MCB 150 Exam 2

cellular respiration

breaking down food/glucose to produce energy/ATP (adenosine triphosphate)

glycolysis

breaking down glucose into pyruvate and occurs in the cytoplasm of all living cells

aerobic respiration

what cells undergo when oxygen is present

anaerobic respiration

what cells undergo when oxygen is not present, but an alternative electron acceptor exists

fermentation

what cells may undergo when oxygen is not present and no alternative electron acceptor exists

mitochondrion matrix

where enzymes of the krebs cycle reside and where pyruvate oxidation happens, DNA and ribosomes

outer membrane

50% protein, 50% lipid by weight, most abundant protein channels porins

intermembrane space (IMS)

composition of ions and small molecules is the same as the cytoplasm

inner membrane

site of ATP generation, 70% protein (no porins),

pyruvate oxidation

breaking down pyruvate by taking a carboxyl group, making CO2 to make acetyl-CoA

krebs cycle (citric acid cycle)

oxidation of acetyl-CoA, produces 2 CO2, 3 NADH, 1 FADH2, and 1 ATP

electron transport chain

series of 4 protein complexes and other molecules which transfer electrons from electron donors to electron acceptors

chemiosmosis

the movement of ions across a semipermeable membrane bound structure, down their electrochemical gradient

oxidative phosphorylation

uses oxygen to create ATP

allosteric regulator

a substance that binds to a protein at a site other than the active site, altering the protein's function

positive regulator

increases activity of the enzyme

negative regulator

decreases activity of the enzyme

feedback inhibition

activity of an enzyme is inhibited by the end product of a biochemical pathway

first committed step

the first step you can stop without interfering with more than one product

transcription

nucleotide sequence being copied to an RNA intermediate

translation

nucleotide sequence being used to build proteins

central dogma

flow of genetic information from DNA to RNA to protein

chromatin

complex of DNA and proteins that forms chromosomes in the nucleus of eukaryotic cells, "beads on a string"

Chargaff's rules

amount of dNTPs differ between organisms, but amount of A=T and C=G

Rosalind Franklin and Maurice Wilkins

got image of DNA with X-ray crystallography

James Watson and Francis Crick

discovered the double helix model of DNA

origin of replication (ori)

a sequence of bases found in prokaryotes that signals the start site of DNA replication

helicase

enzyme that untwists the double helix of DNA at the replication forks

single stranded DNA binding proteins (SSB)

keeps strands apart for replication to occur

topoisomerase (swivel)

cuts and reglues DNA strands to be able to continue moving helicases in replication

DNA strand synthesis

incoming dNTP is hybridized to parental template and phosphodiester bond formed with 3' end of chain

leading strand

the new complementary DNA strand synthesized continuously along the template strand toward the replication fork in the mandatory 5' to 3' direction away from the ori

lagging strand

the strand that is synthesized in fragments working back toward the ori

Okazaki fragments

small fragments of DNA produced on the lagging strand during DNA replication

DNA polymerase

enzyme that joins individual nucleotides to produce a DNA molecule

primase

enzyme that joins RNA nucleotides to make the primer using the parental DNA strand as a template.

primer

a short stretch of RNA opposite an ss-DNA template

DNA polymerase I

removes RNA primers and replaces them with DNA

DNA ligase

enzyme that forms phosphodiester bonds between DNA fragments together, sealing "nicks"

"X"-dependent "Y"-synthesizing enzyme

"X" = what it's using as a template, "Y" = what it is making

nuclease

enzyme that degrades (hydrolyzes) a phosphodiester linkage

exonuclease

hydrolyzes nucleic acid from the end of a chain

endonuclease

hydrolyzes nucleic acid internally

telomerase

enzyme that catalyzes the lengthening of telomeres

histones

eukaryotic protein molecules that DNA is tightly coiled around in chromatin

nucleosome

bead-like structure in eukaryotic chromatin, composed of a short length of DNA wrapped around a core of histone proteins

chromatosome

nucleosome + H1 histone

euchromatin

less condensed form of eukaryotic chromatin that is available for transcription

heterochromatin

highly condensed form of eukaryotic chromatin

sister chromatids

joined copies of the original chromosome

centromere

region of a chromosome where the two sister chromatids attach

chromosome arms

portions of the chromosome on opposite sides of the centromere

telomeres

ends of chromosomes

RNA polymerase

enzyme that carries out transcription

holoenzyme

E. coli RNA polymerase with 6 subunits

core enzyme

E. coli RNA polymerase subunits without its sigma factor

TATAAT

-10 consensus sequence

TTGACA

-35 consensus sequence

promoter

specific region of a gene where RNA polymerase can bind and begin transcription

terminator

in bacteria, a special sequence of nucleotides in DNA that marks the end of a gene

rho-dependent termination

in prokaryotes, an interaction between RNA polymerase and the rho protein to get it away from DNA

intrinsic termination (rho-independent)

RNA binds with itself, creating a hairpin loop structure

messenger RNA (mRNA)

RNA molecule that carries copies of instructions for the assembly of proteins from DNA to the rest of the cell

ribosomal RNA (rRNA)

type of RNA that combines with proteins to form ribosomes, which are the platform on which protein synthesis occurs

transfer RNA (tRNA)

type of RNA molecule that transfers amino acids to ribosomes during protein synthesis

RNA polymerase I

transcribes rRNA

RNA polymerase II

transcribes mRNA

RNA polymerase III

transcribes tRNA

transcription factors

accessory/regulator proteins that allow RNA polymerase to bind to the promoter sequence

noncoding DNA

in eukaryotes, does not contain genes that encode mRNA/proteins

spacer DNA

noncoding DNA that separates one gene from another

exons

coding segments of eukaryotic genes, "expressing sequences"

introns

noncoding DNA within a gene, "intervening sequences"

small nuclear RNA molecules and proteins (snRNPs)

remove introns and join ends of exons

spliceosome

complex of enzymes that serves to splice out the introns of a pre-mRNA transcript

lariat structure

a ring of intron segments that has been spliced out of a messenger ribonucleic acid molecule by enzymes

thalassemias

defective hemoglobin caused by inaccurate splicing of introns

alternative splicing

not using all exons, creating different mature mRNA, therefore different protein

5' cap

a modified form of guanine nucleotide added onto the 5' end of a pre-mRNA molecule, allows recognition for start of translation

kinase

enzyme that adds phosphate groups

phosphatase

enzyme that removes a phosphate group from a molecule

poly-A tail

a sequence of 50-250 adenine nucleotides added onto the 3' end of an mRNA molecule, providing stability

stop codon

codon that signals to ribosomes to stop translation, UAG, UAA, UGA

aminoacyl tRNA synthetase

an enzyme that joins each amino acid to the appropriate tRNA

ribosomes

site of protein synthesis

70S

prokaryotic ribosome

50S

large subunit of prokaryotic ribosome

30S

small subunit of prokaryotic ribosome

5S rRNA, 23S rRNA, 34 proteins

makeup of the large subunit of prokaryotic ribosomes

16S rRNA and 21 proteins

makeup of the small subunit of prokaryotic ribosomes

80S

eukaryotic ribosome

60S

large subunit of eukaryotic ribosome

40S

small subunit of eukaryotic ribosome

5.8S rRNA, 5S rRNA, 28S rRNA, 49 proteins

makeup of the large subunit of eukaryotic ribosomes

18S rRNA and 33 proteins

makeup of the small subunit of eukaryotic ribosomes

initiation factors

proteins that bring in the large subunit that completes the translation initiation complex

AUG

initiator codon, starts protein synthesis

P (peptidyl) site

binds the tRNA carrying the growing polypeptide chain

A (aminoacyl) site

binds the tRNA carrying the growing polypeptide chain

E (exit) site

binds a tRNA recently stripped of its polypeptide