Units 3+4

Question 1

translation

Answer 1

processing of translating genetic information from the language of nucleotides to the language of amino acids
1. initiation- assembly of ribosome on target mRNA at start codon (AUG)
2. elongation- ribosome facilitates base-pairing of tRNA’s anticodon with their complementary codon in the mRNA, catalyzes the peptide bond between the incoming amino acid and the growing polypeptide, translocates to the next codon and repeats
3. termination- ribosome releases polypeptide when it reaches a stop codon

Question 2

tRNA

Answer 2

performs action of translation by serving as a structural bridge between mRNA and amino acid
1 end has anticodon loop that binds a complementary codon on the mRNA
1 end has an attached amino acid that is associated with that anticodon
hydrogen bonds form within the tRNA’s single RNA strand forming its functional cloverleaf structure (anticodon loop keeps anticodon region from binding to another region on the tRNA)

Question 3

ribosome

Answer 3

molecular machine that facilitates translation made up of ribosomal RNA and proteins
considered a ribozyme because it catalyzes the formation of peptide bonds between amino acids
contains binding sites:
mRNA binding site- channel that the template mRNA can move through
A site- accepts incoming tRNA as it base pairs with codon
P site- ribosome translocates by 1 codon shifting mRNA from A site where peptide bond is catalyzed between amino acid on tRNA and growing peptide chain
E site- translocation again and tRNA exits ribosome

Question 4

kozak consensus sequence

Answer 4

serves as a recognition sequence where ribosome is able to stabilize and begin translation- allows ribosome to determine which AUG is correct

Question 5

UTR

Answer 5

5’ untranslated region before coding sequence and 3’ after, can contain places where other proteins can assemble to activate or repress coding sequence, often sensitive to environmental signals that impact expression of coding sequence

Question 6

erythromycin

Answer 6

blocks polypeptide exit channel preventing chain elongation

Question 7

chloramphenicol

Answer 7

inhibits formation of peptide bond by binding to the catalytic site

Question 8

tetracycline/doxycycline

Answer 8

block binding of tRNA in A site

Question 9

streptomycin

Answer 9

interferes with correct assembly of ribosome in mRNA causing it to be misread

Question 10

immunoblot/western blot

Answer 10

measures amount of specific protein of interest
proteins extracted from cells and separated by size with gel electrophoresis
proteins transferred from gel to stable membrane
membrane is probed with labeled antibody that binds to target protein

Question 11

northern blot

Answer 11

measures RNA levels using oligonucleotide probe

Question 12

protein

Answer 12

polymer of amino acids, peptide bonds form between carboxyl group of one amino acid and amino group of the next

Question 13

amino acid

Answer 13

consists of an amino group, variable R group attached to the alpha carbon and a carboxyl group

Question 14

peptide bonds

Answer 14

rigid and planar due to resonance (partial double bond character), creates a strong bond that holds proteins together and allows them to properly fold

Question 15

N-terminus

Answer 15

free end of polypeptide chain with amino group

Question 16

C-terminus

Answer 16

free end with carboxyl group (read N to C)

Question 17

peptide backbone

Answer 17

structure is same in all proteins

Question 18

amino acid side chains- R groups

Answer 18

create diversity of amino acids, can be polar, polar and negatively charged (acidic), polar and positively charged (basic), nonpolar

Question 19

puromycin

Answer 19

drug that inhibits translation and resembles amino acid tyrosine when it is bound to tRNA, has NH on its carboyxl group instead of an O which makes it a chain terminator, cancer treatment that blocks protein synthesis

Question 20

protein folding

Answer 20

occurs as protein leaves ribosome spontaneously due to interactions between amino acids and the aqueous of the cell

Question 21

secondary structure

Answer 21

formed by interactions (H bonds between NH amine groups and CO carboxyl groups) between different locations on peptide backbone
2 forms- beta sheets and alpha helices

Question 22

beta sheet

Answer 22

H bonds form laterally between 2+ adjacent peptide backbones

Question 23

alpha helices

Answer 23

H bonds form within nearby regions of same peptide backbone

Question 24

tertiary structure

Answer 24

final 3D structure of single polypeptide chain, influenced by noncovalent bonds
proteins can have multiple domains that can often fold and function on their own and perform a specific function

Question 25

electrostatic (ionic) bonds

Answer 25

form between +/- R groups and N and C termini

Question 26

Hydrogen bonds

Answer 26

form between backbone and/or R groups

Question 27

Van der Waals

Answer 27

weak forces between nearby uncharged molecules due to shifts in electron density cloud (but many of them can accumulate to influence folding)

Question 28

hydrophobic effect

Answer 28

nonpolar molecules aggregate with each other to be protected from aqueous environment by polar ones

Question 29

disulfide bonds

Answer 29

covalent bonds between adjacent sulfur atoms in neighboring cysteine groups, strong but do not drive protein folding because they are infrequent (instead help stabilize after structure has formed)

Question 30

quarternary structure

Answer 30

final functional 3D structure created by 2 or more amino acid chains

Question 31

misfolded and unfolded proteins

Answer 31

can no longer function and have returned to their primary structure to form clumps (aggregates), aggregates can form beta strand rich structures that assemble into large filaments (amyloids), involved in neurogenerative diseases

Question 32

molecular chaperone

Answer 32

proteins that create protective environment for proteins to fold properly in, protect them from aggregation by giving time to fold properly

Question 33

proteasome

Answer 33

molecular machine that degrades incompletely folded proteins, contain regulatory domain that acts as a lid to allow only misfolded proteins in, protein is unfolded and catalytic domain cleaves peptide bonds, reg domain cleaves short peptides

Question 34

silent mutation

Answer 34

does not change protein sequence, such as a SNP that leads to same amino acid due to redundancy in codons

Question 35

frameshift mutation

Answer 35

shifts codon sequence by changing number of nucleotides (insertion or deletion)

Question 36

protein regulation

Answer 36

1. by controlling amount of protein by regulating synthesis or degradation, ensures cell does not deplete its resources by accumulating excess amounts, good method if having excess amounts is harmful
2. by controlling activity of protein by regulating localization or enzymatic function, ensures cell does not waste substrates, good method if immediate access to protein is needed, often through conformational changes- forms of protein that are similar

Question 37

allostery

Answer 37

binding of ligand at one site (allosteric site) induces conformational change at active catalytic site regulating the enzyme’s activity, allosteric inhibition or activation

Question 38

feedback inhibition

Answer 38

when enzyme is inhibited by product of a metabolic pathway in which it is part of, product starts to build up and binds to enzyme to control amount

Question 39

post-translational modifications reversible

Answer 39

there are enzymes that add and remove the groups, phosphorylation (addition of phosphate group that induces conformational change to turn on/off activity), lipidation (adds hydrophobic lipids which targets them to be inserted into membranes, ubiquitylation (covalently attaches ubiquitin to lysine, marks protein for degradation by proteasome)

Question 40

transmission genetics

Answer 40

classical genetics, study of transmission of traits from generation to generation

Question 41

genetic mutations

Answer 41

heritable changes in DNA sequence, provide genetic diversity for natural selection to act upon (SNPs, insertions, deletions), mutations in gene create alleles (sequence variants)

Question 42

Wild type allele

Answer 42

allele most commonly found in nature, encodes product with proper function

Question 43

mutant allele

Answer 43

any allele that differs from DNA sequence of WT, do not always correspond to change in phenotype (silent mutations)

Question 44

cystic fibrosis

Answer 44

encoded by mutations in CFTR gene
C- CFTR gene wildtype allele (dominant)
c- CFTR mutant allele (recessive)
ex. of haplosufficiency (one copy of WT allele is enough for normal cellular function and to yield WT phenotype)

Question 45

CFTR

Answer 45

transmembrane protein that regulates mucus production in lungs, located on chromosome 7, F508 indicates loss of phenylalanine at pos. 508 due to codon deletion (loss of function mutant, null mutant)

Question 46

Marfan syndrome

Answer 46

dominant loss-of-function mutation in gene that makes fibrillin resulting in abnormal connective tissue
B- mutant allele that results in defective protein
b- WT allele
ex. of haploinsufficiency (one copy of WT allele is not enough for normal cellular function and to yield WT phenotype)

Question 47

hemizygous

Answer 47

males have one X chromosome so only have 1 copy of all X-linked genes, if male inherits one loss of function X-linked mutant allele his phenotype would be mutant

Question 48

gain of function mutation

Answer 48

when mutation gives protein new function, dominant, if function is beneficial mutation is often selected for, can also lead to disadvantage (toxic function, unwanted expression)

Question 49

Huntington’s disease

Answer 49

mutant allele of HD gene harbors multiple repeats of CAG glutamine codon (normal protein has 10-26 repeats but disease protein has 30-40), disrupts normal folding as glutamines become attracted to each other and aggregate, aggregates are toxic to cell (gain of function mutation)

Question 50

conditional mutations

Answer 50

expression of mutant phenotype requires a specific environmental condition, can be loss or gain of function
ex. gestational hyperthyroidism- in WT, TSHR is activated by binding of TSH but mutant allele gains ability to also be activated by hCG (hormone expressed only by placenta)

Question 51

incomplete (intermediate) dominance

Answer 51

displaying an intermediate phenotype between homo dom and homo rec.
ex. 4 o clock plants- CR is WT allele for red flower and CW is allele for white folower but CRCW heteros are pink

Question 52

mendelian genetics

Answer 52

one gene=one trait

Question 53

pedigree

Answer 53

used to track traits in genetically related families, to determine genetic contribution of trait and make predictions about an individuals risk for a genetic disease

Question 54

polygenic

Answer 54

when trait is determined by multiple genes

Question 55

epistasis

Answer 55

when trait is determined by interaction between genes and one gene suppresses another

Question 56

ABO blood type

Answer 56

ABO gene encodes for glycosylase that adds different sugars to surface of red blood cells, alleles IA and IB are dominant over i which adds no sugar
ex. of codominance- IAIB gives AB blood type

Question 57

Bombay phenotype

Answer 57

compound H required for addition of terminal sugar, loss of function recessive inhibits synthesis of compound H
hh leads to type O blood no matter ABO genotype because no sugar can be added
ex. of epistasis (one allele masked by another)

Question 58

twin concordance studies

Answer 58

reveal the importance of environmental vs genetic factors on traits since one pair is identical and other is not
concordance- % of twin pairs that share same trait
if concordance is higher in monozygotic twins suggests genetic component to that trait
if concordance is same suggests environmental component

Question 59

GWAS

Answer 59

Involves sequencing genomes of thousands of people, comparing the genomes
of people with a disease/trait vs. people without that disease/trait to identify
single nucleotide polymorphisms (SNPs, changes in the DNA sequence) that are
found significantly more often in people with the disease/trait then in people
without the disease/trait
reveals SNPs that could be located in disease-causing gene, regulatory sequences, non-coding sequences (most likely due to linkage- 2 sequences nearby on chromosome likely to be inherited together)

Question 60

forward genetic screen

Answer 60

mutagenesis in model organism then screened for phenotype of interest

Question 61

reverse genetic screens

Answer 61

identify causation (genotype to phenotype), mutagenesis of gene of interest and identify changes in phenotype