Bio 1030 Final Flashcards
Central Dogma
DNA transcribed into RNA, which is translated into protiens
Protiens
Linear polymers of amino acids -> form 3D structures w/ specific functions
Also called polypeptides
Translation
Process in which sequence of bases in mRNA specifies the order of successive amino acids in the protein chain that is forming
How do proteins evolve?
Through mutation and selections and combining functional units
Amino acid structure
composed of amino group bonded with carbon which is bonded to a carboxyl group and a R group
R group determines which amino acid it is
R groups
20 groups total
Allow amino acids to be grouped by characteristics
R group properties
Hydrophilic/hydrophobic
Basic or Acidic
Polar or non-polar
Hydrophobic Amino acids
Avoid water
Internal in proteins
Bonds stabilized with weak van der waals forces
Hydrophilic Amino acids
Polar molecules -> contain electronegative elements
Tend to be located on outside of protein
Basic/acidic amino acids
Basic - positively charged
Acidic - negatively charged
Tend to bond with each other
strongly polar and hydrophilic
Glycine
special amino acid
non-polar and small
increases flexibility of polypeptide backbone
Proline
special amino acid
R group linked back to amino acid
prevents the protein from being as flexible
Cysteine
Special amino acid
contains a SH group
can loop and bind protein structure
Peptide bonds
Covalent bonds between amino acid monomers
carboxyl group of one amino acid reacts with the amino group of another amino acid, releasing water
Primary structures
Primary: Amino acid sequences
Determines secondary and tertiary structures
Secondary structures
Result from hydrogen bonding between amino acid functional groups
two types:
1. Alpha Helix: polypeptide chain twisted tightly in right-handed coil.
2. Beta Sheet: polypeptide chain folds back on itself
Tertiary Structures
Result from spatial distribution of hydrophilic and hydrophobic R groups as well as other interactions between the R groups
Gives protein 3D shape
Determines protein function
Ribosomes
Where translation takes place
Consist of a small subunit and large subunit
Determines correct reading frame of codons
Codon
A group of three adjacent nucleotides coding for a single amino acid
Ribosome Large Subunit
includes 3 binding sites for molecules of tRNA
A (aminoacyl)
P (peptidyl)
E (exit)
tRNA
conduct translation
contain 70-90 nucleotides
bonds back with itself
3 bases in loop make up the anticodon
tRNA synthetases
Connect specific amino acids to specific tRNA molecules
uncharged with no amino acid attached
Anti-codon
interaction with codon determines base pairing
First base in the codon in mRNA pairs with the last base in the anticodon (must be antiparallel)
Codon that starts translation is AUG
Translation Process
- Initiation
- Elongation
- Termination
Initiation factors
bind to the 5’ cap of the mRNA
bring up tRNA charged with methionine
Next tRNA joins ribosome and scans the mRNA until the first AUG is encountered
Elongation
1.Once the new tRNA is in place, a coupled reaction takes place in which the bond connecting the Met to its tRNA is transferred to the amino group of the next amino acid in line as the first peptide bond is formed.
2.The new peptide is now attached to the tRNA in the A site.
3.Formation of the peptide bond requires multiple proteins in the large subunit, but the RNA in the large subunit is the actual catalyst.
4.The ribosome then shifts one codon to the right, which moves the uncharged tRNA (Met) to the E site and the peptide bearing tRNA to the P site, freeing the A site for the next charged tRNA in line.
5.The tRNA in the E site is ejected.
6.A covalent bond forms between the amino acid bonded to the tRNA in the A site and the next amino acid.
7.The subunit moves down one codon.
Termination
1.The process continues until one of the stop codons is encountered (UAA, UAG, UGA).
2.When the stop codon is encountered, a protein release factor binds to the A site of the ribosome, causing the bond connected to the polypeptide of the tRNA to break.
3.The breaking of the bond creates the carboxyl terminus of the polypeptide and completes the chain.
Selection of Proteins
1.These mutations can be retained or eliminated through selection based on the ability of individuals with the mutation to survive and reproduce.
2.If the mutation improves protein function, the individual will reproduce more successfully than others, and the mutation will eventually spread throughout a population over time.
Mutation
Any heritable change in genetic material
Heritable
Mutation is stable and therefore passed on through cell division
RNA mistakes
Not-heritable and common
Single nucleotide polymorphism
single change in the genome
linked SNP: occur outside of the gene and to not affect protein function
Non-coding SNP: Occur in regulatory region of gene. Doesn’t change amino acid sequence
Coding SNP: occur in coding region and alter the protein’s function (change amino acid sequence)
Silent Coding SNP: occur in coding region but do not alter protein’s amino acid sequence
Polymorphisms
Any genetic difference among individuals that is present in multiple individuals in a population
Alleles
different forms of a gene, make up the genotype
Somatic Mutation
Mutations within the body
non-heritable
Affect a area of the body
Germline mutation
Affects every cell in the body
heritable
half the gametes of the organism will contain the mutation
Genetic Risk factor
A mutation that increases the risk of disease within an individual
Categories of Mutations (broad)
Small scale (DNA level)
-Nucleotide substitution/point mutation
*Synonymous (silent) -> doesn’t change amino acids
*Nonsynonymous -> changes amino acids
-frameshift
Large scale (Chromosomal mutations)
-Insertion
-deletion
Point mutations
Transitions:
Base pair changes to one within the same category (eg. Adenine to Guanine)
Doesn’t change size of nucleotide
harder to detect and more common due to this
Transversions:
Base pair changes to one from the other group (eg. Adenine to cytosine)
easier to detect
Effect of Point Mutations
Silent: no effect
Missense: results in amino acid substitution
(can be conservative - substitute amino acid has similar properties to normal, or non-conservative - substitute properties are different)
Nonsense: Substitutes stop codon instead of amino acid
Frameshift mutations
Insertion/deletion of nucleotide
may result in shifting the reading frame or insertion of stop codon
Insertion and Deletions
Small insertions or deletions involve several nucleotides
-In non-coding DNA, has little effect
-In coding regions, effect based on size
If it occurs in exact multiple of 3 -> means amino acids are entirely added or removed
Transposable Elements
Transposons are DNA sequences that can move from one position to another in the genome
Discovered by Dr. Barbara McClintock in 1944
Copy-Number Variation
Common form of genetic variation
regions involved are large and include one or more genes
in coding regions results in tandem copies of the same gene
Gene duplication and divergence
Process of creating new genes from duplicates of old ones
Important in evolution
Divergence
Slow accumulation of differences between duplicate copies of a gene that occurs on an evolutionary timescale
Gene family
Multiple rounds of duplication and divergence leading to a group of genes with related functions
Chromosomal Insertions/deletions
Insertion (Duplication):
a. a region of the genome is present twice
b. generally less harmful than deletion
With a deletion, a region of the chromosome is missing.
a. A deletion may result from a replication error or the joining of breaks that may have occurred on either side of the deleted region.
b. Because chromosomes occur in homologous pairs, a deletion in one chromosome can persist in a population.
c. However, in general the larger the deletion, the smaller the chance of survival.
Inversions
part of chromosome is flipped
Reciprocal Translocation
join segments from nonhomologous chromosomes
in formation - both chromosomes broken and terminal segments are exchanged
breaks in large genomes common in non coding DNA
mutagens
Cause mutations, typically spontaneous
Principle of segregation
members of a gene pair (alleles) separate equally into gametes
principle of independent assortment
different gene pairs segregate independently of one another
gene
encoding region of DNA
Allele
variant of gene, 2 together make up genotype
Genotype
two alleles
phenotype
how the gene is expressed
Transmission genetics
how genetic differences among individuals are passed down from generation to generation
blending inheritance
past view
traits of offspring resemble the ‘average’ of the parents traits
problem: rare variants have no opportunity to increase in frequency even if they survive and reproduce more, because blending inheritance says they will gradually disappear over time
Modern transmission genetics
proposed by mendel
says genes, not traits that are transmitted in inheritance
shown between 1856 and 1864
True breeding
physical appearance of the offspring in each successive generation is identical to the previous one
Parental generation
cross between two true-breeding strains
F1 generation
generation produced by breeding of parental generation, trait produced is dominant
F2 generation
cross between F1 generation - resulted in 3:1 ratio of dominant to recessive trait
Incomplete dominance
phenotype of the heterozygous genotype is intermediate between the homozygous genotypes
resulting genotype and phenotype ratio of cross of Xx and Xx is 1:2:1
Pedigree of dominant allele
affected individual is equally likely to be male/female
typically only one affected parent
half of offspring are affected
no carriers -> gene always expressed if you have it
Pedigree of recessive allele
can skip generations (one or more)
females/males equally likely to be affected
parents may be unaffected
typically presents from famial matings
Uncommon inheritance patterns
traits that do not follow mendel’s law
Y-linked genes
Genes that pass traits from father to son
Cannot cross over with X chromosome
Sex chromosomes
special pair of unmatched chromosomes -> determine sex
only small region of homology between human sex chromosomes -> allows them to line up and segregate from each other during anaphase of meiosis 1
*contributes to pattern of sex linked traits in pedigrees
X-linked genes
genes on the X chromosome
more common than Y linked genes
Features of X-linked inheritance
Affected almost always males as only need one copy of gene to be affected
affected males have unaffected sons and carrier daughters
Genetic linkage
occurs when genes are close together on the same chromosome
Not linked
Genes are far apart on same chromosome
genes are on separate chromosomes
recombinant chromosomes
crossing over occurs, resulting in 2 recombinant chromosomes and 2 non recombinant strands after meiosis
nonrecombinant chromosomes
all resulting chromosomes have original allele combinations
more common in linked chromosomes as crossover is less likely to occur
Frequency of recombination
frequency ranges from 0 (crossing over never takes place) to 50 (crossing over always takes place)
linked genes have a recombination frequency between 0 to 50%
Genetic Maps
frequencies of combination are additive under short distances, allow distance between genes to be inferred
Inheritance of mitochondria DNA
Genes move with the organelle during cell division, independent of segregation of chromosomes in the nucleolus
Passed through maternal line
Mitochondrial haplotype remains intact through successive generations as no recombination between mitochondrial genomes takes place
Chloroplast inheritance
can be passed through either male/female line -> depends on species
