Exam 1 Flashcards
3 reasons mutations spread
- social (ex: found attractive)
- selective advantage
- small population
why is genetics one of biology’s unifying principles?
all organisms use genetic systems that have a number of features in common
why do we care about genetics?
- we all possess genes/variants that influence our lives in significant ways
- genetic selection impacts agriculture
- pharmaceuticals
- medical (inherited diseases)
divisions of genetics
- molecular
- transmission
- population
molecular genetics
- chemical nature of DNA
- how information is encoded, replicated, and expressed
- central dogma
transmission genetics
heredity and how traits pass from one generation to the next and the relationship of chromosome to heredity and gene mapping
population genetics
collection of genes in a population and the genetic variation over geography over time
unifying principle
all organisms use similar genetic systems
GENOME
complete set of genetic instructions for any organism
all genomes are composed of ________
(ex: ____ and _____)
nucleic acids
ex: DNA and RNA
examples of model organisms
fruit fly, mouse, bacteria, worms, plants, yeast
WHAT MAKES A GOOD GENETIC MODEL?
- short generation time
- large but manageable number of progeny
- adaptability to lab environment
- ability to be housed and propagated inexpensively
when paleobiologist study DNA thousands of years old why can they not get 100% of the DNA/full DNA traits of parents?
- DNA decays overtime
- there are some genes that are the same so you cannot code to one parent or the other
WHAT IS NEEDED FOR INHERITANCE?
- information storage
- information copying (replication)
- information retrieval (translation)
- ability to vary
3 PARTS OF THE CHEMICAL STRUCTURE OF DNA AND RNA
- pentose sugar
- nitrogenous base
- phosphate group
pentose sugar
- 5 carbons
- DNA = deoxyribose
- RNA = ribose
deoxyribose vs ribose
- deoxyribose = H attached to 2’ C
- ribose = OH attached to 2’ C
nitrogenous bases
- adenine (A)
- guanine (G)
- cytosine (C)
- thymine (T)
- uracil (U)
purine and examples
- double ring
- adenine (A) and guanine (G)
pyrimidine and examples
- single ring
- cytosine (C), thymine (T), uracil (U)
pyrimidines are C U T from purines
pyrimidine(single ring) are C(cytosine) U(uracil) T(thymine) from purines(double ring)
nucleosides
nitrogenous bases are lined to the sugar by the 1’ carbon of the pentose sugar
nucleoside vs nucleotide
nucleoside: 2 pairs (base and sugar)
nucleotide: 3 pairs (base, sugar, phosphate)
where is the phosphate group attached to the pentose sugar?
attached to the 5’ carbon
purpose of the phosphate group
allows for two nucleotides to be linked creating a stream of information that DNA encodes (cleaved to create the phosphodiester bond)
polynucleotides
Covalent bonds between a phosphate group of one nucleotide and the 3’ carbon of the next nucleotide’s sugar
phosphodiester bonds
covalent bonds between a phosphate group of one nucleotide and the 3’ carbon of the next nucleotide sugar (5’ to 3’ linkage)
polarity of the DNA/RNA backbone
information is flowing through the 5’ to 3’ direction
complementary base pairs
- A to T
- G to C
- A to U (RNA only)
number of hydrogen bonds in complementary base pairs
- A to T = 2 hydrogen bonds
- G to C = 3 hydrogen bonds
strong or weak: phosphodiester bond
strong
strong or weak: hydrogen bond
weak
which bond is stronger, A to T or G to C?
G to C because they have 3 bonds
how did Watson and Crick discover the molecular model of DNA?
used all available information about chemistry
STRUCTURE OF DNA
- double helix (2 strands)
- antiparallel strands (directionality)
- base complementary (holds strands together)
_____ base pairs between each turn of the helix
10
in DNA what is the wider and thinner grooves called?
- wider = major groove
- thinner = minor groove
why are grooves important in DNA?
grooves are important for binding other molecules and the regulation of genes
1 C value
a single set of genes, HAPLOID content
2 C value
two copies of every base pair/gene (Mom and Dad), DIPLOID content
what does C mean (1C and 2C)?
C = content = total number of bases
–> there are millions of bases
1C or 2C: gametes (egg OR sperm)
1C
1C or 2C: sperm and egg combined
2C
what does “N” mean?
number of chromosome molecules in a cell
most cells are 2N and 2C meaning they are…
diploid (ex: 46 in humans)
egg and sperm cells are 1N and 1C meaning they are…
haploid (ex: 23 in humans)
how can several feet of DNA fit into a very small nucleus?
compact it!
to compact prokaryotes and bacteria…
supercoiled (like a phone line)
topisomerases
enzymes that break the double helix backbone and rotate the ends (using energy), needed for supercoiling
negative supercoiling
compact (turn) counterclockwise - easier
positive supercoiling
compact (turn) clockwise
chromatin
DNA with a protein scaffold
histones
net positive charge so that they attract to the negatively charged DNA (DNA wraps around it)
how is the DNA packaged?
how does it condense during cell division
- assembly of the nucleosome (DNA + protein)
- multiple nucleosomes are coiled together and stacked on top of each other
- chromatin is further packed by protein scaffolding forming a chromosome
when do chromosomes form?
only when the cell is dividing
karyotype
representation of all the chromosomes in the organism
2 types of chromatin
- euchromatin
- heterochromatin
EUCHROMATIN
hold active genes
(parts of the chromosome that are going to do something, so they are made accessible and less compact and uncoiled except during cell division, stains light)
HETEROCHROMATIN
holds inactive genes
(stains dark and more condensed)
2 types of heterochromatin
- constitutive heterochromatin
- facultative heterochromatin
constitutive heterochromatin
having the power to establish or give organized existence to something (maintain chromosome structure, telomeres and centromeres)
facultative heterochromatin
capable of but not restricted to particular function or made of life (has potential to be condensed… ex: X chromosome inactivation)
centromeres
located at the center of the chromosome, used by cells during cell division to ensure each daughter cell gets a copy of each chromosome
telomeres
located at the ends of the chromosomes, a repeated sequence that can be lost when the cell divides so important information is not lost
heteroplasmic cells
different kinds of mitochondria in the cell
homoplasmic cells
same kind of mitochondria in the cell
(good to have in case of possible mutations)
3 models of DNA Replication
- conservative
- dispersive
- semi-conservative
conservative
one double helix is unchanged by the process, the other is completely new
dispersive
each strand is a mix of old and new DNA (pieces dispersed)
semi-conservative
one strand of double helix is conserved the other is new
what is the model of DNA replication?
semi-conservative
4 RAW MATERIALS NEEDED FOR DNA SYNTHESIS
- template
- enzymes
- raw materials (substrates - A C T G)
- Mg 2+ ions
DNA polymerase
catalyzes the formation of phosphodiester bonds
(joins the 3’-OH group of the last base to the incoming 5’-phosphate)
phosphodiester bonds: strong or weak
covalent, strong
SYNTHESIS DIRECTION
5’ to 3’
characteristics of creating a new strand of DNA/RNA
complementary and antiparallel
replication fork
double stranded DNA exposure allowing for replication to occur in the 5’ to 3’ direction
leading strand
continuous coding strand
lagging strand
discontinuous coding strand
Okazaki fragments
short sections of DNA formed at the time of discontinuous synthesis of the lagging strand during replication of DNA
5 KEY ELEMENTS OF EACH REPLICATION FORK
- helicase to unwind DNA
- single stranded binding proteins to protect single stranded DNA
- gyrase to remove strain ahead of the form
- primase to synthesize RNA primer
- DNA polymerase
Key features of DNA replication in eukaryotes
- occurs in the nucleus during S phase
- initiated by RNA primers
- occurs in 5’ –> 3’ direction
- semiconservative
- initiation at many points
origins of replication
initiations of replication at many points to have replication occur faster
what happens to histones during replication?
histones disassemble but stay in the cell to be reused and new histones are made for the new DNA
what direction does exonuclease activity occur in?
3’ to 5’
phases of the cell life cycle
- During G1, the cell grows
- cells may enter G0, a nondividing phase
- after G1/S checkpoint, the cell is committed to dividing
- in S, DNA duplicates
- in G2, the cell prepares for mitosis
- after the G2/M checkpoint the cell can divide
- mitosis and cytokinesis (cell division) take place in the M phase
5 Phases of the cell life cycle
- G1
- G0
- S
- G2
- Mitosis
G1 Phase
chromosome morphology changes from condensed to dispersed due to a change in the coiling of fibers
G0 Phase
neither growing or progressing
(muscle cells and neurons stay here)
S Phase
DNA untwists and replicates
G2 Phase
DNA condenses
Mitosis
formation of two cells from one cell, daughter cells
5 STAGES OF MITOSIS
- Interphase
- Prophase
- Metaphase
- Anaphase
- Telophase
Interphase
- stage 1 of mitosis
- nuclear membrane present, chromosomes relaxed
Prophase
- stage 2 of mitosis
- chromosomes condense
- 2 sister chromatids become detectable
Metaphase
- stage 3 of mitosis
- chromosomes are arranged on metaphase plate
- microtubules from chromosomes to kinetochore
- used for karyotyping
Anaphasse
- stage 4 of mitosis
- sister chromatids separate
- chromosomes move toward opposite poles
Telophase
- stage 5 of mitosis
- sister chromatids drive at opposite poles
- nuclear membranes form
- chromosomes relax and lengthen
Meiosis
sexual reproduction, creates sex cells
2 phases of meiosis
- Meiosis 1
- Meiosis 2
Meiosis 1
prophase 1, metaphase 1, anaphase 1, telophase 1, cell division (NO separation of sister chromatids)
Meiosis 2
prophase 2, metaphase 2, anaphase 2, telophase 2, cell division (centrosomes split to have haploid gametes)
why are siblings so different?
during meisosis chromosomes cross over (recombinant) during prophase 1 and have independent assortment
transcription
DNA into RNA
RNA polymerase
catalyzes production of RNA using DNA as a template
(A U C G)
RNA is syntheisized ___________, DNA is read ____________
5’ - 3’ , 3’ - 5’
where does transcription occur
the nucleus
DNA vs RNA: composed of nucleotides
both = yes!!
DNA vs RNA: type of sugar
- DNA = deoxyribose
- RNA = ribose
DNA vs RNA: nucleotides joined by phosphodiester bonds
both = yes!!
DNA vs RNA: presence of free 2’-OH
- DNA = NO
- RNA = YES
DNA vs RNA: bases
- DNA = A G C T
- RNA = A G C U
DNA vs RNA: double or single stranded
- DNA = usually double
- RNA = usually single
DNA vs RNA: secondary structure
- DNA = double helix
- RNA = many types
DNA vs RNA: stability
- DNA = stable
- RNA = easily degraded
messenger RNA (mRNA)
instructions to make a protein (each protein has a unique mRNA)
transfer RNA (tRNA)
translates intrusions into protein “language”
ribosomal RNA (rRNA)
machine that builds a protein
small nuclear RNA (snRNA)
mostly modify mRNAs (lots and lots of them)
structure of tRNA
- stem/loop structure
- section that recognizes AA
- section that allow RNA to be recognized and position AA to make a peptide bond
rRNA structure
2 subunits (large and small)
collinearity of the central dogma
predictive relationship between the RNA and a protein
KEY COMPONENTS NEEDED FOR TRANSCRIPTION
- DNA template
- the raw materials (ribonucleotide triphosphate) needed to build a new RNA molecule
- the transcription apparatus, consisting of the proteins necessary for catalyzing the synthesis of RNA
RNA synthesis is _______________ and _______________ to the template strand
complementary and antiparallel
RNA POLYMERASE
copies (transcribes) DNA to RNA
3 main types of RNA polymerases
- RNA Pol I
- RNA Pol II
- RNA Pol III
RNA Pol I
transcribed rRNA
RNA Pol II
transcribed mRNA
RNA Pol III
transcribes tRNA
RNA polymerase funnel and pore
where rNTPs (nucleotides) enter
chromatin - remodeling complexes
reposition the nucleosomes allowing transcription factors and RNA polymerase to bind to promoters and initiate transcription
promoter
sequence that transcription machinery recognizes and binds (specific sequence, not transcribed)
coding region
the sequence that is copied (transcribed) from DNA to RNA
terminator
specific sequences that indicate transcription should stop, generally transcribed
genes can be turned on and off depending on:
- time in development (TDF)
- nutrients (ADH)
- stress
core promoter
on DNA, required for transcription, site where basal transcription machinery binds
regulatory promoter
located upstream of the core promoter, transcription factors and regulatory factors can bind here, affects the rate of transcription
enhancers
distal locations can also enhance transcription (can be upstream or downstream)
initiation (transcription)
if the promoter (core and regulatory) and enhancers “say so”, a protein - coding gene is transcribed
(polymerase and other factors are bound)
elongation (transcription)
keep adding nucleotides
termination (transcription)
for RNA Pol II there is no specific termination sequence, can continue for 100s-1000s of base pairs
gene
unit of information that encodes a genetic characteristic
introns
non coding region of the DNA between 2 regions that can code
introns must be _______ out by snRNPs (small nuclear ribonucleoproteins) in a splicesome
spliced
what happens if there is an error is translation?
does NOT change the DNA, but could affect the protein
5’ UTR
translatiion
does not code for a protein, ribosome binds here
3’ UTR
not transcribed into a protein, affects stability of mRNA
post-transcriptional modifications
1 addition of 5’ cap
2. addition of Poly-A tail
3. introns spliced out
5’ cap
addition of methylate guanines to the 5’ end of RNA to increase stability
Poly- A Tail
addition of adenines to the 3’ end after cleavage
how can the Poly A Tail adjust the half life?
- more As = longer half life
- less As = shorter half life
splicing
removal of introns (allowing for the DNA and RNA to be collinear)
splicesome
large complex structure that comes in to remove introns and splice exons together
the number of genes is _____ strongly correlated with organismal complexity, however _______ size and number is correlated to complexity
NOT, intron
why would exons be put together with alternating splicing / cleavage? leaving some exons out?
different functions
why not change the order of the exons? why can this not occur?
splicesome moves down a linear molecule and puts them back together in linear fashion, physically the splicesome could not change the order (but it can skip)
proteins
functional molecules of the cell, function determined by structure based off AA
how many AA?
20
parts of an amino acid
- amino group
- carboxyl group
- R group
what part of the amino acids structure is different in each AA?
the R group
primary structure of a protein
sequence of AA
secondary structure of a protein
interactions between AA (a-helix, B-sheets)
tertiary structure of a protein
structures after folding makes a 3D shape
quaternary structure of a protein
more than one polypeptide
the function of a protein is determined by __________________
its 3D shape
codon
3 bases to encode an amino acid
how many possible amino acid combinations?
64, 3 bases and 20 AA
(allows for redundancy)
start codon
- AUG - methionine
- NOT ALWAYS THE FIRST CODON, YOU HAVE TO LOOK FOR IT IN THE SEQUENCE
stop codons
- UAA, UAG, UGA
- NO tRNA FOR STOP CODONS, THIS IS WHAT CAUSES TRANSLATION OF THE SEQUENCE TO END
degenerate
more than one codon for each AA
wobble
typically the 3rd base of the codon can vary
synonymus (wobble)
change in the DNA sequence does NOT change the AA
non-synonumus (wobble)
change in DNA sequence CHANGES AA
nonsense (wobble)
changes in DNA introduces a STOP CODON
reading frame
code is read in three’s
ribosome
the machinery the makes proteins (made up of a large and small subunit)
4 Phases of Protein Synthesis
- tRNA charging (binding tRNA to AA)
- initiation: start of translation
- elongation: synthesis of polypeptide chain
- termination: ending of synthesis
aminoacyl-tRNA synthetase
enzyme that attached an AA to a tRNA
(each is specific to a particular AA)
5’ Cap
protection and recognition for the ribosome to bind in initiation of protein synthesis
the _______ __________ scans the mRNA until it finds the start codon
initiation complex
initiation complex
ribosome small unit, initiation factors, initiator tRNA
ribosome reads mRNA moving _____________
5’ to 3’
ribosome has 3 sites that can be occupied
- Aminoacyl (A) site
- Peptidyl (P) site
- Exit (E) site
Aminoacyl (A) site
where charged tRNAs enter the ribosome
Peptidyl (P) site
where peptide bond is formed
premature stop codon
mutation that moves the stop codon to be too early in the sequence
removal of the stop codon
could make an unnecessary amount of a protein
mutation
inherited change in genetic information, the descendants that inherit the change may be cells or organisms
2 categories of mutations
- somatic mutations
- germ line mutations
somatic mutations
occurs after conception occurring in any cell except germ cells and therefore not passed to offspring
germ line mutations
occurs in germ cells and transmitted to offspring
mutations: some are beneficial, some are detrimental, some are neutral. WHY?
dependent on the environment and location of the mutation in the gene
is a plant or animal more affected by their environment (mutational changes)?
plants because they are not able to move
2 classifications of mutations
- physical nature of the variant
- consequence of the variant
base substitution
alteration of a single nucleotide
base substitution types
- transitions
- transversions
base substitution: transitions
substitution of purine for a purine OR substitution of a pyrimidine for a pyrimidine
base substitution: transversions
substitution of purine for pyrimidine OR substitution of pyrimidine for purine
purine (ex)
double ring carbon structures (A and G)
pyrimidine (ex)
single ring carbon structures (C, U, T)
missence
change in AA
nonsense
add a stop codon
silent
no change in AA
neutral mutation
missence mutation that changes one AA for another chemically similar AA
loss of function mutation
results in complete or partial absence of a normally functioning protein (nonsense-premature stop codon)
lethal mutation
result is so drastic an organism cannot survive
how can a lethal mutation pass on?
the biological purpose of life is to transmit DNA, so the mutation kills you after reproductive age
indels
insertion/deletion of one or more bases (can cause a frameshift)
what type of indel would be less consequential?
if it were to be in a multiple of 3 because it would either add or remove 1 AA, so the protein can sometimes still function
expanding nucleotide repeats
mutations in which the number of copies of a set of nucleotides increases
causes of mutations: replicative
the wrong base gets incorporated during DNA replication
causes of mutations: strand slippage
newly synthesized strand loops out on the new strand in the addition of the nucleotide on the new strand or the template strand loops out resulting in the omission of one nucleotide on the new strand (common in repeat bases)
causes of mutations: depurination
loss of a purine base from a nucleotide
causes of mutations: deamination
loss of an amino (NH2) group from a base
causes of mutations: mutagen
any environmental agent that significantly increases the rate of mutation above the spontaneous mutation rate
what affect can UV have on replication?
produces thymine dimers that block replication
common 4-step pathway for DNA Repair
- detection
- excision
- polymerization
- ligation
common 4-step pathway for DNA Repair: step 1
detection!
The damaged section of the DNA is recognized
common 4-step pathway for DNA Repair: step 2
excision!
make a nick and exonuclease removes error
common 4-step pathway for DNA Repair: step 3
polymerization!
DNA polymerase replaces the nucleotides that were removed
common 4-step pathway for DNA Repair: step 4
ligation!
ligase going over and filling in any “holes” / seals the nicks
how many hydrogen bonds between A and T
2 H bonds
how many hydrogen bonds between A and U
2 H bonds
how many hydrogen bonds between C and G
3 H bonds
