode the amino acid sequence information

protein factors

facilitate some of the steps of translation

ribsosome structure

built from dissociable subunits, the large and small subunits

ribosome site for protein synthesis

mRNA-binding site, A, P, and E sites

A (aminoacyl) site

binds tRNA with attached amino acid

P (peptidyl) site

where the tRNA carrying the growing peptide resides

E (exit) site

from which tRNAs leave the ribosome after discharging their amino acid

anticodons

permit tRNA molecules to recognize codons in mRNA by complementary base pairing

where translation of the polypeptide begins

N-terminus

initiation factors (IF1, IF2, and IF3)

bind to the small (30S) ribosomal subunit

Shine-Dalgarno sequence

consists of 3-9 purines located upstream of the start, the mRNA binds in the proper orientation due to this sequence

N-formylmethionine (fMet)

used to initiate translation; only its carboxyl group can bind to another amino acid

initiator tRNA

binds the P site of the small subunit by action of IF2 plus GTP

70S initiation complex

formed when IF3 is released and the 30S initiation complex binds to the large (50S) subunit

internal ribosome entry sequence (IRES)

a sequence of mRNA that allows ribosomes to initiate protein synthesis internally, independent of the 5’ cap

steps of elongation

binding of aminoacyl tRNA to the ribosome

peptide bond formation 

translocation

binding of aminoacyl tRNA to the ribosome

brings a new amino acid into position to be joined to the peptide chain

peptide bond formation

links the amino acid to the growing polypeptide

elongation factors

EF-Tu and EF-Ts are necessary for elongation to begin

location of the start codon as elongation begins

P site (the next codon is at the A site)

what begins elongation

tRNA with an anticodon complementary to the second codon binds the A site

translocation

the process in amino acid synthesis where the ribosome moves along the mRNA strand by one codon after a peptide bond is formed

protein release factors

recognize stop codons and stop translation, bind mRNA stop codons at the A site

molecular mimicry

the phenomenon where the shape of protein release factors is similar to tRNAs

mutation

any change in nucleotide sequence of a genome

base-pair substitution

can alter a codon (this is the case in sickle-cell anemia)

missense or nonsynonymous mutation

encodes for the “wrong” amino acid (changes an amino acid)

nonstop mutation

when a base-pair substitution alters a stop codon to an amino acid codon

nonsense mutation

the mutation changes an amino acid codon to a stop codon

indels

genetic mutations that result from the insertion or deletion of one or more DNA base pairs in a DNA sequence

frameshift mutation

caused by the insertion or deletion of nucleotides in a DNA sequence, but not a multiple of three

silent or synonymous mutations

affect the third base of the codon and results in no change of amino acid

nonsense-mediated decay

used in eukaryotic cells to destroy mRNAs containing premature stop codons, mammals use the EJC to do this

nonstop decay

an RNA-degrading enzyme binds the empty A site of the ribosome and degrades the defective mRNA

result of an mRNA lacking a stop codon

translation becomes stalled

tmRNA

an RNA that has a tRNA domain that gets charged, and an mRNA domain that has a stop codon

posttranslational modification

in bacteria, N-formyl group is removed and the methionine at the N-terminus is often removed

in eukaryotes, the methionine at the N-terminus is often released

central nervous system (CNS)

consists of the brain and spinal cord

peripheral nervous system (PNS)

comprises other sensory or motor components

main types of cells in the nervous system

neurons

glilal cells

neruons

send and receive electrical impulses (nerve impulses)

sensory neurons

responsible for the detection of stimuli

motor neurons

transmit signals from the CNS to the muscles and glands, have multiple branched dendrites and a single long axon

interneurons

signals and transmits information between parts of the nervous system

glilal cells

encompass a variety of cell types, are the most abundant type of cell in the CNS

microglia

fight infections and remove debris

oligodendrites and schwann cells

form the insulating myelin sheath around neurons of the CNS and peripheral nerves

astrocytes

control access of blood-borne components into the extracellular fluid around the nerve cells, forming the blood-brain barrier

neuron cell body

includes the nucleus and other endomembrane components

dendrites

receive signals

axons

conduct signals

myelin sheath

a fatty, insulating layer that surrounds nerve axons, allowing electrical impulses to be transmitted quickly and efficiently down the nerve

nodes of Ranvier

a gap in the myelin sheath of a nerve

synaptic boutons

transmit the signal to the next cell, a neuron, muscle, or gland

purpose of myelination

it decreases the ability of the neuronal membrane to retail electrical charge (decreases capacitance), allows nerve impulses to spread farther and faster

synapse

the junction between a nerve cell, gland, or muscle cell

neurotransmitters

chemical messengers that carry information across the synapse

presynaptic cell

the cell producing the signal

postsynaptic cell

the cell receiving the signal

membrane potential

a difference in electrical charge across the cell’s plasma membrane

resting potential

the membrane potential of a neuron not sending signals (at rest, cells normally have excess negative charge on the inside and positive charge on the outside of the cell)

Na⁺/K⁺ pump

maintains the voltage by pumping sodium ions out of the cell and potassium ions into the cell

leak channels

allow potassium to diffuse out of the cell, increasing the numbers of anions left behind without counterions (this is how the resting membrane potential is maintained)

action potential

a rapid, temporary electrical signal that travels along the membrane of excitable cells

during, the membrane potential changes from negative to positive and then back again in a very short time

patch clamping

permits the recording of ion currents passing through individual channels, developed by Erwin Neher and Bert Sakmann