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BIO Final Section 4
the enddddd BIO311C
131
Biology
Undergraduate 3
12/11/2012

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Term
cells can control what genes are expressed and what genes are not expressed
Definition
gene regulation
Term
In all organisms, regulation allows adjustment of the level of ______ synthesis to meet the needs of the cell/organism
Definition
protein
Term
_______ allows differential expression of genes
1. Developmental pathways
2. Specialization of cell and tissue types
Definition
gene regulation
Term
Transcription
Degrade mRNA
Translation
Degrade protein
Inhibit protein function


these are all ways that genes are ____
Definition
REGULATED
Term
All the genes in the metabolic pathway are under the same “controller” – the ___ concept
Definition
operon
Term
several genes can share the same _____
Definition
promoter!
Term
The regulatory “switch” is a segment of DNA called an ______ usually positioned within the promoter
Definition
operator
Term
An ____ is the entire stretch of DNA that includes the operator, the promoter, and the genes that they control
Definition
operon
Term
operons can be ____ regulated.
operon is switched off by the regulatory (repressor) protein.
Definition
negatively
Term
operons can also be _____ regulated – operon is switched on by the regulatory protein
Definition
positively
Term
negative regulation can be either ____ or ____
Definition
inducible or repressible
Term
_____ type of negative regulation. gene expression is usually on. Is turned off when a repressor binds to the operator.
Example: the trp operon
Definition
repressible
Term
type of negative gene regulation.... _____ gene expression is usually off. Is turned on when the repressor is inactivated. ____ inactivates the repressor.
Example: the lac operon
Definition
inducible...inducer
Term
A small percentage of any lactose present isomerizes to _____
Definition
allolactose
Term
A molecule called an _____ INactivates the repressor to turn the lac operon on
Definition
inducer
Term
Lactose absent, repressor active, operon _____
Definition
off
Term
_____ enzymes usually function in catabolic pathways; their synthesis is induced by a chemical signal
Definition
inducible
Term
Regulation of the trp and lac operons involves ____ control of genes because operons are switched off by the active form of the repressor
Definition
negative
Term
Tin positive regulation the regulatory protein acts directly on the operon to switch _____ gene transcription.
Definition
ON
Term
if lactose and glucose is also present, the rate of lac operon transcription will be ____
Definition
low
Term
But if lactose is present AND glucose is low, then ____accumulates.
Definition
cAMP
Term
Active CAP = increased rate of transcription of _____ operon genes
Definition
Lac
Term
in positive regulation Activated CAP attaches to the promoter of the lac operon and increases the affinity of RNA polymerase, thus accelerating ____
Definition
transcription
Term
When glucose levels increase, ____ detaches from the lac operon, and transcription returns to a normal rate
Definition
CAP
Term
Eukaryotic gene expression can be regulated at ______ stage
Definition
any
Term
In multicellular organisms gene expression is also essential for cell specialization, i.e cells regulate _____ as well as when genes are expressed
Definition
where
Term
muscle cell DNA = _____ cell DNA
Definition
nerve
Term
Errors in gene expression can lead to diseases including _____
Definition
cancer
Term
Chromatin
Transcription
mRNA processing
Degrade mRNA
Transport of mRNA out of nucleus
Translation
Post-translational protein modifications
Degrade protein
Inhibit protein function

all of these ways are also ways that ____ can regulate gene expression
Definition
eukaryotes
Term
Genes within highly packed _____chromatin are usually not expressed
Definition
hetero
Term
Chemical modifications to histones and DNA of chromatin influence both chromatin structure and gene expression
_____lation
____lation
_____lation
Definition
acetylation
methylation
phosphorylation
Term
_______lation of histone tails promotes loose chromatin structure that permits transcription
Definition
acetylation
Term
the addition of phosphate groups (phosphorylation) next to a methylated amino acid can also loosen ______
Definition
chromatin
Term
The addition of methyl groups (methylation) can condense ______
Definition
chromatin
Term
Methylation of DNA prevents its ______
Definition
transcription
Term
DNA methylation is the addition of a methyl group to the base ____
Definition
cystine
Term
the _______ code hypothesis proposes that specific combinations of modifications, as well as the order in which they occur, help determine chromatin configuration and influence transcription
Definition
histone code hypothesis
Term
according to histone code: Methylation of histone or of DNA usually turns a gene ______
Acetylation of histone usually turns a gene _____
Definition
methylation = OFF
acetylation = ON

phosphorylation = DEPENDS
Term
DNA ____lation can cause long-term inactivation of genes in cellular differentiation
It also In genomic imprinting, ____lation regulates expression of either the maternal or paternal alleles of certain genes at the start of development
Definition
methylation & methylation
Term
_______ modifications do not alter DNA sequence.
Definition
chromatin
Term
Chromatin modifications do not alter DNA sequence. However, they may be passed to future generations of cells

This type of inheritance of traits transmitted by mechanisms that do not directly involve the nucleotide sequence is called
Definition
epigenetic inheritance
Term
segments of noncoding DNA that critically help regulate transcription by binding certain proteins
Definition
control elements
Term
Control elements for the initiation of eukaryotic transcription can be located near ____ or far ______from the actual DNA sequence to be transcribed.
Definition
proximal ....distal
Term
A transcription _____ is a protein that binds to an enhancer and stimulates transcription of a gene

Bound ones cause mediator proteins to interact with proteins at the promoter
Definition
activator
Term
Bending the DNA by proteins enables ________ to influence a promoter hundreds or thousands of nucleotides away.
Definition
enhancers
Term
“Activators” bind to enhancer DNA sequences and then the _____ proteins then the general transcription factors.
Definition
mediator
Term
Some transcription factors function as _______, inhibiting expression of a particular gene
Definition
repressors
Term
A particular combination of ____ elements can activate transcription only when the appropriate activator proteins are present
Definition
control
Term
Unlike the genes of a prokaryotic operon, each of the coordinately controlled eukaryotic genes has its own _____ and control elements
Definition
promoter
Term
The life span of mRNA molecules in the cytoplasm is a key to determining ______ synthesis
Definition
protein
Term
_____yotic mRNA is more long lived than ____karyotic mRNA
Definition
eukaryotic lives longer than prokaryotic
Term
Degradation of mRNA usually begins with shortening the _______
Definition
poly A tail
Term
The initiation of translation of selected mRNAs can be blocked by regulatory proteins that bind to sequences or structures of the mRNA
Within 5’ UTR, these proteins can prevent _______ attachment
Definition
ribosome
Term
translation of all mRNAs in a cell may be regulated ______
Definition
at the same damn time!
Term
Many _____ must be processed before becoming active proteins.
Definition
polypeptides
Term
Protein degration often involves a small protein called ______ which is added to the larger protein. This is the “kiss of death.” The protein then enters a proteasome which is the “death chamber.”
Definition
ubiquitin
Term
It is important that proteins be _____ when their usefulness is over or their function fulfilled
Definition
degraded
Term
Noncoding _____ play multiple roles in controlling gene expression
Definition
RNAs
Term
A significant amount of the genome may be transcribed into _______
they also regulate gene expression at two points: mRNA translation and chromatin configuration
Definition
noncoding RNAs
Term
_______ are small single-stranded RNA molecules that can bind to mRNA
These can degrade mRNA or block its translation
Definition
Micro RNA.....Mirna
Term
Multicellular organisms depend on cell _______ for:
Development from a fertilized cell
Growth
Repair
Definition
division
Term
Cell division in unicellular organisms = _____
Definition
reproduction
Term
Make copies of existing cells =_______
Diploid
Identical
Somatic
Definition
mitosis
Term
__________= division of the cytoplasm in either mitosis or meiosis
Definition
cytokinesis
Term
Make gametes = ________
Haploid
Different from original cell
Gametes
Definition
meiosis
Term
_______= the linear DNA molecule + its associated protein also composed of chromatin.
Definition
chromosome
Term
Where the sister chromatids are most closely attached is at the ____
Definition
centromere
Term
Cell growth
Replication of DNA
Preparation of chromosomes for cell division


all of these happen in the ____ phase of cell cycle
Definition
interphase
Term
Interphase (about ______% of the cell cycle) has three subphases:
G1 phase (“first gap”)
S phase (“synthesis”)
G2 phase (“second gap”)

The cell grows during all three phases, but chromosomes are duplicated only during the ____ phase
Definition
90% of cell cycle is interphase. chromosomes are only duplicated in the S phase
Term
Protein structure associated with centromere
Attachment point for microtubules of the spindle

these describe the ____
Definition
kinetochore
Term
In ______phase, sister chromatids separate and move along the kinetochore microtubules toward opposite ends of the cell
Definition
anaphase
Term
: At which end do kinetochore microtubules shorten during anaphase?
Definition
at the end of which is attached to the kinetochore
Term
The results of fusing cells at two different phases of the cell cycle suggest that molecules present in the cytoplasm of cells in the ____ or ____ phase control the progression of phases.
Definition
S or M phase
Term
the frequency of cell division depends on the ______
Definition
type of cell
Term
G1: stay or leave?
S: to replicate or not to replicate?
G2: stay or leave?
Mitosis: Are we there yet?

these are all controlled by the _____ signals in the _____
Definition
chemical signals in the cytoplasm
Term
the cell cycle control system has specific ______ where the cell cycle stops until a go-ahead signal is received
Definition
checkpoints
Term
restriction point (mammals)
If “go-ahead” signal received at _____, then cell completes entire cycle
If not, cell exits cell cycle and switches to non-dividing state
Definition
G1
Term
________ are important intrinsic regulators of the cell cycle...which are classified as cyclin-dependent kinases (Cdks)
Definition
protein kinases
Term
Cyclin-dependent kinases need another molecule called ______ in order to be active.
Definition
cyclin
Term
Cyclin + Cdk =_______ This protein complex triggers a cell’s passage past the G2 checkpoint into the M phase
Definition
MPF (maturation-promoting factor)
Term
Phosphorylate proteins to start mitosis and also activates proteases that degrade cyclins.
Definition
MPF..maturation promoting factor
Term
_______ can be influenced by internal & external factors:
nutritional status
hormones
chemical signals
Definition
regulation
Term
internal factor example occurs At ________phase checkpoint.
Anaphase does not occur until all kinetochores have been attached to microtubules. Molecular signals are released that cause the sister chromatids to remain attached together until all kinetochores have been attached.
Definition
M
Term
this is an example of an ____ factor checkpoint: Growth factors are proteins released by certain cells that stimulate other cells to divide
Definition
external
Term
Another example of external signaling is _______-dependent inhibition, in which crowded cells stop dividing
Definition
density dependent inhibition
Term
Most animal cells also exhibit ______ dependence, in which they must be attached to a substratum in order to divide
Definition
anchorage
Term
Cancer cells lose control over cell ______
- They can migrate to other parts of the body
- They often lose density and/or adhesion dependence.
Definition
division
Term
_________ cells don’t depend on response to these signals like growth factors. Instead they grow almost continuously.
Definition
cancer
Term
A _______ is a large mass of cells.
Definition
tumor
Term
______ tumors resemble the tissue they grow from, grow slowly, and remain localized. they are not cancerous
Definition
benign
Term
_________ tumors do not resemble the tissue they grow from and may have irregular structures.
Cancer cells can invade surrounding tissue and travel through the bloodstream or lymph system.
Definition
malignant
Term
_______, or spreading, can cause organ failure and is hard to treat.
Definition
mestasis
Term
__________ genes
Encode proteins that inhibit abnormal cell division
genes that help prevent uncontrolled cell growth

Mutations of these DO contribute to cancer
Definition
tumor-suppressor
Term
Genes that normally regulate cell growth and division during the cell cycle
Includes genes for growth factors, their receptors, and the intracellular molecules of signaling pathways

these are one of the two types of genes that are associated wtih _____
Definition
cancer
Term
Normal genes involved in controlling cell division. They do not cause cancer.

these are called
Definition
proto-oncogenes
Term
_______ are genes which no longer control cell division properly.
Definition
oncogenes
Term
Mutations that make a proto-oncogene excessively active convert it to an ______, which may promote excessive cell division and cancer
Definition
oncogene
Term
if norml cell signaling is interrupted... gene thats involved in signal cascade that produces protein which stimulates cell cycle
Definition
ras gene
Term
_______ gene – a tumor suppressor gene.
Definition
P53
Term
______ gene prevents a cell from passing on mutations due to DNA damage
Definition
P53
Term
At the DNA level, a cancerous cell is usually characterized by at least one active oncogene and the mutation of several __________ genes
Definition
tumor supressor
Term
Chromosomes may ______ genes before separating
Process = crossing over
Produces additional genetic diversity
Definition
trade
Term
In a diploid cell, every chromosome has a ________
Definition
homologue
Term
In _______ the sister chromatids separate. Each cell gets one of the sister chromatids from each homologue
Definition
mitosis
Term
In _______ each cell gets only one of the sister chromatids from only one of the homologues
Definition
meiosis
Term
Meiosis I is preceded by ____phase, when the chromosomes are duplicated to form sister chromatids
Definition
interphase
Term
_____ in prophase 1= homologous chromosomes loosely pair up, aligned gene by gene
Definition
synapsis
Term
crossing over and synapsis all happen in ______ of meiosis 1
Definition
prophase
Term
group of 4 chromosomes is a
Definition
tetrad
Term
Each tetrad usually has one or more _________, X-shaped regions where crossing over occurred
Definition
chiasmata
Term
do the sister chromatids in anaphase 1 stay attached?
Definition
in anaphase YES
Term
Metaphase 2= Because of crossing over in meiosis I, the two sister chromatids of each chromosome are no longer ______
Definition
genetically identical
Term
At the end of meiosis 1 & 2, there are four daughter cells, each with a _____ set of unreplicated chromosomes
Definition
haploid
Term
the _______ cortex consists of protein strands joining duplicated chromosomes between sister chromatids
Definition
synaptonemal
Term
= manipulation of organisms or their components to make products
Definition
biotechnology
Term
Using bacteria to produce copies of eukaryotic genes =
Definition
cloning
Term
gene cloning Makes use of ________= small circular DNA molecules found in bacteria. These are separate from the bacterial chromosome.
Definition
plasmids
Term
the plasmid is an example of a cloning ________
Definition
vector!
Term
How do you isolate the specific gene that you want to clone from the vast number of genes on all the chromosomes?
Definition
DNA library....make a bunch of copies of DNA

or genomic library... chop up all the DNA and grow them in plastids
Term
________ enzymes =
Needed to make DNA fragments for cloning
Needed to “open up” the plasmid so the DNA fragments can insert.
= Endonucleases found in bacterial cells
Definition
restriction
Term
Bacterial restriction enzymes cut DNA molecules at specific DNA sequences called __________
Definition
restriction sites
Term
The most useful restriction enzymes cut DNA in a staggered way, producing fragments with ______ ends
Definition
sticky ends
Term
Seal the fragment to the plasmid with _____
the superglue!
Definition
DNA ligase
Term
in cDNA libraries Bacteria can’t splice out the _____. so its Useful to have the “processed” DNA
Definition
introns
Term
the clone that contains the gene that you are seeking i.e. the
Definition
B-globulin gene
Term
in order to screen for the beta globulin gene you need a _____ acid probe
Definition
nucleic acid probe
Term
You have to have some idea of at least part of the sequence of the gene you are seeking
Work backwards from amino acid sequence of the protein
Use known genes from related species
Can be DNA or RNA, but is single stranded
Probe is labeled so you can track it


all these need to happen in order to screen for the
Definition
beta globulin gene
Term
Gene will insert at the restriction site and therefore be near the______ because genes need these to be expressed
Definition
PROMOTERS
Term
To sequence an entire _____ the DNA is first cut into fragments about 500 base pairs (bp) long.
Definition
genome
Term
The Human Genome Project used two approaches:
_____sequencing &
_______ sequencing
Definition
hierarchical and shotgun
Term
in _______ sequencing, short marker sequences are identified—ensuring that every DNA fragment would have a marker.
Definition
hierarchical
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