Nucleotides are the building blocks of nucleic acids and consist of a nitrogenous base, a pentose sugar, and a phosphate group. Nucleotides play important roles as the monomers of nucleic acids DNA and RNA, as well as energy carriers like ATP and cofactors like NAD. Nucleic acids such as DNA contain the genetic information to direct protein synthesis and RNAs carry out important cellular functions such as protein translation. The structures of nucleotides and nucleic acids allow for specific base-pairing interactions that are crucial for information storage and transfer.
The slide has some brief introduction to nucleotide chemistry, History, General features of nucleotides, Nomenclature, Individual properties of bases, Classification
and Synthetic analogues of biomedical importance.
The slide has some brief introduction to nucleotide chemistry, History, General features of nucleotides, Nomenclature, Individual properties of bases, Classification
and Synthetic analogues of biomedical importance.
This is a continuation of the earlier slide with a name "Nucleotides". Please refer to the previous mentioned slide before moving to this slide for a better overall concept on nucleotides and nucleic acids.
Ab Initio Protein Structure Prediction is a method to determine the tertiary structure of protein in the absence of experimentally solved structure of a similar/homologous protein. This method builds protein structure guided by energy function.
I had prepared this presentation for an internal project during my masters degree course.
This is a lecture slide for MBBS, BDS, paramedical as well as for those who are interested in molecular biology, molecular life sciences, biochemistry, medical biochemistry, general biochemistry etc.
For the more elucidated and connected information, try to refer to the nucleic acids slides.
protein structure prediction methods. homology modelling, fold recognition, threading, ab initio methods. in short and easy form slides. after one time read you can easily understand methods for protein structure prediction.
Nucleic acid-DNA and RNA
Gene-part of DNA
Functions of DNA
RNA-Functions, different types of RNA-Ribosomal RNAs (rRNAs), Messenger RNAs (mRNAs), Transfer RNAs (tRNAs)-Other RNA-Small nuclear RNA (snRNA), Micro RNA (miRNA), Small interfering RNA (siRNA), Heterogenous RNA (hnRNA).
Nucleic acid-nucleotides-nucleoside
Components of nucleotide-a nitrogenous (nitrogen-containing) base (pyrimidine and purine), (2) a pentose, and (3) a phosphate
Structure of pentose sugar, and 5 major bases (cytosine, thymine, uracil-pyrimidine bases and adenine, guanine-purine bases).
Deoxyribonucleotides and Ribo nucleotides-Molecular structure of deoxyadenosine monophosphate (dAMP), deoxyguanosine monophosphate (dGMP), deoxythymidine monophosphate (dTMP), deoxycytidine monophosphate (dCMP) and Adenosine monophosphate (AMP), Guanosine monophosphate (GMP), Cytosine monophosphate (CMP) and Uridine monophosphate (UMP), Watson crick base pairing, Hoogsteen base pairing,
Helical structure-Heterocylic N -Glycosides, Syn and Anti Conformers, detailed structure of single strand and double stranded DNA.
DNA Nucleotides and Tautomeric Form-Tautomers of Adenine, Cytosine, Guanine, and Thymine
Template strand, non coding strand and coding strand
Hydrogen bonds, phosphodiester linkage, hydrolysis of DNA and RNA.
Different forms of DNA-A, B, and Z forms.
Palindrome sequence, Linear DNA, Cruciform DNA, H DNA (Triplex DNA), Denaturation of DNA, Hyperchromicity, Tm, Renaturation of DNA, Tertiary structure of DNA, Difference of DNA and RNA, RNA structural elements, primary. secondary and tertiary structure of RNA. Detailed structure and functions of tRNA, mRNA, rRNA, miRNA, siRNA, hn RNA, snRNA.
Nucleic acid hybridization, C0t analysis, Buoyant density of DNA, Isopycnic centrifugation.
The skin is divided into two parts: the superficial part, the
epidermis; and the deep part, the dermis (Fig. 1.4). The
epidermis is a stratified epithelium whose cells become flat
tened as they mature and rise to the surface. On the palms of
the hands and the soles of the feet, the epidermis is extremely
thick, to withstand the wear and tear that occurs in these
regions. In other areas of the body, for example, on the ante
rior surface of the arm and forearm, it is thin. The dermis is
composed of dense connective tissue containing many blood
vessels, lymphatic vessels, and nerves. It shows considerable
variation in thickness in different parts of the body, tending
to be thinner on the anterior than on the posterior surface.
It is thinner in women than in men. The dermis of the skin
is connected to the underlying deep fascia or bones by the
superficial fascia, otherwise known as subcutaneous tissue.
The skin over joints always folds in the same place, the
SKIN CREASES (Fig. 1.5). At these sites, the skin is thinner
than elsewhere and is firmly tethered to underlying struc
tures by strong bands of fibrous tissue.
The appendages of the skin are the nails, hair follicles,
sebaceous glands, and sweat glands.
The nails are keratinized plates on the dorsal surfaces of
the tips of the fingers and toes. The proximal edge of the
plate is the root of the nail (see Fig. 1.5). With the exception
of the distal edge of the plate, the nail is surrounded and
overlapped by folds of skin known as nail folds. The sur
face of skin covered by the nail is the nail bed (see Fig. 1.5).
Hairs grow out of follicles, which are invaginations
of the epidermis into the dermis (see Fig. 1.4). The folli
cles lie obliquely to the skin surface, and their expanded
extremities, called hair bulbs, penetrate to the deeper part
of the dermis. Each hair bulb is concave at its end, and
DNA and RNA molecules are linear polymers built from individual units called nucleotides connected by bonds called phosphodiester linkages. DNA and RNA are used to store and pass genetic information from one generation to the next.
Transcript: Selling digital books in 2024: Insights from industry leaders - T...BookNet Canada
The publishing industry has been selling digital audiobooks and ebooks for over a decade and has found its groove. What’s changed? What has stayed the same? Where do we go from here? Join a group of leading sales peers from across the industry for a conversation about the lessons learned since the popularization of digital books, best practices, digital book supply chain management, and more.
Link to video recording: https://bnctechforum.ca/sessions/selling-digital-books-in-2024-insights-from-industry-leaders/
Presented by BookNet Canada on May 28, 2024, with support from the Department of Canadian Heritage.
Epistemic Interaction - tuning interfaces to provide information for AI supportAlan Dix
Paper presented at SYNERGY workshop at AVI 2024, Genoa, Italy. 3rd June 2024
https://alandix.com/academic/papers/synergy2024-epistemic/
As machine learning integrates deeper into human-computer interactions, the concept of epistemic interaction emerges, aiming to refine these interactions to enhance system adaptability. This approach encourages minor, intentional adjustments in user behaviour to enrich the data available for system learning. This paper introduces epistemic interaction within the context of human-system communication, illustrating how deliberate interaction design can improve system understanding and adaptation. Through concrete examples, we demonstrate the potential of epistemic interaction to significantly advance human-computer interaction by leveraging intuitive human communication strategies to inform system design and functionality, offering a novel pathway for enriching user-system engagements.
Connector Corner: Automate dynamic content and events by pushing a buttonDianaGray10
Here is something new! In our next Connector Corner webinar, we will demonstrate how you can use a single workflow to:
Create a campaign using Mailchimp with merge tags/fields
Send an interactive Slack channel message (using buttons)
Have the message received by managers and peers along with a test email for review
But there’s more:
In a second workflow supporting the same use case, you’ll see:
Your campaign sent to target colleagues for approval
If the “Approve” button is clicked, a Jira/Zendesk ticket is created for the marketing design team
But—if the “Reject” button is pushed, colleagues will be alerted via Slack message
Join us to learn more about this new, human-in-the-loop capability, brought to you by Integration Service connectors.
And...
Speakers:
Akshay Agnihotri, Product Manager
Charlie Greenberg, Host
Securing your Kubernetes cluster_ a step-by-step guide to success !KatiaHIMEUR1
Today, after several years of existence, an extremely active community and an ultra-dynamic ecosystem, Kubernetes has established itself as the de facto standard in container orchestration. Thanks to a wide range of managed services, it has never been so easy to set up a ready-to-use Kubernetes cluster.
However, this ease of use means that the subject of security in Kubernetes is often left for later, or even neglected. This exposes companies to significant risks.
In this talk, I'll show you step-by-step how to secure your Kubernetes cluster for greater peace of mind and reliability.
State of ICS and IoT Cyber Threat Landscape Report 2024 previewPrayukth K V
The IoT and OT threat landscape report has been prepared by the Threat Research Team at Sectrio using data from Sectrio, cyber threat intelligence farming facilities spread across over 85 cities around the world. In addition, Sectrio also runs AI-based advanced threat and payload engagement facilities that serve as sinks to attract and engage sophisticated threat actors, and newer malware including new variants and latent threats that are at an earlier stage of development.
The latest edition of the OT/ICS and IoT security Threat Landscape Report 2024 also covers:
State of global ICS asset and network exposure
Sectoral targets and attacks as well as the cost of ransom
Global APT activity, AI usage, actor and tactic profiles, and implications
Rise in volumes of AI-powered cyberattacks
Major cyber events in 2024
Malware and malicious payload trends
Cyberattack types and targets
Vulnerability exploit attempts on CVEs
Attacks on counties – USA
Expansion of bot farms – how, where, and why
In-depth analysis of the cyber threat landscape across North America, South America, Europe, APAC, and the Middle East
Why are attacks on smart factories rising?
Cyber risk predictions
Axis of attacks – Europe
Systemic attacks in the Middle East
Download the full report from here:
https://sectrio.com/resources/ot-threat-landscape-reports/sectrio-releases-ot-ics-and-iot-security-threat-landscape-report-2024/
GDG Cloud Southlake #33: Boule & Rebala: Effective AppSec in SDLC using Deplo...James Anderson
Effective Application Security in Software Delivery lifecycle using Deployment Firewall and DBOM
The modern software delivery process (or the CI/CD process) includes many tools, distributed teams, open-source code, and cloud platforms. Constant focus on speed to release software to market, along with the traditional slow and manual security checks has caused gaps in continuous security as an important piece in the software supply chain. Today organizations feel more susceptible to external and internal cyber threats due to the vast attack surface in their applications supply chain and the lack of end-to-end governance and risk management.
The software team must secure its software delivery process to avoid vulnerability and security breaches. This needs to be achieved with existing tool chains and without extensive rework of the delivery processes. This talk will present strategies and techniques for providing visibility into the true risk of the existing vulnerabilities, preventing the introduction of security issues in the software, resolving vulnerabilities in production environments quickly, and capturing the deployment bill of materials (DBOM).
Speakers:
Bob Boule
Robert Boule is a technology enthusiast with PASSION for technology and making things work along with a knack for helping others understand how things work. He comes with around 20 years of solution engineering experience in application security, software continuous delivery, and SaaS platforms. He is known for his dynamic presentations in CI/CD and application security integrated in software delivery lifecycle.
Gopinath Rebala
Gopinath Rebala is the CTO of OpsMx, where he has overall responsibility for the machine learning and data processing architectures for Secure Software Delivery. Gopi also has a strong connection with our customers, leading design and architecture for strategic implementations. Gopi is a frequent speaker and well-known leader in continuous delivery and integrating security into software delivery.
Key Trends Shaping the Future of Infrastructure.pdfCheryl Hung
Keynote at DIGIT West Expo, Glasgow on 29 May 2024.
Cheryl Hung, ochery.com
Sr Director, Infrastructure Ecosystem, Arm.
The key trends across hardware, cloud and open-source; exploring how these areas are likely to mature and develop over the short and long-term, and then considering how organisations can position themselves to adapt and thrive.
Slack (or Teams) Automation for Bonterra Impact Management (fka Social Soluti...Jeffrey Haguewood
Sidekick Solutions uses Bonterra Impact Management (fka Social Solutions Apricot) and automation solutions to integrate data for business workflows.
We believe integration and automation are essential to user experience and the promise of efficient work through technology. Automation is the critical ingredient to realizing that full vision. We develop integration products and services for Bonterra Case Management software to support the deployment of automations for a variety of use cases.
This video focuses on the notifications, alerts, and approval requests using Slack for Bonterra Impact Management. The solutions covered in this webinar can also be deployed for Microsoft Teams.
Interested in deploying notification automations for Bonterra Impact Management? Contact us at sales@sidekicksolutionsllc.com to discuss next steps.
Builder.ai Founder Sachin Dev Duggal's Strategic Approach to Create an Innova...Ramesh Iyer
In today's fast-changing business world, Companies that adapt and embrace new ideas often need help to keep up with the competition. However, fostering a culture of innovation takes much work. It takes vision, leadership and willingness to take risks in the right proportion. Sachin Dev Duggal, co-founder of Builder.ai, has perfected the art of this balance, creating a company culture where creativity and growth are nurtured at each stage.
UiPath Test Automation using UiPath Test Suite series, part 4DianaGray10
Welcome to UiPath Test Automation using UiPath Test Suite series part 4. In this session, we will cover Test Manager overview along with SAP heatmap.
The UiPath Test Manager overview with SAP heatmap webinar offers a concise yet comprehensive exploration of the role of a Test Manager within SAP environments, coupled with the utilization of heatmaps for effective testing strategies.
Participants will gain insights into the responsibilities, challenges, and best practices associated with test management in SAP projects. Additionally, the webinar delves into the significance of heatmaps as a visual aid for identifying testing priorities, areas of risk, and resource allocation within SAP landscapes. Through this session, attendees can expect to enhance their understanding of test management principles while learning practical approaches to optimize testing processes in SAP environments using heatmap visualization techniques
What will you get from this session?
1. Insights into SAP testing best practices
2. Heatmap utilization for testing
3. Optimization of testing processes
4. Demo
Topics covered:
Execution from the test manager
Orchestrator execution result
Defect reporting
SAP heatmap example with demo
Speaker:
Deepak Rai, Automation Practice Lead, Boundaryless Group and UiPath MVP
FIDO Alliance Osaka Seminar: Passkeys and the Road Ahead.pdf
Nucleotides- 13
1. Nucleotides and nucleic acids
10/10/05
1
Fig. 8-1, 8-19, 8-25
Nucleotides are the building blocks of nucleic acids
Nucleotides also play other important roles in the cell
Nucleotide
DNARNA
2. Roles of nucleotides
10/10/05
2
• Building blocks of nucleic acids (RNA, DNA)
•Analogous to amino acid role in proteins
• Energy currency in cellular metabolism (ATP:
adenosine triphosphate)
• Allosteric effectors
• Structural components of many enzyme
cofactors (NAD: nicotinamide adenine
dinucleotide)
3. Roles of nucleic acids
10/10/05
3
• DNA contains genes, the information needed to
synthesize functional proteins and RNAs
• DNA contains segments that play a role in regulation of
gene expression (promoters)
• Ribosomal RNAs (rRNAs) are components of ribosomes,
playing a role in protein synthesis
• Messenger RNAs (mRNAs) carry genetic information
from a gene to the ribosome
• Transfer RNAs (tRNAs) translate information in mRNA
into an amino acid sequence
• RNAs have other functions, and can in some cases
perform catalysis
4. Structure of nucleotides
10/10/05
4 Fig. 8-1
A phosphate group
Nucleotides have three characteristic components:
A nitrogenous base
(pyrimidines or purine)
A pentose sugar
10. Structure of nucleotides
10/10/05
9
Below is the general structure of a nucleotide. The
pentose sugar, the base, and the phosphate moieties
all show variations among nucleotides.
Know this!
12. Ribose
10/10/0511
Fig. 8-3
• Ribose (β-D-furanose) is
a pentose sugar (5-
membered ring).
• Note numbering of the
carbons. In a nucleotide,
"prime" is used (to
differentiate from base
numbering).
5
1
23
4
13. Ribose
10/10/0512
Fig. 8-3
• An important derivative of
ribose is 2'-deoxyribose, or
just deoxyribose, in which
the 2' OH is replaced with
H.
• Deoxyribose is in DNA
(deoxyribonucleic acid)
• Ribose is in RNA
(ribonucleic acid).
• The sugar prefers
different puckers in DNA
(C-2' endo) and RNA C-3'
endo).
17. Major bases in nucleic acids
10/10/05
16 Fig. 8-2
• Among the pyrimidines, C
occurs in both RNA and
DNA, but
• T occurs in DNA, and
• U occurs in RNA
Know these!
• The bases are
abbreviated by their first
letters (A, G, C, T, U).
• The purines (A, G) occur
in both RNA and DNA
18. Some minor bases
10/10/05
17
Fig. 8-5
• 5-Methylcytidine occurs in DNA of animals and higher plants
• N6
-methyladenosine occurs in bacterial DNA
Fig. 8-5
20. Variation in phosphate group
10/10/05x
Fig. 8-6, 8-42
• Adenosine 3', 5'-cyclic
monophosphate (cyclic AMP,
or cAMP) is an important
regulatory nucleotide.
• In hydrolysis of RNA by
some enzymes,
ribonucleoside 2',3'-cyclic
monophosphates are isolable
intermediates;
ribonucleoside 3'-
monophosphates are end
products
• Another variation - multiple
phosphates (like ATP).
cAMP
19 10/10/05
21. Nucleotides in nucleic acids
10/10/05
20
• Bases attach to the C-1' of ribose or deoxyribose
• The pyrimidines attach to the pentose via the N-1 position of
the pyrimidine ring
• The purines attach through the N-9 position
• Some minor bases may have different attachments.
22. Deoxyribonucleotides
10/10/0521
Fig. 8-4
2'-deoxyribose sugar
Deoxyribonucleotides are abbreviated (for example) A, or
dA (deoxyA), or dAMP (deoxyadenosine monophosphate)
Phosphorylate the 5' position
and you have a nucleotide(here,
deoxyadenylate or
deoxyguanylate)
with a base (here, a purine,
adenine or guanine)
attached to the C-1'
position is a
deoxyribonucleoside
(here deoxyadenosine and
deoxyguanosine).
24. Ribonucleotides
10/10/05
23 Fig. 8-4
• The ribose sugar with a
base (here, a pyrimidine,
uracil or cytosine) attached
to the ribose C-1' position
is a ribonucleoside (here,
uridine or cytidine).
• Phosphorylate the 5'
position and you have a
ribonucleotide (here,
uridylate or cytidylate)
• Ribonucleotides are abbreviated (for example) U, or UMP
(uridine monophosphate)
28. Nucleic acids
10/10/05
27 Fig. 8-7
Nucleotide monomers
can be linked together via a
phosphodiester linkage
formed between the 3' -OH
of a nucleotide
and the phosphate of the
next nucleotide.
Two ends of the resulting poly-
or oligonucleotide are defined:
The 5' end lacks a nucleotide at
the 5' position,
and the 3' end lacks a nucleotide
at the 3' end position.
29. Sugar-phosphate backbone
10/10/05
28
Berg Fig. 1.1
• The polynucleotide or nucleic acid backbone thus consists of
alternating phosphate and pentose residues.
• The bases are analogous to side chains of amino acids; they vary
without changing the covalent backbone structure.
• Sequence is written from the 5' to 3' end: 5'-ATGCTAGC-3'
• Note that the backbone is polyanionic. Phosphate groups pKa ~ 0.
30. The bases can take syn or anti positions
10/10/05
29 Fig. 8-18b
31. Sugar phosphate backbone conformation
10/10/05
30 Fig. 8-18a
• Polynucleotides have
unrestricted rotation about most
backbone bones (within limits of
sterics)
• with the exception of the sugar
ring bond
• This behavior contrasts with the
peptide backbone.
• Also in contrast with proteins,
specific, predictable interactions
between bases are often formed:
A with T, and G with C.
• These interactions can be
interstrand, or intrastrand.
32. Compare polynucleotides and polypeptides
10/10/05
31
• As in proteins, the sequence of side chains
(bases in nucleic acids) plays an important
role in function.
• Nucleic acid structure depends on the
sequence of bases and on the type of ribose
sugar (ribose, or 2'-deoxyribose).
• Hydrogen bonding interactions are
especially important in nucleic acids.
34. DNA structure determination
10/10/0533
• Franklin collected x-ray
diffraction data (early 1950s)
that indicated 2 periodicities
for DNA: 3.4 Å and 34 Å.
• Watson and Crick proposed a 3-
D model accounting for the data.
35. DNA structure
10/10/05
34
Fig. 8-15
• DNA consists of two helical
chains wound around the
same axis in a right-handed
fashion aligned in an
antiparallel fashion.
• There are 10.5 base pairs, or
36 Å, per turn of the helix.
• Alternating deoxyribose and
phosphate groups on the
backbone form the outside
of the helix.
• The planar purine and
pyrimidine bases of both
strands are stacked inside
the helix.
36. DNA structure
10/10/05
35
Fig. 8-15
• The furanose ring usually is
puckered in a C-2' endo
conformation in DNA.
• The offset of the
relationship of the base pairs
to the strands gives a major
and a minor groove.
• In B-form DNA (most
common) the depths of the
major and minor grooves are
similar to each other.
37. Base stacking in DNA
10/10/05
36
Berg Fig. 1.4; 5.13
• C-G (red) and A-T (blue) base
pairs are isosteric (same shape
and size), allowing stacking along
a helical axis for any sequence.
•Base pairs stack
inside the helix.
38. DNA strands
10/10/05
37
Fig. 8-16
• The antiparallel strands of DNA are
not identical, but are complementary.
• This means that they are positioned
to align complementary base pairs: C
with G, and A with T.
• So you can predict the sequence of
one strand given the sequence of its
complement.
• Useful for information storage and
transfer!
• Note sequence conventionally is given
from the 5' to 3' end
39. B,A and Z DNA
10/10/0538
Fig. 8-19
• B form - The most common
conformation for DNA.
• A form - common for RNA
because of different sugar
pucker. Deeper minor groove,
shallow major groove
• A form is favored in conditions
of low water.
• Z form - narrow, deep minor
groove. Major groove hardly
existent. Can form for some DNA
sequences; requires alternating
syn and anti base configurations.
36 base pairs
Backbone - blue;
Bases- gray
41. RNA has a rich and varied structure
10/10/05
40 Fig. 8-26
Watson-
Crick base pairs
(helical segments;
Usually A-form).
Helix is secondary
structure.
Note A-U pairs in
RNA.
DNA can
form
structures
like this as
well.