BIOSC 0160 FINAL EXAM STUDY GUIDE
All certain *
Experiment:a question which science posesto Nature
livingthings share attributes SPONCH
Measurement:
recordingofNature's answer 1. Response
to the environment (natural selection & evolution) importantto human
2. Cellular Structure (structure --
function) biochemistry
*
Dr. Robert's 5Rules 3.Replication(Information flow,
exchange& storage)
4. energy to maintain structure)
1. evolution
Energy(ability to
acquired use
2. homeostasis 5. Homeostasis in systems)
(emergent
properties
3. OSMOSis (blood volume blood
-
pressure)
4.Conformation (shape -
unique function) < The Structure of DNA). Watson & Crick: double helix
5. Trade-o ffs Mendel's "heridarity factors" associated with specific traits
(genes)
-
4
down regulation:
plenty signal, so reduce
quantity hypothesis
"One-gene-one-polypeptide" (Beadle & Tatu m)
4
is faint, so
postulated that determine structure of polypeptide
up signal
regulation: putup more
genes -
ability &
blw reproductive (there is an
genes- carried on chromosomes
production
clutch size)
optimum
chromosomes
=
DNA+ proteins
Mendel factors" associated with specific traits
"hereditary genes
-
Ist
law: Segegration Griffith:virulence can be transferred from dead bacteria -
cells ofa non-virulent strain
4 heat
duringmeiosis, of live heat-killed +
the alleles a gene pair separate equally lives-strain
strain R-strain
↓ killeds-strain S-strain
into (2 copies 1 from each parent) death healthy healthy death
-
gametes
means that each carries allele type
gamete only one
of the parent'sgene to its Avery,McLeod, McCarthy:
DNA is element
pair offspring the
transforming
·
before meiosis I, each of the
homologous
chromosomes by subjectingsamples to catabolic enzymes for RNA & protein
replicates (makes sister chromatids)
RNase Protease DNase
at the end of meiosis I, the 2 chromosomes ↓ ↓ ↓ ...
DNA, no virulence
are segegrated no
transformed transformed
into separate cells xtransformation
daughter
S-strain bacteria S-strain bacteria
at the end of meiosis II, each haploid gamete contains one
&
member of each pair of homologous chromosomes,
Chase:
thus one allele for each
gene (four haploidgametes) Hershey& DNA: primary genetic
material (1952)
Law of Assortment
Independent
·
usedphosphorons
& sulfur
each chromosome sorts I if only blu proteins&DNA DIC both contains
independentlyduringmeiosis nitrogen, could not
distinguish Nitrogen
RR RR used viral infection to identify DNAas the infections
Ur Ur
cycle agent
YYyy YY
yy
32P label DNA. 355 label protein
-
2 L
RRFr RRFr phosphorouswas found in cells, became radioactive
YY yY YY
yy
<not sulfur
v
r,
2
RY RYry ry By
Ey Only 32P was recovered from bacteria -
transformation requiresDNA
4 than if the are other
When followingmore a single trait, attacks
Bacteriophage: bacteria
*
genes
bacteria & use them phage
on
separate chromosomes, all outcomes are equally likely Phage:viruses
* that infect to create more
Base Purines pyrimidines Chargaff
Base
P (T 2]
+
(A
=
G]
+
Base +
Sugar - t P
- A T
STY(A]=
ribose or
deoxyribose Nucleoside
Nucleotide [G] [C] =
OH
S
[A+T] (G =
+C]
phosphate G (sometimes!)
H2C5' 0 OH'
4
* I'base
H
H H
PrimaryStructure: DNA is formed by nucleotides in a backbone connected
GC 3 hydrogen
fla+
=
+
H
by covalent bonds blu the 3'c on ribose & the phosphate
attached
next
3 2
T androgen
=
nucleotide's OH 1 to the bit of the next nucleotide
phosphate group
secondarystructure: (double helix) function of the Hbonds thatform bly the creates
major & minor grooves
↓
purine-pyrimidinepairs mostDNA-protein
interactions
, semi-conservative Replication ->
only matches the observations
hydrogen
bonds: link nitrogenousbases
· on speed & efficacyof replication
bonds:form
phosphodiester the DNAbackbone; requires more
energyto break u
·
Conservative Replication
DNA Replicationduring S-phase
·
u
mitosis
·
M Meselson Stahl: semiconservative
-
Dispersive Replication
G2 used isotopesof nitrogenthat could be incorporated
G1
-
DNASynthesis u
bacterial
into
growth& separated on gradients :
S
Topois omera seto separate strands * of
ori-origins replication
-
Multiple
helicase
Helicase -
helix enzyme; untwist *
replication forks move away from each other
↓
Single-strand
bindingprotein
-
hold strands apart primace
↓
Frimase -
make a
primer (session of RNA) DNA Polymerase DNA
polymerase efficiency
is increased by the protein ring known
↓
DNA Polymerasefinds RNA primer; -
reads old strand, oversee as the "slidingclamp"
matching Exonuclease
3'end
pairs;adds new nucleotides to
growingstrand as ↓ binds to the DNA
cenergy) DNA
which results of ligase
triphosphates in release pyrophosphate 4DNA Polymerase binds to DNA-clamp complex
"
DNA ligase tie(ligate) Okazaki fragments
-
keeps the DNA polymerase stay bound to DNA
4
who clamp: 7100 phosphodiesterbonds
[Steps
of Replication] we clamp: 15000 bonds
1. DNAis untwisted, unzipped& held apart(topoisomerase,helicase. SSBP(
2. Primace creates short (often RNA) to match the
primer sequences open DNA
strand
-
3. DNA
Polymerasesadd new nucleotides to the free 3' ends of each "finishing problem" does not affect bacteria bic of its circular chromosome
primer
With every replication,
4. DNAPolymerases pop out
primers & add new nucleotides in their
space laggingtelomere gets shorter, no
place
5. DNAPolymerasescontinue to the 3' ends of DNA to bind RNA
addingnew nucleotides primer
4
ties
6. DNA
ligase fragments
together
Out
keeps CUHing DNA
primersthan Codinginfo lost (senescence, death)
lagging requires many more
leading eventually.
ligase is more active on laggingstrand prevented by telomerase
has itto
DNApol-I: self check mechanism that confirms matching antiparellel strands of DNAallows
copy of itself
a *
proper make exact
during new strand assembly
Mismatch pairs or damaged nucleotides are found by repair "black
Alkaptonuria: urine disease"
proteins& removed Mendelian autosomal recessive inheritance
<bacterial *the
relationship
blw
gene& metabolic product
was further codified by experiments
single "chromosome" &
single ori with Neurosporamold
·DNApolymerase III adds nucleotides to the & DNA anneals mutant strains developedthat require nutritional supplementation
primer ligase
4
the Okazaki while
fragments together Polymerase I removes
DNA the
primer matrix: results demonstrate the order of metabolic processes requiredfor growth
One
gene,one-enzyme
<Central DogmaL
·Genomic DNAis sequesteredin nucleus
genes are synthesized,processed
RNA of individual in the nucleus ·RNAviruses can use
(single-stranded)
I
themselves as
·
transcripts
In mRNA -
translated into for transcription
cytoplasm, polypeptide template
& sent to
Polypeptides
are processed destination Retroviruses use an to make
·
·
can enzyme, reverse transcriptase,
a DNA of their RNA
copy genome
, read 3'-5
& tRNA & DNA3' 5'
Ribsomal RNACrRNA) Cytoplasm binds mRNA proteinsynthesis
I
built5'-3'
MRNA 5' 31
MessengerRNA (mRNA) cytoplasm carrier of
gene sequence Tran sl ation
TransferRNACtRNA) cytoplasm adaptor blu mRNA &
protein sequences
Transcription
MicroRNA [miRNA) nucleus/cytoplasm regulatestranscription & translation 1. Initiation
I Elongation
Small 2.
interferingRNA RNAS Transcription
&
(SiRNA)
nucleus/cytoplasm regulates other
Processing
3.Termination
Small nuclear RNA Nucleus mediates MRNA
CSURNA) processing
Creverses
-> apply mRNA to DNA
DNAhybridization splicing is predictable,removal subunits that
may be included during
some of the gene is translated into finished protein a diff. Transcription
event
only
(noncoding"
introns")
&
Ap poly A tail added to MRNA Transcription RNAEditing
modified GTP promoter ·SNRNPs: used to fold
(splice)
protects MRNA transport & serves as a
·
TATA
BOX Introns & Exons
turing
landmark duringtranscription ·RNA Polymerase
·MRNA
Termination Sequence * ribosome:
staging area for polypeptidesynthesis
translation Asite: "Arrive"
5'Cap &
poly Atail
first nucleotides P site: "process"
only the are requiredto specify
the amino acid E site: "exit"
·tRNAs contain
bindingsites for both nucleic acid & protein termination, instead of tRNA, stopcodons bind a "release factor"
to the ER surface & release
canticoding
matchingantiparallel
-
synthesizing export proteins bind
the lumen
polypeptideinto its
synthetase
Aminoacyl-tRNA is responsible for loadingamino acids
Onto their appropriate tRNA
(charges
tRNA) Endomembrane system:
1. amino acid is ATP continuous membrane nucleus-endoplasmic reticulum
chargedwith
2. Pyrophosphate
is released nucleus. ERCSmooth, rough), Golgi apparatus, lysosomes, endosomes, vesicles
3.Activated aminoacid- AMP binds the matchingtRNA,
for the synthesizedin
AMP is released GolgiApparatus:
responsible modification of material the ER
4. The highenergy bond bIw tRNA & amino acid fuels cis-receives productsfrom ER; trans releases products
in vesicles
peptidebond formation Phosphorylation:
added phosphate
group
alter the shape ofthe protein
Glycosylation:
adding sugars is importantfor &
targeting recognition
to fold
ER
Rough protein structure clearing the polypeptide
proteolysis: allows the
fragments into diff. Shapes
studded w/ ribosomes 1. Primary
& are sites for 2. helix
protein synthesis Secondary:
2 &
SMOOthER 3.Ter ti a r yH: bond & Disulfide bonds
site for & 4.
lipid synthesis
·
Quaternary
chemical modification of
proteins
All certain *
Experiment:a question which science posesto Nature
livingthings share attributes SPONCH
Measurement:
recordingofNature's answer 1. Response
to the environment (natural selection & evolution) importantto human
2. Cellular Structure (structure --
function) biochemistry
*
Dr. Robert's 5Rules 3.Replication(Information flow,
exchange& storage)
4. energy to maintain structure)
1. evolution
Energy(ability to
acquired use
2. homeostasis 5. Homeostasis in systems)
(emergent
properties
3. OSMOSis (blood volume blood
-
pressure)
4.Conformation (shape -
unique function) < The Structure of DNA). Watson & Crick: double helix
5. Trade-o ffs Mendel's "heridarity factors" associated with specific traits
(genes)
-
4
down regulation:
plenty signal, so reduce
quantity hypothesis
"One-gene-one-polypeptide" (Beadle & Tatu m)
4
is faint, so
postulated that determine structure of polypeptide
up signal
regulation: putup more
genes -
ability &
blw reproductive (there is an
genes- carried on chromosomes
production
clutch size)
optimum
chromosomes
=
DNA+ proteins
Mendel factors" associated with specific traits
"hereditary genes
-
Ist
law: Segegration Griffith:virulence can be transferred from dead bacteria -
cells ofa non-virulent strain
4 heat
duringmeiosis, of live heat-killed +
the alleles a gene pair separate equally lives-strain
strain R-strain
↓ killeds-strain S-strain
into (2 copies 1 from each parent) death healthy healthy death
-
gametes
means that each carries allele type
gamete only one
of the parent'sgene to its Avery,McLeod, McCarthy:
DNA is element
pair offspring the
transforming
·
before meiosis I, each of the
homologous
chromosomes by subjectingsamples to catabolic enzymes for RNA & protein
replicates (makes sister chromatids)
RNase Protease DNase
at the end of meiosis I, the 2 chromosomes ↓ ↓ ↓ ...
DNA, no virulence
are segegrated no
transformed transformed
into separate cells xtransformation
daughter
S-strain bacteria S-strain bacteria
at the end of meiosis II, each haploid gamete contains one
&
member of each pair of homologous chromosomes,
Chase:
thus one allele for each
gene (four haploidgametes) Hershey& DNA: primary genetic
material (1952)
Law of Assortment
Independent
·
usedphosphorons
& sulfur
each chromosome sorts I if only blu proteins&DNA DIC both contains
independentlyduringmeiosis nitrogen, could not
distinguish Nitrogen
RR RR used viral infection to identify DNAas the infections
Ur Ur
cycle agent
YYyy YY
yy
32P label DNA. 355 label protein
-
2 L
RRFr RRFr phosphorouswas found in cells, became radioactive
YY yY YY
yy
<not sulfur
v
r,
2
RY RYry ry By
Ey Only 32P was recovered from bacteria -
transformation requiresDNA
4 than if the are other
When followingmore a single trait, attacks
Bacteriophage: bacteria
*
genes
bacteria & use them phage
on
separate chromosomes, all outcomes are equally likely Phage:viruses
* that infect to create more
Base Purines pyrimidines Chargaff
Base
P (T 2]
+
(A
=
G]
+
Base +
Sugar - t P
- A T
STY(A]=
ribose or
deoxyribose Nucleoside
Nucleotide [G] [C] =
OH
S
[A+T] (G =
+C]
phosphate G (sometimes!)
H2C5' 0 OH'
4
* I'base
H
H H
PrimaryStructure: DNA is formed by nucleotides in a backbone connected
GC 3 hydrogen
fla+
=
+
H
by covalent bonds blu the 3'c on ribose & the phosphate
attached
next
3 2
T androgen
=
nucleotide's OH 1 to the bit of the next nucleotide
phosphate group
secondarystructure: (double helix) function of the Hbonds thatform bly the creates
major & minor grooves
↓
purine-pyrimidinepairs mostDNA-protein
interactions
, semi-conservative Replication ->
only matches the observations
hydrogen
bonds: link nitrogenousbases
· on speed & efficacyof replication
bonds:form
phosphodiester the DNAbackbone; requires more
energyto break u
·
Conservative Replication
DNA Replicationduring S-phase
·
u
mitosis
·
M Meselson Stahl: semiconservative
-
Dispersive Replication
G2 used isotopesof nitrogenthat could be incorporated
G1
-
DNASynthesis u
bacterial
into
growth& separated on gradients :
S
Topois omera seto separate strands * of
ori-origins replication
-
Multiple
helicase
Helicase -
helix enzyme; untwist *
replication forks move away from each other
↓
Single-strand
bindingprotein
-
hold strands apart primace
↓
Frimase -
make a
primer (session of RNA) DNA Polymerase DNA
polymerase efficiency
is increased by the protein ring known
↓
DNA Polymerasefinds RNA primer; -
reads old strand, oversee as the "slidingclamp"
matching Exonuclease
3'end
pairs;adds new nucleotides to
growingstrand as ↓ binds to the DNA
cenergy) DNA
which results of ligase
triphosphates in release pyrophosphate 4DNA Polymerase binds to DNA-clamp complex
"
DNA ligase tie(ligate) Okazaki fragments
-
keeps the DNA polymerase stay bound to DNA
4
who clamp: 7100 phosphodiesterbonds
[Steps
of Replication] we clamp: 15000 bonds
1. DNAis untwisted, unzipped& held apart(topoisomerase,helicase. SSBP(
2. Primace creates short (often RNA) to match the
primer sequences open DNA
strand
-
3. DNA
Polymerasesadd new nucleotides to the free 3' ends of each "finishing problem" does not affect bacteria bic of its circular chromosome
primer
With every replication,
4. DNAPolymerases pop out
primers & add new nucleotides in their
space laggingtelomere gets shorter, no
place
5. DNAPolymerasescontinue to the 3' ends of DNA to bind RNA
addingnew nucleotides primer
4
ties
6. DNA
ligase fragments
together
Out
keeps CUHing DNA
primersthan Codinginfo lost (senescence, death)
lagging requires many more
leading eventually.
ligase is more active on laggingstrand prevented by telomerase
has itto
DNApol-I: self check mechanism that confirms matching antiparellel strands of DNAallows
copy of itself
a *
proper make exact
during new strand assembly
Mismatch pairs or damaged nucleotides are found by repair "black
Alkaptonuria: urine disease"
proteins& removed Mendelian autosomal recessive inheritance
<bacterial *the
relationship
blw
gene& metabolic product
was further codified by experiments
single "chromosome" &
single ori with Neurosporamold
·DNApolymerase III adds nucleotides to the & DNA anneals mutant strains developedthat require nutritional supplementation
primer ligase
4
the Okazaki while
fragments together Polymerase I removes
DNA the
primer matrix: results demonstrate the order of metabolic processes requiredfor growth
One
gene,one-enzyme
<Central DogmaL
·Genomic DNAis sequesteredin nucleus
genes are synthesized,processed
RNA of individual in the nucleus ·RNAviruses can use
(single-stranded)
I
themselves as
·
transcripts
In mRNA -
translated into for transcription
cytoplasm, polypeptide template
& sent to
Polypeptides
are processed destination Retroviruses use an to make
·
·
can enzyme, reverse transcriptase,
a DNA of their RNA
copy genome
, read 3'-5
& tRNA & DNA3' 5'
Ribsomal RNACrRNA) Cytoplasm binds mRNA proteinsynthesis
I
built5'-3'
MRNA 5' 31
MessengerRNA (mRNA) cytoplasm carrier of
gene sequence Tran sl ation
TransferRNACtRNA) cytoplasm adaptor blu mRNA &
protein sequences
Transcription
MicroRNA [miRNA) nucleus/cytoplasm regulatestranscription & translation 1. Initiation
I Elongation
Small 2.
interferingRNA RNAS Transcription
&
(SiRNA)
nucleus/cytoplasm regulates other
Processing
3.Termination
Small nuclear RNA Nucleus mediates MRNA
CSURNA) processing
Creverses
-> apply mRNA to DNA
DNAhybridization splicing is predictable,removal subunits that
may be included during
some of the gene is translated into finished protein a diff. Transcription
event
only
(noncoding"
introns")
&
Ap poly A tail added to MRNA Transcription RNAEditing
modified GTP promoter ·SNRNPs: used to fold
(splice)
protects MRNA transport & serves as a
·
TATA
BOX Introns & Exons
turing
landmark duringtranscription ·RNA Polymerase
·MRNA
Termination Sequence * ribosome:
staging area for polypeptidesynthesis
translation Asite: "Arrive"
5'Cap &
poly Atail
first nucleotides P site: "process"
only the are requiredto specify
the amino acid E site: "exit"
·tRNAs contain
bindingsites for both nucleic acid & protein termination, instead of tRNA, stopcodons bind a "release factor"
to the ER surface & release
canticoding
matchingantiparallel
-
synthesizing export proteins bind
the lumen
polypeptideinto its
synthetase
Aminoacyl-tRNA is responsible for loadingamino acids
Onto their appropriate tRNA
(charges
tRNA) Endomembrane system:
1. amino acid is ATP continuous membrane nucleus-endoplasmic reticulum
chargedwith
2. Pyrophosphate
is released nucleus. ERCSmooth, rough), Golgi apparatus, lysosomes, endosomes, vesicles
3.Activated aminoacid- AMP binds the matchingtRNA,
for the synthesizedin
AMP is released GolgiApparatus:
responsible modification of material the ER
4. The highenergy bond bIw tRNA & amino acid fuels cis-receives productsfrom ER; trans releases products
in vesicles
peptidebond formation Phosphorylation:
added phosphate
group
alter the shape ofthe protein
Glycosylation:
adding sugars is importantfor &
targeting recognition
to fold
ER
Rough protein structure clearing the polypeptide
proteolysis: allows the
fragments into diff. Shapes
studded w/ ribosomes 1. Primary
& are sites for 2. helix
protein synthesis Secondary:
2 &
SMOOthER 3.Ter ti a r yH: bond & Disulfide bonds
site for & 4.
lipid synthesis
·
Quaternary
chemical modification of
proteins
