Genetics test 2 Flashcards
structure of protein
a sequence of amino acids. They are joined by peptide bonds (the thing elena showed me)
structure of amino acids
N terminus on the left (amino group), hydrogen in middle top, C terminus on right (carboxyl group) and variable group (R group) on bottom.
how amino acids are linked together to form a polypeptide
The peptide bond
different levels of protein structure
Primary, secondary, tertiary, quaternary (see notes for structure)
Explain how the structure of RNA allows it to participate in a variety of cellular functions
Consists of a large number of linked, repeating, nucleotides. They can fold into many shapes. There are also many types of RNA
List the different classes of RNA
mRNA
tRNA
rRNA
miRNA
mRNA
carries coding instructions (in cytoplasm and nucleus)
tRNA
plays crucial roles during protein synthesis(in cytoplasm)
rRNA
plays crucial roles during protein synthesis(in cytoplasm)
miRNA
typically regulate stability of specific mRNAs(in nucleus and cytoplasm)
major components required for transcription
Template (ssDNA), raw materials (ribonucleic triphospates), enzymes and other proteins
Give the substrate for transcription and how it is used to create a polyribonucleotide chain
Ribonucleoside triphosphates are used as the substrates in RNA synthesis. Two phosphate groups are cleaved from a ribonucleoside triphosphate, and the resulting nucleotide is joined to the 3′-OH group of the growing RNA strand
Identify the parts of a typical transcription unit
Stretch of DNA encoding mRNA and sequences necessary for transcription
DNA Transcription general principles:
- Transcription is a selective process; only certain parts of the DNA are transcribed at any one time
- RNA is transcribed from a single strand of DNA. Within a gene, only one of the two DNA strands—the template strand—is usually copied into RNA
- The transcribed RNA molecule is antiparallel and complementary to the DNA template strand.
- always in 5’ to 3’ direction
- Transcription depends on RNA polymerase. RNA polymerase consists of a core enzyme, which is capable of synthesizing RNA, and other subunits that may join transiently to perform additional functions e.g. sigma factor enables the core enzyme of RNA polymerase to bind to a promoter and initiate transcription
- Promoters contain short sequences crucial to the binding of RNA polymerase to DNA; these consensus sequences are interspersed with nucleotides that play no known role in transcription
Transcription is always in the___ direction
Transcription is always in the 5′→3′ direction, meaning that the RNA molecule grows at the 3′ end
three major stages of transcription in bacteria
Initiation, elongation, termination
Initiation bacteria
Promoter recognition
Formation of transcription bubble
Creatorion of first bonds between rNTPs
Escape of transcription apparatus from promotoer
Elongation
DNA is threaded through RNA polymerase; polymerase unwinds + adds new nucleotides to 3’end, rewinds DNA at trailing end
Termination
Recognition of end. The terminator ends it.
Understand the concept of colinearity between genes and proteins and how this gave scientists a clue about the presence of introns and exons in eukaryotic DNA
The thing elena showed me!!
Be able to differentiate exons and introns
Introns go, exons stay. (introns light, exons dark)
Explain the types of processing that occur in pre-mRNA
Moving from primary transcript to mature transcript (pre-mRNA to mRNA). This is done in 3 steps; 5’ capping, 3’ capping and intron splicing
Describe the 5’ cap and its function
A methylguanine is attached to pre-mRNA. This protects it and helps create stability
Describe the poly(A) tail, how it is added, and its function
A bunch of adenine is added to nucleotides at the 3’ end where the cleavage is (where it is likely to break). This creates stability.
Describe how introns are removed from pre-mRNA
By RNA splicing. The spliceosomone cuts the introns in a loop and connects exons
Summarize the different regions of a typical mRNA molecule
5’ untranslated region, protein region (made up of codons), and 3’ untranslated region
Explain what we mean by “the genetic code”
How genetic info is interpreted by protein
Explain how the genetic code is redundant
Multiple codons can code for the same protein
Explain how the reading frame of a gene is determined
By triplets?
Explain what is meant by the universality of the code
All species use the same 4 bases?
Describe the process of elongation, by which amino acids are added to the growing polypeptide chain according to the codons contained in the mRNA
Elongation requires initiation, charged tRNA, elongation factors, peptide bonds, and energy
Describe the process by which amino acids are assembled into a protein through translation of an mRNA
tRNA charging, initiation of teranslation, elongation, and termination
Describe the process of termination that occurs when a ribosome encounters a stop codon
Termination codon stops synthesis
Explain why regulation of gene expression is important and list and explain the different levels at which gene regulation may occur
It prevents protein synthesis from occurring when not necessary. It regulates it. The types
* Operons- on and off switches
* Regulatory elements- DNA sequences that affect expression of DNA to which they are linked
* Operator
* Structural genes
* Regulatory genes
Understand how gene regulation in eukaryotes brings about cell differentiation
Cells are different because they do not all make same proteins
Structural genes
proteins that play a structural or functional role in the cell
Regulatory genes
RNA or protein that interacts with DNA and affect transcription or translocation
Regulatory elements-
DNA sequences that affect expression of DNA to which they are linked
Explain how operons control transcription in bacterial genes
On and off switch
Negative inducible
turned on by repressor.
Positive inducible
activator turns it on
Negative repressible-
repressor turns it off
Positive repressible
activator turns it off
lac operon controls
the metabolism of lactose as an example of a negative inducible operon
glucose affects
transcription through catabolite repression as an example of positive inducible operon
trp operon controls
the biosynthesis of tryptophan as an example of a negative repressible operon
Enhancers/silencers-
enhance or silence transcription. This has a huge impact on cell identity
Activators
stimulate transcription. Faster transcription=more protein
Repressors
compete w activators by blocking, competing, interfering, etc.
Insulators
block the action of enhancers
Understand how insulators limit the long-range action of enhancers
They block the action of enhancers
Histone methylation
addition or removal of methyl group (-CH3). Some result in increased transcription rate BUT most often they repress transcription.
* H3= histone, K4=lysine 4,3 methyl groups
Histone acetylation
addition or removal of acetyl group (-COCH3). This results in increased transcription
Describe modifications to chromatin structure that affect gene expression in eukaryotes (molecular changes that lead to epigenetic effects)
DNA methlyation, histone modifications, and chromatin remodeling
Epigenetics
inheritance of variation above and beyond DNA sequence. the study of how your behaviors and environment can cause changes that affect the way your genes work
Neutral mutation
similar amino acid
Loss of function mutation
structure of protein or regulatory problems
Gain of function mutation
new gene product or produced in inappropriate tissue/time
Conditional mutation
only certain conditions
Lethal mutation
as it sounds…
Germ-line mutations
heritable mutations
Somatic mutation
not heritable mutations
Gene mutations
relatively small DNA lesions that affect a single gene
Chromosome mutations
large scale mutations (affect chromosome structure or number of chromosomes)
Base substitution
single nucleotide is changed
types of base substitutions
transition, transversion, silent, nonsense, and missense
Transition-
purine substituted for other purine or pyrimidine substituted for pyrimidine
Transversion -
purine substituted for a pyrimidine or vice versa
Silent-
no amino acid change (still encodes for correct thing)
Nonsense-
premature stop
Missense
different amino acid
Insertion and deletion
addition or removal of 1 or more nucleotides
types of insertion and deletions
Frameshift mutation and In-frame mutation
Frameshift mutation
affect the reading frame
In-frame mutation
leave reading frame intact (usually 3)
Expanding nucleotide repeats
increase in repeated nucleotides(usually 3 nucleotides)
Mutations arise from…
Mispairings, insertions and deletions, deamination (loss of an amino group from a base) or depurination (loss of a purine…there is a blank spot and A is place in replicated strand).
direct reversal repair
Happens when DNA is being replicated. It is like an autocorrect.
mismatch repair (what, protein, how, when, if impaired)
- Corrects replication errors including mispaired bases and small indels
- Sensor protein:Msh2(aka MutS)senses a mistake (finds the base that IS methalyated bc that is the correct one)
- How: remove + replace a section of newly synthesized DNA
- When: mainly right away after DNA replication
base-excision repair(what, protein, how, when, if impaired)
- What: corrects abnormal bases and modified bases (issues that aren’t considered significant to the DNA helix structure)
- Sensor protein: DNA glucosylase
- How: removes single damaged base
- When: mainly in G1 phase
- If impaired: neurological issues, cancer risk, etc
*
nucleotide-excision repair(what, protein, how, when, if impaired)
- What: corrects bulky DNA damage (distorts structure)
- Sensor: XPC-Rad23bcomplex
- How: remove + replace section of DNA
- When: before DNA replication
- If impaired:predisposition to skin cancer
*
homologous recombination(what, protein, how, when, if impaired)
- Corrects: double strand breaks
- Sensor: MRN complex
- How: remove some from broken ends invade the other chromosome + replicate to this one
- When: s/G2 phase when sister chromatids exist
- If impaired: breast cancer risk
non-homologous end joining(what, protein, how, when, if impaired)
Corrects: double strand breaks
Sensor: KU heterodimer
How: remove some nucleotides at end. Ligase and polymerase stitch it up. This is VERY imprecise
When: when sister chromatids are not available
If impaired: sever immunodeficiency
Mismatch repair, base excision repair, and nucleotide excision repair all…
Are when there is a template strand
Homologus recombination and non-homologous end joining all…
Are when template is not available
Incomplete dominance
the phenotype is in between homozygoters and can be differentiated from them (pink flower instead of white or red?)
Codominance
the heterozygotes simultaneously expresses phenotypes of both homozygotes (spotted cow)
Penatreance
when some individuals who carry a variant express the trait while others dont
Expressivitivity
degree to which a trait is expressed. Can be affectred by other genes or environmental factors
Epistasis
effect og genme interaction is that one gene masks (hides) effect of other gene at different locus
Blood types- h allele is epistatic to IA, IB, and i
Sex restricted
autosomal genes expressed in only one sex (tail feathering is limited to roosters (XY)and is recessive)
Sex influenced
autosomal gnes but expressed differently in XX vs XY indifiduals (male goats beard is dominant and female goats it is recessive)
Genic
Genotypes at one or more loci influence sex (ie plants, fish, etc)
Chromosomal: XX-XO, XX-XY, ZZ-ZW
Sex is dependent on the presence or absence of particular chromosome
Environmental
Influenced to some degree by environmental factors (ie invertebrates, turtles, etc)
genotypic frequencies
f(AA)= number of AA/total number
allelic frequencies with two alleles
= #of copies of allele/# copies of alleles at locus
solve Hardy-Weinberg law
p2+2pq+q2 (q+p=1)
Similarities and differences (bacteria and eukaryotes): Promoter/consensus sequences
Same main process (initiation, elongation, and termination.) but it is more complex in eukaryotes. Elongation is the same in both.
Similarities and differences (bacteria and eukaryotes):Initiation
- In bacteria polymerase recognizes and binds directly to promoter
- In eukaryotes the promoter is not immediately recognized and accessory proteins help. This uses transcription factors, which are the accessory proteins and they control the rate of transcritiption
*
Similarities and differences (bacteria and eukaryotes):RNA polymerase
Bacteria polymerase has one and eukaryotes have multiple types of polymerase
Similarities and differences (bacteria and eukaryotes): Termination
- bacteria : both rho-dependent and rho-independent
- Eukaryotes: multiple termination factors
Describe how different proteins can result from the same pre-mRNA through alternative processing
Join exons in different ways and orders, resulting in different proteins.
Outline the process of tRNA charging
The process of attaching a specific amino acid group to its specific tRNA
initiation of translation
transcription apparatus assembles on the promoter and begins RNA synthesis.
* mRNA binds to the small subunit of the ribosome
* Initiator tRNA binds to the mRNA through base pairing- codon-anticodon
* large ribosomal subunit joins initiation complex
*ps 5’cap and polyAtail are in eukaryotes
Outline the structure and function of a typical operon
2 or more protein-coding genes that are regulated by a single promoter. In it is promoter and structural genes, Its function is to control transcription
List ways that gene regulation in bacterial and eukaryotic cells differ
In bacteria, operons and regulatory elements control gene regulation. In eukaryotic, transcription factors regulate gene expression. Both have activators and repressors
Understand what we mean when we say that genes are coordinately expressed in eukaryotic cells
In Eukaryotic cells, a single gene can be activated by many regulatory elements. Also, and single stimuli can activate many genes. This means one genotype can result in many phenotypes
Describe the role of RNA splicing and degradation in gene regulation
Splicing helps a gene be a functional protein by getting rid of introns. Alternative splicing helps create many possible options. Degradation can change how much of protein can be synthesized. Protein synthesized= mRNA synthesized-mRNA degraded. Degradation gets rid of transcripts that arent needed.
Explain how transcription factors affect the initiation of transcription
They bind to sites on DNA
chromatin remodeling
remodeling chromatin to expose binding sites and transcription factors of specific genes, this changes chromatin structure and changed gene expression
low glucose =
higher CAP (if there is not enough glucose, ATP (energy) levels fall and it is broken down into CAP (CAMP activator protein) and can now bind to DNA and increase RNA binding efficiency, including transcription.
Predict the effects of different types of mutations on transcription of structural genes in negative/positive and inducible/repressible operons
Look at photo for this one. The key on my notes
Understand the general mechanisms of the different pathways of DNA repair
- Damage sensing proteins sense the damage.
- Excision protein either removes one base or a short stretch
- Dna polymerase or ligase patches DNA back up.
How to determine proportions of offspring produced when penetrance is incomplete
N individuals with phenotype/n of individuals with genotype x 100
Genetic Nondiscrimination Act.
protects individuals against discrimination based on their genetic information in health coverage and in employment
Understand the importance of the human genome project and its relationship to single-nuclotide polymorphisms
- The Human Genome Project (HGP) identified many single nucleotide polymorphisms (SNPs), which are small variations in DNA that occur between genomes
- Scientists study SNPs to identify genetic contributors to diseases and other traits. For example, SNPs can help predict how an individual will respond to certain drugs, their susceptibility to environmental factors like toxins, and their risk of developing diseases.
Explain the Hardy-Weinberg law and its assumptions and how “breaking” those changes allelic frequency in the population
Assumes that genetic variation in a population will remain constant from one generation to the next in the absence of distributing factors
