Final: Modules 12 and 13

Question 1

Describe the basic structure of amino acids

Answer 1

All amino acids have the same basic structure:
Carbon atom (α –carbon) attached to amino group, carboxylic (acid) group, hydrogen[all amino acids], and side chain [for different amino acids]

Question 2

How the peptide bond forms between amino acids.

Answer 2

Amino acids are held together by peptide bonds. Covalent bonds that hold amino acids bonds called peptide bonds.
The amino group of one amino acid is joined to the carboxyl group of another amino acid

Question 3

State the different levels of protein structure

Answer 3

There are 4 levels of protein structure:
1. primary: sequence of amino acids in polypeptide,
2. secondary: First layer of folding of a polypeptide
Caused by interactions (hydrogen bonds) between two nearby amino acids. Two kinds of secondary structure
α (alpha) helix and β (beta) pleated sheet
One or both found in most proteins,
3. tertiary: Overall 3 dimensional shape of polypeptide
Includes secondary structures and other interactions between different parts of the protein
- Determined by specific interactions between different R group of different amino acids.
Primary structure (sequence of amino acids in polypeptide):
determines final structure of protein
Higher levels of structure determined by specific interactions between R groups (side chains) on different amino acids, and
4. quaternary: Overall structure of protein formed when 2 or more folded polypeptides chains are associated with one another
Proper structure is necessary for proper function of proteins

Question 4

Describe how the different levels of protein structure are related to function.

Answer 4

The structure of the protein sets the foundation for the interaction with other molecules which determines the function.

Question 5

Explain how alternative splicing generates different proteins with similar (but not identical) functions

Answer 5

Since exons code for different domains, and these domains have different functions:
Proteins created by alternative splicing have different combinations of functions

Question 6

Describe the basic structures of tRNAs, including where the amino acid binds (3’ end) and where the anticodon is.

Answer 6

tRNA molecule: single RNA strand, about 80 nucleotides long
Much of a tRNA is base-paired to itself
Has stretches of complementary bases that bind to each other by hydrogen bonds
tRNAs are often drawn as so looks like a cloverleaf
(2-dimensional structure)
Actual 3-dimensional structure: looks like the letter “L”
The anticodon is at the bottom.

Question 7

Explain how tRNAs “read” the codons in mRNA

Answer 7

The genetic code in mRNAs is translated into proteins using tRNAs
tRNAs (transfer RNAs): match the codon with the correct amino acid for that codon.
One end: carry amino acid
Other end: recognizes the codon in the mRNA for that amino acid

Question 8

how the anticodon works

Answer 8

tRNAs use their anticodons to recognize and bind to codons
Anticodon: Three bases on tRNA complementary to mRNA codon for that amino acid
Anticodon binds to codon via hydrogen bonds

Question 9

how the anticodon is oriented relative to the mRNA

Answer 9

Same as binding between DNA strands: Antiparallel
and Complementary

Anticodons are often written 3’🡺 5’
since mRNA is written 5’🡺3’
The anticodon sequence is complementary to the mRNA, using base pairs in the anti-parallel direction.

Question 10

what “wobble” means in regard to tRNA binding to codons, and how it is related to the fact that many amino acids are encoded by codons that only differ in the third position

Answer 10

Wobble pairing: when tRNA binds to codon with different nucleotide in 3rd position
Wobble pairing lets one tRNA recognize multiple codons for the amino acid it carries

Question 11

Know what tRNA charging is, and the role that aminoacyl-tRNA synthetases play in charging

Answer 11

binding of amino acids to transfer RNAs
tRNA charging: when amino acids are joined to their tRNAs by specific enzymes
To be used in translation, tRNAs need to be bound to their amino acid. For each amino acid, there is an enzyme called aminoacyl-tRNA synthetase
These aminoacyl-tRNA synthetases: attaches amino acids to tRNAs

Question 12

Explain how the reading frame of a gene is determined.

Answer 12

Three ways in that a sequence can be read in groups of three.
Called reading frames
Each of 3 ways: encodes a different sequence of amino acids
Reading frame is determined by start codon: AUG

Question 13

If given a genetic code and an mRNA sequence, write the amino acid sequence that would be translated from the sequence.
And, if given a genetic code and an amino acid sequence, write a mRNA sequence that would code for those amino acids

Answer 13

The codons are written 5′→3′, as they appear in the mRNA

The amino acids specified by each codon

Question 14

If given a codon, state the sequence of the anticodon that recognizes that codon (including labeling the 5’ and 3’ ends)

Answer 14

The codons are written 5′→3′, as they appear in the mRNA

The amino acids specified by each codon

Question 15

If given an anticodon:
state the sequence the codon that it recognizes and
(if given a genetic code) state which amino acid is carried by that tRNA

Answer 15

The codons are written 5′→3′, as they appear in the mRNA

The amino acids specified by each codon

Question 16

Describe the position of the open reading frame, 5’ UTR, and 3’UTR in mRNAs

Answer 16

Protein coding region: located in middle of mRNA
Called Open reading frame (ORF)
contains codons for amino acids that make up the protein encoded by the gene transcribed into that RNA
Begins with AUG
Regions outside of ORF do not code for amino acids:
The 5’ untranslated region (5’ UTR): from the 5’ end of RNA to last base before AUG start codon.
The 3’ untranslated region (3’ UTR): from the stop codon to the 3’ end of the mRNA.

Question 17

Explain how translation is initiated including the 4 components that assemble to form translation initiation complex.

Answer 17

Initiation of translation are components needed for translation are gathered together on the ribosome
In both prokaryotes and eukaryotes, initiation requires assembly of 4 things:
1. Initiator tRNA: tRNA that recognizes the start codon
Carries Methionine (Met)
2. Small subunit of the ribosome
3. Large subunit of the ribosome
4. mRNA

Question 18

Describe in detail how ribosome binding and recognition of AUG differs in prokaryotes and eukaryotes

Answer 18

In prokaryotes:
Ribosome binding and start of
translation occurs at the same place
at Shine-Dalgarno sequence
tRNA carries modified methionine
- f-Met

In eukaryotes:
Ribosome binding is initiated at one place, and translation begins somewhere else
Small subunit and tRNA bind to the 5’ CAP
Then scan along until they find an AUG (in context of Kozak sequence), then begin translation
tRNA carries regular methionine (fMet)

Question 19

Describe the function of the Shine Dalgarno sequence in initiation of translation in bacteria, state where it is located, and state what would happen to initiation in bacteria if it were not present

Answer 19

In bacteria: The Shine–Dalgarno consensus sequence
Binds small unit of ribosome
Shine–Dalgarno consensus sequence in bacterial cells:
Located just upstream of the start codon
Recognized by rRNA in the small unit of ribosome
Positions ribosome over start codon
covers 30-40 nucleotides

Question 20

State that 5’CAP is required for binding of ribosomes in eukaryotes, that the poly A tails helps with the binding

Answer 20

In eukaryotes: 5’ CAP to bind, Kozak sequence to start
Small subunit of ribosome initiates binding at 5’ CAP
Then scans until they find an AUG is surrounded by a consensus sequence (called the Kozak sequence)
5’-ACCAUGG-3

Question 21

Describe the process of elongation, by which amino acids are added to the growing polypeptide chain according to the codons contained in the mRNA

Answer 21

Elongation of polypeptide: amino acids added one at a time to polypeptide chain

Question 22

State when in the process a peptide bond is formed

Answer 22

Peptide bonds form between the amino group of the amino acid attached to the A-site tRNA and the carboxyl group of the amino acid attached to the P-site tRNA.

Question 23

If given a diagram like the ones on the PowerPoint slides showing elongation:
identify the mRNA, amino acids, polypeptide chain, tRNA, and ribosome
state which tRNA is leaving the ribosome and which is entering the ribosome

Answer 23

In a diagram, mRNA: has the codon.
The amino acids: the circle that attaches to the top of tRNA.
polypeptide chain: is a chain that keeps building.
tRNA: it looks like a clover
The tRNA that’s leaving: the polypeptide chain will continue to shift
The tRNA that’s entering the ribosome: aa-tRNA(the next tRNA with an amino acid)

Question 24

Describe the process of termination that occurs when a ribosome encounters a stop codon, including the role of release factors (RFs).

Answer 24

There are 3 Termination (stop) codons:
UAA
UAG
UGA
The termination codons do not code for any amino acids

A release factor is a protein that allows for the termination of translation by recognizing the termination codon or stop codon in an mRNA sequence.

Question 25

the meaning of the term codon

Answer 25

three nucleotides that encode an amino acid

Question 26

that the code is degenerate, and what that means

Answer 26

Refers to the fact that the genetic code contains more codons than are needed to specify all 20 common amino acids.
The degeneracy of the genetic code means that the code is redundant: amino acids may be specified by more than one codon.

Question 27

that the code is unambiguous, and what that means

Answer 27

This means that each codon codes for just one amino acid (or start or stop).

Question 28

State that, in any given cell, only a subset of genes are expressed

Answer 28

In any given cell at a given time:
only a specific subset of genes are expressed
In human cells: 5,000- 15,000 genes out of ~ 21,000 genes

Differences in protein expression reflect function of that cell.

Question 29

Explain the difference between constitutive (“housekeeping”) genes and regulated genes

Answer 29

Constitutive genes: are always “on,”
They are expressed at the same rate, regardless of environment
Many constitutive genes are “housekeeping genes”:
control the ability of DNA to replicate, express itself, repair itself, control protein synthesis, facilitate much of an organism’s central metabolism.

Regulated genes: can be turned “on” and “off”
They are only expressed as needed
May be expressed at basal level, expression is then increased or decrease in response to signals

Question 30

Explain in general terms how that gene expression can be controlled at different levels, including the alteration of chromatin structure, transcription, mRNA processing, RNA stability, and RNA interference.

Answer 30

Changing chromatin from heterochromatin to euchromatin
Allows transcription factors and RNA polymerase to access genes
Transcription of that gene is activated
Changing chromatin from euchromatin to heterochromatin:
Prevents transcription factors and RNA polymerase from accessing genes
Transcription of that gene is repressed

Question 31

Explain the differences (both in structure and in ability to express genes) between euchromatin and heterochromatin, and the role that altering chromatin structure plays in gene regulation of eukaryotes

Answer 31

Euchromatin: Less condensed and Transcriptionally active

Heterochromatin:
More condensed and Mainly transcriptionally inactive
Convert from heterochromatin to euchromatin by altering chromatin structure

Question 32

Describe how chromatin-remodeling complexes affect gene expression by altering chromatin structure without changing the DNA or the histones, and explain why re-positioning of nucleosomes is required for transcription to occur.

Answer 32

Chromatin remodeling: Moves with nucleosomes so that RNA polymerase can access genes
Performed by large protein complexes chromatin-remodeling complexes
Chromatin-remodeling complexes:
1. Large protein complexes that acts as a motor
2. Move a segment of DNA from inside nucleosomes to region between nucleosomes
3. Allow transcription factors and RNA polymerase to bind
- Transcription can occur

Question 33

Explain how transcription factors affect the initiation of transcription, and be able to explain it using the following terms: basal transcription apparatus, activators, regulatory promoters, enhancers, silencers, insulators, TADs and mediator complex.
If given a diagram of a stretch of DNA with enhancers, insulators, and genes, be able to state which genes are turned on and which are not.

Answer 33

Transcription is regulated by proteins called transcription factors.
Transcription factors: proteins produced in cytoplasm, then migrate into the nucleus
In nucleus, they interact with DNA and activate transcription.
These transcription factors only interact with specific genes
So, when a cell want to turn on a gene, it makes a transcription factor specific for that gene
Basal level of transcription: occurs when basal transcription apparatus is bound to core promoter
Basal transcription apparatus: RNA polymerase, basal transcription factors, other proteins

Regulatory promoter: just upstream of the core promoter.
Has different combinations of consensus sequences
These sequences bound by transcriptional activator proteins:
activator proteins then interact with basal transcription apparatus; dramatically increase rate of transcription.
Allows cells to express certain genes at high levels in response to specific signals

Transcriptional activator proteins: bind to specific DNA sequences and increase transcription.
Regulatory promoter sequences:
just upstream of core promoter
2. Enhancer sequences:
distant from gene being transcribed
Both interact with basal transcription apparatus
Results in higher level of transcription

Silencers are sequences that block expression of a gene
Like enhancers silencers:
can be far away from the gene they control
are position and orientation independent
contain binding sites for specific transcription factors
these transcription factors are called repressors

Insulators may function by causing loops of chromatin that form interacting regions of genes and regulatory elements
Can create TAD with “neighborhoods” of regulatory elements and genes that can physically interact but are insulated from regulatory elements in TADs

Although enhancers are far away from the promoter: transcriptional activator proteins bound to enhancers are able to interact with the basal transcription apparatus.
This is possible because of:
Bending of DNA
Interactions through proteins called mediator proteins.

Question 34

Explain in general terms how a DNA binding proteins can recognize specific sequences in DNA

Answer 34

DNA binding proteins: bind to DNA sequences and affect their expression
Certain regions of the proteins (DNA binding domains):
Are responsible for binding to DNA
Make hydrogen bonds to nucleotides BUT
Do NOT disrupt bonds between strands

Question 35

Explain how eukaryotic cells use response elements in regulatory promoters to coordinately express genes in eukaryotic cells.

Answer 35

Binding of activators to response elements in regulatory promoters or enhancers can:
Directly turn on genes
Indirectly turn on genes by turning on other transcriptional activators that then turn on those genes

Question 36

Describe the three major ways that gene expression is controlled at a post-transcriptional level.

Answer 36

1. Alternative RNA splicing pathways
   Control how much of a certain protein is made by determining which protein exact protein is produced
2. Degradation of RNAs based on their stability
   Control how much of a certain protein is made by how long the mRNA exists
3. RNA interference:
   Control how much of a certain protein is made by blocking gene expression at different points in the pathway (depending on type of mRNA)

Question 37

Describe the role of RNA degradation and stability in influences the amount of protein that is made from that mR

Answer 37

Degradation of RNAs based on their stability
Control how much of a certain protein is made by how long the mRNA exists.

mRNAs usually have proteins on polyA tail and 5’-cap
protect both ends from ribonucleases
Proteins that induce degradation remove these proteins
RNA degradation usually begins at 5’ CAP

Question 38

Discuss in general terms how RNA interference brings about gene regulation: the ways in which miRNAs and siRNAs silence the expression of specific genes.

Answer 38

RNA interference (RNAi):
Important cellular mechanism to regulate gene expression
Used by cells to block expression of specific genes
control expression of the cell’s own genes
block invasion of the genome by viruses and transposons

1. Begins with double stranded RNAs (ds RNA)
   Similar/identical sequence to RNA being targeted
2. dsRNA is diced (cut) into small fragments RNA
   Cut by protein called Dicer
3. Small fragments bind to protein that removes one of the 2 strands (so now single stranded RNA
   Proteins + ssRNA = RNA-induced silencing complex (RISC)
4. RISC binds to the mRNA being silenced
   by base pairing to ssRNA

When protein/interfering RNA complex binds to target RNA, blocks expression in different ways
Different types of RNAi block gene expression in different ways:
miRNAs: Block target RNA from being translated
Some siRNAs: Cause target RNA to be degraded
Other siRNAs: Block transcription by attracting enzymes that methylate the DNA that codes for that mRNA

Question 39

Understand and be able to explain how epigenetic changes similar and how they are different from mutations including the fact that they:
can be passed to other cells (and sometimes to future generations)
are caused by permanent changes to chromatic structure
do NOT involve changes to the sequence of the DNA of the genome.

Answer 39

Epigenetic changes:
Alterations in gene expression (and therefore phenotypes) that:
Can be passed from one cell to another during mitosis BUT
These are NOT mutations
do not involve changes to the sequence of DNA

Epigenetic changes are changes that alter chromatin structure determine whether or not a gene is transcribed

Changes seen in later life were NOT due to mutations in sequence of DNA
Were caused by changes in gene expression
Caused by permanent changes in chromatin
This was one of the early studies that lead to the field of epigenetics

Question 40

For DNA methylation:
State what bases are usually modified by methylation and describe what CpG islands are.
Be able to explain the relationship between the presence of methylated cytosines and the level of transcription.
be able to explain role of the Dnmt3 gene, “royal jelly” and methylation in the development of queen bees.

Answer 40

Chromatin can be changed by DNA methylation
DNA methylation: addition of methyl groups to nucleotide bases
Most common: methylation of cytosine
produces 5-methylcytosine

Methylation of DNA: most common on cytosine bases adjacent to guanine nucleotides
two methylated cytosines sit diagonally across from each other on opposing strands
Called “CpG islands”
Often found near transcription start sites for genes

Queen bees are larger and live 20x as long as worker bees
Honeybee queens and workers have identical sequences in their genomes:
Differences in phenotypes due to methylation

Queen bee: Eat royal jelly
All other (worker bees) do not
Royal jelly: activates genes that are not expressed in worker bees
silences the expression of gene called Dnmt3
Protein encoded by Dnmt3: blocks expression of those genes by methylating them
In queen bees: Royal jelly inactivates Dnmt3
so many genes normally methylated (and inactive) in worker bees are expressed in Queen bees

Question 41

For histone modification:
state how adding certain molecules to the histones alters that interactions, and how changing can increase or decrease transcription
describe the effect that histone acetylation has on chromatin structure and transcription
explain what is meant by the histone code.

Answer 41

Transcription of a gene can be increased or decreased by modifying histones by covalently attaching small modules
Many modifications are to tail of histones: the part that interacts with negatively charged phosphates in DNA backbone

Addition of negatively charged modifications
Loosens interaction with DNA; Increases transcription

Transcription of a gene can be increased or decreased by modifying histones
Small modules are added to histones
Common histone modifications include addition of:
Phosphates groups
Methyl groups
Acetyl groups
Ubiquitin

Many modifications are to the tail of the histones
Part that interacts with negatively charged phosphates in DNA backbone

Histone code: sum of modifications to histones that determine which genes are expressed
Certain modifications on specific amino acids of the histone increase transcription
Others decrease transcription

Some modifications directly influence chromatin structure
Other modifications recruit proteins that then alter chromatin structure

Question 42

For RNA molecules that affect chromatin structure and gene expression:
Know that RNA molecules often cause epigenetic changes indirectly
Be able to explain the role of the long noncoding RNA Xist in inactivation of one of the X chromosomes in female mammals.
You do NOT have to know about the other three RNAs involved in X inactivation discussed in lecture and in your textbook

Answer 42

X chromosome: silenced by long noncoding RNAs (lcRNAs)
involves region of X chromosome called X-inactivation center
Inactivation starts at X-inactivation center, spreads to rest of X
Involves lncRNA called Xist “X-inactive specific transcript”

RNA molecules involved in epigenetic changes effect chromatin structure and gene expression
Most of these RNAs appear to have an indirect effect:
silence genes by causing DNA methylation and/or histone modification

Example: inactivation of X chromosome in females by long noncoding RNA

Question 43

Understand that epigenetic changes occur naturally in response to environmental factors, know that there are many different factors other than can cause epigenetic changes, and understand that:

Answer 43

epigenetic changes are the reason for phenotypic differences between genetically identical monozygotic twins

environmental chemicals may produce epigenetic effects that are passed to later generation

early life experiences can produce epigenetic changes that have long-lasting effects on behavior.

Question 44

Describe the role of RNA splicing in influencing the amount of a specific protein produced by a cell

Answer 44

Two types:
1. Alternative splicing: when single pre-mRNA is spliced in different ways
produce alternative types of mRNA
different proteins are produced from the same DNA sequence.
2. Multiple 3′ cleavage sites: 2 or more potential sites for cleavage and polyadenylation
use of the different sites produces mRNAs of different lengths

Question 45

State what is meant by the terms epigenetics and epigenome

Answer 45

Epigenetics
An emerging area of genetics that studies how an individual’s behaviors and environment can alter expression of their genes
Epigenetics explains how experiences during one’s life can have permanent effects
Provides new understanding of ”Nature vs Nurture”
Both positive and negative experiences cause epigenetic changes

Epigenome:
All epigenetic modifications within the genome of an individual organism