exam 2 Flashcards
x ray crystallography
makes DNA into crystals and shine x-ray light through to find structure and functions of biological molecules.
DNA double helix
nucleotides covalently linked into strands that contain any sequences of nucleotides in any order; complementary strand binds through H bonds and twisted into double helix
purine nucleotides
A and G
pyrimidine nucleotides
T and C
how are complementary base pairs linked
hydrogen bonds
DNA strand directions
antiparallel; 5’ end of one stand line up with 3’ end of the other
3’ end
3 carbon bonded to phosphate; OH group on end
5’ end
5 carbon bonded to phosphate group; phosphate on the end
what links together nucleotides in the strand
phosphodiester bonds (phosphate-sugar-phasphate-sugar)
DNA replication
- separate 2 strands of DNA
- used as template for new strand
- new strand create; reverse complement
what kind of model does DNA replication follow?
semi conservative model
DNA polymerase
enzyme that matches complementary nucleotides to template and binds new strand
central dogma
base pair matching used for information flows from dna -> rna -> protien
DNA polymerase
dna replication enzyme that matches complementary nucleotides to template and builds new strand
which direction does dna polymerase build new strand
5’ -> 3’
where was is template strand read
3’ -> 5’
helicase
enzyme that breaks hydrogen bonds between nitrogenous bases of double stranded dna (unzips)
replication fork
area where double helix is opened and where the replication of DNA will actually take place
replication bubble
formed because 2 helicase working in opp directions -> 2 replication forks -> creates bubble
origin of replication
specific dna sequence where helicases and polymerases start replication; proteins distinguish by specific nucleotide sequence
*creates neg feedback loop
origin of replication; prokaryotes
1 origin of replication bc small circular chromosomes
origin of replication; eukaryotes
many origins of replication because larger linear chromosomes
supercoiling
winding up of dna strands (problem separating the replicates)
topoisomerase
enzyme that cuts strands of dna allowing them to unwind, then rejoins them
rna polymerase
brin in first rna nucleotide for replication
what is the problem with dna polymerase?
it cannot start dna replication on its own; only can elongate the nucleotide
primase
builds short rna primer that dna polymerase can add to
*type of rna polymerase
dna ligase
joins the 2 replicated dna fragments
replication of the leading strand
chases helicase
replication of the lagging strand
fragments created bc replication keeps stopping and starting since polymerase can only work 5’ -> 3’
tolemere
end of linear chromosome
*only in eukaryotes
centromere
middle of a linear chromosome
overhang
telomere is single stranded which is less stable -> if nothing done then cell looses nucleotides every division
tolemerase
enzyme that adds nucleotides to template strand where the extended rna primer overhang can bind
what cells have tolemerase
cells that replicate often; germ line cells (reproductive), stem cells and cancer cells
what factors make tolemers get shorter
stress and age
*skin cells don’t have telomerase -> aging?
dna replication in lab
1) get bacteria to grow plasmid dna
or
2) dna replication in test tube via pcr
polymerase chain reaction (pcr)
amplifies part of a dna strand; used template dna, mixture of dNTP’s (triphosphate dna nucleotides) and dna primers; heat cycles and amplify
mRNA
messenger rna; used to make protein
transcription
process of using dna template to make rna
transcription: amplification
make many mRNAs from 1 gene (template region of DNA)
*many proteins made from 1 mRNA
transcription: control
can change/ control whether or not to make mRNA from DNA and/or how much is translated
transcription: evolution
earliest cells might not have had dna; mrna directly made proteins
*rna world hypothesis
transcription requirements
rna polymerase (so no primer needed)
dna-rna binding in transcription is…
temporary (dna only used as template)
how many mrna can be made from 1 dna template
many!
transcription unit
a region of dna used as a template for a type of rna ; from promoter to terminator
how many transcription units per chromosome
100s-1000s
genes
regions of dna that define the coding info for a protein
promoter dna
nucleotides bound by rna polymerase that signify the starting point of the transcription unit
transcription factors
proteins that bind to dna and recruit rna polymerase/ give it directions
tata box promoter
recruits and directs dna polymerase; located upstream of where transcription starts
terminator dna
where transcription stops
transcription in prokaryotes
no nucleus/ membrane bound sections to move mRNA in and out of; translation begins before transcription ends (5’ end once made attaches to ribosome)
polyribosome
ribosome attached to an mRNA
transcription in eukaryotes
transcription in nucleus separated from translation; nucleus -> cytoplasm -> ribosomes
why is mRNA modified in eukaryotes
to help with stability and export out of the nucleus
mRNA modifications
- 5’ cap: modified nucleotide 5’ - 5’
- poly- A tail: binds to proteins at 3’ end to stabilize, recognize/mark and export from nucleus
primary transcript of mRNA
mRNA before modifications (5’ cap and poly-A tail)
rna processing
removal of non coding introns and splicing together of remaining exons (coding regions)
introns
non coding regions of rna that are spliced out
-thinner than exons
-spliced out at splice site/ exon- intron junctions
exons
coding regions of rna (thicker than introns)
spliceosome
protiens and small nuclear rna (snRNA) that remove introns
what are snRNAs
ribozymes
alternative splicing
rna keep different exons in different cells -> get diff mRNA proteins from same dna template
how can ribosomes be isolated
-can be seen by e- microscope
-cell fractionalization
cell fractionlization
separating cell components by density; create density gradient using sugar solution
ribosomes
cell structure that makes proteins;
-made of ribosomal rna (rRNA) and proteins
-have large and small subunits
codon
nucleotide triplet in mrna that amino acids are coded with
what way do ribosomes build and read amino acids
build: 5’ -> 3’
read: 3’ -> 5’
experiment that discovered codons
feed radioactive amino acids to cell-> look what radioactive proteins were made
start codon; and what does it match with?
AUG/ ATG
*matches with initiator tRNA anticodon
stop codons
TAA, TAC, TGA
*nonsense codons
release factor
protein that bonds to stop condon; releases polypeptide
codon steps
1) linear sequence mrna has triplet codons
2) ribosome attaches and reads mrna codon sequence
3)recognize triplet -> bring in right amino acids (reverse complement)
adaptors
tRNA (transfer rna) that binds to mrna codon and amino acid
anticodon
reverse complement rna that binds to codon in mrna -> brings in attached amino acid
aminoacyl trna
amino acid bound to trna amino acid attachment site
aminoacyl trna synthases
enzymes that attach amino acids to the correct tRNA.
*specific enzyme for each type of trna
untranslated regions (utr)
5’ utr: before start codon
3’ utr: after stop codon
translation in prokaryotes
1 mrna can code for several different proteins
operons
several consecutive start/stop regions in 1 mrna; cluster of genes transcribed from the same promoter to give a single mRNA carrying multiple coding sequence
what recognized intron-exon splice sites
small nuclear rna (snRNA)
info for nucleotide sequence for snRNA comes from….?
dna
mutation
dna nucleotide changes that lead to permanent, heritable changes in genome
what causes mutations (3)
1) bad replication; mistakes in dna polymerase proofreading
2) chemical/ radiation damage to bases/ dna strands
3) viruses and transposable elements that hijack/ jump around dna damaging it
point mutations
change in or gain/loss of single nucleotide base
point mutations: synonymous mutation
mutated nucleotide that codes for same amino acid -> no change in protein/ silent mutation
point mutations: missense mutation
change nucleotide that leads to the wrong amino acid being made
point mutations: nonsense mutation
change in nucleotide sequence makes stop codon -> incomplete protein
point mutations frameshift mutation
deletion or insertion of nucleotide -> changes how codon triplets are read
*frame stays the same if 3 nucleotides added together
mutations in non coding regions
impacts mRNA made
*could disrupt stop codon, protomer/terminator dna, splice sites, etc
transcriptional regulation
use transcription factor proteins to help or inhibit dna polymerase to increase or decrease transcription of nearby genes
example of gene regulation: Lac operon
*beta galacto sidase breaks down lactose -> glucose
*repressor protein binds to operator site -> repress
how can lactose be broken down into glucose
- presence of lactose; allosterically binds to repressor transcription factor to allow for transcription
*other transcription factors act;; CRP or cyclic AMP (cAMP)
CRP
activator transcription protein; active when low levels of glucose (bring lactose in even when repressor is repressing)
cAMP
non protein molecule; second messenger whose levels of abundance carry info about how much glucose there is
cAMP levels and glucose
- glucose high = cAMP low
- glucose low = cAMP high (signal for more lactose to be broken down)
enhancer dna
transcription factor that stimulates transcription
silencer dna
transcription factor that represses transcription
do transcription factors have to be close to promoter to impact transcription
no
chromatin remodeling
change chromosome shape by wrapping dna into nucleosomes
what carries out chromatin remodeling
histone proteins
impact of chromatin remodeling
more densely packed dna makes it harder to transcribe
what do acetyl groups on histone do
cause less winding of dna, therefore more transcription
*taking off acetyl groups silences transcription/ gene expression
dna modifictions
change gene expression
dna methylation
adding a methyl group to silence region gene expression
*temporary and does not change genetics
epigenetic change
changes in transcription factors that do not genetically modify/ alter nucleotide sequence
*stays consistent through cell division
microRNA
binds to mRNA after transcription to trigger destruction or to block translation
what 2 things can mutations impact
1) can change recognition sites for transcription factor binding (promoter, enhancer, silencer dna)
2) can change the transcription factor itself
chromatin
strands of chromosomes (dna, histones, transcription factors)
nucleolus
site of rRNA synthesis in the middle of the nucleus; not membrane bound
inner and outer envelopes
2 lipid bilayers of the nucleus perforated by nuclear pores
how to transport proteins to diff parts of the cell
use signal sequence -> bind to carrier protein for specific part of cell -> transport protein
importin
a protein that imports proteins bound to it into nucleus
exportin
protein that shuttles a protein out of the nucleus
nuclear import signal sequence
specific amino acid sequence on a protein being transferred that binds to importin via lock and key interaction
endoplasmic reticulum
network of membrane enclosed tubes/dishes that is continuous with the outer nucleus membrane
smooth er
-has no ribosomes (so not involved with protein synthesis)
-has enzymes that synthesize lipids, steroids, carbohydrates
- Calcium ion storage place (pumps in with membrane pumps)
rough er
has ribosomes -> synthesises proteins
rough er secretion
secretion signal sequence on protein binds to SRP receptor -> secretion by exocytosis -> ER lumen
where do proteins go after the rough er and how do they get there
they go to the golgi apparatus via vesicals
golgi apparatus
stacks of flattened membrane that modifies/ process proteins
golgi apparatus cis face
innermost face
golgi apparatus trans face
outermost face
how does the golgi modify proteins
- cleave; split into 2
- covalently link other proteins together; disulfide bonds
-glycosylation: adding sugars to protein
how do vesicles know where to go
proteins on outside of vesical
lysosome
digestive enzymes that break up macromolecules; mini stomach in cell
lysosome pH
acidic inside of lysosome so things can be broken down; H+ pumps move H+ into lysosome from cytosol
how are vesicles moved
moved by motor proteins along the cytoskeleton
cytoskeleton
intracellular roads and fibers made up of many proteins
microtubules
thick hollow tubes in cytoskeleton
what are microtubules made of
alpha and beta tubulin proteins
how do microtubules move things
- lengthening and shortening
-motor proteins
-slide past each other using cilia (lots of short structures) and flagella (one long structure)
what motor proteins do microtubules use
kinesin or dynein
cilia and flagella
bendable projections of membrane organized into ring with a 9-fold array of stable doublet microtubules; pairs connected by dynein motor protein
what do microtubules do during cell division
move chromosomes
microfilaments and function
finest/ thinnest part of the cytoskeleton used for:
-rapid cell shape change
- intracellular movements (* cytoplasm streaming)
- muscle contraction
what are microfilaments made of
double helix made of actin proteins; shortened and lengthened by actin removal
microfilaments motor proteins
myosins
how do microfilaments move things
-motor proteins
-move things along microfilaments
-slide microfilaments past each other
actin extensions
- pseudopodia
-filopodia
-lamellipodia
cytoplasmic streaming
acitive (needs energy) movement of cytoplasm to deliver things to parts of the cell
prokaryotic cell division
fission
why is prokaryotic cell division so much simpler than eukaryotic
dna in 1 circular chromosome in prokaryotic but in eukaryotic it is in multiple linear chromosomes
fission mechanism
-replicate cytoplasm
-replicate dna
-each copy of dna attach to one side of membrane -> seperate through cell elongation
number of eukaryotic chromosomes
set number per species
*humans: 46 per somatic cell (not sex cell)
mitotic spindle
microtubules used in mitosis to separate sister chromatids to either side of the cell; separate chromosomes for daughter cells
what do microtubules do
arrange and move chromosomes
where do microtubules attach to chromosomes
kinetochore; specialized point of centromere
what do non kinetochore microtubules do
build cage
spindle poles (of the microtubules cage)
centriole pairs
spindle pole organization
centriole pair w/ centrosome; chromatids attached to single chromosome at centromed
kinetochore
proteins surrounding centromere
how does spindle move chromatids (2)
1) shortening; microtubules disassemble at kinetochores
2)sliding along microtubules using motor proteins
Interphase (G1, S, G2)
cells grows and replicates dna to prepare for cell division
Prophase
-winding up of dna into chromosomes
Prometaphase
nuclear envelope breaks down (stored to be reformed later); spindle starts to form
Metaphase
chromosomes attach to spindle fibers and line up in center
Anaphase
spindle pulls sister chromatids to either end of the cell
Telophase
separates duplicated genetic material
cytokinesis
subdivision of cytoplasm into 2 cells
animal cell cytokinesis
cleavage furrow; pinches cell in middle -> 2 cells
plant cell cytokinesis
cell plate; form new membrane from vesicles fusing in middle of cell
*cannot do cleavage because of rigid cell wall and turgor pressure
cell cycle
life cycle of cells; G1, S phase, G2, M phase
cell cycle checkpoints
protein complexes throughout the cell cycle that monitor activity/ make sure everything is going right
G1 checkpoint
make sure cell large enough/ with enough neutrance; decide whether or not to divide
G2 checkpoint
check if all of the DNA replicated correctly
M checkpoint
check that all chromosomes are attached to spindle microtubules
MPF
complex of 2 proteins that drives cell through G2 checkpoint
how are checkpoints regulated
by “clock” protein cyclin; protein synthesised at a steady pace with specific thresholds
*disappears after mitosis; restarts clock
cyclin dependant kinase (CDK)
protein that cyclin binds to and activates tp create active MPF
why do cells reproduce to make non genetically identical offspring
genetic variation can make a species more resistant and have better chances of survival
prokaryote reproduction -> genetically varied offspring
1) transformation: specialized channels take up DNA from outside -> incorporated into prokaryote chromosome
2) conjugation: bits of dna transfer between prokaryotes
how do prokaryotes transfer bit of dna between each other
pili
how do eukaryotes produce genetically varied offspring
cell fusion during fertilization
diploid
pairs of homologous chromosomes (4 chromatids)
ex of diploid cell
somatic cell
haploid
only 1 homologue (2 sister chromatids)
ex of haploid cell
sperm and egg cells (gametes)
homologous chromosome
2 chromatids joined by centromere with same genes in same regions BUT different versions of the gene/ different alleles
alleles
one of two or more alternative forms of a gene that arise by mutation and are found at the same place on a chromosome
meiosis
diploid cell -> 4 haploid cells
meiosis 1
meiotic spindle lines up homologous chromosomes next to each other -> separate homologous chromosomes
*sister chromatids stay together!
what do chromosome synapses do
pair sister chromatids together
*prophase
tetrad/ bivalent
4 sister chromatids/ 2 chromosomes together; recognize similar dna/ nucleotide sequences -> join together
*metaphase
crossing over
dna from 1 homologue breaks and joins with other chromosome -> non parental chromosomes (mixes genes from both chromosomes)
meiosis 2
sister chromatids separate -> 4 haploid cells
*no dna replication before
mendel 1865 experiment
breeding pea plants and observing inheritance of traits (flower color, seed color, seed shape)
true breeding parents
offspring keep traits unless you allow/ breed for cross fertilization
alleles
different versions of the same gene
*homologous chromosomes with certain gene in the same region -> different alleles
mendel’s law of segregation
the 2 alleles in the parent segregate from each other during formation of gametes; equal probability of passing on either allele
homozygotic
2 of the same allele (recessive or dominant)
heterozygotic
2 different alleles
mendel’s law of independent assortment
the way 1 set of alleles separate from each other into gametes has no impact on the separation of another set of alleles
*if genes on different chromosomes
phenotype
physical traits individual has
genotype
genetic information individual has passed on from parents
how to determine genotype; homozygous dominant vs heterozygous dominant
test cross; breed with homozygous recessive
dihybrid cross
cross 2 heterozygous genes on different non homologous chromosomes (independent assortment)nat the same time
dihybrid cross genotype ration
9:3:3:1
what does independent assortment increase
genetic variation
how to see all of the genetic possibilities
punnett square
diagram to see what genotype is dominant
pedigree
incomplete dominance
heterozygote has phenotype that is intermediate/ in between homozygotes
ex. white + red -> pink
co dominance
different alleles give qualitatively different dominate traits -> see both traits
ex. blood type (A and B carbohydrates)
transfusion reaction
immune response to unfamiliar blood type cells
O blood type
no carbohydrates on blood cells
universal blood receiver
AB
universal blood donor
O
several mutant alleles of the same gene
can inhibit, increase or completely change protien function
several mutant alleles of the same gene nomenclature
gene name ^ xxx (superscript)
pleiotropy
single mutant allele affects many tissues and processes
ex. beta globin gene mutation causes blindness, liver failure and heart attacks
specialization
organs for production of nutrient filled egg (ovary) or mobile sperm (testes)
hermaphrodites
have both reproductive organs; can vary over time or exist at the same time
autosomes
non sex chromosomes
humans: 22 pairs
sex chromosomes
make genetic choice between making sperm or egg
- XX makes ovaries -> egg
- XY makes testes -> sperm
SRY gene
gene on Y chromosomes that encodes transcription factor that directs development of testes and hormone testosterone
sex linked genes
XY is hemizygous for X- linked gene allele and Y- linked gene allele
hemizygotic
individual who has only one member of a chromosome pair or chromosome segment rather than the usual two
X- linked gene
gene on X chromosome
Y- linked gene
gene on y chromosomes
why are males more likely to inherit recessive X linked genes
dependent on only 1X allele because only have 1 X chromosome
x linked mutations
more likely to be passed onto males because there are only genes expressed on the one X chromosome
sex influenced traits
autosomal mutation influenced by sex physiological factors (ex. sex hormones)
*not on sex chromosome
pedigree symbols
circle: XX
square: XY
shades indicate the phenotype
x linked recessive trait passing on
male: only mother must have trait on 1 X chromosome
female: both parents must possess trait on X chromosome
y linked trait
all XY offspring of XY with the trait will also inherit the trait
how are X Y chromosomes paired during meiosis
pairing must be between similar segments of DNA; 40 shared genes between X and Y on tip of chromosome
what is the region of similar DNA used to pair X and Y chromosomes called
pseudo- autosomal
dosage compensation
XX have double the X linked genes as XY which produces 2x as much mRNA (BAD)
dosage compensation; mammals
random inactivation of 1 X chromsome in XX individuals
what are the inactive X chromosomes called (used for dosage compensation)
barr bodies
how are barr bodies made
histones wrap chromosome so tightly it silences transcription so cannot make mRNA
epigenetic mosaic
different mix in gene expression; heterozygous XX expresses both genes
nondisjunction
chromosome separation fails during meiosis (either stage) and produces unequal gametes
gametes produced by nondisjunction
aneuploidies
trisomy
3 of one chromosome; leads to birth defects (only 3 survivable ones)
momsomy
only 1 of one chromosome; not survivable to birth on autosomal chromosomes
trisomy ex
down syndrome; trisomy on chromosome 21
nondisjunction in sex chromosomes
XXY
XXX
X
* ONLY SURVIVABLE HUMAN MONOSOMY
XYY
XXY
1 barr body; reduced testes, testosterone and fertility
XXX
2 barr bodies
X
no barr bodies; only survivable human monosomy
XYY
both Y active; extra fertile testes and could lead to more severe defects
fruit fly gene nomenclature
x+ = dominant/ normal
x or x- = mutant
named after the mutant form
recombinant
non parental chromosome; crossing over has occurred
crossing over
parts og homologous chromosomes in meiosis 1 cross and make tetrad; chromosome recombine at chiasm and forms non parental chromosome
*more genetic variability is added
tetrad
4 connected chromatids; the point where homologous chromosomes exchange genetic material by the process of crossing over
independent assortment test cross
equal amount of all 4 gametes
where on gene must crossing over occur for genes linked on the same chromosome
in between the 2 genes of interest
*happens more commonly when genes further apart
unit for mapping matants
centimorgans/ map units= % of offspring with non parental geneotype
50 map units
50/50 chance of recombinant or parental chromosomes
- less than 50 = recombinant
- greater than 50 = parental
polygenic trait
one phenotype caused by more than 1 gene; mutation in all genes causes phenotype
what does polygenic inheritance lead to
quantitative variation in interiable quantitative trait
epistasis
complex interactions between genes and traits
when one gene turns the entire pathway off, how is that gene described
that gene is epistatic to the other genes in the polygenic inheritance
how to determine genetic vs. environmental influence
twin tests; monozygotic (identical) vs. dizygotic (fraternal)
concordance
the probability that both twins have a certain phenotype given that one has the characteristic
cadherin
cell adhesion molecule
mitochondrial gene inheritance
male and female offspring of an affected XX parent show the trait; mother to child
*XY parents never transmit the trait to their offspring
what does the signalling cell produce
signaling molecule known as the receptor
what do ligands produce
signaling cell (which the signalling molecule binds to)
kinase function
type of protein adds a phosphate group to another protein
inheritance by non nuclear chromosomes
genetic inheritance from dna from semi autonomous organelles (chloroplasts and mitochondria)
does non dna information pass down through fertalization; epigenetics/ gene expression
as of now we don’t think so; dna methylation and gene expression lost after fertilization
protist
single celled
colony
collection of individual cells
multicellularity
collection of eukaryotes that has a more complex organizational structure than colonies; interconnectedness and communication.
how does a multicellular organism forms
single cells goes through division -> leads to differentiation of cells (specialization)
cell signaling
coordination between cells in multicellular organisms
fungi cell signaling
cytoplasmic connections; breaks in cell wall so cytoplasms are directly connected and anything can go through (proteins, organelles, etc)
syncytial arrangment
cells fused together so things can fow between them; direct cytoplasm connections
animal cell signaling
gap junctions; small pores that can pass small molecules between cells (ions, monomers, cAMP)
plant cell signaling
plasmodesmata; large pores used to pass large molecules between cells (proteins, mRNA, etc)
extracellular signaling
cell communication outside of the cell via signaling molecules
ligands
a signaling molecule that binds to receptor protein -> trigger response in cell
signal transduction pathway
The chains of molecules that relay intracellular signals
ligand example; steroids
-easily diffuses across membrane (not normally the case)
-binds and activates receptor proteins
-receptor- steroid complex becomes active transcription factor
- binds to specific enhancer dna
- stimulates transcription
factors in information flow (4)
1) specificity of signal/receptor pathway
2) scale of impact (part or whole cell)
3) feedback (pos or neg)
4) amplification caused?
amplification
enzymes in pathway receive and amplify protein at every step; pos feedback
what receptors exhibit amplification
- transcription factors
- protein kinase
- cyclases
- G proteins
- secondary messengers
secondary messengers
non protein messengers; cAMP, Ca2+, ions, lipids, gasses. etc
G proteins
family of proteins that act as molecular switches inside cells
G protein coupled receptors
activates G proteins by breaking bond with GDP and binding protein with GTP
inactive g protein
bound to GDP
active g protein
bound to GTP
ex of g protein activation
adrenaline; activates alpha G protein -> activates adenylyl cyclases -> makes cAMP -> activates protein kinase A -> increases heart rate
