Exam 4 Genetics flashcards checklist

What does gene expression mean?

Production of a functional gene product

What does constitutive expression mean

Needed for survival; constitutive genes and housekeeping genes needed for survival

What is a methyl group?

CH3

What nucleotide is methylated in prokaryotes

Adenine (Influences transcription)

What is a domain in the context of a protein?

A domain is a part of a protein that can fold independently and has its own function.

What is a motif in the context of a protein?

Supersecondary structure and is the collection of adjacent secondary structure found in a protein

Which groove does motifs bind to

the major groove

operon

DNA sequence with multiple genes that are lined together under one promoter. That can be observed through prokaryotes.

Polycistronic RNA

mRNA formed has coding sequence of all genes

What are the parts of an operon

Promoter, operator, inducer, repressor

What does the promoter within an operon do?

DNA sequence that initiates transcription

What does an operator do?

DNA sequence that controls transcription of gene

What does a repressor do?

Protein that binds to the operator and prevents transcription of genes

What does an inducer do?

Molecule that counteracts repressor function

What does the regulatory protein do?

Can act as a repressor (negative control) or activator (positive control) where it stimulates transcription if it acts as an activator or inhibits transcription if it was a repressor

corepressor

Substance that inhibits transcription in a repressible system of gene regulation; usually a small molecule that binds to a repressor protein and alters it so that the repressor is able to bind to DNA and inhibit transcription

What is the purpose of the lac operon

Metabolize lactose

In which scenario is lac operon desirable

Glucose levels must be low and lactose must also be present.

What are the three genes in the lac operon

lacZ, lacY, lacA

How is lac operon regulated in the absence of lactose and glucose

No transcription occurs.

How is lac operon regulated in the presence of lactose and glucose?

Very low levels of transcription. CAMP is not made where CAP cannot bind to DNA

How is lac operon regulated in presence of lactose and absence of glucose?

High levels of transcription occur. CAMP is made and attached to CAP to bind with DNA sequence at CAP site which is before the promoter.

Who is the inducer of lac operon and what is its function?

The allolactose is the inducer; the function of the allolactose is to bind to the lac repressor.

Role of the CAP protein

The role of the CAP protein is to help RNA polymerase bind to the promoter.

Role of cAMP

cAMP (Cyclic AMP) helps the CAP protein bind to the DNA sequence before the promoter

What is the purpose of the trp operon?

Controls the biosynthesis of tryptophan in the cell
(Controls the ability to make tryptophan)

In what scenario is trp operon expression desirable?

It is desirable when tryptophan levels are low and repressed when high

Parts of trp operon: Must know names and locations of promoter, operator, and all 5 trp genes

5 trp genes: trpE, trpD, trpC, trpB, trpA

How is trp operon regulated in absence of tryptophan?

When tryptophan levels are low, the cell must make their own tryptophan. No repressor will bind to the operator since repressor needs tryptophan for binding which RNA polymerase will

How is trp operon regulated in presence of tryptophan?

When the tryptophan levels are present then transcription will be repressed, due to the tryptophan acting as a co-repressor.

Who is the corepressor of trp operon and what is its function?

Tryptophan is the corepressor of the trp operon; tryptophan binds to the repressor so the trp repressor binds to the operator where it shuts down transcription.

What is attenuation?

Attenuation helps the repressor repress transcription at a much higher level. It is a type of gene regulation in some bacterial operons where transcription is initiated but terminated prematurely before transcription of structural genes.

Why is attenuation required?

Attenuation is needed to completely shutdown transcription; it will help the repressor.

Which secondary structure causes termination of transcription?

3+4

What type of termination is observed: rho-dependent or rho-independent?

rho-independent

What does constitutive expression mean?

-This is needed for survival; housekeeping genes are also needed for survival.

What is a methyl group?

CH3

What nucleotide is methylated in eukaryotes?

Cytosine

What are CpG islands

If many CpG sequences show methylation. CpG is cytosine that is adjacent to guanine commonly methylated

What happens when DNA gets methylated?

Methylation of DNA is usually associated with repression of transcription where heterochromatin is formed.

What is chromatin remodeling?

Chromatin remodeling occurs to make DNA more accessible for transcription to occur. Heterochromatin represses transcription. Euchromatin allows transcription to occur.

Who aids in modeling chromatin and how can chromatin be remodeled?

Chromatin-remodeling complexes

What are the three covalent modifications that are done in histones?

- Acetylation (Lys)(Lysine)(K)
- Phosphorylation (Ser)(Serine)(S)
- Methylation (Lys/Arg)(Lysine or Arginine)

What part of the histones gets post-translationally modified

Histone N-terminal tails

Enzyme for Acetylation (know what an acetyl group is)

The enzyme is HAT; Histone acetyl transferases

Enzyme for deacetylation

Histone deacetylase complexes (HDACs)

enzyme for methylation

Histone methyltransferases (HMT)

Enzyme for demethylation

Histone demethylases

Which histone modifications tend to promote transcription and which histone modifications prevent transcription

Acetylation of histones promotes transcription and methylation of histones prevents transcription.

What does the histone code mean?

Combinations of covalent modifications signal specific outcomes

Basal transcription apparatus:

Complex of transcription factors, RNA polymerase, and other proteins that assemble on the promoter and are capable of initiating minimal levels of transcription.

Core promoter:

DNA sequence located immediately upstream of a eukaryotic gene, to which the basal transcription apparatus binds.

Regulatory promoter

DNA sequence located immediately upstream of the eukaryotic core promoter; contains consensus sequences to which transcriptional regulator proteins bind.

What does an enhancer sequence do

Promote transcription

What does a silencer do

Repress transcription.

What does an insulator do

The insulator represses transcription.

transcriptional activators

bind to enhancers

Transcriptional Coactivators:

Link activators with basal transcription apparatus

Transcriptional repressors:

Bind to the repressor

Transcriptional corepressor

Bind to transcription factors and prevent transcription

Mediator:

Protein that enables transcription regulatory proteins to contact RNA polymerase indirectly

Role of exonic/intronic splicing enhancers and silencers in splicing

influence use of splice sites as Splicing factors prefer one spice site over another. They help to promote or repress the use of particular splice sites during the process of RNA splicing, resulting in alternative splicing outcomes.

Proteins that play a role in splice site selection

SR proteins which are a group of serine and arginine proteins that regulate alternative splicing of pre-RNA

Regulation of gene expression by regulating mRNA degradation

The more stable the mRNA the higher chance of it being around longer where more proteins are made. MRNA that is less stable are rapidly degraded to translate a lesser number of proteins. 5' and 3' UTR determines the stability of mRNA.

Role of siRNA and miRNA in gene regulation

Regulation of gene expression through RNA interference

Different methods by which siRNA and miRNA can regulate gene expression

-Cleavage of mRNA
-Inhibition of translation
-Transcriptional silencing
-Degradation of mRNA

Translational level of gene expression

- Availability of ribosomes
-Translation initiation factors
- Charged tRNA
- Elongation factors

Methylation

Adding methyl groups (In eukaryotes the cytosine will be methylated)
Normally occurs in CPG islands

Demethylation

The removal of methyl groups

Phosphorylation

The addition of a phosphate group

Dephosphorylation

removal of a phosphate group

Ubiquitination

The addition of a small protein to a protein

Glycosylation

Addition of sugars to proteins
Aids in anchoring the proteins in the cell membrane

Acetylation

Addition of acetyl groups
In histones this is associated with the loosening of chromatin

Deacetylation

removal of acetyl groups

Lipidation

Addition of fatty acids to proteins
Usually added to proteins that are destined to be secreted (delivered) to extracellular environment

Proteolysis

Cleaving of proteins

Reasons why Mendel was successful in understanding heredity

Mendel was successful as he used scientific and quantitative methods in his experiments.

Sepals

enclose the flower

Petals

often brightly colored

Stamen

the male reproductive organ of a flower

Anther

the part of a stamen that contains the pollen.
Male reproductive

What is female reproductive organ of a flower?

carpel/pistil

stigma of flower

This is where the pollen is deposited

What is style?

Acts as a buffer against pollen contamination.

What is the ovary?

The ovary contains the ovule.

What is the ovule?

The ovule is where the (female gamete) is found in the egg cell. The ovule houses the egg cells.

What is self-pollination?

Self-pollination is the transfer of pollen from anther of a flower to stigma of same flower or flower of same plant

What is cross pollination?

Cross pollination is the transfer of pollen grains from anther of flower of one plant to stigma of a flower of another plant

What occurs in fertilization

Pollen germinates to form pollen tubes where male gametes go through the tube and reach the ovule. It fuses with the egg cell to form a zygote where it forms into an embryo and resides in a seed.

Allele

one or more alternative forms of a gene

Trait (Phenotype)

The appearance or manifestation of a characteristic

Homozygous

Containing the same types of alleles of a gene

Heterozygous

Containing two different types of alleles of a gene

Dominant

Out of two alternative traits, this trait will appear (F1)

Recessive

Out of two alternative traits, this trait will not appear (F1)

Skip a generation

Ratio for the monohybrid cross when both parents are heterozygous

3:1

Ratio for the dihybrid cross when both parents are heterozygous

9:3:3:1

What does the principle of segregation state

Alleles of a gene segregate (separate) during gamete formation and are rejoined at random, one from each parent, during fertilization

Principle of Independent Assortment:

Two traits separate independently of each other OR the alleles of a gene segregate independently of other genes