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94 Cards in this Set

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gene =
series of DNA nucleotides

**generally, ONE gene => ONE pp, mRNA, rRNA, or tRNA**
prokaryotes have one copy
*of each gene*

while euk's have >1 copy of some genes
euk infrastructure:
nucleus, mitochodria, and other membrane-bound organelles

larger
prok infrastructure:
mesosomes;

no nucleus or other complex, bound organelles
both euk's and prok's have
ribosomes
central dogma:
DNA => RNA => protein
a small variation in a genome
can make a huge difference
genome =
the complete set of genes of an organism

can also refer to the content of one set of chromosomes
DNA
a nucleic acid made up of many nucleotides which differ from each other only by their N-bases

(the P's and pentoses of all the nucleic acids are the same)
"upstream" (DNA):
toward the 5' end
DNA is written
5' to 3'

at the end of 3', C3 is attached to an OH
DNA runs antiparallel
side by side but in opposite directions
"base-pairing"
the H-bonding between nitrogenous bases

length of DNA is measured in base-pairs
A2T,
C3G
Replication
ONCE in a cell's life cycle, (not life) it replicates its DNA

it's semi-conservative; one new strand, one old strand paired at the end
replisome
group of proteins that governs replication
replication proceeds in
BOTH directions from an origin

each direction produces a leading strand and a lagging strand
**a single euk chromosome contains multiple origins on each chromosome**
prok's have a SINGLE ORIGIN on their circular chromosome
***DNA-polymerase can only run 3' to 5' ***
that's why the lagging strand occurs
with the lagging strand, DNA-polymerase starts adding nucleotides to the RNA primer CLOSEST to the helicase
and works its way back
***in what direction does DNA-polymerase read the original strand?***
3' to 5'

so that the new strand is made 5' to 3'
DNA-polymerase
puts the nucleotides on to make the new strand

but CANNOT INITIATE a new strand; **needs RNA primer**
DNA-polymerase requires
a primer

primase creates the RNA primer
DNA replication is both
fast and accurate
exonuclease
a subunit of DNA-polymerase

removes nucleotides from the new strand if they are mismatched , b/c it proofreads
telomeres
TTAGGG repeated, that protects chromosomes from being eroded by multiple rounds of replication
where does transcription take place?
Either in the nucleus or mit. matrix, b/c DNA can't leave them
initiation
beginning of transcription
prok's have ONE type of initiation factor

(also: one copy of each gene, one origin of replication)
euk's have three, one for each type of RNA
***promoter***
a sequence of DNA nucleotides *within the strand* that tells RNA-polymerase where to begin transcription

**transcription requires a promoter**

once the RNA-polym recognizes the promoter, elongation can start
*RNA-polymerase transcribes ONLY the _________________
TEMPLATE strand of the double helix*

(the coding strand resembles the universal code sequence of RNA)
errors in transcription are higher than in DNA replication
but b/c it's in RNA, it's not passed down to progeny
RNA-polymerase moves along the 3' to 5' direction,
which means the new strand that it BUILDS is 5' to 3'
termination of transcription
requires a **special termination sequence** and special proteins to dissociate RNA-polymerase from DNA
****the amount of a given protein within a cell is related to how much of its mRNA is transcribed****
negative example: mRNA is degraded soon after transcription, so no more of that specific protein is made

positive example: many of the same kind of protein can be transcribed from a single mRNA => amplifying effect
genetic regulation occurs at transcription
genes are activated or deactivated at transcription

via *activators* or *deactivators*, which bind to DNA close to the promoter
operon
prok's only

a sequence of bacterial DNA containing an operator, a promoter, and related genes

the genes of an operon are transcribed on one mRNA

the operator, when bound with a repressor, makes it so that the operon's DNA is not transcribed
for prok's, what determines which genes get turned on or off is
the external environment
prok. mRNA copies several genes together in a single transcript
=> proteins that work together being translated at the same time to work on the same function
euk mRNA codes for only one
protein
in prok's, mRNA will be translated directly to protein,
while tRNA and rRNA go through processing

in euk's, all three go through processing
initial mRNA arrived at via transcription is called the *primary transcript*
aka pre-mRNA
pre-mRNA is processed in 3 ways:
1. addition of nucleotides

2. deletion of nucleotides

3. modification of nitrogenous bases
before the **euk** mRNA is completely transcribed,
the 5' end is capped

5'-cap = attachment site in protein synthesis,

as well as protection against degradation

the 3' end is a Poly-A tail, also to protect from degradation by exonucleases
*pre-mRNA is much longer than*
the mRNA that's actually translated into a protein
**before leaving the nucleus, the primary transcript is split into introns and exons**
**introns stay in the nucleus, get degraded

exons leave it to be translated**
snRNP's
**enzyme-RNA complexes**

make the spliceosome

cuts the introns off the pre-mRNA, splices the exons together

exons may be spliced in different orders to code for different proteins => variety
the sequences of DNA that code for mRNA introns and exons
are also called Introns and Exons
to denature DNA means to
separate the two strands of the double helix

via high heat, high [ion], low pH
nucleic acid hybridization:
DNA prefers to be double stranded and will look for a complementary partner

=> DNA-DNA, DNA-RNA (if the second strands are complementary)

(RNA-RNA also possible)
restriction enzymes
cut nucleotides out at specific sequences
methylation is usually associated with
inactivation of genes

but also used to protect good DNA from the bacteria's own restriction enzymes
restriction site
DNA sequences that a bacteria will cut with restriction enzymes, for example if a sequence is viral

restriction sites are typically palindromic - the sequence reads the same forwards and backwards
most restriction enzymes cleave DNA unevenly,
leaving a single strand with no complement out in the open

ends like these can connect to other single strands
recombinant DNA
DNA formed by combining parts from different organisms/chromosomes
scientists create recombinant DNA, use a vector to transfer it to bacteria
vector = vehicle, typically a plasmid
plasmid
a segment of DNA independent of a bacterium's chromosomes and capable of replication
once a vector is inside a bacterium
you reproduce the bacterium, thereby reproducing your recombinant DNA
library =
collection of bacteria possessing your recombinant DNA

(to clone means to derive a population from a single cell)
PCR
polymerase chain rxn

**much faster way of cloning**

DNA to be cloned is placed into a mixture with many copies of DNA primers,

- the mixture is heated to 95 C to denature the DNA

- then cooled to 60 C => the primers hybridize to the DNA

- nucleotides and heat-resistant DNA polymerase added, mixture heated to 72 C

=> polymerase doubles the amount of DNA

==> then repeat this procedure many times with the same polymerase to continue doubling your DNA
Southern blotting
identifies specific sequences of DNA by nucleic acid hybridization

1. chop up DNA

2. use an electric field to separate pieces according to size

3. blot onto a membrane

4. add a radioactive probe made from DNA or RNA, which attaches (hybridizes) with the target fragment

5. visualize it with radiographic film
Northern blotting
just like Southern blotting, but to find RNA
Western blotting
detects proteins with antibodies
RFLP
restriction fragment length polymorphism

humans have different restriction sites

used to identify criminals
the genetic code is unambiguous and degenerative;
unambiguous = one codon corresponds to one AA

degenerative = more than one codon can code for a specific AA
the start codon:
AUG
the stop codons:
UAA, UAG, UGA

aka termination codons
***understand that a single codon always codes for only one AA;***
but there may be more than one codon that codes for a certain AA
a sequence of nucleotides is written
5' to 3'

***
translation
protein synthesis

all three major RNA's participate:

- mRNA is the template, tRNA sequesters the AA that corresponds to its anticodon, and rRNA (with proteins) makes up the ribosome
ribosome
consists of a large subunit and small subunit

prok. ribosomes: 30S and 50S subunits => 70S

euk. ribosomes: 40S and 60S => 80S
nucleolus
a special organelle that manufactures ribosomes

(prok's don't possess a nucleolus)
what's tRNA's "start" anticodon?
**CAU**

the opposite of AUG start codon, and read backwards (so that C~G, etc.)
initiation (of translation)
- a tRNA containing the start anticodon sequesters methionine (which corresponds to AUG) into the P-site

- the initiation complex forms as large and small (and proteins) join together
elongation (of translation)
- a tRNA with an AA comes into the A-site (*at the expense of two GTP's*)

- the C-terminus of methionine attaches to the N-terminus of the next AA via dehydration; the second tRNA now has both AA's

- translocation: the ribosome shifts 3 nucleotides along the mRNA toward its 3'; the tRNA that carried methionine moves to the E site; the tRNA with both of the AA's moves to the P site
(translocation requires another GTP)

- next tRNA with next AA comes in

- **the elongation process continues until a stop codon reaches the P site**
termination (of translation)
the polypeptide is freed from the tRNA

and the ribosome breaks up
even as the polypeptide is being translated, it's folding
assisted by chaperones
post-translational modifications:
- sugars, lipids, or P's may be added to AA's

- chain may be cleaved

- other pp's may join to form quaternary structure
***translation begins on a free-floating ribosome***
***a signal peptide (20-AA sequence) at the beginning of the tranlated pp may direct the ribosome to attach to the ER,

in which case the pp is injected into the lumen

the signal peptide is recognized by the signal-peptide recognition particle (SRP)***
if, during translation, the ribosome attaches to the ER,
the pp is destined for the ER lumen

pp's injected into the lumen may be secreted from the cell via the Golgi
OR remain partially attached to the membrane
cancer
unrestrained growth of cells

tumor = mass of cancer cells; malignant if it impairs organ function
metastasis
cancer cells separate from the tumor and enter the circulatory system, establish tumors in other parts of the body
proto-oncogenes:
*genes* that stimulate normal growth in human cells

can be converted to oncogenes by UV radiation, chemicals, or simply random mutations
oncogenes:
genes that cause cancer
mutagens that cause cancer are called
carcinogens
in animals, DNA is found only in
the nucleus and the mitochondria
histones
proteins around which DNA wraps
nucleosome
8 histones wrapped in DNA
chromatin
the entire DNA/protein/little bit RNA complex

supercoiled into chromosomes

chromosomes must be uncoiled to be transcribed
euchromatin
chromatin that can be uncoiled and transcribed

only coiled during nuclear division
there are 46 chromosomes in the nucleus of human cells
both before replication and after replication, by convention
diploid means
the cell contains homologous pairs
any cell that doesn't contain homologous pairs =
haploid cell
homologues
in humans, each chromosome possesses a partner that codes for the same traits

although the traits are the same, the actual genes can be different

e.g. same trait is eye color, but one chromosome codes for blue eyes, the other for brown